Related papers: flippy: User friendly and open source framework fo…
Lipid vesicles appear ubiquitously in biological systems. Understanding how the mechanical and intermolecular interations deform vesicle membrane is a fundamental question in biophysics. In this article we developed a fast algorithm to…
An emerging theme across many domains of science and engineering is materials that change shape, often dramatically. Determining their structure involves solving a shape optimization problem where a given energy functional is minimized with…
Fractures are ubiquitous in the subsurface and strongly affect flow and deformation. The physical shape of the fractures, they are long and thin objects, puts strong limitations on how the effect of this dynamics can be incorporated into…
Development of models and dedicated numerical methods for dynamics in fractured rocks is an active research field, with research moving towards increasingly advanced process couplings and complex fracture networks. The inclusion of coupled…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
Cellular membranes are a heterogeneous mix of lipids, proteins and small molecules. Special groupings of saturated lipids and cholesterol form a liquid-ordered phase, known as `lipid rafts,' serving as platforms for signaling, trafficking…
Water-phospholipid interactions at the lipid bilayer/water interfaces are of essential importance for the dynamics, stability and function of biological membrane, and are also strongly associated with numerous biological processes at the…
Whether live cell membranes show miscibility phase transitions (MPTs), and if so, how they fluctuate near the transitions remain outstanding unresolved issues in physics and biology alike. Motivated by these questions we construct a generic…
A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with…
The elastic properties of two-component bilayer membranes are studied using a coarse grain model for amphiphilic molecules. The two species of amphiphiles considered here differ only in their length. Molecular Dynamics simulations are…
Phosphatidylinositol phosphates (PIPs) are membrane phospholipids that play crucial roles in a wide range of cellular functions. However, there is a dearth of experimental data in the literature on PIPs because their investigations are not…
Atomistic simulations were performed on hydrated model lipid multilayers that are representative of the lipid matrix in the outer skin (stratum corneum). We find that cholesterol transfers easily between adjacent leaflets belonging to the…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Understanding interactions between membranes requires measurements on well-controlled systems close to natural conditions, in which fluctuations play an important role. We have determined, by grazing incidence X-ray scattering, the…
The biological membrane, which compartmentalizes the cell and its organelles, exhibit wide variety of macroscopic shapes of varying morphology and topology. A systematic understanding of the relation of membrane shapes to composition,…
Cells are defined by lipid membranes that differ in their structure across the tree of life. While the membranes of most bacteria and eukaryotes consist of single-headed bilayer lipids, the membranes of archaea are composed of mixtures of…
SkyPy is an open-source Python package for simulating the astrophysical sky. It comprises a library of physical and empirical models across a range of observables and a command-line script to run end-to-end simulations. The library provides…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
Multiphysics processes in fractured porous media is a research field of importance for several subsurface applications and has received considerable attention over the last decade. The dynamics are characterised by strong couplings between…
We propose a very simple but realistic enough model which allows to include a large number of molecules in molecular dynamics MD simulations of these bilayers, but nevertheless taking into account molecular charge distributions, flexible…