Meenakshi Dutt, Rutgers, The State University of New Jersey
Durba Sengupta, National Chemical Laboratory
Sanket A. Deshmukh, Virginia Tech
Igor V. Pivkin, University of Lugano
National Science Foundation
BM03.01: Multiscale Modeling of Soft Materials and Interfaces I
Sanket A. Deshmukh
Monday AM, November 26, 2018
Sheraton, 2nd Floor, Back Bay B
8:00 AM - BM03.01.01
Effects of Molecules Organization on the Mechanical Properties of Wood
Kai Jin1,Markus Buehler1
Massachusetts Institute of Technology1Show Abstract
Wood is a biological material with outstanding mechanical properties resulting from its hierarchical structure across different scales. While the cellular structure and the winding angle between the stiff cellulose fibrils and the wood cell axis have been reported to be key factors for its high stiffness and strength at light weight, the role of the molecular organization of its chemical components: cellulose, hemicellulose and lignin, is still to be fully understood. At the molecular scale, most of the hemicellulose molecules attach on the surface of the stiff crystalline cellulose fibrils, while lignin molecules fill the rest space. By applying a recently developed full atomistic model of the wood cell wall material, we studied how wood benefits from this intriguing molecular organization by intentionally varying the material distribution so that hemicellulose and lignin are randomly mixed or lignin molecules attach on the cellulose surface. It is found that better adhesion between the cellulose fibrils are achieved with the material distribution found in natural wood. Further detailed studies on individual molecules reveal that the hemicellulose show higher adhesion than lignin with cellulose and the three-dimensional structure of lignin originates its higher rigidity. Moreover, the covalent crosslinks between hemicellulose and lignin molecules enhance the load transferring between them. Therefore, the material distribution found in natural wood forms a pathway for load transferring that materials with stronger interactions are paired together. Our study reveals the molecular principles that wood adapts to achieve the outstanding mechanical properties at the macro-scale, which could shed light on the design of composite materials.
8:15 AM - BM03.01.02
The Effect of Cargo Topology on Microcompartment Assembly
Farzaneh Mohajerani1,Michael Hagan1
Brandeis University1Show Abstract
Bacterial Microcompartments (BMC) are roughly icosahedral shells found in bacteria that sequester enzymes involved in certain metabolic processes. Experiments suggest that some BMCs assemble by a pathway in which the enzymatic cargo first undergoes phase separation, after which the shell assembles around the dense cargo droplet. Other types of BMCs assemble in a single step, with simultaneous cargo coalescence and shell assembly. Computational studies suggest that the strength of interactions between cargo particles are a key determinant of the assembly pathway. However, the physical origins of these interactions remain unclear; in particular, whether they result from direct attractions between enzymes or are mediated by scaffolding proteins.
In this presentation we describe coarse-grained computational and theoretical modeling to study the effect of cargo interactions and cargo topology on microcompartment assembly. We present results of dynamical simulations that compare shell assembly when cargo coalescence is driven by direct cargo-cargo attractions or scaffold-mediated attractions. We find that cargo properties can dramatically influence assembly pathways. Depending on conditions, the presence of cargo may increase or decrease shell size in comparison to the intrinsic protein curvature. This result may explain recent experiments on different BMC systems in which empty BMC shells were respectively smaller or larger than full shells. In comparison to direct cargo-cargo attractions, our simulations identify a richer set of assembly behaviors for scaffold-mediated cargo attractions, and suggest that there are experimentally distinguishable differences between the two classes of systems. Understanding factors that control encapsulation of cargo by self-assembling shells is the first step for reengineering BMCs to construct drug delivery vehicles or customizable nanoreactors that encapsulate a programmable set of enzymes.
8:30 AM - BM03.01.03
Development of Coarse-Grained Polystyrene and Poly(acrylic acid) Models—From Monomers to Polymer
Yaxin An1,Karteek Bejagam1,Sanket A. Deshmukh1
Virginia Tech1Show Abstract
The self-assembly process of polymers and peptide amphiphile usually involves large time (~microseconds) and length (~micrometers) scales. Modeling of such a process using all-atom (AA) classical molecular dynamics (MD) simulations is a challenge. Coarse-graining is a technique to overcome these challenges, in which a group of atoms is represented by a bead. In this work, the coarse-grained (CG) models of the monomer’s analogues of polystyrene (PS), i.e. ethylbenzene, and that of poly(acrylic acid) (PAA), i.e. propionic acid, are developed firstly to reproduce their corresponding experimentally measured properties at 300 K. A 2:1 mapping scheme is used to map a ethylbenzene molecule to be a C2E bead and three BZ beads, while a propionic acid molecule was represented by a C2E bead and a COOH bead. The C2E bead represents the ethyl group in ethylbenzene and propionic acid, and three BZ beads constitute the phenyl group, and the COOH bead represent the carboxylic acid group. The bonded interaction parameters are obtained by matching the bond length distributions with all AA mapped trajectories. The nonbonded parameters of the C2E and BZ beads were taken directly from our previously developed hydrocarbon and benzene models, while the nonbonded parameters of the COOH bead was optimized to reproduce the density (ρ), self-diffusion coefficient (D), enthalpy of vaporization (Hv), and surface tension (γ) of propionic acid at 300 K. The ρ, Hv, D, γ of CG ethylbenzene and propionic acid models were in good agreement with their corresponding experimental values. The free energies of hydration (ΔGhydr) of ethylbenzene and propionic acid are within 10% of their experimental values. Finally, CG PS and PAA polymer models with 30 monomer units were constructed. The conformation of these polymer chains in a CG water model was studied at 300 K by MD simulations. Results of these CG MD simulations were in good agreement with those of the AA simulations.
8:45 AM - BM03.01.04
Understanding Polyethylene Cross Linking with Dicumyl Peroxide (DCP) via Large Scale Molecular Dynamics Simulations with ReaxFF Reactive Force Fields
Dundar Yilmaz1,Dooman Akbarian1,Adri Duin1
The Pennsylvania State University1Show Abstract
Polyethylene (PE) is one of the widely used commercial polymers. Cross linking improve many properties of PE such as high dielectric strength, mechanical strength, low water permeability.
Cross-linked PE (XLPE) has emerged as the insulator of choice for high-voltage direct current (HVDC) power transmission cables due to its favorable dielectric properties, low water permeability, structural integrity at high temperature and chemical resistance.
Dicumyl Peroxide (DCP) has been used as an accelerating agent in cross linking PE. We investigated cross linking mechanisms and mechanical and electrical properties of XLPE systems using large scale molecular dynamics simulations. We first started with a non-reactive force field to understand diffusion of DCP molecules into the PE matrix with and without the influence of external electric field. Second, we employed eReaxFF to investigate cross linking mechanisms. ReaxFF reactive force fields first developed for hydrocarbons and later ported to different systems such as ceramics, metals and their oxides and provided precise results for those systems. eReaxFF is an extension to ReaxFF in which electrons are treated explicitly in a pseudo classical manner. We adopted a previous ReaxFF reactive force field and developed eReaxFF reactive force field to capture DCP-PE interactions, and investigated reaction mechanisms of crosslinking of PE via DCP under the external electric field using large scale molecular dynamics simulations. We investigated the effects of different parameters such as temperature, density, pressure and the ratio of peroxides to polyethylene on the formation of byproducts, distribution of functional groups and cross-linking. Furthermore we investigatedmechanical ( tensile strength, bulk modulus) and electrical properties ( dielectric strength ) of the cross linked PE.
9:00 AM - BM03.01.05
Modeling the Influence of Emergent Interactions Between Nascent Oligomers on the Sequences of Step-Grown Copolymers
Kateri DuBay1,Zhongmin Zhang1
University of Virginia1Show Abstract
The sequences of synthetic copolymers are notoriously difficult to control, and numerous complex protocols have been developed to help us do so. However, we lack a comprehensive understanding of what governs the sequential incorporation of different monomers into a chain for even the simplest of copolymerizations. To learn more, we performed coarse-grained modeling of a linear, step-growth copolymerization between two monomers. Our results demonstrate that transient associations and emergent self-organization among the reacting monomers and nascent oligomers can exert considerable influence over the sequential arrangement of monomers in the resulting chains, even when reaction barriers between the different monomer pairs are held constant. The magnitude of the effect we observe for differing co-monomer attractions can be explained by an emergent phase separation among the nascent oligomers – a phase separation that is both initiated and limited by the copolymerization.
9:15 AM - BM03.01.06
Computational and Experimental Studies of Peptide: Silica Interactions
Carole Perry1,Victor Volkov1
Nottingham Trent Univ1Show Abstract
Structural properties of bioinorganic composites are of contemporary research interest in fields such as drug delivery, bone repair and biomimetics. While being a key material in bio-engineering applications, silica may be either hazardous or biocompatible depending on parameters such as particle size, shape or surface properties. Effective simulation at the quantum level of large silica-based bio-composites is necessary to gain a deeper insight into the properties of such materials. How to bridge between structural extraction from large scale classical simulation to predictions by quantum chemistry for silica based structures is the focus of our contribution. In this presentation we present MD and DFT simulation data, complemented by experimentally derived vibrational and optical spectroscopic data for the study of (a) 2nm silica nanoparticles, (b) the possible effects of local fields next to such nanoparticles and (c) the interaction of silica with 7-mer peptides.
9:30 AM - BM03.01.07
Predicting Viscoelasticity, Strength and Fracture for Ideal Reversible Polymer Networks
German Parada1,Xuanhe Zhao1
Massachusetts Institute of Technology1Show Abstract
Ideal Reversible Polymer Networks have well-controlled network structures similar to ideal covalent networks but exhibit transient properties due to the presence of reversible crosslinks. We have developed a theory to describe the mechanical properties of these ideal reversible polymer networks under small shear deformation, and have predicted that the networks behave as a single Maxwell element of a spring and a dashpot in series, with the instantaneous shear modulus and relaxation time determined by the concentration of elastically-active chains and the dynamics of reversible crosslinks, respectively. Due to the use of short polymer chains, we expected no contributions from polymer chain entanglements or chain relaxation, as the Rouse relaxation time is much shorter than the reversible crosslinks’ characteristic time. The theory also provided general methods to (i) independently control the instantaneous shear modulus and relaxation time of the networks, and to (ii) quantitatively measure kinetic parameters of the reversible crosslinks, including reaction rates and activation energies, from macroscopic viscoelastic measurements. The theory and methods were validated experimentally using a 4-Arm polyethylene glycol hydrogel system. We have also employed the theoretical and experimental system developed to characterize the fracture modalities and mechanical properties under large uniaxial deformation at varying loading rates.
9:45 AM - BM03.01.08
Revisiting the Strong Stretching Theory for pH-Responsive Polyelectrolyte Brushes
Harnoor Sachar1,Siddhartha Das1
University of Maryland, College Park1Show Abstract
Polyelectrolyte chains grafted to a substrate attain a brush like configuration above a critical grafting density. Polyelectrolyte brushes (PE) have gained significant attention in the last few decades due to a myriad of applications like flow control, biosensing, current rectification, ion manipulation etc. We present a self-consistent model of backbone charged pH-responsive PE brushes using the Strong Stretching Theory (SST). State of the art theoretical model (we refer to it as model 1) for the pH-responsive PE brushes assume a Boltzmann distribution for hydrogen ions both inside and outside the PE layer. In other words, the effect of the coupling between the brush ionization and local hydrogen ion concentration is not considered. This is a major limitation of the existing theory that has been hitherto overlooked. We propose a new theory that self-consistently calculates the correct hydrogen ion distribution by accounting for the appropriate coupling between the brush ionization and local hydrogen ion concentration. We obtain a pair of coupled ordinary differential equations in electrostatic potential and hydrogen ion concentration that are solved numerically to obtain (a) the monomer profile, (b) the distribution of chain ends, (c) the electrostatic potential, and (d) the hydrogen ion distribution. Our results indicate a larger deviation from the results of model 1 at lower bulk salt concentrations and higher pH values. The self-consistent theory always predicts a smaller brush height in comparison to that predicted by model 1. In addition, we observe an enhanced biasness of the monomer concentration profile towards the base than the brush tip.
10:30 AM - BM03.01.09
Multiscale Modeling of Polymer at Solid and Soft Interfaces
The University of Manchester1Show Abstract
The prediction of the adsorption and dynamics properties of polymers at solid and soft interfaces is an important technological and biological problem. Solid interfaces are indeed present in all polymer composites (where particles are dispersed into a polymeric matrix with the aim of improving its mechanical and rheological properties) but also relevant for many applications such as for coating. Polymers adsorb also at liquid interfaces in many industrial processes, such as liquid/liquid extractions, solvent displacement methods, or emulsifications, and also when used for biological applications, such as drug nanocarriers, biocompatibilizers, or protective coatings.
In this talk we will present a set of multiscale approaches developed over the years to predict the adsorption properties of polymers at solid surfaces (specifically carbon black) and soft interfaces (liquid/liquid and lipid membrane).
The aim of the multiscale technique is to balance the need to retain important chemical details allowing long simulations and ultimately to identify design rules to predict the polymer/interface adhesion properties as a function of surface roughness and polymer composition.
M. Zaki, P. Carbone, Langmuir 2017,33, 13284
T. Taddese, P. Carbone, J. Phys. Chem. B, 2017, 121, 1601
T. Taddese, D. L. Cheung, P. Carbone, ACSMacro Lett., 2015, 4, 1089
T. Taddese, P. Carbone, D. L. Cheung, Soft Matter, 2015, 11, 81
11:00 AM - BM03.01.10
Effect of Structural and Material Heterogeneity on Failure in Fibrous Materials
Sai Deogekar1,Mohammad Islam1,Catalin Picu1
Rensselaer Polytechnic Institute1Show Abstract
Fiber networks occur abundantly at all length scales in the biological and non-living worlds. Various applications of such fibrous materials require them to maintain their structural integrity. Hence, an accurate understanding of the factors affecting failure at system subscale is important. Since these materials are structurally stochastic, heterogeneity plays a major role in determining the dominant failure mechanism and affects strength and toughness of the material. In addition, most of these networks naturally occur as composites (e.g. in various types of tissue). Previously, we studied the effect of heterogeneity in the strength of the inter-fiber bonds on the overall network strength. In this work we study the effect of structural heterogeneity and network architecture, on the macroscopic strength and strain-at-failure. We observe that increasing the structural heterogeneity increases the strain-at-failure while the strength remains unaffected. Thus, we propose to use structural disorder of these materials to control their toughness. Further, we investigate the behavior of network-based composites formed by embedding spherical inclusions, rigid or deformable, in a fibrous network. A small fraction of inclusions strongly affects the network stiffness and alters drastically the microscopic deformation and failure mechanisms. This is due primarily to the confinement effect of inclusions on the deformation of the network.
11:15 AM - BM03.01.11
Simulating Polymers with Reactive MD—Cross-Linking, Stress/Strain, Degradation, Solvation
Fedor Goumans2,Adri van Duin1,Nick Austin2
The Pennsylvania State University1,Software for Chemistry & Materials (SCM)2Show Abstract
Reactive molecular dynamics techniques such as ReaxFF afford insight at the atomistic level for complex chemical processes as well as for material properties which involve chemical bond breaking and formation. We will discuss recent developments in the ADF-ReaxFF software in the context of polymers.
A new bond boost method enables the atomistic simulation of cross-linking processes such as epoxy resin hardening at reasonable time scales. The cross-linking densities from these simulations are in good agreement with experiments.
Stress/strain properties and yield points can be obtained with ReaxFF while straining the system, including the underlying atomistic processes. Similarly, degradation rates and mechanisms under extreme conditions can be simulated with ReaxFF.
Finally we will discuss how the information from reactive MD runs, in particular the dynamic charges, may be used to refine our COSMO-RS thermodynamic predictions for solubilities and related properties.
11:30 AM - BM03.01.12
Diffusioosmotic and Thermoosmotic Transport in Nanochannels Grafted with End-Charged Polyelectrolyte Brushes—Continuum Calculations and Molecular Dynamics Simulations
Siddhartha Das1,Raja Maheedhara1,Parth Rakesh Desai1,Haoyuan Jing1,Harnoor Sachar1
University of Maryland1Show Abstract
Liquid flows in nanocahannels grafted with polyelectrolyte brushes have been invariably retarded owing to the significant drag force imparted by the PE brushes. In a recent study, we proposed a paradigm shift in this understanding – we showed that for nanochannels grafted with end-charged brushes (having a charge density of σ), the electroosmotic (EOS) transport got massively augmented as compared to the brush free nanochannels having a wall charge density of σ. We argued that the presence of the end-charged brushes localized the charge density of the induced electric double layer (EDL) and hence localized the EOS body force away from the nanochannel wall, thereby ensuring a massive manifestation of the EOS body force eventually enforcing a larger EOS transport. Here we report our first Molecular Dynamics (MD) simulations based verification of this phenomenon. Furthermore, we carry out continuum calculations for the diffusioosmotic (DOS) and thermooosmotic (TOS) transport in such end-charged PE-brush-grafted nanochannels in presence of an axial concentration and an axial temperature gradient respectively to establish that these transports too get enhanced due to the corresponding enhancement in the induced EOS transport. Furthermore, MD simulations are carried out to validate the continuum findings.
BM03.02: Multiscale Modeling of Soft Materials and Interfaces II
Sanket A. Deshmukh
Monday PM, November 26, 2018
Sheraton, 2nd Floor, Back Bay B
1:30 PM - BM03.02.01
Effect of Solvent on the Molecular Structure and Electrical Conductivity of DNA
Busra Demir1,Sumeyye Gokce1,Hashem M. Mohammad2,Sunil R. Patil3,Yuanhui Li4,Josh Hihath4,M. P. Anantram2,Ersin Emre Oren1
TOBB University of Economics and Technology1,University of Washington2,College of Engineering Pune (COEP)3,University of California Davis4Show Abstract
DNA is a promising molecule for molecular electronics due to its unique electronic and self-assembly properties. Understanding the nature of electrical conductance of DNA is essential for rational design and engineering of these soft materials for use in molecular electronics. The structure of double-stranded DNA (dsDNA) is known to be sensitive to solvent conditions and thus its electrical conductivity. Here, we first used Molecular Dynamics (MD) simulations to determine both the transformation path and the stable molecular conformations of DNA (CCCGCGCCC and TTTATATTT) in various solvent (water-ethanol mixtures) conditions. The MD trajectories revealed that there is a specific ethanol concentration, below which the B form DNA is stable. Above this threshold value, which also depends on the sequence, we observed that A form DNA is the stable form. These observations also validated by the circular dichroism experiments for the same DNA sequences. The MD simulations also revealed that for extremely high ethanol concentrations the DNA helix is destabilized and collapsed. We then selected representative structures along the transformation path using structural clustering algorithms, and calculate the wave functions near the HOMO-LUMO gap using Density Functional Theory (DFT). Finally, we used Green’s functions based transport modelling to analyze conductivity of DNA. Our calculations reveal that the solvent conditions is an important factor that determines the device characteristics because it can significantly change the conformation and conductance of the DNA.
1:45 PM - BM03.02.02
Determining the Binding Mechanisms of All 20 Natural Amino Acids to (hkl) Facets of Hydroxyapatite as a Function of pH
Sam Hoff1,Juan Liu1,Hendrik Heinz1
University of Colorado Boulder1Show Abstract
Mineralization of hydroxyapatite is a complex and highly controlled process involving interactions of biological and mineral components. Understanding the basic interactions between individual amino acids and hydroxyapatite at the (001) and (020) surfaces at pH 7 and 5 is a crucial step in understanding the mineralization process and potentially aiding in designing peptides to direct and control growth of bone allograft and biomimetic materials. In our study, a combination of steered and unrestrained molecular dynamics simulations using the CHARMM36 and Interface force field parameters are used to study the dynamic nature of hydroxyapatite as well as the binding conformations of N and C capped amino acids. The results indicate that charged amino acids have a distinctly higher affinity to the mineral surface than non-charged amino acids. Binding site preferences, conformations, and the effects of pH and surface facet on the affinities are reported, and significant differences for Arginine, Glutamic Acid, Aspartic Acid, and Lysine quantified. The trends provide valuable insight into the affinity and binding mechanism of the building blocks of larger biological structures such peptides and proteins onto hydroxyapatite surfaces. The results will be useful in designing peptides to target specific bone facets for growth or suppression as well as potentially offering the ability to target specific bone sites where infections exist.
2:00 PM - BM03.02.03
Elucidation of the Induced Chirality of Dansylglycine by Its Interaction with Human Serum Albumin
Aguinaldo Souza1,Izabelle Amorin Ferreira Boza1,Valdecir Ximenes1,Maurício Yoguim1,Nelson Morgon2,Ignez Caracelli3
Sao Paulo State University - UNESP1,Campinas State University2,Federal University at São Carlos3Show Abstract
Human serum albumin (HSA) plays an important role in the transport of substances with pharmacological properties due to their high plasma concentration and specificity, placing it as the fundamental protein responsible for the pharmacokinetic implication of the drugs. The dansylglycine amino acid derivative (DG) is a fluorescent marker specific for the II site on the HSA. In addition, when binding to the protein, DG acquires chirality, a feature that can also be used to characterize the binding site of new compounds in albumin. This work aimed to elucidate the induction of chirality in the DG by its bonding to the HSA. Experimental Electronic Circular Dichroism (ECD) spectra of DG (100 μM) in the absence or presence of HSA (30 μM) in 50 mM sodium phosphate buffer pH 7.0 were obtained in a Jasco J-815 spectropololarimeter at 25 o C. The spectra were obtained with a resolution of 1 nm and a scanning speed of 50 nm/min. The theoretical ECDs were simulated using the Density Functional Theory (DFT) approach with the hybrid functional B3LYP and CAM-B3LYP in the base set 6-311 ++ G (2d, p) and the implicit Solvation Model based on Density (SMD) for the solvents ethanol, methanol, acetonitrile, water and tetrahydrofuran; the calculations were performed with the Gaussian09 program. The DG-HSA complex formation in buffer resulted in the appearance of a positive ECD spectrum centered at 346 nm. Considering that the ICD signal should arise from a chiral conformation of the DG acquired by binding in the protein, calculations were initially performed to obtain the stable conformations focusing on the inversion of configuration centered on the nitrogen atom: alpha-amino group. However, both configurations: R and S showed similar and positive ECD signals. Calculations of the potential energy surface (PES) of the DG were performed, focusing on the dihedral angles formed by the bonding of the -N(CH3)2 group of the naphthalene ring. The analysis of the various conformations obtained and their respective theoretical ECDs revealed that the 150 ° dihedral (ECD positive centered at 320 nm) presented excellent similarity with the experimental spectrum. On the other hand, the 80° dihedral showed a signal of the ECD spectrum opposite to that observed experimentally. In addition, we observed that the nitrogen atom of the -N(CH3)2 group presented the greatest contribution to the HOMO-LUMO transition that gives rise to the n-pi * electronic transition involved in the generation of the ECD signal. The molecular docking analysis, using the GOLD 5.5 program, of the complexation between DG and HSA revealed a conformation with a dihedral similar (150 °) to that obtained theoretically (DFT) and whose ECD is in agreement with the experimental result. In conclusion, through the study of the possible conformations for dansylglycine and the calculation of its theoretical ECD, it was possible to identify the origin of the ECD signal obtained by the complexation between DG and HSA.
2:15 PM - BM03.02.04
Understanding Malaria Pathogenesis Through Coarse-Grained Computational Modeling
Sulin Zhang1,Yao Zhang2,Leann Tilley3,Ju Li4,Subra Suresh5
The Pennsylvania State University1,Northwestern University2,The University of Melbourne3,Massachusetts Institute of Technology4,Nanyang Technological University5Show Abstract
A normal human red blood cell (RBC) is characterized by two distinct features: high deformability and discocyte shape, which underlie its biological functions, demonstrated by the repeated transit of RBCs (diameter ~8 mm) through narrow capillaries and and 1-2 mm interendothelial slits in the spleen. These two distinct features of RBCs can be comprised genetically or in a variety of pathological conditions, leading to severe RBC diseases. Here we present a coarse-grained RBC membrane model integrating an one-agent-thick lipid bilayer model and a string-of-bead spectrin network model to simulate the change of deformability of the infected RBCs by the malaria parasites (plasmodium falciparum). In particular, we show how malaria parasites harness several materials principles simultaneously to render the RBC losing its deformability during asexual stage (disease-causing stage) and how the parasites alter the entropy of the spetrin network to enable the RBC regain the deformability during the sexual stage (disease-transmission stage). Our simulation results suggest potential targets for the development of new antimalarial therapies
3:15 PM - BM03.02.06
Structure and Dynamics of Polymers in Ionic Liquids
University of Wisconsin1Show Abstract
Ionic liquids have generated considerable excitement for their varied potential applications and their interesting physical properties. The viability of ionic liquids (ILs) in materials applications is limited by their lack of mechanical integrity, which may be provided by mixing them with a polymeric material. Recent experiments on polymers in ILs have unearthed a wealth of interesting phenomena that raise fundamental questions. This talk focuses on computational studies of PEO in imidazolium ILs. We develop a physically motivated first principles force field for PEO and [BMIM] [BF4]; this force field is in quantitative agreement with experiment with no adjustable parameters. Based on the same quantum calculations we develop a hierarchy of united atom models with decreasing resolution and increasing computational efficiency. Microsecond simulations are required to obtain converged properties of the polymer, which displays a combination of ring-like and extended conformations. The simulations show the existence of a lower critical solution temperature which arises from conformational restrictions on the polymer molecules at low temperatures.
3:45 PM - BM03.02.07
Behavior of Polyethylene Glycol in Bulk and in Water as Studied by Multi-Scale Simulations
Trakya University1Show Abstract
Polyethylene glycol (PEG) is an important polymer that has an enormous area of application especially in biomedical field such as drug carrier agent, hydrogel, and tissue engineering material. A thorough understanding of the molecular structure of PEG at different environments is important to devise better routes to develop materials with desired purposes. Although, PEG has been a widely studied material its molecular structure in bulk and in aqueous environment has been poorly investigated. In this work, we strive to perform multi-scale molecular simulations in order to study the physical behavior and molecular structure of PEG in dry environment and interacting with water. We initially perform Dissipative Particle Dynamics (DPD) simulations to create the structure of PEG. Later, we perform reverse-mapping of the atomistic coordinates to perform atomistic molecular dynamics simulations in order to observe the chain configurations and material properties of PEG.
DPD simulations result in successful prediction of the negative volume excess of PEG upon mixing with water. Here, we use a recent extension of the DPD method, where the non-bonded potential of DPD is modified by a Morse potential term to mimic the intermolecular attraction. The parameterization of the Morse potential is done by a mapping of the mixing energies of different hydrogen bonding bead pairs and from radial distribution functions (RDF) for the energy and equilibrium hydrogen bond length terms, respectively. DPD simulations yield preferential attraction of some chemical groups to water as quantified by radial distribution functions. Moreover, PEG chain structure is observed to deviate significantly from a random coil structure as a result of the end-to-end distances and radius of gyration values. Moreover, DPD simulations reveal that water plays a significant role in increasing the flexibility of PEG chains. The helical structures of PEG chains are quantified and a significant helicity of PEG chains is noted with a higher fraction in wet environment.
The reverse-mapped coordinates of DPD simulations of bulk PEG structure are used in atomistic simulations to compute the material properties such as coefficient of thermal expansion, elastic modulus and Poisson’s ratio. The computed coefficient of thermal expansion is in line with the experimental prediction. The computed values mainly reveal that PEG becomes more elastic and less compressible upon addition of water. In addition, the experimental aggregation of water in PEG is observed from MD simulations. In all, the multi-scale procedure predicts the structural and material properties of a widely used PEG in dry and wet environment. The procedure presented herein can be applied to similar materials to gain a molecular and macroscopic understanding of their properties.
4:00 PM - BM03.02.08
Machine Learning Methods to Design Next-Generation Gas Separation Membranes
Columbia University1Show Abstract
Machine Learning (ML) has been used for quite some time in analyzing large sets of data in a variety of disciplines in order to make predictions on new data. Although gas permeability data has been collected for polymer membranes for decades, only hundreds of data points are available in the literature out of the thousands of possibilities. In order to address the intractability of running thousands of different gas permeability studies, we use ML to build a model on existing data and predict which untested polymers are most likely to achieve superior gas separation performance.
4:30 PM - BM03.02.09
Using Gel Actuated Smart Capsules for Particle Capture
Svetoslav Nikolov1,Alberto Fernandez-Nieves1,Alexander Alexeev1
Georgia Institute of Technology1Show Abstract
Advancements in nanotechnology over the last two decades have allowed researchers to tackle a number of critical biomedical problems on the microscale, like site-specific drug delivery and micro-sensing. Microdevices which can selectively capture nanoparticles at a given rate are particularly interesting as they are critical for the development of enzymatic bioreactors which are used in many in vivo micro-sensing applications. These devices could also be used for origin of life studies, where the ability to bring in particles at predefined rates can be used to carry out complex chemical reactions. In our work, using dissipative particle dynamics, we leverage the large volume changes of microgels to design a novel microdevice which can be used for nanoparticle capture. Our device is made up of a perforated rigid spherical shell that is embedded with a spherical microgel. Upon application of an external stimulus the gel swells, expanding through the perforated holes and making contact with the external nanoparticle rich solution. After removal of the external stimulus the microgel collapses into the shell interior, bringing along with it nanoparticles from the external solution. The area around each of the perforations is functionalized with a polymer brush which is used to achieve chemical gating, when the gel is in the collapsed state. We study how the capture rate depends on the swelling period and gel-nanoparticle interactions and we quantify the optimal swelling period which maximizes capture rates.
Project supported by the National Science Foundation of U.S.A. (DMR-1255288, TG-DMR180038, and DGE-1650044)
BM03.03: Poster Session: Multiscale Modeling of Soft Materials and Interfaces
Sanket A. Deshmukh
Monday PM, November 26, 2018
Hynes, Level 1, Hall B
8:00 PM - BM03.03.01
Confinement Effect of Nanoscale Biological Systems
Nima Rahbar1,Arvand Navabi1
Worcester Polytechnic Institute1Show Abstract
The nanoscale molecular dynamics of the confined organic matrix in the biological material, nacre and its contribution to the exceptional toughness of this biomaterial has been studied. While under stress, the dynamics of the nanoscale structure of nacre have significant influence on the energy dissipation of the system and ultimately on the fracture toughness of the material. For better understanding these mechanisms, a solution of the c-domain consensus of the protein, Lustrin A, was confined between two ceramic layers of aragonite by employing molecular dynamics computations. Then the aragonite walls were subjected to shear, and the polymeric system responded by unfolding. This study reports increase in the energy dissipated through unfolding mechanisms of the protein system as the confinement size decreases. The dominant energy dissipation method in larger systems transition from unfolding to polymeric interactions and entanglements.
8:00 PM - BM03.03.02
2D Powerless Capillary Microchannel Device for Efficient Capture of Circulating Tumor Cells
Northeastern University1Show Abstract
Introduction: Liquid biopsy of circulating tumor cells (CTCs) can help find cancer at an early stage and determine whether treatment is effective or not. Secondary microscale features such as micropillars, microstripes and silicon nanowires, microfluidic channels can be functionally modified with cell selective species such as anti-epithelial cell adhesion molecules (Anti-EpCAM) and aptamers to enhance efficacy of CTC capture. However, the surface bound cell adhesion molecules have less flexibility to interact with receptors over-expressed on the surfaces of flowing cancer cells, leading to low capture efficiency. Meanwhile, the microfluidic devices require sophisticated processes to make and accessory such as pumps and tubing to work, which makes microfluidic device not an ideal tool for point-of-care diagnosis and prognosis.
This work describes a method for efficient capture of CTCs from human whole blood using a two dimensional (2D) capillary microfluidic device modified with long chain polymers that have cell-adhesive terminals. The height of microchannel is designed to approximate the diameter of single cells. Given its low cost, easy operation, repeated usage, and zero-power consumption, this device would find its use at points-of-care.
Results: CEM cells solution with PBS was studied in channels with different heights and capture efficiency is inversely proportional to channel height to the second power which agrees well with the modeling of cell sedimentation in channels. Cells are injected in channels by flow and the flow filling time in our device is not long enough to let all the cell settling. The 30 μm channel can achieve 95% capture efficiency. This optimal parameter was applied in cell capture in human blood. Figure 2 shows fluorescence images of CEM cells captured on folic acid modified channel The capture efficiency of the channel has calculated to be 88.3 ± 14.6% for CEM cells in spiked blood with concentration of 5×106 cell/ml and 90±4% with concentration of 5,000 cell/mL. CEM cells are found firmly attached on the substrate. The capture efficiency agrees well with the assumed theory of cell rolling and cell sedimentation.
Conclusions: Circulating tumor cells (CTCs) spiked in human blood can be captured efficiently with 2D capillary microchannel device which was modified with polymer brush. Blood or cell suspension can be sucked in the channel by capillary force. The kinetics of channel filling for buffer solution containing cells agreed with theoretical models. The capture efficiency decreases with increased height of channel due to cell rolling and tethering in microchannels. In high channel, less cells are captured by cell rolling and tethering while more cells have ligand receptor reaction by cell settling. The polymer brush modified glass can be easily dissembled for further analysis of captured cells. This non-sealing and pump-less device does not have blocking or leaking problems as normal fluidic device.
8:00 PM - BM03.03.03
The Effect of Microenvironment Stiffness on Oligodendrocyte Differentiation
Massachusetts Institute of Technology1Show Abstract
Understanding how a cell senses its environment is key to understanding how it acts and responds to different stressors, such as changes of pH, temperature, or concentration of small molecules. Oligodendrocytes are a type of glial cell found in the central nervous system; they are responsible for wrapping axons in myelin, a sheath that allows neurons to effectively transmit electrical impulses in the brain. Oligodendrocyte dysfunction leads to debilitating diseases such as multiple sclerosis. Polystyrene petri dishes, which are currently used to culture and study these cells, are poor models of the brain (e.g. the Young’s Modulus of polystyrene is approximately 106 times larger than that of the brain). It is hypothesized that this lack of biomimicry may contribute to inaccurate or incomplete understandings of oligodendrocyte and myelin biology, as well as hinder the pace of therapeutic development. The goal of this research is to help bridge that gap of understanding by studying the effect of various mechanical cues on the differentiation and myelination of human oligodendrocyte cells. Here we fabricate and characterize various substrates that recapitulate key physical properties of the oligodendrocyte microenvironment. Human oligodendrocytes are derived from induced pluripotent stem cells and cultured in these engineered microenvironments. The extent of differentiation and myelination is assessed via immunocytochemistry and fluorescence microscopy. These results may help lead to more effective methods to culture human oligodendrocytes, and shed light on how these cells may respond to pathological mechanical changes in the in vivo environment.
8:00 PM - BM03.03.04
Continuous Elasto-Capillary Clustering of Tilted Nano-Pillars
Sang Moon Kim1,Junsoo Kim2,Seongmin Kang3,Daeshik Kang4,Segeun Jang5,Seung Eon Moon6,Hong Nam Kim5,Hyunsik Yoon7
Incheon National University1,Harvard University2,Chungnam Univ.3,Ajou Univ.4,Korea Institute of Science and Technology5,Electronics and Telecommunications Research Institute6,Seoul National University of Science and Technology7Show Abstract
Complex structures of clustered micro/nano pillars from the elastocapillarity have been extensively studied for the application of mechanical electrical micro system devices and sensors systems. Herein, we investigate the unidirectional clustering property of initially slanted nanopillars. The deionized water droplet was dispensed onto the slanted nanopillars fabricated by using of Faraday cages and was dried off to generate cluster formation of the patterns. We observed non-continuous clustering of the low-tilted (initial tilting angle of ~0° and ~15°) nanohairs and unidireictional clustering of the nanopillar arrays with tilting angles of ~30° and ~45°. We proposed theoretical model to analyze the unidirectional cluster formation and set a criterion for a unidirectionality. Furthermore, we predicted the shape of clustered pillars for the case of the non-continuous clustered pillars based on our proposed model.
8:00 PM - BM03.03.05
Investigation of Self-Assembly of Polypeptoids in Aqueous Solution—From Atomistic to Coarse-Grained Simulations
Pu Du1,Revati Kumar1
Louisiana State University1Show Abstract
Polypeptoids or poly N-substituted glycines are a type of peptidomimetic polymers that are highly tunable, and hence an ideal model system to study self-assembly as a function of chemical groups in aqueous soft matter systems. In this study, atomistic simulations were performed on sequence-defined ionic peptoid block copolymers consisting of a hydrophobic and a hydrophilic segment (with one singly charged and the remaining uncharged polar groups) in aqueous solution. These studies revealed that the placement of the charged moiety on the polymer chain affected the micellar structure and shape. However, the computational expense limits simulation times and system sizes to a hundred nanoseconds and tens of nanometers, respectively, necessitating the development of coarse-grained models to study more complex polypeptoids with multiple types of hydrophilic side groups. A coarse-grained (CG) model for N, N-dimethylacetamide (DMA), which represents the polypeptoid backbone, is developed as a step towards developing a CG model of the complex polypeptoids system. The DMA CG model is parameterized to reproduce the structural properties of DMA liquid as well as a dilute aqueous solution of DMA using a reference all atom model, namely the OPLS-AA force-field. The intermolecular forces are represented by the Stillinger-Weber potential, which consists of both two- and three-body terms that are very short-ranged. The model is validated on thermodynamic properties of liquid and aqueous DMA, as well as the vapor-liquid interface of liquid DMA and the structure of a concentrated aqueous solution of DMA in water. Without long-ranged interactions and the absence of interaction sites on hydrogen atoms, the CG DMA model is an order of magnitude faster than the higher resolution all-atom (AA) model.
8:00 PM - BM03.03.06
Artificial Exosomes—Tailored Conjugation of Fusogen to Lipid/Polymer Hybrid Vesicles for Enhanced Drug Delivery
Jeong Yi Kang1,Jin Woong Kim1
Hanyang University1Show Abstract
The development of a wide spectrum of nanoscale technologies is beginning to change the scientific landscape in terms of disease treatment. The small size, customized surface, improved solubility, and multi-functionality of nanoparticles will continue to open many doors and create new biomedical applications. Indeed, the novel properties of nanoparticles, including carbon nanotube, nanofibers, self-assembling polymeric constructs, liposome, and nano-sized silicon chips, offer the ability to interact with complex cellular functions in new ways. Among them, recent technology pays attention to exosomes, nano-sized vesicles that are released from various types of cells into the extracellular space, since they are able to provide a practical means of intercellular communication and transmission of macromolecules between cells. Moreover, they are able to act as useful vectors for drugs because they are composed of cell membranes, rather than synthetic polymers, and as such are better tolerated by the host. In this study, we propose an exosome-analogous drug delivery system which is established by using lipid/polymer hybrid vesicles with fusogenic peptide conjugates. The lipid/polymer hybrid vesicles are fabricated by co-assembly of phosphatidylcholine and poly(ethylene oxide)-b-poly(caprolactone)-b-poly(ethylene oxide). Thanks to large size and slow dynamics of amphiphilic triblock copolymers at the bilayer membrane, the hybrid vesicles show long-circulating time and high drug loading efficiency. Fusogenic peptide, penetratin, induces vesicular interaction with cell membrane, thus enhancing cellular uptake. To evaluate the cell affinity of fusogenic exosomes, the interaction force between an exosome and a cell is characterized via microscale thermophoresis. Finally, in vitro cell-penetration study demonstrates the practical applicability of our artificial exosome as a remarkable cell delivery nanocarrier.
8:00 PM - BM03.03.07
Systematic Control of Flory-Huggins Interaction Parameter of Block Copolymer Forming Sub-10 nm Perpendicular Lamellar Pattern
Seung Won Song1,Yoon Hyung Hur1,Yeon Sik Jung1
Korea Advanced Institute of Science and Technology1Show Abstract
Directed self-assembly of block copolymer is one of the most promising candidates for sub-10 nm scale lithography due to its cost effectiveness and nanometer scale pattern resolution. However, further improvements of line edge fluctuation and pattern resolution to sub-10 nm region of Poly(styrene-b-methyl methacrylate) (PS-b-PMMA) block copolymer remain as critical challenges. To improve pattern resolution, higher Flory-Huggins parameter (χ) is required. However, too high of χ value induces horizontal lamellar pattern which cannot be used in devices. Therefore, deliberate design of block copolymer with medium χ value is required so that χ value is high enough to achieve sub-10 nm pattern formation and small enough to prevent horizontal lamellar pattern. Here, we suggest a newly designed block copolymer that can form sub-10 nm perpendicular lamellar pattern which is aligned by graphoepitaxy template. The block copolymer was synthesized by reversible addition-fragmentation chain-transfer polymerization copolymerized with fluorine containing monomer, which is hydrophobic. The modified block copolymer showed controlled χ value as the fraction of hydrophobic monomer changed. Block copolymer pattern with sub-10 nm feature size could be achieved due to a three times higher χ value than the conventional PS-b-PMMA. Even though the newly synthesized block copolymer has a high χ value, the polymer could form perpendicular lamellar morphology by short thermal annealing.
8:00 PM - BM03.03.08
Theranostic Pluronic Nanoparticles for Glioblastoma Treatment—Synergic Application of Chemotherapy and Photodynamic Therapy
Diogo Pellosi1,Leonardo de Paula2,Maryanne de Melo2,Danielle Mota1,Giovanni Lima1,Antonio Tedesco2
Federal University of São Paulo1,University of São Paulo2Show Abstract
Despite advances in the fight against cancer, glioblastoma multiform treatment continues inefficient due inhibitory activity of brain-blood barrier (BBB) that causes low efficacy and selectivity for temozolomide (TMZ) chemotherapy. In order to improve therapeutic outcomes aiming side effects reductions the present work followed two strategies: (i) the use of theranostic pluronic nanoparticles and (ii) application of photodynamic therapy (PDT) as adjuvant treatment. Pluronic P85/F127 nanoparticles were engineered as multifunctional theranostic/targeted nanoparticles (m-NP) through the chemical functionalization of its surface with biotin (target moiety) and rhodamine-B (fluorescent probe). The chemical-modified pluronic copolymers self-assembly into m-NP that present the advantage of overcoming BBB and encapsulate multiple cargo for the application of multiple tumor treatment modalities with an optimized drug ratio. In addition, PDT characteristics such as its high selectivity upon light-driven activation and the non-development of cross-resistance mechanisms make it a valuable option as adjuvant for TMZ chemotherapy. m-NPs formulations were firstly optimized to obtain best drug loading conditions (for both TMZ and PDT agent) and formulation long-term stability. In these studies we demonstrated that lyophilization of formulation was the best methodology to obtain a longer shelf life for the proposed system. Due theranostic characteristics of m-NP and PDT agent, in vitro confocal microscopy studies on U87-MG, T98-G, U343 glioblastoma cells and NHI-3T3 fibroblast as control were evaluate in order to understand m-NPs role in uptake and intracellular drugs distribution. Uptake experiments demonstrated that the proposed nanoparticle possess higher affinity toward cancer cell lines in detriment of the non-tumor cell line NHI-3T3. In addition, confocal images revealed a broad intracellular distribution for both m-NP and encapsulated drugs at cells cytoplasm, but not in the nucleus. Blank formulations were not cytotoxic while formulations containing TMZ or PDT agent separately presented a reduced effect in cell viability. Nevertheless, PDT/TMZ concomitant treatment presented high efficiency due their synergic action even at low and safe drug concentrations. As demonstrated by flow cytometry experiments, this synergism is due to the different mechanisms of action of each proposed drug in the cell cycle arrest and their selective/controlled delivery at the intracellular level. In conclusion, these results point m-NP are a promising nanostructure to carry different drugs and selectively release encapsulated cargo in cancer cells.
8:00 PM - BM03.03.09
Computational Design of Dendron-Grafted Soft Materials-Based Nanoparticles
Akash Banerjee1,Meenakshi Dutt1
Rutgers, The State University of New Jersey1Show Abstract
Many drug delivery strategies demand the need for the adsorption and transport of charged, therapeutic biomolecules. These requirements can be met by nanoparticles (NPs) encompassing multiple molecular species that endow electrostatically-induced interfacial binding of specific biomolecules. We are interested in understanding the role of the architecture and composition of the molecular species on the morphological characteristics of the NPs. We study multicomponent NPs encompassing phospholipids and lipids bearing hyper-branched polyelectrolytes (namely, polyamidoamine (PAMAM) dendrons) via the Molecular Dynamics simulation technique. The bonded and non-bonded interactions between the particles is captured by the Martini force field. We examine the impact of interfacial area, dendron generation and relative concentration on the NP morphology. Our studies can potentially guide the design of multicomponent amphiphile-based nanoparticles for applications in medicine and environmental sustainability.
8:00 PM - BM03.03.10
A Multiscale Approach to Study Molecular and Interfacial Characteristics of Colloids
Meenakshi Dutt1,Xiang Yu1
Rutgers, The State University of New Jersey1Show Abstract
The functions of colloidal particles are dictated by interfacial properties which are determined by an interplay of physical interactions and processes spanning multiple spatiotemporal scales. The multiscale characteristics of colloidal particles can be resolved by the hybrid Molecular Dynamics- Lattice Boltzmann technique. This technique enables the resolution of the particle dynamics along with long range electrostatic and hydrodynamic interactions. We have examined the feasibility of an implementation of the hybrid technique to capture the molecular and interfacial characteristics of colloidal particles, such as vesicles. For simplicity, we have examined two types of vesicles whose molecular components have different sustained interactions with the solvent. One of the vesicles encompassed phospholipids and the other vesicle was composed of phospholipids and poly ethylene glycol (PEG)-grafted lipids. The molecular and interfacial characteristics of the phospholipid vesicle and PEGylated, or hairy, vesicles are found to be in good agreement with earlier experimental, computational and theoretical findings. These results demonstrate that the multiscale hybrid technique is suitable for capturing the molecular and interfacial characteristics of colloidal particles. The results of our investigations demonstrate the potential of the hybrid technique in capturing multiscale interfacial characteristics of intra- and inter-colloid interactions in suspensions under different flow conditions, and their relation to molecular properties.
8:00 PM - BM03.03.11
Rational Surface-Anchored Cross-Linking of Nanogel Framework for RhD-Epitopes Stealth Red Blood Cells
Yueqi Zhao1,Mingjie Fan1,Ben Wang1,Ruikang Tang1
Zhejiang University1Show Abstract
The Rhesus D (RhD) as well as A and B antigens are important immunogenic epitopes on red blood cells (RBCs) which need type matching during blood transfusion, and mismatching will lead to fatal reactions. Producing antigen negative RBCs, which are universal for transfusion, are necessary especially in emergent situation. While the conversion of A and B antigens into immunity negative cells have been achieved, however, the transition of D-positive cells to D-negative is still problematic. To solve the problems in transfusion, we developed a rational approach to shield the antigens on the Rh D-positive RBCs for D-negative blood production by using the surface-anchored and cross-linked nanogel framework. A thin and uniform nanogel layer,which is consisted of alginic acid and tyramine, was constructed on individual RBCs catalyzed by surface-anchored enzyme. The physical and biological properties of modified RBCs were similar with native RBCs. More importantly, the D antigens on surface of engineered RBCs were shielded completely by the framework layer, preventing the recognition of immune system both in vitro and in vivo. The distribution of “the D-negative blood” in tissues including heart, liver, spleen and kidney was similar with native ones in blood circulation. The resulting stealthy effects achieve complete sheltering of blood group D antigens on RBCs membrane, providing a potential methodology of cell surface engineering for universal blood transfusion regardless of blood types.
8:00 PM - BM03.03.12
Lipid Morphology in Solid Lipid Nanoparticles
Demi Pink1,Jayne Lawrence2,1,Christian Lorenz1
King's College London1,University of Manchester2Show Abstract
Solid lipid nanoparticles (SLN) first came to attention in 1991 as they were considered promising particles to investigate with regards to potential applications in drug delivery. These nano-colloidal particles are typically spherical and are comprised of a solid lipid core. This solid lipid core is not perfectly crystalline and so it contains defects which can be used to trap and solubilise lipophilic and hydrophobic drug molecules. Surfactant molecules are then utilised to further stabilise the lipid core. The exact properties of SLN depend on their composition and preparation, with lipid and surfactant selection being key in the development of non-toxic, stable nanoparticles. Since SLN properties can be modified by using different lipids and surfactants, SLN can be optimised for encapsulation and delivery of specific molecules. Whilst the potential for their use in healthcare has been the dominant area of research, there are also options for the application of SLN in a range of other industries, including cosmetics and agriculture.
A significant challenge concerning the use of SLN in drug formulations is the tendency of the solid lipids to converge towards a perfectly crystalline lattice when stored over time. This is due to the increased thermodynamic stability this confers. However, the transition towards a perfect crystalline lattice removes the defects in which the drug molecules are stored. This can result in the expulsion of the drug molecules during storage or rapid expulsion of the drug upon administration, potentially rendering them ineffective. The triglycerides used in SLN can exist in 4 distinct conformations and by examining the conformations of triglyceride in the SLN we aim to better understand the mechanisms behind drug encapsulation and drug expulsion.
This work uses molecular dynamic simulations to investigate the overall morphology of the SLN as well as looking closely at the conformation of lipids in solid lipid nanoparticles. Through this we have gained a detailed understanding of the role of lipids within SLN. By modifying the temperature of our simulations we were able to compare the conformations of lipids in both liquid and solid lipid aggregate as well as in the SLN. This simulation worked is paired with experimental work in order to develop a multi-scale and experimentally relevant understanding of solid lipid nanoparticles.
8:00 PM - BM03.03.13
Design Guidelines of Optoelectronics Devices Based Triboelectrification
Abdelsalam Ahmed1,Islam Hassan1,Ali Radhi1,Jean Zu2
University of Toronto1,Stevens Institute of Technology2Show Abstract
Triboelectric nanogenerators (TENGs) are a new power generation technology with high affinity to ambient energy harvesting from the surrounding media. This has driven many researchers towards coupling such technologies into numerous electronic devices, introducing the field of tribophototronics. An analytical framework has been established for practical evaluation of the multiphysics aspects of tribophototronics devices. The work shows the numerous operating modes of TENGs and their impact on the electrical performance from structural, material and ecological perspectives. Scalability, electrical regulatory systems, supply channel control features are presented. The attributed properties of lightweight, low-cost, high material selections will be shown to have a significant impact on tribophototronics devices.
8:00 PM - BM03.03.14
Corrosion Modelling of Ti-20Zr in Body Environment Conditions
Julia Mirza Rosca1,Hosam Sakr1,Alexandru Pascu2,Elena Stanciu2
University of Las Palmas de Gran Canaria1,University Transylvania of Brasov2Show Abstract
Zr alloy was evaluated because it has been suggested as a candidate for human body implant material and was primarily developed in response to concerns of potential cytotoxicity and adverse tissue reactions caused by vanadium and aluminium in the actually used biomaterial Ti-6Al-4V.
The Ti-20Zr alloy (donated by RD&D, Bucharest, Romania) was obtained by vacuum melting. The cylindrical electrodes were obtained and embedded in a resin. The specimens are ultrasonically cleaned using deionized water, and etched in Kroll reagent containing 10 ml of HF, 5 ml of HNO3 and 85 ml of water for microscopic observation, using an Olympus PME 3 – ADL microscope.
The microstructure and microhardness were determinated and the tensile strength was evaluated. The electrochemical behaviour has been evaluated in simulated body fluid (SBF) using Electrochemical Impedance Spectroscopy technique (EIS).
From metallographical images can be observed that the sample has an alpha-beta structure.
From microhardness measurements can be concluded that the alloy formed a hard layer on its surface which greatly improves the wear resistance.
The alloy exhibits brittle fracture and yield stress was equated to ultimate tensile stress. The obtained tensile strength can be considered good in relation with other similar implant materials.
The impedance spectra were fitted with two time constants equivalent circuit and the fitting parameters indicate long-term stability of the passive layers in surgical implant conditions.
The results were confirmed by mechanical approach, in terms of two-layer model of the oxide film, consisting of a thin barrier type inner layer and a porous outer layer. The pronounced porous outer layer is expected to facilitate the incorporation of mineral ions and to improve the resistance to electrochemical corrosion over the potential of relevance for human body conditions.
8:00 PM - BM03.03.15
MD Simulation and Cellular Potts Model for Neuronal Differentiation on Polymeric Nanoscaffolds
Wu Qi1,Pegi Haliti1,Debika Debnath1,Bhushan Dharmadhikari1,Prabir Patra1
University of Bridgeport1Show Abstract
Over the past decades, a great progress has been made in the field of tissue engineering and regenerative medicine especially in the differentiation and proliferation of stem cells into desired lineages in vitro on 2D scaffolds. The purpose of this study is to simulate and design of nanofibrous Polycaprolactone-Graphene (PCL-G) scaffolds, for neuronal differentiation and investigate subcellular and cellular level interactions of cells with the scaffold using MD simulation and Cellular Potts Model (CPM). We explore the interactions between PCL, graphene, and F-actin towards better understanding of neuron cell mobility on PCL-G scaffold. F-actin protein is associated with controlling the mobility and influences the dendritic spines for neuronal cell. Here we use VMD (Visual Molecular Dynamics) for modeling and visualization, NAMD for Molecular Dynamics (MD) computations and Cellular Potts Model (CPM) for cell-cell, cell-scaffold interaction study. After 10ns of MD simulation data and trajectory visualized in VMD, we observed that PCL chains shows affinity towards graphene sheet and try to fit into the graphene sheet. Further, we plan to repeat MD simulations using different sizes of graphene sheet allowing further to investigate the interactions between F-actin and PCL-G. For the CPM simulation, the interactions such as cell-cell, cell-scaffold adhesion and cellular motility contribute to the system’s energy given by a function known as Hamiltonian which manages the lattice rearrangement using the stochastic Monte Carlo’s probabilistic model by minimizing the system’s total energy. In our simulation we set 1 pixel to correspond to 4μm and the time, which is given by Monte Carlo Steps (MCS), to corresponds to 2s of the real experimental time. One simulation is set for as long as 12h to also consider that cells can undergo duplication or apoptotic events. We found out that the cells are moving and changing their shapes, their mobility and growth. More investigations are underway on altering cell-cell and cell-scaffold adhesion energy that can be the key on achieving an alignment of cells on the scaffold and migration afterwards.
8:00 PM - BM03.03.16
Supercoiled DNA with Mismatched Base Pair—Probing the Role of Structural Defect on Plectoneme Pinning by Molecular Dynamics Simulation
Parth Rakesh Desai1,2,Siddhartha Das1,Keir Neuman2
University of Maryland, College Park1,National Institutes of Health2Show Abstract
Mismatched base pairs in DNA can result in mutations. Mismatched base pairs are recognized by the MutS enzyme, which initiates the mismatch repair pathway. MutS recognizes mismatches through a process that involves introducing a sharp bend and flipping out a DNA base at the mismatch site. Single-molecule magnetic tweezers-based DNA supercoiling measurements found that plectonemes nucleate, and are localized, at a mismatch. Localizing the mismatch at the end of the plectoneme loop may facilitate mismatch detection by MutS due to the stabilization of the bent and base-flipped out configuration. The plectoneme end loop containing a mismatch can kink more easily, which reduces the energy of the end loop. However, these experiments were limited to positively supercoiled DNA at salt concentrations of 0.5 M NaCl and higher. Theoretical studies predict that for positively supercoiled DNA under physiologically relevant conditions, i.e., at salt concentrations of 0.2 M NaCl, plectoneme nucleation at the mismatch becomes probabilistic rather than deterministic. Here, we use molecular dynamics simulations to study the effect of a mismatched base pair on DNA supercoiling. We employ the oxDNA model to simulate DNA under torsional stress. The oxDNA model is a coarse-grained model in which each nucleotide is treated as a rigid ellipsoid with three interaction sites. The oxDNA model has been shown to accurately reproduce the response of an intact DNA to both negative and positive torsional stress. To model a mismatched base-pair we eliminate hydrogen bonding between the two nucleotides. Using this modification of the oxDNA model, we first determine the effect of a mismatched base-pair on the bending free energy of a short 15 base-pair DNA and compare the results to atomistic simulations. We find that the bending free energy of a short DNA containing a G-T mismatch is close to the bending free energy predicted by atomistic simulations. We then perform simulations of a 600 base-pair DNA with 0, 2, 4 and 6 consecutive mismatched based pairs. We find that for positively supercoiled DNA at high salt, i.e., 1 M NaCl, the plectoneme always localizes at the mismatch, in good agreement with experiments. Extending this framework to study the case of both positively and negatively supercoiled DNA at 0.2 M NaCl, we find that plectoneme localization at the mismatch indeed becomes probabilistic. We will present the relation between the probability of plectoneme localization and the number of mismatches in addition to an analysis of the shape of end the loop of the plectoneme for different mismatches.
8:00 PM - BM03.03.17
Bioinspired Multifunctional Surfaces for Versatile Optical Applications
Chungnam National University1Show Abstract
The capability of fabricating multifunctional polymeric structures has great advantages to satisfy the increasing demand for flexible and wearable energy conversion devices, electronics and displays. In this work, we have demonstrated a novel fabrication method for structuring bioinspired multifunctional moth-eye TiO2/PDMS pad by using conventional lithography, imprinting, and thin sacrificial layer. It is noted that the embedded TiO2 nanoparticles acted as an effective UV-protector. As a result, the high energy UVB-light is perfectly blocked by the embedded TiO2 nanoparticles and the UVA-light is partially penetrated though the surface. Also, the moth-eye inspired nanostructures on the surface show high transparency in a visible wavelength range as well as self-cleaning effect due to nano-roughness on the surface. Further, we successfully fabricated hierarchical structured surface, where we want, by controlling partially-cured region using the multifunctional polymeric pad with partial blocking property of UVA ray.
8:00 PM - BM03.03.18
Temperature-Independent Zero-Birefringence Polymer and its Compensation Mechanism for Temperature Dependence of Birefringence
Kenji Wada1,Akihiro Tagaya1,Yasuhiro Koike1,2
Keio University1,Keio Photonics Research Institute2Show Abstract
Optical polymers are used as key materials for liquid-crystal displays (LCDs) due to their ease of processing, high transparency, and low-cost. Most of polymers exhibit orientational birefringence because polymer chains tend to become oriented by processing. In LCDs, the birefringence in polarizer protecting films cause light leakage. This light leakage decreases the contrast ratio and increases color shift depending on the viewing angle. Therefore, orientational birefringence of the polymers is ideal to be zero for LCDs. Orientational birefringence is always zero no matter how much a polymer is orientated by processing if intrinsic birefringence Δn0 which is a specific value of each polymer is zero. Our group proposed and synthesized zero-birefringence polymers (ZBPs) which exhibited almost no Δn0 . Recently, we found temperature dependence of Δn0 of the polymers . It becomes a problem for in-car LCDs which generally require no birefringence in the large temperature range from around −40 to 85°C, compared with the range for interior LCDs. However, the mechanism of temperature dependence of Δn0 has not been clarified. For synthesis of temperature-independent zero-birefringence polymers (TIZBPs) which exhibited almost no Δn0 in the wide temperature range, the detail clarification of the behaviors of polymer molecules is necessary. The purpose of this article is clarification of the mechanism of temperature dependence of Δn0 for design and synthesis of TIZBP by the method of birefringence compensation.
Poly(methyl methacrylate (MMA) /benzyl methacrylate (BzMA)) and poly(MMA/phenyl methacrylate (PhMA)) in various composition ratios were synthesized. Then, uniaxial heat-drawn films of these copolymers were made. Absorbance spectrums in IR region of the copolymer films were measured from 25 to 65°C by FT-IR. The spectrums were analyzed to clarify the behavior of main chains and side chains of the polymer in the heating process. Also, Δn0 of the films from 15 to 65°C were evaluated by automatic birefringence measurement system to calculate temperature dependence of Δn0 of them. From the above, it suggested that increasing or decreasing of Δn0 in heating process is related to the orientation behavior of a polymer molecule. Based on the results, the composition of monomers in a system of MMA, BzMA, and PhMA was calculated to compensate birefringence and its temperature dependence for designing a TIZBP. Moreover, poly(MMA/BzMA/PhMA) (39/38/23 wt.%) was synthesized and exhibited almost no intrinsic birefringence Δn0 from 15 to 65°C.
 A. Tagaya, H. Ohkita, T. Harada, K. Ishibashi, and Y. Koike, Macromolecules, 39, 3019-3023 (2006).
 M.D.Shikanai, A.Tagaya, and Y. Koike, Applied Physics Letters, 108, 131902 (2016).
8:00 PM - BM03.03.19
All Atom and Coarse-Grained Molecular Dynamics Simulations of an Interdigitated Multilamellar Phase of a Mixed Surfactant System
Arpita Srivastava1,Ananya Debnath1
Indian Institute of Technology, Jodhpur1Show Abstract
A coarse-grained (CG) molecular dynamics simulation of a cationic surfactant behenyl trimethyl ammonium chloride (BTMAC), co-surfactant (SA) in presence of water is performed at a ratio of 2:1 at 283 K from an all atom (AA) simulation . The CG bonded potentials are derived by the Boltzmann inversion of their respective AA distributions . A good match in the CG and AA bonded distributions validate the bonded potentials derived for the model. The MARTINI non-bonded potentials  are used to obtain the interdigitated (Lßi) multi-lamellar phase as in the AA simulation. The single chain conformational entropies of both BTMAC and SA reveal that around 4% of the molecules have relatively higher entropy than the rest of the molecules, indicating coexistence of both ordered and disordered phases in the bilayer. The molecules with higher entropy and low order parameter are confined to the upper monolayer of a bilayer without flipping to the other layer as evident from their cosine angles with respect to the bilayer normal. The coexistence between ordered and disordered phases is attributed to the oscillation between the bent and stretched conformers of disordered BTMAC molecules with an energy barrier of 5 kJ/mol whereas all ordered molecules stay stretched throughout the simulations. Our calculations show the suitability of MARTINI force field in predicting the phase behavior of interdigitated bilayer and reveal that the coexistence of two phases arise due to the strong interdigitation between two layers dictated by the chain length of shorter SA which do not allow longer BTMAC to flip-flop and traverse. Thus our analysis will be helpful in understanding the multi-component membrane dynamics with various applications in the field of biological membranes, pharmaceuticals or industry.
 Lunkad, R.; Srivastava, A.; Debnath, A. Influence of water concentrations on the phase transformation of a model surfactant/co-surfactant/water system. Chem. Phy. 2017, 483–484, 103–111.
 Peter, C.; Kremmer, K. Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back. Soft Matter 2009, 5, 4357-4366.
 Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, H.J.; The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. Jour. Of. Phy. Chem. B, 2007, 111 (27), 7812–7824.
8:00 PM - BM03.03.20
Mechanical Basis for the Morphology of Fibrillar Aggregates
Thomas Michaels1,L Mahadevan1
Harvard University1Show Abstract
The self-assembly of fibrillar aggregates is of importance in biology, biomedicine and materials science, yet understanding the range of possible shapes for these structures remains an open question. We propose a coarse-grained approach that averages over specific molecular details to suggest that the spatial complexity of self-assembling fibrillar structures is due to the competing effects of (the bending and twisting) elasticity of individual filaments and the adhesive interactions between them. We show that a theoretical framework accounting for this allows us to capture a number of diverse fibril morphologies observed in natural and synthetic systems, ranging from Filopodia to multi-walled carbon nanotubes, and leads to a phase diagram of possible fibril shapes. We also show how the extreme sensitivity of these morphologies can lead to spatially chaotic structures. Together, these results suggest a common mechanical basis for the micronscale fibril morphology as a function of the nanoscale mechanical properties.
8:00 PM - BM03.03.21
Crack Formation in Wet Colloidal Pillars
Justin Beroz1,Alvin Tan1,Ken Kamrin1,A. John Hart1
Massachusetts Institute of Technology1Show Abstract
A basic and well-established assumption about solid materials is that they do not crack when subject to uniform compression. Intuitively, it is paradoxical to imagine how a solid material could conspire to split apart while being uniformly compressed together. In this talk, we present an example of such a case, wherein cracks appear during the drying of vertically freestanding water-saturated colloidal pillars we constructed using a direct-write technique. Paradoxically, the cracks form at the free end, far from the substrate, where the particle network is unconstrained in contracting its volume as it bears compression by a uniform capillary pressure acting at its outer surface. We first detail our experiment results and then provide a theoretical explanation for the cracks based on a dominant balance of wetting energy terms, from which follows a simple relationship between the colloid particle size and pillar dimensions that captures the presence or absence of cracks. Our theoretical result agrees with experiment, and demonstrates that having an evaporating liquid exert the pressure is fundamentally different compared to the typical balance of surface energy and bulk stress considered for dry materials.
8:00 PM - BM03.03.22
sasPDF—Pair Distribution Function (PDF) Analysis of Nanoparticle Assemblies
Chia-Hao Liu1,Ellie Buenning1,Eric Janke2,Igor Coropceanu2,Dmitri Talapin2,Sanat Kumar1,Simon Billinge1,3
Columbia University1,The University of Chicago2,Brookhaven National Laboratory3Show Abstract
Nanoparticle superlattice assemblies (NPSA) are being developed for their special properties in applications such as flat-panel displays. The properties of the resulting assemblies can be further engineered by controlling interparticle spacings and arrangements. It is therefore crucial to be able to determine the structure of these NPSAs as quantitatively and accurately as possible. In general, they may have only short-range (on the nanoparticle length-scale) structural correlations (though some assemblies are highly crystalline), making the quantitative determination of NPSA structure difficult. TEM is popular for visualizing mesoscopic structures. Small angle scattering (SAS) may also be applied. However, conventional analysis of SAS data as so far resulted only in semi-quantitative analyses and TEM images can be subjected to sample bias and are not suitable for sample-average measurements. Atomic pair distribution function (PDF) analysis of x-ray and neutron powder diffraction data is a powerful approach for studying non-periodic structural signals, for example from nanoparticles themselves. It yields local structural information from nanomaterials with high precision and quantitative accuracy. Here we describe how have extended the PDF analysis to the SAS regime, where we can apply similar quantitative modelling methods that are proving powerful at the atomic scale, but to the extraction of structural information about superlattice assemblies. In this presentation, we will present PDF analysis in SAS regime (sasPDF) and we will also present applications of sasPDF techniques to systems with different levels of ordering, from highly crystalline assemblies to isotropic, amorphous polymer coated silica nanoparticles that have promise in gas separation membranes.
8:00 PM - BM03.03.23
Synthesis of Metal and Polymer Nanoparticles for Hybrid Nanoassembling and Functional Properties
The City College of New York1Show Abstract
Nanoscale metal and polymer particles have captured broad attention and allowed enormous technological progress in various fields from biomedical and photonics to catalysis and sensing. In this work, surface-active polymer nanoparticles as well as polymer-polymer and polymer-metal nanoassembly particles are synthesized, and different parameters such as their size, morphologies and assembling strength have been studied. Nanoassembly particles are attractive because of the coupled properties with a large surface to volume ratio. A key challenge is to produce the core shell polymer nanoparticles via single-step processes. To address this concern, here, microfluidics approach and precise interfacial reaction strategies is highly promising, and hence different types of surface layered polymer nanoparticles were obtained in one-step processes. An inner core material is hydrophobic whereas a hydrophilic surface layer (in-situ formed during the polymerization process) swells in the aqueous environment. On other side, polymer-metal nanoassembly particles as well as metal catalyzed metal deposited four layered nanoassembly particles of tuned size and compositions were produced. It is shown that these particles can be used as nano-sensor particles for surface-enhanced Raman spectroscopy.
8:00 PM - BM03.03.24
Toward Self-Healable Multifunctional Coatings Containing Catechol in Hybrid Polysilsesquioxane
Sohyeon Park1,Sungwon Jung1,Jinkee Hong1
Yonsei University1Show Abstract
The polysilsesquioxane (PSQ) is an organic/inorganic hybrid material and has excellent biocompatibility and mechanical properties. Thus, PSQ is regarded as a promising candidate for coating materials for various medical devices. From a medical device point, the ideal coating should have the ability to exert excellent biocompatibility, durability, antimicrobial effect and drug delivery capabilities. However, most of the developed coatings for medical devices were limited in exhibiting this simultaneous ability. Here, we fabricated catechol-functionalized PSQ hybrid coatings with various functions. First, well-defined PSQ matrixes were synthesized by sol-gel reaction using hydrophilic precursors, and catechol groups were functionalized in carboxymethyl cellulose (CMC). Subsequently, the catechol-functionalized PSQ hybrid coatings were prepared by excellent compatibility of organic primers in PSQ to catechol-functionalized CMC. Synthesized PSQs were highly durable and exhibit superhydrophilic properties that contribute to the antimicrobial effect, through their morphological changes. On the other hand, the catechol residues of the coating were initiated and promoted by rapid and strong hydrogen bonding between them when cracks were formed in the coating, and their strong wet adhesive properties also contribute to the regeneration of the coating by generating other noncovalent interactions. We have attempted to introduce a drug delivery function into this self-healable antimicrobial coating. We have also applied this coating to a variety of medical devices and verified their versatility.
8:00 PM - BM03.03.25
Diffusion Modeling for the Predication of Bacterial Patterning on Vascularized Polymers
Caitlin Howell1,Kayla Marquis1,Benjamin Chasse1
University of Maine1Show Abstract
The creation of rationally designed and spatio-temporally controlled surfaces for cell culture is of great interest in the pursuit of the next generation of advanced biointerfaces. Here, we explore the use of COMSOL Multiphysics modeling to calculate the mass transport of antibiotic compounds through a bio-inspired vascularized polymer system, and use this model to predict the growth pattern of a bacterial biofilm on the surface of the polymer. The vascular system geometry, antibiotic concentration, and diffusion coefficients define the model, and are used in conjunction with known bacterial growth parameters such as minimum inhibitory concentration and critical time to determine the final arrangement of the biofilm on the surface. The theoretical models are then compared to an experimental validation. This approach may prove useful in applications such as compact methods for separation of bacterial multi-cultures based on antibiotic resistance or the creation of multiple spatially isolated colonies from a single culture sample for high-throughput testing.
8:00 PM - BM03.03.26
Prediction of Surface Wettability of Fresh and Aged Graphite Surfaces from First-Principles Density Functional Theory Simulations
ChunYu Lu1,ChiaYun Lai1,Mariam Mansouri1,Tuza Olukan1,Harry Apostoleris1,Ibraheem Almansouri1,Matteo Chiesa1
Khalifa University1Show Abstract
Elucidating the surface wettability of graphite has increasing attracted much attention owning to its applications in several engineering fields, including the CMOS industry, energy storage technology and steel casting. However, despite the abundant information in literature, the underlying mechanism for the temporal surface property variations is still not fully elucidated yet, particularly the role played by water vapor. Prediction of the intrinsic surface wettability of graphite from first-principles density functional theory simulations offers an opportunity to clarify the overall evolution. In this study, by combining density functional theory (DFT)-predicted water contact angles and DFT-predicted AFM force-distance curves with experimental temporal observations, we provide conclusive evidence to demonstrate that water adsorption itself causes the graphite surface to be more hydrophobic. This finding helps to explain the variations of surface properties between fresh and aged graphite surfaces in ambient air. Moreover, in this study, we propose a methodology to predict the surface wettability at the nanoscale by linking the adhesive energy at the solid/liquid interface and cohesive energy at the liquid/liquid interface with the DFT AFM-predicted force of adhesion through the Young–Dupre equation.
8:00 PM - BM03.03.27
Investigation on Micromechanical Behavior of Living Cell with FEM Simulation
Guanlin Tang1,Massimiliano Galluzzi1,Yu-Lin Shen2,Florian Stadler1
Shenzhen University1,The University of New Mexico2Show Abstract
Atomic force microscopy (AFM) indentation is a powerful technique to characterize micromechanical properties of soft materials including living cells, such as detecting alterations of single cell rigidity correlated to pathophysiological conditions. However, the mechanical data obtained from deep indentation measurements can be problematic to interpret due to heterogeneity of a cell, nonlinearity of indentation contact, and constitutive relations of hyperelastic soft material. In this work, living MDA-MB-231 cells were indented by spherical probes, and the morphological and mechanical data obtained were adopted to build an accurate finite element model (FEM) for a parametric study. Living cells can be considered as complex multi-layered systems comprising membrane, cytoskeleton layers (actin, tubulin, intermediate filaments), nucleus, and internal organelles. Initially, a 2D-axisymmetric numerical model was constructed with the main purpose of understanding the effect of geometrical and mechanical properties of constitutive parts such as cell body, nucleus, and lamellipodium. Then, a 3D finite element model was constructed to simulate indentation events with an asymmetric misalignment geometry. Deformation field from FEM simulations were directly compared with atomic force spectroscopy to resolve the mechanical convolution of heterogeneous parts and quantify Young’s modulus and geometry of nuclei. The results showed that nuclei of adherent MDA-MB-231 in standard conditions are 3-4 times stiffer than the surrounding cell body. 3D simulations demonstrated the nucleus shifting laterally during asymmetric indentation, underlining how a stiffer nucleus can prevent deformability (and therefore damage) caused by external force stimuli.
8:00 PM - BM03.03.28
Preliminary Multiscale Studies of the Montmorillonite, Amylose, Fatty Acids and Water for Polymer-Clay Nanocomposite Modeling
Felipe Azevedo Rios Silva1,2,Elaine Maia1,Maria José Sales1,Latifa Chebil3,Mohamed Ghoul3
Universidade de Brasília1,Universidade Católica de Brasília2,Université de Lorraine3Show Abstract
More than ever, biodegradable polymers attracts much attention in polymer science.1 Although, some biopolymers, such as starch, presents disadvantages such as poor processability.2 In order to circumvent those disadvantages, researchers mix those polymers with compounds such as clays. This work presents the final part of a theoretical study of a Polymer-Clay Nanocomposite (PCN) composed by: starch, Pequi vegetable oil and montmorillonite (MMT), a phyllosilicate. In the present study, amilose oligomers, oleic, palmitic and stearic acids in the proportion found in the vegetable oil, montmorillonite and water, acting as solvent involved in the experimental medium,2 were studied, as an simplified model, in order to simulate in multiscale their structural and behavioral correlations. The calculations were carried out by Molecular Mechanics, Dynamics (MM/MD) and Dissipative Particle Dynamics (DPD) methods at 363 K3 and variable dynamic times, using Materials StudioTM software. In the dynamic trajectories, the organic molecules organized near the MMT, strongly interacting with it. The MD simulations were used as a basis to calculate the interaction parameters for the DPD model, which showed similar characteristics. The organic material concentrated near the MMT surfaces, what correlated with the MD results, implying in the validity of the model. The new knowledge acquired about those molecular systems, works as a starting point to build more complex models and, if the theoretical work converge with the experimental findings, will encourage further studies in the design of PCNs with biopolymers.
Acknowledgements: This work was supported by CNPq, CAPES, UnB and Université de Lorraine.
1 Silva, F. A. R.; Sales, M. J. A.; Paterno, L. G. ; Ghoul, M.; Chebil, L.; Maia, E. R. .MRS Adv., v. 3, 2018.
2 Silva, F.A.R.; Sales, M. J. A. ; Chebil, L. ; Ghoul, M.; Matos, G. D. R. ; Maia, E. R. MRS Comm., v. 8 (2) 2018.
3 Schlemmer, D.; Angélica, R. S.; Sales, M. J. A.; Compos. Struct. 92, 2010.
8:00 PM - BM03.03.29
Enhanced Icephobic Surface Using Porous Silica Particles
Youngseok Kim1,Mi-jin Kim1,Beom Jin Yoon1,Jin Hwan Kim1,Byungsu Lee2,Daechul Kim2
Korea Electronics Technology Institute1,Kangnam Jevisco Co., LTD.2Show Abstract
Icephobicity is usually defined as the ability to delay and prevent ice nucleation and formation on surfaces induced either by pouring a supercooled water. Formation, adhesion, and accumulation of ice, snow, frost, glaze, rime, or their mixtures can cause severe problems for solar panels, wind turbines, aircrafts, heat pumps, power lines, telecommunication equipment, and submarines. Recently, extremely low ice adhesion was introduced by tailoring the cross-link density of different elastomeric coatings and by enabling interfacial slippage of surface. But, the icephobicity for such surfaces can be short-lived, as the oil may be displaced and removed by water droplets or frost, or during accreted ice removal.
Here, we introduced oil-impregnated silica particles into modified hydrophobic polyurethane. The swelling capacity of oil was greatly increased by the porosity of particles, which promises durability of slippery surface. The roughness of particle-disperedd surface also enhanced hydrophobicity. The measured the interfacial friction force between the ice and the film agreed improved icephobicity with durability
8:00 PM - BM03.03.30
Solvent Induced Coil-to-Globule Conformation Change of a Single Poly(acrylic acid) Chain
Yaxin An1,Karteek Bejagam1,Sanket A. Deshmukh1
Virginia Tech1Show Abstract
Poly(acrylic acid) (PAA) is a polymer with carboxylic acid as pendant side-chains. The conformation of the PAA chains is sensitive to changes in the pH, salt concentration, and solvents, which makes it a good candidate as stimuli-responsive polymers. To investigate the effects of solvents on the structure of the PAA polymers at atomistic level, the all-atom (AA) PAA model was solvated in pure water, pure dimethylformamide (DMF), and mixtures of these two solvents of varying concentrations. Molecular dynamics (MD) simulations were performed to analyze the conformation of the PAA and the local solvent structure around the PAA chain. The radius of gyration (Rg) of the PAA chain in pure water and pure DMF were ~10.0 Å and ~14.0 Å at 300 K, representing its globule-like and coil-like state, respectively. The local structure of the solvents at the polymer-solvent interface was characterized by the radial distribution functions (RDFs) between polymer and solvents. The intra-molecular and inter-molecular hydrogen bonds of PAA, and the hydration free energy of the monomer of PAA in different solvents were calculated to probe the the polymer-polymer interaction and the polymer-solvent interaction. This study of the AA model of PAA paves the way for developing coarse-grained PAA models.
Meenakshi Dutt, Rutgers, The State University of New Jersey
Durba Sengupta, National Chemical Laboratory
Sanket A. Deshmukh, Virginia Tech
Igor V. Pivkin, University of Lugano
National Science Foundation
BM03.04: Multiscale Modeling of Soft Materials and Interfaces III
Tuesday AM, November 27, 2018
Sheraton, 2nd Floor, Back Bay B
8:00 AM - BM03.04.01
Development of Transferable Coarse-Grained Models of Amino Acids
Olivia Conway1,Yaxin An1,Karteek Bejagam1,Sanket A. Deshmukh1
Virginia Tech1Show Abstract
Amino acids are important structural units of biomolecules and biomaterials such as peptides, proteins, and peptide amphiphiles (PAs). The focus of this study is on developing accurate transferable coarse-grained (CG) models of twenty standard amino acids. In CG models a group of a few or several atoms is represented by a bead, which can allow the modeling of processes like self-assembly of biomolecules and biomaterials. A 2:1 to 4:1 mapping scheme, where a CG bead is comprised of two to four heavy atoms and associated hydrogens, is employed to represent functional groups in amino acids. The amino acid backbone is comprised of two beads, while the side chains are comprised of one to five beads. The bonded parameters for the CG model are obtained from atomistic distributions of all-atom models of dipeptides. Nonbonded parameters are optimized using the particle swarm optimization (PSO) method to reproduce experimental properties (e.g. solvation free energy, surface tension, and density) of analogues of the side chains and backbone of the amino acids. In the near future, we plan to utilize these new CG models to construct PAs and simulate their self-assembly in the presence of explicit water models to elucidate the mechanism of their self-assembly. The knowledge gained from our study could then be used to aid the successful development of new PAs with potential applications in the field of drug delivery, regenerative medicine, tissue engineering, and stabilized photosynthetic complexes.
8:15 AM - BM03.04.02
Modeling Surfactant Micellization with Solvent Accessible Surface Area
Hsieh Chen1,Athanassios Panagiotopoulos2
Aramco Services Company: Aramco Research Center-Boston1,Princeton University2Show Abstract
We report a new implicit-solvent simulation model for studying the self-assembly of surfactants, which the hydrophobic interactions were captured by calculating the relative changes of the solvent accessible surface area (SASA) of the hydrophobic domains. Using histogram-reweighting grand canonical Monte Carlo simulations, we demonstrated that this approach allowed us to match both the experimental critical micelle concentrations (cmc) and micellar aggregation numbers simultaneously with a single phenomenological surface tension γSASA for the poly(oxyethylene) monoalkyl ether (CmEn) surfactants in aqueous solutions. Very good transferability was observed that the same model can accurately predict the experimental cmc and aggregation numbers for the CmEn surfactants with alkyl lengths m between 6 and 12, and poly(oxyethylene) lengths n between 1 and 9. The implicit-solvent model with SASA calculations put forward in this study is general and may be applied to study the more complex amphiphilic systems such as the surfactants with branched alkyl chains, or the surfactant and hydrocarbon mixtures.
8:30 AM - BM03.04.03
Data-Driven Ultrafast Prediction of the Protein’s Natural Frequency Spectrum by Machine Learning
Zhao Qin1,Markus Buehler1
Massachusetts Institute of Technology1Show Abstract
Proteins are one of the basic biopolymers that can be generally found in many different forms in the body of living organisms. A protein molecule is usually composed of one or several polypeptide chains that combine to form a certain folded three-dimensional protein structure. The protein structures are easily excited by external force causing vibration or structural transition. One efficient way to extract the natural frequency of a protein is normal mode analysis (NMA), which provides the frequency and normal modes of the most general motion of a protein structure. However, NMA can be difficult for large protein structures since it will be both compute and memory intensive to solve the eigenvector and eigenvalue of the Hessian matrix, which is a square matrix composed of second-order partial derivatives of the potential energy function of all the constituting atoms of the protein structure. Here, we developed a machine-learning algorithm that allows us to efficiently compute the vibrational spectra of a protein without solving the hessian matrix nor using any chemical force field. To build the algorithm, we wrote our own code to compute and build a database of the first 70 normal modes of over 100,000 protein structures available in the Protein Data Bank by using NMA in a consistent manner. We train our algorithm by randomly pick up 80,000 proteins out of the database (80%) and explore the correlation between their natural frequency and the other structural features of the protein (size and secondary structure content) that are easier to be measured with a convolutional neural network. We test the performance of the machine-learning model by predicting the natural frequency of the rest 20,000 protein structures (20% of the database) by giving their structural features. We find the predictions given by our algorithm can largely explain the natural frequency of these protein structures, especially for their low-frequency region (<20 cm-1). The correlation coefficient between the predicted frequency and the frequency given by NMA is over 0.9, demonstrating the reliability of this machine learning algorithm. This method will be useful to obtain the natural frequencies of protein structures without knowing their detailed atomic geometry, which may be helpful for the analysis of a frequency spectrum and the quick recognition of the unknown chemical molecules. Besides frequency prediction, we conclude the presentation with the demonstration of a new musical instrument, the EigenProt, that creates complex sounds based on the vibrations of more than a 100,000 protein structures.
8:45 AM - BM03.04.04
Neural Coarse Graining for Molecular Dynamics Simulations
Wujie Wang1,Rafael Gomez-Bombarelli1
Massachusetts Institute of Technology1Show Abstract
Molecular dynamics (MD) simulations provide key insights into the microscopic behavior of materials and, as a predictive tool, allow theory-driven design of functional materials. However, because of the large temporal and spatial scales involved in thermodynamic and kinetic phenomena in materials, atomistic simulations are often computationally infeasible. Coarse graining methods are widely used to tackle the challenge of expensive atomistic simulations. Current coarse graining methods require intensive manual tuning to determine both the coarse graining rules and the force field parametrization . Inspired by recent works that achieve deep learning based accelerated calculation in Density Functional Theory , molecular kinetics  and free energy landscape calculations , we propose an alternative data-driven framework utilizing auto-encoders to map the atomistic trajectory into a latent space of coarse grained “super-atoms”. By training on data from atomistic molecular dynamics trajectories or electronic structure calculations, this approach adopts stochastic gradient optimization of the coarse-graining rules, the force field parametrization and the up-resolution rules. Thus, it can provide parameters for large scale coarse-grained calculations and also map the coarse-grained trajectory back to dynamic information with atomistic details. Through this approach, systematic coarse graining pipelines can be built for fast molecular dynamics simulations and high-throughput predictions of the thermodynamics and kinetics of materials.
WG Noid, Perspective: Coarse-grained models for biomolecular systems WG Noid The Journal of Chemical Physics 139, 090901 (2013)
Chmiela, S. et al. Machine learning of accurate energy-conserving molecular force fields. Sci. Adv. 3, e1603015 (2017).
 Wehmeyer, C. & Noé, F. Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics. (2017).
Schneider, E., Dai, L., Topper, R. Q., Drechsel-Grau, C. & Tuckerman, M. E. Stochastic Neural Network Approach
for Learning High-Dimensional Free Energy Surfaces. Phys. Rev. Lett. 119, 150601 (2017).
9:00 AM - BM03.04.05
A Hierarchal Approach to Understand Kevlar Using Quantum and Classical Molecular Dynamics
Subodh Tiwari1,Sungwook Hong1,Paulo Branicio1,Rajiv Kalia1,Aiichiro Nakano1,Priya Vashishta1
Univ of Southern California1Show Abstract
The outstanding strength-to-weight ratio of para-aramid fibers, such as Kevlar and Twaron, can be largely attributed to their high content of p-phenylene terephthalamides (PPTA) crystals. Here, we perform non-adiabatic shock loading on large PPTA crystal models along different low-index crystallographic directions using quantum molecular-dynamics simulations. Results reveal an anisotropic shock response displaying elastic, plastic, and phase transformation from crystalline to para-crystalline configuration.
A reactive forcefield is developed and verified based on the shock data obtained using quantum molecular dynamics. Further, we performed reactive forcefield simulation to include the effect of chain end in PPTA. The simulation results provide an atomistic view on the shock absorbing mechanism during shock in para-aramid synthetic fibers.
9:15 AM - BM03.04.06
Using Particle Swarm Optimization to Develop Lennard-Jones Parameters Between Hexagonal Boron Nitride and Water
Preeya Achari1,Karteek Bejagam1,Sanket A. Deshmukh1
Virginia Tech1Show Abstract
Hexagonal boron nitride (BN) has shown great potential in lubrication, electronic devices, sensors, and as an additive for cosmetic products due to its light weight, thermodynamic and chemical stability, great strength-to-weight ratio, and increased resistance to oxidation. Its used in microfluidic and nanofluidic applications at the molecular level demands accurate force-field parameters to describe the interactions between BN and water molecules. In this study, particle swarm optimization (PSO) and machine learning (ML) were coupled with molecular dynamics (MD) simulations to accelerate the development of Lennard-Jones (LJ) parameters, which are used to describe the non-bonded interactions between a water droplet and a sheet of hexagonal BN. Three commonly used water models, namely, SPC, SPC/Fw, and SPC/E were employed to describe water, while the BN sheet was modelled using REBO potential. The LJ parameters were optimized to reproduce the nanoscopic contact angle of water on the BN sheet.
9:30 AM - BM03.04.07
Coupling Lattice Boltzmann and Molecular Dynamics—A Versatile Tool for the Study of Soft-Matter Hydrodynamics
Burkhard DuenwegShow Abstract
The talk outlines the methodology of Lattice Boltzmann (LB) simulations for hydrodyamics, and its stochastic version to include thermal fluctuations. To study colloidal dispersions, polymer solutions, and similar systems, a particle system is run by Molecular Dynamics, and coupled to the LB background by a Stokes friction force and a Langevin force. The method can be shown to represent both statistical mechanics and hydrodynamics fully consistently. A particularly successful application was the solution of the problem of hydrodynamic screening in semidilute polymer solutions. If time permits, the talk will also outline new (and so far not yet fully successful) attempts to base stochastic LB rigorously and approximation-free on the underlying Boltzmann entropy that governs the statistical mechanics of the system.
10:30 AM - BM03.04.08
State of Trapped Matter Inside Graphene Nanobubble
Petr Zhilyaev1,Evgeny Iakovlev1,Iskander Akhatov1
Skolkovo Institute of Science and Technology1Show Abstract
Graphene nanobubbles are formed when material is trapped between graphene and atomically flat substrate. Van der Waals interaction between graphene and the substrate results in the high pressures up to 1 GPa inside the grapahene nanobubble. Such extreme pressures and confinement could lead to phase transition in trapped material. Here we present multiscale model that describes both the state of matter inside the graphene nanobubble and its mechanical properties. Adhesion energies and their dependence on the thermodynamics parameters is calculated on atomstic level, energy is evaluated in continuum. We apply developed model to the graphene nanobubble on the graphite substrate with argon inside. Super critical state of argon is predicted at room temperature for graphene nanobubbles with radius in range from 100 to 500 nm. Gas phase of argon is emerged inside graphene nanoubbles with radius greater than 500 nm.
10:45 AM - BM03.04.09
Interfacial Effects on Free Volume, Mobility and Glassiness
Jane Lipson1,Ronald White1,Jeffrey DeFelice1
Dartmouth College1Show Abstract
Finite homogeneous materials are contained by interfaces, whose influence on bulk properties is typically unremarkable. However, as the interfacial presence begins to dominate, for example in an ultrathin film or a sample loaded with nanoparticles, significant perturbations in behaviour may result. While it is evidently the material in very close proximity to an interface - e.g. within several nanometers - that is directly affected, the consequences can extend tens of nanometers into the sample. As a result, sample averaged properties might be significantly different from those of the bulk.
This talk will focus on links between changes in local mobility and free volume as interfaces are introduced, and how those changes translate into altering dynamic relaxation and the glass transition. We have recently shown that the Cooperative Free Volume (CFV) theory can resolve bulk dynamic relaxation data over a broad temperature and pressure range, including the span from Arrhenius to non-Arrhenius behaviour. Most recently, we have turned to studying thin films, and found intriguing connections between interfacial confinement and pressure. Application of CFV analysis to experimental dielectric relaxation data will be described, as well as prediction of trends.
The work discussed will also include simulation results using our simple Limited Mobility (LM) model. Here the focus will be on predicting interfacial effects caused by introducing additives into a bulk sample. The LM data reveal connections between the un/favourability of short-range polymer-additive interactions and sample-wide changes in glassiness and local mobility. The LM predictions show good agreement when tested both against experimental data and relative to results from more detailed simulation treatments.
11:15 AM - BM03.04.10
From Small to Large to Very Large—Multi-Scale Modeling of Biomolecular Structures in Implicit Solvent
Virginia Tech1Show Abstract
Water is as important to biomolecular simulations as it is to biology. However, accurate treatment of solvation effects explicitly, by representing solvent as discrete particles, can be computationally expensive. A popular alternative that can speed-up practical simulations is based on representing solvent as a continuum: solvent effects on the biomolecule in question are accounted for implicitly, at various levels of approximation. Molecular simulations within this so-called implicit solvent can speed up conformational search dramatically. Here I will discuss the foundations of the methodology and some of its new multi-scale variants. I will also discuss applications across many length scales: from atomistic simulations of the folding of small proteins to studies aimed at understanding chromatin compaction and dynamics at the level of the entire cell nucleus.
11:45 AM - BM03.04.11
Understanding the Thermomechanical Response of Polymer Nanocomposites via Predictive Coarse-Grained Modeling
North Dakota State University1Show Abstract
Understanding and predicting the thermomechanical responses of polymer materials are challenging as their responses are greatly influenced by many factors, such as interfacial energy and filler volume fraction, giving rise to the presence of nanoscale interfaces. To overcome the spatiotemporal limitations of atomistic modeling, we have recently established an atomistically informed coarse-graining technique, called energy-renormalization approach, to achieve temperature transferability for coarse-grained (CG) modeling. Here, we employ our CG models to investigate how the nanoscale interface and free surface influence the mechanical and glass transition properties of polymer films and nanocomposites. Taking cellulose nanocrystal and poly(methyl-methacrylate) (PMMA) nanocomposites as a relevant model system, we present a multi-scale framework built upon our CG approach and machine learning algorithms to allow the prediction of thermomechanical properties of nanocomposite as a function of interfacial energy and filler volume fractions. Our established multi-scale framework is validated by recent experiments and breaks new ground in predicting key structure-property relationships for polymer nanomaterials.
BM03.05: Multiscale Modeling of Soft Materials and Interfaces IV
Sanket A. Deshmukh
Tuesday PM, November 27, 2018
Sheraton, 2nd Floor, Back Bay B
1:30 PM - BM03.05.01
Nanostructure and Interfacial Characterisation Using Image Classification and Machine Learning
Amanda Barnard1,Baichuan Sun1
Restricting materials informatics to the numerical parameters output from conventional materials modelling software restricts us to a subset of machine learning methods capable of uncovering structure/property relationships and driving materials discovery and design. Presented here is a simple way of converting materials structures in to unique image-based fingerprints suitable for image processing methods that does not require subjective pre-assessment of the data and selection of descriptors by the user. This combination of methods is shown to classify the morphologies of in a meaningful way, and predict the correlation with the functional properties in agreement with other machine learning methods that required user intervention. This image-based, rather than feature list-based, description of nanoparticle surfaces can be extended to more complex interfaces including macromolecules.
2:00 PM - BM03.05.02
A Multiscale Model for Solute Diffusion in Hydrogels
Eneko Axpe1,Giovanni Offeddu2,Yin Chang3,Doreen Chan1,David Merida4,Eric Appel1
Stanford University1,Massachusetts Institute of Technology2,University of Cambridge3,University of the Basque Country, UPV/EHU4Show Abstract
Currently, solute diffusion in hydrogels is modeled by at least one of three main theories (hydrodynamics, free volume and obstruction theory), proceeding from distinct diffusion mechanisms. However, a comprehensive predictive model is lacking, so that time and capital intensive trial-and-error procedures are used to test the viability of hydrogel applications. In this presentation, a model for the diffusivity of solutes in hydrogels that combines the three main theories will be introduced. The model is verified by a combination of (i) positron annihilation lifetime spectroscopy (PALS) to measure the sub-nanoscopic free volume, (ii) instrumented indentation to quantify mesh size, and (iii) fluorescence recovery after photobleaching (FRAP) to quantify the diffusivity of dextran solutes of different sizes in poly(ethylene glycol) hydrogels with various mesh sizes. The model presented here outperforms traditional models.
2:15 PM - BM03.05.03
Multiscale Modeling Framework with Application to the Facet Capsule Ligament and Podocytes
Jacob Merson1,Sai Deogekar1,William Tobin1,Catalin Picu1,Mark Shephard1
Rensselaer Polytechnic Institute1Show Abstract
A multiscale strategy is presented which is used to model various types of biological structures such as the cervical facet capsular ligament (FCL), and the podocyte; a cell responsible for filtration in the kidney. This strategy allows the micromechanical representation of the biological tissues as collagen networks, and the direct use of the detailed geometry obtained through various microscopy techniques.
In the FCL we start from the observation that the volume of the ligament is divided in a patchwork of sub-domains, each having a different direction of preferential fiber orientation. Such preferential orientation produces hydrostatic stress amplification and increased fluctuations. We construct a model based on the FCL geometry and perform a parametric study to determine the effect of the preferential orientation on the overall mechanical properties, and microscale fiber reorientation. This study is pertinent because the microscale fiber reorientation has been linked to FCL damage and pain. The multiscale method is also applied to study the deformation of podocytes due to capillary distention. This study is relevant for podocyte degeneration which is associated with degradation of renal function. We determine the threshold strain beyond which such degradation is expected.
2:30 PM - BM03.05.04
Rheology and Relaxation of Entangled Polymers in Strongly Nonlinear Extensional Flows
Mark Robbins1,Thomas O'Connor1,Austin Hopkins1,Nicolas Alvarez2
Johns Hopkins Univ1,Dept Chemical Engineering2Show Abstract
Nonlinear extensional flows are common in polymer processing but remain challenging theoretically because dramatic stretching of chains deforms the entanglement network far from equilibrium. Tube and slip-link models that describe flow of melts near equilibrium must be enriched to describe these states, but it is not clear what physics is missing. Here, we address this problem by performing coarse-grained simulations of extensional flows in entangled polymer melts for Rouse-Weissenberg numbers Wi=0.06-52 and Hencky strains >6. Simulations reproduce experimental trends in extensional viscosity with time, rate and molecular weight. Studies of molecular structure reveal an elongation and thinning of the confining tube with increasing Wi. The rising stress is quantitatively consistent with the decreasing entropy of chains at the equilibrium entanglement length. Molecular weight dependent trends in viscosity are related to a crossover from the Newtonian limit to a high rate limit that scales differently with chain length. Stress relaxations from steady state reveal chains rapidly retract and recover their equilibrium tube diameter even when chain primitive paths are fully aligned and do not intersect. Contrary to some geometric models of entanglement, our results suggest the degree of chain confinement is independent of the orientation of the entanglement network. The results are used to test and constrain generalizations of tube and slip-link models to strongly nonlinear flows.
3:30 PM - BM03.05.05
Integral Equation Coarse-Graining Simulation Approaches for the Mixtures of Polymer Melts—Composition-Dependent Effective Potentials
Mohammadhasan Dinpajooh1,Marina Guenza1
University of Oregon1Show Abstract
Mixtures of polymers with different compositions are of great importance for many technological and industrial applications because as the composition of polymers change, the mixture structure and dynamics can change significantly. Molecular simulations may be used to study polymer mixtures but their properties develop on such an extended range of time and length-scale that they cannot be investigated by atomistic simulations. In this regard, the integral equation coarse-graining (IECG) approach has been developed in which the polymers are either represented as soft spheres or multi coarse-graining (CG) sites, where each CG site consists of a large enough number of monomers to use Gaussian statistics to obtain the intramolecular correlations. The IECG method is based on the liquid state theory and solves the Ornstein-Zernike equation to obtain the intermolecular correlations, and consequently the effective CG potentials. Representing polymer melts with a given degree of polymerization at various resolutions, we use the IECG theory and/or perform the IECG simulations to investigate the properties of the same polymer melt represented by mixtures of CG models at various resolutions. We show that the structural and thermodynamical properties, such as pressure and pair correlation functions, for such mixtures are consistent with pure CG liquids as well as the underlying atomistic simulations. We also address the compositional dependence of the effective IECG potential, along with its range for various types of mixtures.
3:45 PM - BM03.05.06
Replica Exchange Enhanced Self Assembly of Ultrashort Peptides
Srinivas Mushnoori1,Vivek Balasubramanian1,Doaa Altarawy2,Benjamin Pritchard2,Shantenu Jha1,Meenakshi Dutt1
Rutgers, The State University of New Jersey1,Virginia Tech2Show Abstract
Replica-Exchange (RE) is a class of simulation techniques used to enhance sampling and comprehensively explore phase space of simulations. Originally proposed using Monte Carlo methods, RE techniques have since found their way into Molecular Dynamics (MD) methods, particularly for addressing problems of large, complex biomolecular systems. RE simulations are generally used for exploring single proteins or peptides, but seldom to explore assembly. Assembly of biomolecules constitutes a class of physical processes which are especially susceptible to kinetic traps. RE provides enhanced sampling that aids the systems in overcoming these kinetic traps. In this study, we apply the REMD technique to the assembly of ultrashort peptides and explore the morphological diversity of the supramolecular structures.
4:00 PM - BM03.05.07
Bridging Time Scales with Variationally Enhanced Sampling
Max Planck Institute for Polymer Research1Show Abstract
The usefulness of atomistic simulations is generally hampered by the presence of several metastable states separated by high barriers leading to kinetic bottlenecks. Transitions between metastable states thus occur on much longer time scales than one can simulate. Numerous enhanced sampling methods have been introduced to alleviate this time scale problem, including methods based on identifying a few crucial order parameters corresponding to the relevant slow degrees of freedom and enhancing their sampling through the introduction of an external biasing potential .
Here we will discuss Variationally Enhanced Sampling , a generally applicable enhanced sampling method where an external bias potential is constructed by minimizing a convex functional. We present numerous examples from physics, chemistry, and materials science which show the flexibility and practicality of the method [3-6]. We will furthermore show how the variational property of the method can be used to extend the method in various innovative ways, e.g.: to obtain kinetic information from atomistic simulation ; to accelerate nucleation events by employing models from classical nucleation theory ; to parameterize coarse-grained phenomenological models from microscopic simulations ; and to incorporate experimental information into molecular simulations.
We will also introduce the VES code , an open-source library for the PLUMED 2 plugin that implements methods based on Variationally Enhanced Sampling.
 O. Valsson, P. Tiwary, and M. Parrinello, Annu. Rev. Phys. Chem. 67 159-184 (2016) [doi: 10.1146/annurev-physchem-040215-112229]
 O. Valsson and M. Parrinello, Phys. Rev. Lett. 113 090601 (2014) [doi: 10.1103/PhysRevLett.113.090601]
 G. Piccini, J. McCarty, O. Valsson, and M. Parrinello, J. Phys. Chem. Lett. 8, 580–583 (2017) [doi: 10.1021/acs.jpclett.6b02852]
 P. M. Piaggi, O. Valsson, and M. Parrinello, Phys. Rev. Lett. 119, 015701 (2017) [doi: 10.1103/PhysRevLett.119.015701]
 F. Palazzesi, O. Valsson, and M. Parrinello, J. Phys. Chem. Lett. 8, 4752-4756 (2017) [doi: 10.1021/acs.jpclett.7b01770]
 C. Perego, O. Valsson, and M. Parrinello, J. Chem. Phys. 149, 072305 (2018) [doi: 10.1063/1.5024631]
 J. McCarty, O. Valsson, P. Tiwary. and M. Parrinello, Phys. Rev. Lett. 115 070601 (2015) [doi: 10.1103/PhysRevLett.115.070601]
 P. Piaggi, O. Valsson, and M. Parrinello, Faraday Discuss. 195 557–568 (2016) [doi: 10.1039/C6FD00127K]
 M. Invernizzi, O. Valsson, and M. Parrinello, Proc. Natl. Acad. Sci. USA 114 3370-3374 (2017) [doi: 10.1073/pnas.1618455114]
4:15 PM - BM03.05.08
Hiking on the Energy Landscape—All-Atom Computational Understanding of the Universality of Long Timescale Phenomena and Rare Events in Non-Equilibrium Matter—Metal, Water and Protein
University of Illinois at Urbana-Champaign1Show Abstract
In the last few years, we have developed an all-atom metadynamics method, which allows intelligently sampling statistically rare events in complex materials, and a Relaxation-Excitation Mode Analysis (REMA) theoretical framework, which links the computationally sampled statistics of the energy landscape to experimentally measurable two-point correlation functions. This synergistically integrated experimental and computational approach opened the way for qualitatively examining a range of non-equilibrium matter and the associated complex processes that occur over a very long timescale, such as the viscous flow of supercooled liquids and glasses, nucleation and crystal growth, the folding of polypeptide chains into structured proteins, the self-assembly of micro-units into functional objects, and aging and degradation of materials. In this talk, first I will show the intriguing energy landscape characteristics of three apparently-different systems: glass-forming metallic liquids, water, and protein; then, I will describe our quantitative investigations of how confinement blocks the transition pathways on the energy landscape of proteins and thus prevents their thermal unfolding/denaturation.
4:30 PM - BM03.05.09
Multiscale Modeling of Fibrils in Bone—Bridging Collagen-Mineral Interaction to Macroscale Properties
Dinesh Katti1,Kalpana Katti1
North Dakota State University1Show Abstract
Bone is an essential biological nanocomposite found in the human body that plays a vital role in providing structural integrity and mobility to the human body. Bone displays structural hierarchy spanning from the molecular scale to the macroscale, beginning with well-organized arrays of collagen molecules and nanoscale hydroxyapatite which in turn form the fibrils followed by concentric lamella and the osteon and finally the macroscopic bone. The role of molecular interactions between the nanosized hydroxyapatite and collagen on the mechanics of collagen is evaluated using molecular dynamics simulations. In addition, detailed steered molecular dynamics studies on the mechanics of full length collagen of 300nm size, are conducted and the impact of inter-chain molecular interactions on the structure of collagen and mechanics on the collagen are mechanistically evaluated. The mechanical response obtained from molecular scale studies are incorporated into a 3D finite element model of fibril using a hierarchical multiscale modeling approach. Simulations using the finite element models of collagen fibril are conducted to study the elastic and inelastic response of the fibril. These simulations provide an insight into key mechanisms that influence the mechanics of fibril and indicate that the molecular scale interactions at collagen-mineral interfaces have a significant impact on the mechanics of the fibril. Further, we report the role of crosslink densities in collagen fibrils on the mechanics of the fibril. These studies are vital towards understanding ageing and diseases in bone.
4:45 PM - BM03.05.10
Structural Evolution in Polymer Nanocomposite Fibers—A Molecular Dynamics Simulation Approach
Sojeong Heo1,Jeong-Eun Lee1,Seunggeol Lee2,Han Gi Chae1
UNIST1,Pusan National University2Show Abstract
Carbon nanotube (CNT)-based polymer nanocomposites have often been processed into fibers because fibrous shapes are one of the best methods of fully exploiting the anisotropies and structures of CNTs. Among various types of polymer-CNT nanocomposite fiber, polyacrylonitrile (PAN) has been among the most studied polymeric system because it strongly interacts with CNTs and is the most common source of high-performance carbon fibers. In order to understand the structural evolution and related mechanical properties under extensional flow, molecular dynamics (MD) simulations were performed on polyacrylonitrile–single-wall carbon nanotube (PAN-SWNT) nanocomposites, to a draw ratio of two, which mimics fiber-spinning and drawing processes. Two SWNT(5,5)- and SWNT(10,10)-containing nanocomposite systems, as well as a control PAN, were constructed. Higher stresses were observed in both nanocomposite systems. In addition, higher Young’s (4.76 GPa) and bulk (4.09 GPa) moduli were observed when the smaller-diameter SWNT(5,5) was used, compared to those of PAN-SWNT(10,10) (4.41 GPa and 3.96 GPa, respectively), suggesting that SWNT(5,5) resists stress better. Furthermore, we also observed the formation of void structures at both ends of the SWNTs, especially for the large-diameter SWNT(10,10); these voids became larger in the drawing direction with increasing draw ratio and may adversely affect the mechanical properties of the nanocomposite fibers.