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We present a simple coarse-grained bead-and-spring model for lipid bilayers. The system has been developed to reproduce the main (gel-liquid) transition of biological membranes on intermediate length scales of a couple of nanometres and is…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
Critical lateral pressure for a pore formation and phase diagram of porous membrane are derived analytically as functions of the microscopic parameters of the lipid chains. The derivation exploits path-integral calculation of the free…
All simulation approaches eventually face limits in computational scalability when applied to large spatiotemporal domains. This challenge becomes especially apparent in molecular-level particle simulations, where high spatial and temporal…
We discuss the computational performance of the adaptive resolution technique in molecular simulation when it is compared with equivalent full coarse-grained and full atomistic simulations. We show that an estimate of its efficiency, within…
Using Couette and Poiseuille flow, we extract the temperature dependence of the slip length, $\delta$, from molecular dynamics simulations of a coarse-grained polymer model in contact with an attractive, corrugated surface. $\delta$ is…
We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair interactions between them. The pair potentials…
The rich thermotropic behavior of lipid bilayers is addressed using phenomenological theory informed by many experiments. The most recent experiment not yet addressed by theory has shown that the tilt modulus in DMPC lipid bilayers…
The correct accounting for thermal effects is always a challenge when one needs to make quantitative predictions for any laser applications. In such complicated devices as quantum cascade lasers temperature strongly affects the operational…
The membrane curvature of cells and intracellular compartments continuously adapts to enable cells to perform vital functions, from cell division to signal trafficking. Understanding how membrane geometry affects these processes in vivo is…
A minimalist simulation model for lipid bilayers is presented. Each lipid is represented by a flexible chain of beads in implicit solvent. The hydrophobic effect is mimicked through an intermolecular pair potential localized at the…
For solving the discretized three-temperature energy linear systems, Xu et al. proposed a physical-variable based coarsening two-level iterative method (PCTL algorithm) in 2009 and verified its efficiency by numerical experiments in…
Near a critical point, the time scale of thermally-induced fluctuations diverges in a manner determined by the dynamic universality class. Experiments have verified predicted 3D dynamic critical exponents in many systems, but similar…
Droplet interface bilayers are a convenient model system to study the physio-chemical properties of phospholipid bilayers, the major component of the cell membrane. The mechanical response of these bilayers to various external mechanical…
The cryopreservation of biological materials is a highly complex process, as it involves numerous factors such as the cooling and thawing procedures, the administration of cryoprotective agents (CPAs), as well as the type and composition of…
Superpositioning of relaxation data as a function of the product variable TV^{\gamma}, where T is temperature, V the specific volume, and {\gamma} a material constant, is an experimental fact demonstrated for approximately 100 liquids and…
Active learning (AL) reduces the amount of labeled data needed to train a machine learning model by intelligently choosing which instances to label. Classic pool-based AL requires all data to be present in a datacenter, which can be…
We present a simple and highly adaptable method for simulating coarse-grained lipid membranes without explicit solvent. Lipids are represented by one head-bead and two tail-beads, with the interaction between tails being of key importance…
The averaged absorbed power density (APD) and temperature rise in body models with nonplanar surfaces were computed for electromagnetic exposure above 6 GHz. Different calculation schemes for the averaged APD were investigated.…
Accurate prediction of temperature evolution is essential for understanding thermomechanical behavior in friction stir welding. In this study, molecular dynamics simulations were performed using LAMMPS to model aluminum friction stir…