相关论文: Cluster phases of membrane proteins

We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids,…

We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by…

The phase behavior of colloid-polymer mixtures, and of solutions of globular proteins, is often interpreted in terms of a simple model of hard spheres with short-ranged attraction. While such a model yields a qualitative understanding of…

A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…

We investigate the phase diagram of a fluid of hard-core disks confined to the surface of a sphere and whose interaction potential contains a short-range attraction followed by a long-range repulsive tail (SALR). Based on previous works in…

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 present a minimal model of plasma membrane heterogeneity that combines criticality with connectivity to cortical cytoskeleton. Our model is motivated by recent observations of micron-sized critical fluctuations in plasma membrane…

Superconductivity, superfluidity, condensation, cluster formation, etc. are phenomena that might occur in many-particle systems. These are due to residual interactions between the particles. To explain these phenomena consistently in a…

Motivated by the biologically important and complex phenomena of A\beta\ peptide aggregation in Alzheimer's disease, we introduce a model and simulation methodology for studying protein aggregation that includes extra-cellular aggregation,…

We propose a model that leads to the formation of non-equilibrium finite-size domains in a biological membrane. Our model considers the active conformational change of the inclusions and the coupling between inclusion density and membrane…

Much progress has been made in elucidating the inner workings of voltage-gated ion channels, but less understood is the influence of lipid rafts on gating kinetics. Here we propose that state-dependent channel affinity for different lipid…

The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…

We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the…

We present molecular dynamics (MD) simulations results for dense fluids of ultrasoft, fully-penetrable particles. These are a binary mixture and a polydisperse system of particles interacting via the generalized exponential model, which is…

We show through rigorous calculations that dielectric microspheres can be organized by an incident electromagnetic plane wave into stable cluster configurations, which we call photonic molecules. The long-range optical binding force arises…

Liquid-liquid phase separation plays a major role in the formation and maintenance of various membrane-less subcellular structures in the cytoplasm and nucleus of cells. Biological condensates contain enhanced concentrations of proteins and…

In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…

The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…

We present a field theory to describe the composition of a surface spontaneously exchanging matter with its bulk environment. By only assuming matter conservation in the system, we show with extensive numerical simulations that, depending…

The transport of individual entities through interconnected structures is a process of practical relevance both in biology and technology. Examples are given by diffusive dynamics of molecules in porous structures. In soft environments,…