Related papers: Molecular Dynamics Simulations of Lipid Bilayers: …
Experiments reveal that structural transitions in thin sheets are mediated by the passage of transient and stable mobile localized elastic excitations. These ``crumples'' or ``d-cones'' nucleate, propagate, interact, annihilate, and escape.…
Smoothing short-wavelength charge density variations can stabilize explicit electrostatic particle-in-cell (PIC) plasma simulations against grid heating and cold beam instabilities, which cause unphysical heating when the Debye length is…
We have adapted a set of classification algorithms, also known as Machine Learning, to the identification of fluid and gel domains close to the main transition of dipalmitoyl-phosphatidylcholine (DPPC) bilayers. Using atomistic molecular…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We investigate the behavior of colloidal suspensions with different volume fractions confined between parallel walls under a range of steady shears. We model the particles using molecular dynamics (MD) with full hydrodynamic interactions…
Fundamental understanding of macroscopic properties of polymer nanocomposites (PNCs) remains difficult due to the complex interplay of microscopic dynamics and structure, namely interfacial layer relaxations and three-dimensional…
In biological membranes, alpha-tocopherols ({\alpha}-toc; vitamin E) protect polyunsaturated lipids from free radicals. Although the interactions of {\alpha}-toc with non-oxidized lipid bilayers have been studied, their on oxidized bilayers…
In this article we propose and investigate a hierarchy of mathematical models based on partial differential equations (PDE) and ordinary differential equations (ODE) for the simulation of the biophysical phenomena occurring in the…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
Water contained within biological membranes plays a critical role in maintaining the separation between intracellular and extracellular environments and facilitating biochemical processes. Variations in membrane composition and temperature…
We have constructed a model for the kinetics of rupture of membranes under tension, applying physical principles relevant to lipid bilayers held together by hydrophobic interactions. The membrane is characterized by the bulk compressibility…
With the great development of parallel computing techniques, the particle-particle (PP) model has been successfully applied in a number of plasma applications. Comparing to particle-mesh (PM) models, for example the widely used…
A dynamical rearrangement in the electronic structure of a molecule can be driven by different phenomena, including nuclear motion, electronic coherence or electron correlation. Recording such electronic dynamics and identifying their fate…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
The capability to simulate a two-way coupled interaction between a rarefied gas and an arbitrary-shaped colloidal particle is important for many practical applications, such as aerospace engineering, lung drug deliver and semiconductor…
Ultracold dipolar molecules hold great promise for the creation of novel quantum states of matter, but the realization of long-lived molecular bulk samples with strong dipole-dipole interactions has remained elusive. Here, we realize a…
We investigate finite-size effects on diffusion in confined fluids using molecular dynamics simulations and hydrodynamic calculations. Specifically, we consider a Lennard-Jones fluid in slit pores without slip at the interface and show that…
Kinetics of dislocations is studied by means of computer simulation during intensive plastic deformation. The dynamical effect in the form of soliton-like wave of sharply disrupted interparticle bonds is observed. Along with it, micropores…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
Plastic deformation In crystalline materials is controlled by the motion and interactions of dislocations [AND 17]. Discrete Dislocation Dynamics (DDD) simulations have now existed for about 25 years to investigate plastic flow at the…