Simulating Stress-Strain Behavior by Using Individual Chains: Uniaxial Deformation of Amorphous Cis- and Trans-1,4-Polybutadiene.

This work develops a probability-based numerical method for quantifying mechanical properties of non-Gaussian chains subject to uniaxial deformation, with the intention of being able to incorporate polymer-polymer and polymer-filler interactions. The numerical method arises from a probabilistic approach for evaluating the elastic free energy change of chain end-to-end vectors under deformation. The elastic free energy change, force, and stress computed by applying the numerical method to uniaxial deformation of an ensemble of Gaussian chains were in excellent agreement with analytical solutions that were obtained with a Gaussian chain model.

Computing Individual Area per Head Group Reveals Lipid Bilayer Dynamics.

Lipid bilayers express a range of phases from solid-like to gel-like to liquid-like as a function of temperature and lipid surface concentration. The area occupied per lipid head group serves as one useful indicator of the bilayer phase, in conjunction with the two-dimensional radial distribution function (i.e.

Generation and Computational Characterization of a Complex Lipid Bilayer.

Studies indicate a crucial cell membrane role in the antibiotic resistance of . To simulate its membrane structure and dynamics, a complex molecular-scale computational representation of the lipid bilayer was developed. Phospholipid types and their amounts were optimized by reverse Monte Carlo to represent characterization data from the literature, leading to 19 different phospholipid types that combine three headgroups [phosphatidylglycerol, lysyl-phosphatidylglycerol (LPG), and cardiolipin] and 10 tails, including iso- and anteiso-branched saturated chains.

Computational Study of Helical and Helix-Hinge-Helix Conformations of an Anti-Microbial Peptide in Solution by Molecular Dynamics and Vibrational Analysis.

Many classical antimicrobial peptides adopt an amphipathic helical structure at a water-membrane interface. Prior studies led to the hypothesis that a hinge near the middle of a helical peptide plays an important role in facilitating peptide-membrane interactions. Here, dynamics and vibrations of a designed hybrid antimicrobial peptide LM7-2 in solution were simulated to investigate its hinge formation.

Planarity and out-of-plane vibrational modes of tryptophan and tyrosine in biomolecular modeling.

Tryptophan and tyrosine are amino acids that play significant roles in the folding processes of proteins at water-membrane interfaces because of their amphipathic heteroaromatic rings. Employing appropriate heteroaromatic molecular structures is essential for obtaining accurate dynamics and predictive capabilities in molecular simulations of these amino acids. In this study, molecular dynamics simulations that applied the most recent version of the CHARMM36 force field were conducted on aqueous solutions of tryptophan and of tyrosine.

Effect of pressure profile of shock waves on lipid membrane deformation.

Use of shock waves to temporarily increase the permeability of the cell membrane is a promising approach in drug delivery and gene therapy to allow the translocation of macromolecules and small polar molecules into the cytoplasm. Our understanding of how the characteristics of the pressure profile of shock waves, such as peak pressure and pulse duration, influences membrane properties is limited. Here we study the response of lipid bilayer membranes to shock pulses with different pressure profiles using atomistic molecular dynamics simulations.

ROSE bitumen: Mesoscopic model of bitumen and bituminous mixtures.

We present a mesoscopic model for bitumen and bituminous mixtures. The model, which is based on dissipative particle dynamics, consists of different dynamical entities that represent the different characteristic time scales. Through the stress relaxation function, the mechanical properties of the model are investigated.

Hydrodynamic relaxations in dissipative particle dynamics.

This paper studies the dynamics of relaxation phenomena in the standard dissipative particle dynamics (DPD) model [R. D. Groot and P.

Dynamics and Structure of Bitumen-Water Mixtures.

Systems of Cooee bitumen and water up to 4% mass are studied by molecular dynamics simulations. The cohesive energy density of the system is shown to decrease with an increasing water content. This decrease is due mainly to an increase in the interaction energy which is not high enough to counterbalance the increase in volume due to the addition of water.

Viscosity, relaxation time, and dynamics within a model asphalt of larger molecules.

The dynamics properties of a new "next generation" model asphalt system that represents SHRP AAA-1 asphalt using larger molecules than past models is studied using molecular simulation. The system contains 72 molecules distributed over 12 molecule types that range from nonpolar branched alkanes to polar resins and asphaltenes. Molecular weights range from 290 to 890 g/mol.

Frequency analysis of stress relaxation dynamics in model asphalts.

Asphalt is an amorphous or semi-crystalline material whose mechanical performance relies on viscoelastic responses to applied strain or stress. Chemical composition and its effect on the viscoelastic properties of model asphalts have been investigated here by computing complex modulus from molecular dynamics simulation results for two different model asphalts whose compositions each resemble the Strategic Highway Research Program AAA-1 asphalt in different ways. For a model system that contains smaller molecules, simulation results for storage and loss modulus at 443 K reach both the low and high frequency scaling limits of the Maxwell model.

Relaxation time, diffusion, and viscosity analysis of model asphalt systems using molecular simulation.

Molecular dynamics simulation was used to calculate rotational relaxation time, diffusion coefficient, and zero-shear viscosity for a pure aromatic compound (naphthalene) and for aromatic and aliphatic components in model asphalt systems over a temperature range of 298-443 K. The model asphalt systems were chosen previously to represent real asphalt. Green-Kubo and Einstein methods were used to estimate viscosity at high temperature (443.

Packing of simulated friction modifier additives under confinement.

Molecular dynamics simulations have been conducted to obtain detailed information regarding molecular structure and packing of surfactant-like "friction modifier" (FM) chains adsorbed to two confining surfaces under sliding conditions. The simulations are interpreted via the density profile, position-dependent fluctuations in the density profile, and parallel, interlayer position correlation functions. Heterogeneous FM structures were obtained.