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Force fields form the basis for classical molecular simulations and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small molecule chemistry makes it a challenge to build and parameterize a suitable force field. The Open Force Field Initiative is a combined industry and academic consortium developing a state-of-the-art small molecule force field. In this report industry members of the consortium worked together to objectively evaluate the performance of the force fields (referred to here as OpenFF) produced by the initiative on a combined public and proprietary dataset of 19,653 relevant molecules selected from their internal research and compound collections. This evaluation was important because it was completely blind; at most partners, none of the molecules or data were used in force field development or testing prior to this work. We compare the Open Force Field "Sage" version 2.0.0 and "Parsley" version 1.3.0 with GAFF-2.11-AM1BCC, OPLS4 and SMIRNOFF99Frosst. We analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical data. We show that OPLS4 performs best, and the latest Open Force Field release shows a clear improvement compared to its predecessors. The performance of established force fields such as GAFF-2.11 was generally worse. While OpenFF researchers were involved in building the benchmarking infrastructure used in this work, benchmarking was done entirely in-house within industrial organizations and the resulting assessment is reported here. This work assesses the force field performance using separate benchmarking steps, external datasets, and involving external research groups. This effort may also be unique in terms of the number of different industrial partners involved, with 10 different companies participating in the benchmark efforts.

To date, no extensive study of the phase diagram for binary fluid mixtures in dissipative particle dynamics (DPD) has been published. This is especially pertinent for newer parameterization schemes where the self-self interaction, or the effective volume, of different particle types is varied. This work presents an exhaustive study of the parameter space concerning DPD particles with soft interaction potentials. Moreover, we propose a closed-form coexistence equation or binodal curve that is inspired by the Flory-Huggins model. This equation describes the phase diagram of all binary mixtures made up out of monomers, homopolymers, and the mixtures thereof when self-self interactions are varied. The mean absolute percentage error (MAPE) of the equation on simulated data, including validation simulations, is 1.02%. The equation can a priori predict the phase separation of mixtures using only DPD interaction parameters. The proposed coexistence equation can therefore be used to directly validate interaction parameters resulting from novel parameterization schemes, including coarse graining and equations of state, without the need for additional simulations. Finally, it is shown that the choice of bond potential markedly influences phase behavior.

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesoscale to continuum. Reasons for its popularity are that it provides a wide variety of particle interaction models for different materials, that it runs on any platform from a single CPU core to the largest supercomputers with accelerators, and that it gives users control over simulation details, either via the input script or by adding code for new interatomic potentials, constraints, diagnostics, or other features needed for their models. As a result, hundreds of people have contributed new capabilities to LAMMPS and it has grown from fifty thousand lines of code in 2004 to a million lines today. In this paper several of the fundamental algorithms used in LAMMPS are described along with the design strategies which have made it flexible for both users and developers. We also highlight some capabilities recently added to the code which were enabled by this flexibility, including dynamic load balancing, on-the-fly visualization, magnetic spin dynamics models, and quantum-accuracy machine learning interatomic potentials. Program Summary Program Title: Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) CPC Library link to program files: https://doi.org/10.17632/cxbxs9btsv.1 Developer's repository link: https://github.com/lammps/lammps Licensing provisions: GPLv2 Programming language: C++, Python, C, Fortran Supplementary material: https://www.lammps.org Nature of problem: Many science applications in physics, chemistry, materials science, and related fields require parallel, scalable, and efficient generation of long, stable classical particle dynamics trajectories. Within this common problem definition, there lies a great diversity of use cases, distinguished by different particle interaction models, external constraints, as well as timescales and lengthscales ranging from atomic to mesoscale to macroscopic. Solution method: The LAMMPS code uses parallel spatial decomposition, distributed neighbor lists, and parallel FFTs for long-range Coulombic interactions [1]. The time integration algorithm is based on the Stormer-Verlet symplectic integrator [2], which provides better stability than higher-order non-symplectic methods. In addition, LAMMPS supports a wide range of interatomic potentials, constraints, diagnostics, software interfaces, and pre- and post-processing features. Additional comments including restrictions and unusual features: This paper serves as the definitive reference for the LAMMPS code. References [1] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117 (1995) 1–19. [2] L. Verlet, Computer experiments on classical fluids: I. Thermodynamical properties of Lennard–Jones molecules, Phys. Rev. 159 (1967) 98–103.

Thermoplastic polyurethanes (TPUs) are useful materials for numerous applications due in part to their outstanding resilience and ability to dissipate energy under large mechanical deformation. However, the mechanistic understanding of the origins of these mechanical properties at the molecular level remains elusive, largely due to the complex, heterogeneous structure of these materials, which arises from the segregation of chemically distinct segments into hard and soft domains. In this work, molecular simulations are used to identify the mechanism of mechanical response under large tensile deformation of a common thermoplastic polyurethane comprising 4,4′-diphenylmethane diisocyanate and n-butanediol (hard segment) and poly(tetramethylene oxide) (soft segment), with atomic resolution. The simulation employs a lamellar stack model constructed using the Interphase Monte Carlo method established previously for semicrystalline polymers, which models the interfacial zone between hard and soft domains with th...

This work addresses the large strain behaviors of thermoplastic polyurethanes (TPUs) spanning a range of fractions of hard and soft contents in both experiment and theoretical modeling. The key mechanical features involve a combination of elasticity and inelasticity, and are quantified experimentally under a broad variety of loading scenarios. A finite deformation constitutive model is then presented to capture the main features of the stress-strain data, which are strongly dependent on fractions of hard and soft contents. The stress-strain behavior of these TPUs is characterized by highly nonlinear rate-dependent hyperelastic-viscoplasticity, in which substantial energy dissipation is accompanied by shape recovery as well as softening. Agreement between the model and the experimental data for the representative TPUs provides physical insight into the underlying deformation mechanisms in this important class of soft materials that exhibit both elastomeric and plastomeric characteristics.

Thermoplastic polyurethanes constitute a versatile family of materials with a broad variety of engineering applications. However, connection between their chemical structure and mechanical properties remains elusive, in large part due to their heterogeneous nature, arising from segregation of chemically distinct segments into separate domains, with resulting complex morphologies. Using atomistic simulations, we examine the structure and mechanical properties of a common family of thermoplastic polyurethanes (TPU) comprising 4,4′-diphenylmethane diisocyanate and n-butanediol (hard segment) and poly(tetramethylene oxide) (soft segment). A lamellar stack model previously developed for the study of semicrystalline polymers is applied here for the first time to a phase-segregated copolymer. Equilibrium structure and properties were evaluated for TPUs with different ratios of hard and soft components, using a combination of Monte Carlo and molecular dynamics simulations. Stress–strain behaviors were then evalua...

We use molecular simulations with a united atom force field to examine the effect of short chain branching (SCB) on the noncrystalline, interlamellar structure typical of linear low density polyethylene (LLDPE). The model is predicated on a metastable thermodynamic equilibrium within the interlamellar space of the crystal stack and accounts explicitly for the various chain topologies (loops, tails, and bridges) therein. We examine three branched systems containing methyl, ethyl, and butyl side branches and compare our results to high density polyethylene (HDPE), without branches. We also compare results for two united atom force fields, PYS and TraPPE-UA, within the context of these simulations. In contrast to conventional wisdom, our simulations indicate that the thicknesses of the interfacial regions in systems with SCB are smaller than those observed for a linear polyethylene without branches and that branches are uniformly distributed throughout the interlamellar region. We find a prevalence of gauche...

We report molecular simulation, at the atomistic level, of crystalline 4,4′-diphenylmethane diisocyanate (MDI) with n-butanediol (BDO) as chain extender, henceforth denoted as MDI/BDO, which is one of the most important components of thermoplastic polyurethanes. This work studies the structure and properties of crystalline MDI/BDO at equilibrium and under deformation. An atomistic molecular model of the MDI/BDO unit cell was constructed from fractional coordinates available for related model compounds and space group symmetry, and bulk properties of the subsequently equilibrated crystal were estimated by molecular dynamics. Overall stress-strain behavior of the crystal to small strains was simulated. The full stiffness matrix of crystalline MDI/BDO was extracted, allowing for the complete characterization of the linear elastic behavior of the crystal. Keywords: Atomistic simulation; Crystal elasticity; Polyurethane

We report the use of atomistic simulation to study semicrystalline poly(tetramethylene oxide) (PTMO), which is one of the major components of thermoplastic polyurethanes. This work reports the first application of an Interphase Monte Carlo model previously developed for polyethylene to a more complex chemistry involving heteroatoms, about which much less is known experimentally. The interface between the crystalline and amorphous domains of PTMO has been modeled in detail, complete with the equilibrium distributions of tails, loops and bridges. In doing so, a criterion has been established for selecting the relevant interface between domains, and a methodology developed that identifies the energetically most favorable interface in a heterogeneous material. A representative sample of configurations was then simulated by molecular dynamics, and analysis of deformation to small strains at different strain rates is described. Estimation of the full stiffness matrix of semicrystalline PTMO is reported for the ...

In this review, we sketch the materials modeling process in industry. We show that predictive and fast modeling is a prerequisite for successful participation in research and development processes in the chemical industry. Stable and highly automated workflows suitable for handling complex systems are a must. In particular, we review approaches to build and parameterize soft matter systems. By satisfying these prerequisites, efficiency for the development of new materials can be significantly improved, as exemplified here for formulation polymer development. This is in fact in line with recent Materials Genome Initiative efforts sponsored by the US government. Valuable contributions to product development are possible today by combining existing modeling techniques in an intelligent fashion, provided modeling and experiment work hand in hand.

© 2018 Elsevier Ltd In the present work we have performed classical molecular dynamics modelling to investigate the effects of different types of force-fields on the stress-strain and yielding behaviours in semi-crystalline lamellar stacked linear polyethylene. To this end, specifically the all-atomic optimized potential for liquid simulations (OPLS-AA) and the coarse-grained united-atom (UA) force-fields are used to simulate the yielding and tensile behaviour for the lamellar separation mode. Despite that the considered samples and their topologies are identical for both approaches, the results show that they predict widely different stress-strain and yielding behaviours. For all UA simulations we obtain oscillating stress-strain curves accompanied by repetitive chain transport to the amorphous region, along with substantial chain slip and crystal reorientation. For the OPLS-AA modelling primarily cavitation formation is observed, with small amounts of chain slip to reorient the crystal such that the chains align in the tensile direction. This force-field dependence is rooted in the lack of explicit H-H and C-H repulsion in the UA approach, which gives rise to underestimated ideal critical resolved shear stress. The computed critical resolved shear stress for the OPLS-AA approach is in good agreement with density functional theory calculations and the yielding mechanisms resemble those of the lamellar separation mode. The disparate energy and shear stress barriers for chain slip of the different models can be interpreted as differently predicted intrinsic activation rates for the mechanism, which ultimately are responsible for the observed diverse responses of the two modelling approaches.

Machine-cast thermoplastic polyurethanes are strained and monitored by small-angle X-ray scattering (SAXS). They are prepared from 4,4′-methylene diphenyl diisocyanate, 1,4-butane diol, and polytetrahydrofuran. Upon stretching hard domains are destroyed. Most stable are the domains of materials with a hard-domain content (HSC) of 30%. Domain stability decreases with increasing HSC and crosslinking. Most materials show stability up to a strain 0.6. At higher strain, the apparent long period decreases for the materials with HSC = 30%. Correlated hard domains, the “strain probes” relax as others are destroyed. The fraction of relaxing probes and their ultimate relaxation decrease with increasing HSC. Chord distribution functions computed from the SAXS exhibit the same sequence of static long-period bands. The band positions form a Fibonacci series, related to the underlying polyaddition process. This indicates a nearly quasicrystalline arrangement of stringed hard domains, identified as the strain probes of the discrete SAXS. At strains

When straining polyurethane elastomers (PUEs), it is often observed that the long-period peak of the small-angle X-ray scattering (SAXS) does not shift normally. An explanation is indicated for some PUEs in the real-space chord distribution. It exhibits a sequence of constant long-period bands. The band positions form a Fibonacci sequence. This relates to the underlying chemical synthesis by polyaddition of hard and soft modules, indicating a nearly quasiperiodic setup in sequences of stringed hard domains. These sequences appear to be the probes provided by SAXS for the study of morphology evolution in such PUEs. Should a regular-as-possible arrangement of physical crosslinks optimize a property of the material, then in the synthesis the mole fractionnHof hard modules should be chosen to benH= τ/(1 + τ) ≃ 0.62, where τ is the golden ratio.

This work demonstrates how the geometric and topological characteristics of substructures within heterogeneous materials can be employed to tailor the mechanical responses of soft crystals under large strains. The large deformation mechanical behaviors of elastomeric composites possessing long-range crystalline order are examined using both experiments on 3D-printed prototype materials and precisely matched numerical simulations. The deformation mechanisms at small and large strains are elucidated for six sets of morphologies: dispersed particles on each of the simple cubic, body-centered cubic or face-centered cubic lattices, and their bi-continuous counterparts. Comparison of results for the six types of morphologies reveals that the topological connectivity of dissimilar domains is of critical importance for tailoring the macroscopic mechanical properties and the mechanical anisotropy.

Monte Carlo molecular simulations are reported to investigate the amorphous region between crystalline lamellae of isotactic polypropylene ( iPP). It is the first such study in which consideration is given to the nature of pendant side groups on the polymer chain. The crystalline lamellae are modeled after the R2 crystal of iPP, while the interphase and amorphous domains are equilibrated with respect to both spatial and topological degrees of freedom. A united atom force field is used to describe the interactions between the methyl, methylene, and methyne moieties that constitute a polypropylene molecule. Mass density and bond orientational order profiles, distributions of chain populations, interphase thicknesses, interfacial energies, local conformations as characterized by torsional angle sequences, and chain reentry statistics are studied for three different temperatures. Our results match well with the available experimental data and provide a molecular level understanding of the semicrystalline interphase for isotactic polypropylene. A comparison with linear polyethylene (PE) reveals the effects of chemical architecture on the crystal -amorphous interphase in semicrystalline polymers. Semicrystalline polymers have found widespread use due to their excellent mechanical and barrier properties. The crystal- lization of polymers corresponds to a first-order phase transi- tion, 1 similar to other substances. However, a significant difference between long chain molecules and their low molecular weight counterparts lies in the kinetics of the crystallization process, because of which the complete incorporation of polymer molecules into the ordered crystalline state is rarely achieved. Thus, "semicrystalline" polymers are structurally nonhomoge- neous materials and invariably consist of an intimate mixture of crystalline and amorphous phases. These polymers exhibit properties that are a consequence of the combined attributes of ordered (crystalline) and disordered (amorphous) constituent regions, with the unique feature that both crystalline and noncrystalline elements are topologically connected by chains that meander their way from region to region. A comprehensive understanding of the behavior of semicrystalline polymers thus demands extensive knowledge not only of the individual phases but also the interplay between them. The existence and lamellar nature of semicrystalline polymers have been known for approximately half a century. 2-8 Various facets that describe the state of the semicrystalline system can be identified, including the gross morphological structure, degree

We describe a method to determine the mechanical and thermodynamic properties of the interface between a polyethylene crystal and melt by united-atom Monte Carlo simulations. In particular, the {201} fold surface is studied in the temperature range 380–450 K. The interface properties are defined by using the concept of a sharp Gibbs dividing surface, which in turn is used to define the interface internal energy and the interface stresses. We find that the internal energy of the interface is of the order 0.3–0.35 J/m 2 . The interface stresses are anisotropic for the {201} crystal surface with values of approximately −0.27 and −0.4 J/m 2 for the xx - and yy -components, respectively. By way of the Herring equation, the surface tension of the fold surface is independent of shear strains in the interface. The temperature and strain derivatives of the interface properties are also measured and discussed in detail. The influence of the interface internal energy and of phase change contributions on the macroscopic heat capacity of the semi-crystalline material is examined.

Polysulfone based on bisphenol A has been extensively used as a material for membrane-based gas separation. For polymers with aromatic rings in their backbones, such as polysulfones and polyimides, changing the connecting bond positions from meta to para seems to increase their permeability and diffusivity to gases. Cavity size distributions of three isomer pairs (PSF and 3,4′-PSF, PSF-P and PSF-M, 6FDA-6FpDA and 6FDA-6FmDA) are calculated through molecular simulation. The diffusivity of small molecules in these isomers is also obtained by molecular dynamics. For all three isomer pairs, the average cavity size in para isomers is larger than in meta isomers. The molecular dynamics determined diffusion coefficients of neon in para isomers are also larger than in meta isomers. These results are consistent with the experimental observation that room-temperature gas diffusion in para isomers is faster than in meta isomers.

We describe a method for determining the thermal and elastic properties of the noncrystalline phase of semicrystalline polymers (the “interphase”) by Monte Carlo simulations. The method is applied to an interphase composed of freely rotating polyethylene-like chains, studied previously by Balijepalli and Rutledge (J. Chem. Phys. 1998, 109, 6523). The isochoric and isobaric heat capacities, Gruneisen coefficients, thermal expansion coefficients, and elastic stiffnesses are reported. The interphase exhibits material properties comparable to that of the corresponding melt, with significant contributions of both enthalpic and entropic origins. Through judicious selection of Monte Carlo moves, we approximate the rate sensitivity of the stiffness normal to the crystal surface, C 33, on time scales that are long and short, respectively, relative to the characteristic time scale of the crystalline αc relaxation.

In this study Monte Carlo simulations are used to determine the solvation properties of model hydrophobic (xenon and hard sphere) and hydrophilic (dimethyl ether) solutes in SPC/E water. Various contributions to the experimental solvation entropy, including the solvent reorganization entropy, have been determined. The main conclusion drawn, which is in accord with solubility data, is that poor solubility correlates with poor solute-water interaction. At room temperature, energy dominates the aqueous solubility of both hydrophobic and hydrophilic solutes, rather than entropy. However, at higher temperatures the solubility can pass through a minimum, and then entropy becomes dominant. Another interesting finding is the presence of larger than expected cavities in water. Two different simulation results support this finding. This unexpected hollow structure in water explains why a hard sphere solute is more soluble in water than in a comparable hard sphere or Lennard-Jones solvent. Hydrogen bonding causes wa...

A new algorithm has been developed for determining the cavity size distribution in liquids. The computational method is based on energetic rather than geometric considerations. It is applicable to any liquid structure, including polymers, that can be simulated by molecular dynamic or Monte Carlo methods. To illustrate its utility, it has been applied to hard sphere (HS) and Lennard-Jones (LJ) fluids, SPC/E water, as well as to the two isomeric polyimides. To verify its ability to locate cavities and to determine cavity size frequency, it has also been applied with success to crystalline systems. Significant differences in liquid structure can be detected among HS, LJ, and SPC/E liquids, particularly at low densities where LJ and SPC/E liquids show evidence of “clustering.” The supercooled LJ liquid clearly reveals the development of a solid phase by the preferential appearance of tetrahedral and octahedral cavities. Cavitation in water under negative pressures can be detected. Differences in cavity size d...

Using accurate equations of state, contributions to the configurational entropy and energy of water are calculated and compared with six simple fluids and a model Lennard-Jones (LJ) fluid. The reorganizational entropy is calculated for the first time for water and other fluids. Comparisons are made at equal reduced densities from the triple point to the gas-liquid critical temperature. A corresponding states principle (CSP), suggested by the van der Waals model, is satisfied for certain configurational properties among the simple and LJ fluids. Saturated simple liquids in states of equal free volume fractions have comparable configurational properties. Water deviates significantly from the CSP in some but not all cases. The normal boiling point of eight simple fluids is seen to be an isofree volume state that occurs at a reduced density (ρ/ρc) of 2.63 ± 0.02, or equivalently, an occupied volume fraction of 0.42. A nearly invariant entropy of vaporization at the normal boiling point among eight simple flui...

Nanoparticles are now more than ever being used to tailor materials function and performance in differentiating technologies because of their profound effect on thermo-physical, mechanical and optical properties. The most feasible way to disperse particles in a bulk material or control their packing at a substrate is through fluidization in a carrier, followed by solidification through solvent evaporation/drying/curing/sintering. Unfortunately processing particles as concentrated, fluidized suspensions into useful products remains an art largely because the effect of particle shape and volume fraction on fluidic properties and suspension stability remains unexplored in a regime where particle-particle interaction mechanics is prevalent. To achieve a stronger scientific understanding of the factors that control nanoparticle dispersion and rheology we have developed a multiscale modeling approach to bridge scales between atomistic and molecular-level forces active in dense nanoparticle suspensions. At the largest length scale, two 'coarse-grained' numerical techniques have been developed and implemented to provide for high-fidelity numerical simulations of the rheological response and dispersion characteristics typical in a processing flow. The first is a coupled Navier-Stokes/discrete element method in which the background solvent is treated by finite element methods. The second is a particle based method known as stochastic rotational dynamics. These two methods providemore » a new capability representing a 'bridge' between the molecular scale and the engineering scale, allowing the study of fluid-nanoparticle systems over a wide range of length and timescales as well as particle concentrations. To validate these new methodologies, multi-million atoms simulations explicitly including the solvent have been carried out. These simulations have been vital in establishing the necessary 'subgrid' models for accurate prediction at a larger scale and refining the two coarse-grained methodologies.« less

Results of large scale nonequilibrium molecular dynamics simulations are presented for nanoparticles in an explicit solvent. The nanoparticles are modeled as a uniform distribution of Lennard-Jones particles, while the solvent is represented by standard Lennard-Jones particles. We present results for the shear rheology of spherical nanoparticles of diameter 10 times that of the solvent for a range of nanoparticle volume fractions. By varying the strength of the interactions between nanoparticles and with the solvent, this system can be used to model colloidal gels and glasses as well as hard spherelike nanoparticles. Effect of including the solvent explictly is demonstrated by comparing the pair correlation function of nanoparticles to that in an implicit solvent. The shear rheology for dumbbell nanoparticles made of two fused spheres is similar to that of single nanoparticle.

Results of large scale equilibrium and non‐equilibrium molecular dynamics (NEMD) simulations are presented for nanoparticles in an explicit solvent. The nanoparticles are modeled as a uniform distribution of Lennard‐Jones particles, while the solvent is represented by standard Lennard‐Jones particles. Unlike hard sphere models, the nanoparticles and solvent do not phase separate for disparate sizes of nanoparticles and solvent, which allows us to study the static and dynamic properties of nanoparticle suspensions with an explicit solvent. Here we present results for nanoparticles of size 5 to 20 times that of the solvent for a range of concentrations from 7 to 40% volume fraction. The nanoparticles are found to segregate to the liquid/vapor interface or repel the interface depending on the relative strength of the nanoparticle/nanoparticle and nanoparticle/solvent interactions. Results from NEMD simulations suggest that the shear rheology of the suspension depends only on the nanoparticle concentration no...

The purpose of this project is to develop tools to model and simulate the processes of self-assembly and growth in biological systems from the molecular to the continuum length scales. The model biological system chosen for the study is the tendon fiber which is composed mainly of Type I collagen fibrils. The macroscopic processes of self-assembly and growth at the fiber scale arise from microscopic processes at the fibrillar and molecular length scales. At these nano-scopic length scales, we employed molecular modeling and simulation method to characterize the mechanical behavior and stability of the collagen triple helix and the collagen fibril. To obtain the physical parameters governing mass transport in the tendon fiber we performed direct numerical simulations of fluid flow and solute transport through an idealized fibrillar microstructure. At the continuum scale, we developed a mixture theory approach for modeling the coupled processes of mechanical deformation, transport, and species inter-conversion involved in growth. In the mixture theory approach, the microstructure of the tissue is represented by the species concentration and transport and material parameters, obtained from fibril and molecular scale calculations, while the mechanical deformation, transport, and growth processes are governed by balance laws and constitutive relations developed withinmore » a thermodynamically consistent framework.« less

We present the first theoretical estimates for thermoelastic properties of the noncrystalline domain (the interlamellar phase) of semicrystalline polyethylene obtained by Monte Carlo simulations. The interlamellar phase is prescribed to be thermodynamically metastable, with the constraints that it have an average density less than that of the crystal and that it be bounded by two static crystalline lamellae oriented with the {201} crystal plane parallel to the interface. Polyethylene was modeled using a realistic united atom force field with inclusion of torsional contributions, and the results are compared to those of prior studies that used a freely rotating chain model. Parallel tempering between 350 and 450 K was used to simulate several isochoric/isothermal ensembles simultaneously and efficiently, from which the heat capacity, thermal expansion coefficients, Grneisen coefficients, and the elastic stiffness tensor were determined at atmospheric pressure. The noncrystalline interlamellar phase exhibits properties intermediate between that of the semicrystalline solid and the amorphous melt.

Stochastic rotation dynamics (SRD) is a relatively recent technique, closely related to lattice Boltzmann, for capturing hydrodynamic fluid flow at the mesoscale. The SRD method is based on simple constituent fluid particle interactions and dynamics. Here we parametrize the SRD fluid to provide a one to one match in the shear viscosity of a Lennard-Jones fluid and present viscosity measurements for a range of such parameters. We demonstrate how to apply the Müller-Plathe reverse perturbation method for determining the shear viscosity of the SRD fluid and discuss how finite system size and momentum exchange rates effect the measured viscosity. The implementation and performance of SRD in a parallel molecular dynamics code is also described.

We present molecular dynamics simulations of the liquid-vapor phase coexistence of pure nanoparticle systems with three different model nanoparticle interactions. Our simulations show that the form of the interaction potential between nanoparticles strongly influences their coexistence behavior. For nanoparticles interacting with an integrated Lennard-Jones potential, the critical temperature and critical density increase with increasing particle size. In contrast, nanoparticles interacting via a Lennard-Jones potential shifted to the surface of the nanoparticle do not exhibit the expected size dependence of the phase diagram. For this model, the critical temperature decreases with increasing nanoparticle size. Similar results were observed for composite nanoparticles, with the interactions truncated at a finite distance.

We perform atomistic simulations on a single collagen molecule to determine its intrinsic molecular strength. A tensile pull simulation to determine the tensile strength and Young's modulus is performed, and a simulation that separates two of the three helices of collagen examines the internal strength of the molecule. The magnitude of the calculated tensile forces is consistent with the strong forces of bond stretching and angle bending that are involved in the tensile deformation. The triple helix unwinds with increasing tensile force. Pulling apart the triple helix has a smaller, oscillatory force. The oscillations are due to the sequential separation of the hydrogen-bonded helices. The force rises due to reorienting the residues in the direction of the separation force. The force drop occurs once the hydrogen bond between residues on different helices break and the residues separate.