A multiscale modeling approach is used to develop an implicit-solvent intermediate resolution model, LIME (Lipid Intermediate Resolution Model), to simulate the behavior of phospholipids in solution. The LIME geometric and energetic parameters are obtained by collecting data from atomistic simulations of a system composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecules and explicit water and then grouping the atoms on DPPC into 14 coarse-grained sites with unique properties. The interactions between coarse-grained sites are represented by hard sphere and square well potentials, as opposed to Lennard Jones potentials, thereby allowing us to use discontinuous molecular dynamics (DMD) , a fast alternative to traditional molecular dynamics. DMD simulations on systems containing 256 DPPC molecules show spontaneous formation of a bilayer from a random solution in less than 4 hours. The structural properties of the DPPC bilayer are accurately reproduced including the area per lipid, bilayer thickness, bond order and mass density profiles. DMD/LIME simulations are also applied to aqueous bilayers composed of two types of phospholipids: those containing phosph-L-serine (PS) head groups and those containing phosphatidylcholine (PC) head groups. Our simulations predict that this system phase-separates in agreement with the results of our collaborator Stavorula Sofou ( Rutgers University) on a similar system, DPPC and 1,2-distearoyl-sn-glycero-3-phospho-L-serine (DSPS).

Gold nanoparticles (AuNPs) have recently emerged as a flexible nanoscale platform for applications in drug delivery, biosensing, and bioimaging. The surface properties of AuNPs can be tuned for desired applications by grafting a protecting ligand monolayer to the AuNP surface. A typical strategy for biological applications is to graft alkanethiol ligands to the surface with some or all of the ligands end-functionalized with hydrophilic end groups to confer aqueous solubility. Recently, gold nanoparticles (AuNPs) protected by a binary mixture of purely hydrophobic and anionic end-functionalized linear alkanethiols were observed to spontaneously penetrate cell membranes via a non-disruptive, non-endocytotic mechanism (1). The propensity for penetration was shown to depend on both the composition and morphology of the mixed ligand monolayer. The observation of non-disruptive penetration is unusual given that the monolayers are highly anionic, unlike cationic cell-penetrating peptides or cationic AuNPs that are known to penetrate cell membranes driven by electrostatic interactions. To the best of our knowledge, no mechanism has yet emerged to explain membrane penetration by anionic, monolayer-protected AuNPs.
In this work, we use a combination of both implicit and explicit simulation models, supported by experiments, to demonstrate that these same AuNPs fuse with single component lipid bilayers. The fusion process leaves the AuNPs embedded within the hydrophobic core of the bilayer, resembling transmembrane proteins. To avoid strong energetic penalties associated with the exposure of charged end groups to the hydrophobic bilayer core, the charged ligands “snorkel” to allow charges to access nearby aqueous interfaces while the hydrophobic alkane backbones of the ligands remain in favorable positions within the bilayer. Particle insertion is thus driven by the hydrophobic effect rather than electrostatic interactions. Free energy calculations indicate that fusion depends on the size of the AuNPs, with a preferred particle size and cutoff size for favorable insertion that are both a function of the particle composition. Atomistic molecular dynamics simulations provide further insight into the kinetics of particle insertion, showing the pathway by which insertion proceeds as a function of particle composition. Finally, experiments show a size dependence for the penetration of AuNPs into cell membranes that is similar to the size dependence predicted for bilayer fusion, implying that fusion may be a critical step for cell penetration. We believe this work improves our understanding of AuNP-bilayer interactions and will enable the design of nanoparticles for drug delivery and biosensing applications based on the relationships between AuNP composition and function outlined here.
(1) A. Verma et al, “Surface-structure-regulated cell-membrane penetration by monolayer-protected nanoparticles,” Nature Materials 7 (2008).

The entropic force between two fluctuating fluid membranes is critically reexamined both analytically and through systematic Monte Carlo simulations. A recent work by Freund [1] has questioned the validity of a well-accepted result derived by Helfrich. We find that, in agreement with Freund, for small inter-membrane separations d, the entropic pressure scales as 1/d, in contrast to Helfrich's result: 1/d^3. For intermediate distances, our calculations agree with that of Helfrich and finally, for large inter membrane separations, we observe an exponentially decaying behavior.
[1] L. B. Freund. PNAS, 110(6): 2047, 2013.

Using computer simulations, we probe how to design a synthetic vesicle that can act as an artificial phagocyte by selectively capturing and encapsulating solutes from the surrounding solvent. Our synthetic phagocyte consists of two components: a stimuli-sensitive microgel particle and a lipid membrane enclosing the microgel. Under the action of an appropriate stimulus, microgel swells and perforates the membrane enabling transport of solutes into the vesicle interior. When the target solutes bind to the microgel surface and the stimulus is removed, microgel deswells, which in turn restores the membrane integrity. As a result, captured solutes are isolated inside the vesicle. In our simulations performed using dissipative particle dynamics, we probe the operation of this artificial phagocyte and examine the conditions leading to the membrane pore formation and closing. Our results will be useful for developing new methods for drug delivery and in-vivo sampling.

Our objective is to design effective controlled-release vehicles for lab-on-chip devices for applications in the areas of bionanotherapeutics, sensing and catalysis. In this presentation we present our results on the role of molecular architecture on the morphology and mechanical properties of bio-inspired soft materials. We focus on four lipid architectures with variations in the head group shape and the hydrocarbon tail length. Each lipid species is composed of a hydrophilic head group and two hydrophobic tails. We characterize the soft material via the thickness, interfacial tension, molecular diffusion, area compression modulus, bending modulus, and total energy of the lipid bilayer. We demonstrate the equilibrium morphology of these bilayer membranes to be determined by factors such as the average area of the lipid, lipid head group orientation, and lipid tail length (Koufos et al., 2013.) We use a Molecular Dynamics-based mesoscopic simulation technique called Dissipative Particle Dynamics that captures the molecular details of the components through soft-sphere coarse-grained models and reproduces the hydrodynamic behavior of the system over extended time scales. The DPD method is highly effective in resolving the dynamics of complex fluids over extended spatiotemporal scales due to the soft-repulsive interaction forces.

We generate bilayers in a large variety of geometries, which resemble unusual cellular shell shapes, by mixing cationic and anionic amphiphiles [1]. We use pH to control the degree of ionization of the amphiphiles and hence their intermolecular electrostatic interactions. At low and high pH, we observe closed faceted vesicles with 2D hexagonal molecular arrangements, while at intermediate pH we observe ribbons with rectangular-C packing of the amphiphiles. That is, pH acts as a switch to control the morphology of the ionic bilayers via transitions in the crystalline lattice. Atomistic simulations explain the observed bilayer interdigitation when the charge fraction of both, cationic and anionic head groups is large, and reveal hexagonally packed tails forming bilayers at low pH, when the fraction of charged cationic head groups is low. Mesoscale geometry coarse-grained simulations at low pH unveil faceted vesicles composed of crystalline facetted faces and liquid-like boundaries. These simulations explain that the observed low symmetry polyhedral vesicle result from the possibility of adjusting the local density of hexagonally packed tails at the polyhedral edges to allow for sharp bends.
[1] Leung et al., ACS Nano, 2012, 6 (12), pp 10901-10909.

We develop a computational model to design and characterize multi-component nanostructured soft biomaterials using the Molecular Dynamics simulation technique. Our objective is to generate a stable vesicle through the self-assembly of amphiphilic lipid molecules using implicit solvent coarse-grained molecular models. The amphiphilic lipid molecules are composed of a hydrophilic head group and two hydrophobic tails. We investigate the dependence of mechanical properties as well as morphological stability of the lipid vesicles on temperature. We show that these lipid vesicles are morphologically stable upon changes in the shape and mechanical properties due to temperature. We have extended the model to investigate two component lipid mixtures to enable the formation of hybrid lipid vesicles through the self-assembly. We find that the degree of phase segregation between the two lipid species is tunable via their distinct effective chemical specificity and molecular architecture. We characterize phase segregation process by analyzing the distribution of the pure species domain populations. We furthermore illustrate that the degree of phase segregation has effects on the structure and mechanical properties of the lipid vesicle. Our findings can be used to design new soft biomaterials for various applications in medicine, sensing and energy.

Remora fish have a unique dorsal pad capable of fast, reversible adhesion to a large range of natural and artificial surfaces. The effectiveness of adhesion is due in part to the pad&’s ability to dynamically conform and adapt to the geometry of its host. Simulations based on measured material properties and geometry can provide useful design metrics for biologically inspired design, and furthermore, serve as platform for virtual experiments. The pad itself consists of a lamellar, composite structure composed of mineralized and soft tissue. In this work, finite element models based on microCT scans and measured viscoelastic material properties elucidate the pad&’s complex moduli frequency spectrum and response to different loading configurations.

We combine the string method with self-consistent field theory to compute the most probable transition pathway, i.e. the minimum free energy path, for the insertion of Janus and protein-like nanoparticles into a polymer membrane bilayer. The method makes no assumptions in the reaction coordinate and overcomes the long timescales challenge associated with simulating rare events. Our study suggests that one approach to building functional polymer-nanoparticle composite membranes with oriented nanoparticles is through electrostatic interactions. In particular, hydrophobic Janus nanoparticles with an asymmetric charge distribution can be made to directionally insert into charged membranes. This process is kinetically driven, and involves overcoming a thermally-surmountable activation barrier, which requires favorable interactions between the nanoparticle and the hydrophilic block of the membrane. In contrast, the insertion of protein-like nanoparticles with alternating hydrophilic- hydrophobic-hydrophilic domains into polymer membranes does not occur as a thermally activated event.
Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy&’s National Nuclear Security Administration under contract DE-AC04-94AL85000.

Droplet spreading is a fundamental physical process that is subject to intensive scientific research and of interest in many technical applications. Particularly interesting phenomena in this context are the spreading of droplets of pure trisiloxane surfactants and the spreading of droplets of their aqueous solution. Pure droplets of trisiloxane surfactants form precursor films with complex shapes that depend on the critical surface tension of the substrate: small variations can lead to double layers, terraced layers, or sandpiles. The spreading velocity of these droplets is controlled by the humidity of the surrounding air. Droplets of aqueous surfactant solutions show the unique and fascinating behavior of superspreading, the greatly enhanced spreading of droplets of aqueous solution on hydrophobic substrates. Despite extensive experimental research, the underlying physics of spreading and superspreading processes are still not well understood.
We perform large-scale molecular dynamics simulations with advanced algorithms and optimized force fields to study the spreading of droplets of pure trisiloxane surfactants and of aqueous solutions on amorphous polymer substrates. The simulation approach, and especially the ability to resolve molecular-scale features, provides insights that cannot be obtained from experiments or other simulation methods. We identify the molecular mechanisms of superspreading, the formation of precursor films, and the influence of humidity on spreading velocities. We address open questions from the scientific literature and relate our findings to theories of precursor formation, spreading, and superspreading.

In conventional theoretical or experimental approaches, DNA-grafted colloids are allowed to self-assemble and then the resulting structures examined. While this empirical approach is useful for a-posteriori understanding the factors governing assembly, it does not allow one to a-priori design DNA-grafted colloids that will assemble into desired structures. Here we present an evolutionary optimization framework for designing the building blocks that will self-assemble into desired crystal structures. The proposed ``design" methodology is validated using known experimental results, promising a rational materials design paradigm with broad potential applications.

The capture of solar radiation for energy production and storage is one of the grand challenges of the next decades. Among the many photo-physical processes involved in the developed solar energy conversion devices, it is the first one, namely the light harvesting (LH) step, which has probably received less attention from the scientific community. Nonetheless, light harvesting represents a key step in natural photosynthetic systems: natural LH proteins allow tuning the absorption spectra of the system and an efficient energy funneling towards the reaction centers, while keeping up an effective photo-protection mechanism. To exploit sunlight efficiently we could integrate these antenna systems into photonic devices, e.g. by combining LH proteins with plasmonic metal nanoparticles (MNPs).
We present a newly developed QM/MM/continuum approach which is designed to model all the different electronic processes (light absorption, inter-pigment and pigment-MNP excitation energy transfers, and emission) quantum-mechanically, always including mutual polarization effects among all the QM (the pigments) and the classical parts (the protein and the MNPs).
The QM description of the pigments is of paramount importance, since it allows us to capture excitonic effects, which are behind the most peculiar features of biological systems: any form of semi-empirical or classical description of pigments, e.g. in terms of point-like dipoles, while working properly for simpler artificial devices, would inevitably miss most of the important physics of bio-hybrid devices.
Applications of the model to the case study of the PCP light harvesting protein on a silver islands film are presented. Our multiscale simulations not only reproduce and interpret the experimental findings but they also allow for suggesting general rules to design novel bio-hybrid devices.

Understanding the recognition and interactions at the interface between titania and peptides is crucial for a wide range of applications ranging from the development of biocompatible materials for medical implants to the design and fabrication of nanomaterials for biotechnological and nanotechnological applications [1-4]. Despite the fact that considerable effort has been directed toward a general understanding of peptide recognition and binding to inorganic materials, a deep understanding of the mechanistic features of recognition and binding at the molecular or atomistic level is far from being accomplished [5]. Although several molecular dynamics (MD) simulation studies of peptide adsorption at the aqueous titania interface have been reported [3,4], efficient conformational sampling of adsorbed peptides at the interface is a great challenge. Advanced sampling techniques are pivotal to the understanding, advancement and optimization of interfacial properties. A recently developed version of the promising Replica Exchange with Solute Tempering (REST2)[6] method has shown great improvement in sampling efficiency of peptides adsorbed at aqueous interfaces, at a fraction of the computational cost [7]. Using this technique, for the first time, we have studied the binding and interaction of two titania-binding dodecameric peptides at the aqueous titania (110) surface. Metadynamics simulations have been used to calculate the free energy of adsorption of the two peptides to the titania surface. The results reveal critical insights into the role of peptide sequence and conformation in the binding to titania surface.
[1] Carravetta V. and Monti S., J. Phys. Chem. B, 2006, 110, 6160-6169.
[2] Evans J. S. et al., MRS Bull., 2008, 33, 514-518.
[3] Schneider J. and Ciacchi L. C., J. Am. Chem. Soc., 2012, 134, 2407-2413.
[4] Skelton A. A. et al., ACS Appl. Mater. Interfaces, 2009, 1(7), 1482-1491.
[5] Puddu V. and Perry C. C., ACS NANO, 2012, 6(7), 6356-6363.
[6] Terakawa T. et al., J. Comput. Chem., 2011, 32, 1228-1234.
[7] Wright L. B. and Walsh T. R., Phys. Chem. Chem. Phys., 2013, 15, 4715-4726.

The chemical bonding of dithiolate molecule on the Au surface has been widely studied for applications in molecular electronics. We perform classical molecular simulations by combining grand canonical Monte Carlo (GCMC) sampling with molecular dynamics (MD) simulation to explore the dynamic gold nanojunctions in a benzenedithiol (BDT) or a Alkenedithiol (ADT) solvent. A model system has been built according to the experimental setup. The system involves the long-range elasticity of the gold electrodes in BDT or ADT solvent. The total number of gold atoms in the system is 832. The two layers at the far ends of the gold tips are kept rigid, and the atoms between them are dynamic. The upper gold tip is connected to a driving support through a spring and follows a driven dynamics motion due to the pulling of the driving support. Combining Grand Canonical Monte Carlo (GCMC) and Molecular Dynamics (MD) Simulations In order to reflect the experimental environment, in our simulation we propose a method of combining GCMC and MD techniques alternatively to keep the BDT or ADT density at a bulk value during the pulling process. Temperature is controlled at 298K. The equilibrium absorption configuration obtained from GCMC run then is taken as the input for the MD simulations. After the 0.3 nano meter retraction MD simulation run is finished, MD is switched back to GCMC for a new equilibrium adsorption run based on the configuration of the system from MD. These two procedures proceed alternatively until the breakage of gold single atomic contact begins to form. According to the experiment, we remove all the nonbonded BDT or ADT molecules and stretching without the insertion and deletion of new BDT or ADT molecules. We observe the formation mechanism of single Au-BDT-Au junction.

A large number of practical processes in nanotechnology involve the interactions of metals and peptides(1). However, the current understanding of the atomistic behavior of the aqueous peptide-metal interface is far from complete. In this work, we present atomistic simulations of the aqueous peptide-gold interface. The recently developed GolP-CHARMM force field(2) is employed to model the peptide-metal interactions due to its ability to capture the dynamic polarization of gold atoms, chemisorbing and the hybridized carbon-gold atoms. These features result in an accurate representation of the peptide binding in gold. Intensive Replica Exchange Solute Tempering(3) (REST) simulations were performed for a set of 12 different peptides(4). From the simulations, clustering analysis, contact motifs, Ramachandran plots, and the most probable conformations are obtained. These results expand the current understanding of the single residue binding and show the relevance of the contact residues and the role of entropy in peptide binding. The simulations reveal that the total binding strength is more than simply the sum of multiple anchoring residues, and that the position of the anchoring residues has a significant impact on the conformational entropy. These findings provide guidelines in the development of new peptide sequences that efficiently bind to gold interfaces.
(1) Sarikaya, M.; Tamerler, C.; Jen, A.K.Y.; Schulten, K.; Baneyx, F., Nat. Mater. 2003, 2, 577.
(2) Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R., J. Chem. Theory Comput. 2013, 9, 1616.
(3) Terakawa, T.; Kameda, T.; Takada, S., J. Comput. Chem. 2011, 32, 1228.
(4) Tang, Z.; Palafox-Hernandez, J. P.; Law, WC.; Swihart, M. T.; Prasad, P. N.; Knecht, M. R.; Walsh, T. R., ACS Nano, under review.

The synthesis of biologically-inspired macromolecules with well-defined sequence, dispersity and assembly function has large potential for applications ranging from delivery vehicles of medical therapeutics, sensing applications, to scaffolds for tissue regeneration. Here we report the progress of our work in exploiting the ability of a specific DNA polymerase, terminal deoxynucleotidyl transferase (TdT), to polymerize long chains of single strand DNA (ssDNA) and to incorporate unnatural nucleotides with useful functional groups into the growing polynucleotide chain. Specifically we report on a method that allows the facile synthesis of amphiphilic ssDNA biomacromolecules (0.6 to 2.7 kilobases) via enzymatic polymerization of mononucleotides. The amphiphilicity arises from the synthesis of hydrophilic homopolynucleotides and the modification of hydrophobic, unnatural nucleotides into the extended ssDNA chain. We synthesize these ssDNA polynucleotides by a two-step enzymatic polymerization reaction in which the MW and composition are controlled by the ratio of monomer to initiator concentration and the type of nucleotides, respectively. The hydrophobicity, resulting from incorporation of unnatural nucleotides, can be tuned to drive the assembly of these polynucleotides into star-like, hairy micelles. We used high resolution AFM and cryo-TEM imaging to directly visualize the star-like micelle morphologies with a condensed core and hairy corona. In addition, we investigated the hydrodynamic radius (Rh) of homopolynucleotides and polynucleotides amphiphiles that form micelles by dynamic light scattering (DLS). Finally we report on simulations in which a coarse-graining computational method was used to represent the amphiphilic polynucleotides, and we show that they form star-like micelles with relatively condensed core and hairy corona.

Cyclic peptide nanotubes (CPNs) are self-assembled supramolecular systems with outstanding mechanical properties (Ruiz et al. Nanotechnology, 2013). CPNs are excellent candidates as biomimetic synthetic nanopores that could serve as artificial ion channels because they offer precise control of the pore diameter and the nanotube outer surface chemistry, as well as interior polarity through nonstandard mutations presented in the amino acid sequence (Hourani et al. JACS 2011).
One successful strategy to generate CPN based thin nanoporous membranes for applications such as carbon capture or low energy water desalination is through co-assembly of polymer conjugated CPs with block copolymers (Xu et al. ACS Nano 2013). Experimental results suggest that the conjugated polymer helps to prevent lateral aggregation of CPNs and increase processability in solution and in polymer thin films. However, our simulations validated by experiments also show that polymer conjugation introduces a free energy penalty to the binding energy of the CPs, that if not well-tuned, can hamper the nanotube formation. Building on this finding, here we investigate whether the free energy penalty associated with the polymer conjugation can be leveraged to direct the self-assembly of functionalized CPs towards a defined stacking sequence. To illustrate this point, we present a theoretical framework and molecular dynamics simulations to explain the self-assembly of conjugated-CPs and show how the conjugation degree can indeed be used to control the self-assembly stacking sequence. We use coarse-grained molecular MD and a single energy barrier kinetic model to quantify the free energy penalty induced by the polymer conjugates. Replica exchange simulations are implemented to enhance the sampling of the energy space of a coarse-grain model of the conjugated-CPs, thereby reproducing the stacking sequences that corresponds to thermodynamic and kinetic limits. Our results provide a theoretical framework for precisely controlling the self-assembled stacking sequence of CPs with different polarity, paving the way for generating artificial transmembrane peptide assemblies with tunable interiors and exteriors.

Ionomer melts have unique mechanical and electrical properties due to the formation of nanoscale ionic aggregates in the polymer matrix. However, the relationships between ionomer chemistry, morphology, and ion transport are poorly understood. To elucidate the ionic aggregate morphology, we have performed molecular dynamics simulations of a series of polyethylene-based model ionomer melts, in which the spacing between functional groups is precisely controlled. We vary the polymer-bound ion chemistry (methylimidazolium, sulfonate and carboxylate), the counterion type, the neutralization level, and the length of the spacer. The simulations provide new insights into the shape, size and composition of ionic aggregates. In particular, we observe a wide variety of aggregate morphologies, ranging from small spherical aggregates to string-like shapes and large percolated networks. The structure factors calculated from simulation agree well with available X-ray scattering data. Depending on the morphology, the simulation and experimental scattering curves can be well fit with a modified hard sphere or modified hard cylinder model. These fits, combined with the simulation data, provide the first (indirect) experimental evidence of string-like aggregate morphologies in ionomer melts.
This work was performed, in part, at the Center for Integrated Nanotechnologies, an Office of Science User Facility operated for the U.S. Department of Energy (DOE) Office of Science. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy&’s National Nuclear Security Administration under contract DE-AC04-94AL85000.

The design and manipulation of mesoscale assemblies is a promising area of emerging research, which requires the ability to understand and harness the van der Waals-London dispersion (vdW-Ld) interactions that arise in these systems. This is achieved by measuring the interband optical properties of materials, computing their vdW-Ld interaction potentials, and establishing an open-source software platform for the calculation and distribution of these results.
Previous work enabled us to understand vdW-Ld interactions between objects with simple geometries, such as solid substrates, rods and spheres, as well as more complex anisotropic systems such as carbon nanotubes. This understanding laid a foundation for our current research on a range of biological and biologically relevant materials, including collagen, AlPO₄, and SiO₂. We have focused on AlPO₄ because of the strong electron localization in the phosphate complex ion, which provides insights into the role of phosphates in the electronic structure of biological systems; SiO₂, which has a similar electronic structure, is presented for comparison.
The interband optical properties of AlPO₄ and SiO₂ have been derived from Vacuum Ultraviolet (VUV) spectroscopy and spectroscopic ellipsometry. Ab initio calculations, based on the local density approximation of density functional theory, and further analyses, based on Lifshitz theory, give us insights into the electronic structures, interband transitions and vdW-Ld interaction potentials for SiO₂, AlPO₄, and collagen. These results, along with the new interaction geometries, have been incorporated into our open-source Gecko Hamaker software.
Further studies will apply this same methodology to bovine serum albumin and DNA oligonucleotides, including the determination of interband optical properties through VUV spectroscopy and ab initio methods, as well as direct determination of interaction strengths via static light scattering measurements of biomolecules in solution. These results will facilitate the mesoscale material design.

DNA template can trigger the self-assembly of metal or semiconductor nanoparticles into programmable molecular architectures. The performance of DNA-nanoparticle system strongly depends on the size and ligand chemistry of nanoparticles. We performed molecular dynamics simulations to investigate the effect of colloidal gold nanoparticle (GNP) ligands charge and polarity on the ability to bind DNA molecules. We tailored the surface of GNP by introducing different terminal functionality to thiolated ligands, such as hydrophobic, polar and charged groups. We found that uncharged GNPs and GNPs with cationic ligand charge density of less than 10% can only bind to the minor groove of DNA. Whereas GNPs with ligands charge density of higher than 10% can bind to major or minor groove. Binding to major groove result in significant distortion and wrapping of DNA around the GNP. The distortions of the DNA helical structure strongly depends on the ligand charge density. Also at higher nanoparticle concentration and low charge densities, the ligand hydrophobicity can disrupt the hydrogen bonding between base pairs of DNA strands and leads to unwinding of DNA helix. We observed that by tuning the cationic charge density and concentration of GNP we can control the binding modes and DNA structural modifications.

Via computational modeling, we investigate the mechanism of strain recovery in dual cross-linked polymer grafted nanoparticle networks. The individual nanoparticles are composed of a rigid spherical core and a corona of grafted polymers that encompass reactive end groups. With the overlap of the coronas on adjacent particles, the reactive end groups form permanent or labile bonds, and thus form a “dual cross-linked” network. We consider the strain recovery of the material after it is allowed to relax from the application of a tensile force. Notably, the existing labile bonds can break and new bonds can form in the course of deformation. Hence, a damaged material could be “rejuvenated” both in terms of the recovery of strain and the number of bonds, if the relaxation occurs over a sufficiently long time. We show that this rejuvenation depends on the fraction of permanent bonds, strength of labile bonds, and maximal strain. Specifically, we show that while an increase in the labile bond energy leads to formation of a tough material, it also leads to delayed strain recovery. Further, we show that an increase in the fraction of permanent bonds not only enables faster recovery but also yields improved recovery even after multiple stretch-relaxation cycles.

Recently, hydrogel have found to be promising biomaterials since their porous structure and hydrophilicity enables them to absorb a large amount of water. In this study the role of water on the mechanical properties of hydrogel are studied using ab-initio molecular dynamics (MD) and coarse-grained simulations. Condensed-Phased Optimized Molecular Potential (COMPASS) and MARTINI force fields are used in the all-atom atomistic models and coarse-grained simulations, respectively. The crosslinking process is modeled using a novel approach by cyclic NPT and NVT simulations starting from a high temperature, cooling down to a lower temperature to model the curing process. Radial distribution functions for different water contents (20%, 40%, 60% and 80%) have shown the crosslinks atoms are more hydrophilic than the other atoms. Diffusion coefficients are quantified in different water contents and the effect of crosslinking density on the water diffusion is studied. Elasticity parameters are computed by constant strain energy minimization in mechanical deformation simulations. It is shown that an increase in the water content results in a decrease in the elastic moduli. Finally, using the knowledge of nanomechanical behavior, continuum hyper elastic model of contact lens were used for three different loading scenarios.

Using molecular dynamics simulation, we investigated constant strain rate deformation behavior of a model hydrogel consisting of a single polymer network in which the ratio between the number of physical and chemical cross-links was varied. The physical cross-links were modeled as clusters of acrylic acid (AA) groups connected by hydrophilic flexible chains. Chemical cross-links were represented as permanent bonds between selected segments of neighboring chains and were added after the physical cross-links were formed. The structural parameter used was the number of chemical cross-links related to the number of physical clusters (cpc). Slightly cross-linked networks up to cpc=0.7 exhibitted no change in their mechanical response compared to the pure physically cross-linked gel. A moderately chemically cross-linked network gel with cpc = 1.58 exhibitted deformation behavior similar to a double network hydrogel. The strongly crosslinked networks with cpc > 3.02 behaved as purely chemically cross-linked network gel over the entire deformation range. The strongest effect of chemical cross-links on the non-linear deformation response of the hydrogels, was obtained for physical and chemical cross-links set as far apart as possible. The addition of 64 crosslinks to the simulation box composed of 1600 non-solvent atomic groups, switched the character of the deformation response from that for a physical to that for a chemically cross-linked network gel.
The molecular mechanism of the hybrid cross-linked hydrogel deformation consisted of (i) hopping of AA groups between neighbouring clusters, (ii) cluster reorientation and (iii) combination of the two. The AA groups hops exhibited relaxation times of 10-5 - 10-4 ns and the reorientation was slower ranging from 10-3.5 to 10-3 ns. The relaxation times for the third process resulting in a significant remodeling of the original network structure, comprising of both the hops and reorientation, ranged from 1 ns to the maximum simulation time of 100 ns. The redistribution of the force between chemical cross-links was more efficient than that between purely physical cross-links. .
In conclusion, we believe that the analysis of our model hydrogel could be instructive for the preparation of tough single chemistry hydrogels. The model can provide leads for designing extent and spatial arrangement of chemical cross-links of reversible bond hydrogels with prescribed deformation behavior similar to that obtained for double network hydrogels.
Acknowledgements
J. Zidek, and J. Jancar acknowledge European Regional Development Fund (CEITEC, CZ.1.05/1.1.00/02.0068), A. M. acknowledges support by CECAM at MPIP during his stay at the Institute.

A new class of porous polyarylamide polymer films that contain s-dibenzocyclooctadiene (DBCOD) moieties can generate unconventional thermal contraction that is completely reversible under low-energy stimulation. They possess an extremely large negative thermal expansion coefficient (NTE) of approximately -1200 ppm/K under ambient conditions, much higher than the best previously known NTE materials at these operating conditions. Significantly, the NTE value remains unchanged after extended cycling. Density-functional theory calculations revealed that the spectroscopic change with temperature and macroscopic thermal contraction is due to the conformational changes of the DBCOD moiety, from the thermodynamic global minimum (twist-boat) to a local minimum (chair). This contention is further supported by the calorimetry analysis indicating that the conformational change is the origin of this abnormal thermal shrinkage. The observed giant and stable NTE that can be triggered by low and penetrating energy sources have the potential to generate high mechanical energy output otherwise unattainable. This newly identified thermally agile molecular subunit opens a new pathway for creating NIR-based macromolecular switches and motors, as well as enabling ambient thermal and photothermal energy storage and conversion.

Liquid crystal elastomers (LCE) are functional soft materials consisting of weakly crosslinked polymer networks with embedded liquid crystalline (mesogenic) molecules. Consequently, LCE are characterized by a pronounced coupling between macroscopic strain and orientational mesogenic order. As the latter can be controlled by external stimuli such as temperature, electric field, or ultraviolet light, LCE have great potential for application as sensors and actuators [1]. Here we present large-scale molecular simulations of swollen main-chain LCE [2,3]. The simulated experiments include temperature scans, stress-strain runs, and the application of an external electric field. Our isostress Monte Carlo simulations are capable of reproducing isotropic, nematic, and smectic phases, as well as a stress-induced isotropic-to-nematic transition [2]. Moreover, a transversal electric field is seen to induce nematic director rotation resulting in orientational stripe domains [3]. We use our simulation output to connect to typical experimental observables, such as sample dimensions, specific heat, deuterium magnetic resonance spectra, and scattered X-ray patterns.
[1] M. Warner and E. M. Terentjev, Liquid Crystal Elastomers, Oxford University Press, Oxford, 2003.
[2] G. Ska#269;ej and C. Zannoni, Soft Matter 7, 9983 (2011).
[3] G. Ska#269;ej and C. Zannoni, Proc. Natl. Acad. Sci. USA 109, 10193 (2012).

There has been a growing need for synthetic polymers with optimized mechanical responses and energy dissipation characteristics that can be implemented as tissue simulants. Such "soft materials" can serve as test media for examining effects of ballistics on soft-tissues, and enable design of devices and protective garments that minimize blunt impact trauma. The limited mechanical tunability of current tissue simulant gels to replicate the energy dissipation capacity and rates of biological soft-tissues highlights the importance of further investigations. Furthermore, experimental measurements are inefficient and insufficient as stand-alone approaches to match impact responses of new materials to those of biological tissues. Here, we validated a multi-scale finite element model against impact experiments for synthetic polymer gels intended as candidates for mechanical simulants of soft-tissue. Importantly, using a bi-layer system of dissipative and nondissipative materials, we decoupled the two design metrics of impact resistance and energy dissipation capacity. These computational predictions provide promising prospects for tunable design of soft-tissue simulant materials.

Recently developed theoretical approach is presented in this work with the aim to design stimuli-responsive hydrogels and optimize their swelling properties. Among many possible interesting applications of such gels is a mucoadhesive drug delivery. The structure and as a result delivery properties of these gels are modulated by external impulses.
Using molecular theory and molecular dynamics we also demonstrate in this work that the presented approach allows us to apply it on understanding the barrier properties of mucus towards sexually transmitted diseases. Mucus is a gel like substance that consists of water, electrolytes, amino acids and highly glycosylated proteins called mucins. It acts as a sensor towards incoming pathogens, and signals to epithelium in response to sensing such dangers. The mucus layer can naturally modify its barrier properties. For example, cervical mucus properties change regularly during the menstrual cycle, providing variable resistance towards viruses.
Mucus structure varies a lot for different parts of the body. Since there is very little and not enough information about exact structure of mucus we begun from modeling mucus by a structure of stimuli responsive hydrogels such as poly(methacrylic acid-grafted-poly(ethylene glycol)) gels (P(MAA-gEG)) which were previously proposed as a good protein and drug delivers[1].
Here we present results of our recent studies: the variations of binding properties of synthetic stimuli responsive hydrogels as a result of environment changes like pH, salt concentration and volume fraction of the gel.
1. L. Serra, J. Doménech and Nicholas A. Peppas, European Journal of Pharmaceutics and Biopharmaceutics 71 (2009) 519-528.

Nematic Liquid Crystal Elastomers (NLCE) are lightly cross-linked polymeric materials that exhibit rubber elasticity and liquid-crystalline orientional order. We investigated the thermal response and microstructure of several samples of side-chain NLCEs which had varying chemical compositions. Real-time synchrotron wide-angle X-ray scattering (WAXS) during thermal treatment showed that the materials were highly anisotropic with a fiber-like diffraction pattern. The isotropic to nematic transition temperature showed a dependence on the chemical composition. Transition temperatures from WAXS were correlated with thermal properties, using differential scanning calorimetry, and with optical properties, using polarizing optical microscopy and transmission ellipsometry. In the low temperature nematic phase, we investigate how the stress-strain behavior depends on the chemical composition and thermo-mechanical history of the samples.

Inclusion of colloidal particles into a nematogenic material functionalizes defects as carriers of cohesion, self-assembly and manipulation in the resulting composite material. One of the commonly used particle types are spheres, treated to enforce homeotropic surface alignment -- they form structures with just enough degrees of freedom to allow for complex entangled structures, but still follow models that are easy to formulate. Depending on the geometry of the confinement and arrangement of the dispersed spheres, entangled particle clusters can be assembled, ranging from disordered clusters, one-dimensional wires, two-dimensional regular arrays and finally opal-like 3D colloidal crystals.
We focus on structures that enforce disclination lines with a constant director field cross section with a winding number of -1/2. In these systems, the main phenomenological building elements are so-called ``rewiring sites'', where the disclinations are free to choose the way they connect to each other, while away from these sites, the disclination geometry is enforced by the confining surfaces of in the inclusions. The rewiring sites appear in highly symmetric tetrahedral and cubic forms and their enumeration is an elementary question of elementary geometry and symmetry groups. As a result, they can be used to predict the possible structures, use them as templates for numerical modeling, and lead the process of experimental assembly.
We review the rewiring sites from topological and geometric point of view, and demonstrate the numerical models of their appearance in the nematic colloids.

We study propagation of elastic waves in layered media undergoing finite deformation. Applied deformation influences the wave propagation in two ways: first, as a material undergoes deformation, its microstructure evolves; second, the presence of stress can influence wave propagation. By application of Bloch-Floquet technique we have derived an exact analytical solution for elastic wave propagation in flat layers. However, when layered materials are compressed along the layer direction, a buckled shape may developed upon attending a critical load. Further compression beyond the critical strain may lead to the wrinkling of the interfacial layer. Thus, a system of periodic scatterers can be created. These scatterers reflect and interfere with waves. To analyze the wave propagation in the media with wrinkled interfacial layers, a finite element model was developed. By means of the numerical analysis we demonstrate that the topology of wrinkling interfacial layers can be controlled by deformation and used to produce band-gaps and to filter frequencies. Since the microstructure change is reversible, the mechanism can be used for tuning and controlling wave propagation by deformation.

References
[1] Kushwaha, M.S. and Halevi, P. and Dobrzynski, L. and Djafari-Rouhani, B. Acoustic band structure of periodic elastic composites. Phys. Rev. Lett., 71(13):2022-2025, 1993.
[2] Li, Y. and Kaynia, N. and Rudykh, S. and Boyce, M. C. Wrinkling of Interfacial Layers in Stratified Composites. Adv. Eng. Mater., 2013.

Transport of nano-scale particulate materials in polymeric network is the key phenomenon that determines their efficacy as delivery system. Nano-rheological measurements detect the movement of a particle through polymeric systems and providing direct way to probe local polymer dynamics. We study sub-diffusive motion of probe particles and coupling between particle transport properties in polymer solutions at various concentrations analytically and numerically. Applied Diffusing Wave Spectroscopy technique allows characterizing dynamic mobility of particles with the size range from tens nanometers to microns in various natural polymeric systems that represent biological matrices. It was shown that well known Stokes - Einstein model cannot be applied to describe the mobility of particle in semi-diluted polymer solutions and gels because the diffusivity of particle is not inversely proportional to the bulk viscosity. Our results show that there are several distinct regimes of particle mobility corresponding to the various arrangements of polymeric molecules in the solutions and melts. Measured mobility coefficients for the embedded nanoparticles are in good correspondence with De Genes scaling theory. Based on obtained data, we propose simple criteria that allow rational design of the various nanocomposite materials.