Related papers: Simple Model of Membrane Proteins Including Solven…
We report a numerical simulation of the phase diagram of a simple model for membrane proteins constrained to move in a plane. In analogy with the corresponding three dimensional models, the liquid-gas transition becomes metastable as the…
The properties of the solvent affect the behavior of the solution. We propose a model that accounts for the contribution of the solvent free energy to the free energy of globular proteins in solution. For the case of an attractive square…
A microscopic model is proposed for the interactions between sickle hemoglobin molecules based on information from the protein data bank. A Monte Carlo simulation of a simplified two patch model is carried out, with the goal of…
In this paper, phase field models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic…
We propose a model describing liquid-solid phase coexistence in mixed lipid membranes by including explicitly the occurrence of a rippled phase. For a single component membrane, we employ a previous model in which the membrane thickness is…
We report theoretical and simulation studies of phase coexistence in model globular protein solutions, based on short-range, central, pair potential representations of the interaction among macro-particles. After reviewing our previous…
We present a single-particle Lennard-Jones (L-J) model for CO2 and N2. Simplified L-J models for other small polyatomic molecules can be obtained following the methodology described herein. The phase-coexistence diagrams of single-component…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the…
Several recent imaging experiments access the equilibrium density profiles of interacting particles confined to a two-dimensional substrate. When these particles are in a fluid phase, we show that such data yields precise information…
We present computer simulations of a system of purely repulsive soft colloidal particles interacting via the Hertz potential and constrained to a two-dimensional plane. This potential describes the elastic interaction of weakly deformable…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
In this work we examine thermodynamics of fluid with "molecules" represented by two fused hard spheres, decorated by the attractive square-well sites. Interactions between these sites are of short-range and cause association between the…
Monte Carlo simulation provides a powerful tool for understanding and exploring thermodynamic phase equilibria in many-particle interacting systems. Among the most physically intuitive simulation methods is Gibbs ensemble Monte Carlo…
Recent work has highlighted roles for thermodynamic phase behavior in diverse cellular processes. Proteins and nucleic acids can phase separate into three-dimensional liquid droplets in the cytoplasm and nucleus and the plasma membrane of…
The statistical mechanics of flexible two-dimensional surfaces (membranes) appears in a wide variety of physical settings. In this talk we discuss the simplest case of fixed-connectivity surfaces. We first review the current theoretical…
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We have developed a path integral Monte Carlo method for simulating helium films and apply it to the second layer of helium adsorbed on graphite. We use helium-helium and helium-graphite interactions that are found from potentials which…