相关论文: Structural evolution of protein-biofilms: Simulati…

Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…

Preliminary results are presented for the kinetics of phase separation in three distinct models of protein aggregation. The first is a model of the formation of spherical microcrystals of insulin via an initial formation of fractal clusters…

We propose a model of antibiotic diffusion through a bacterial biofilm when diffusion and/or absorption barriers develop in the biofilm. The idea of this model is: We deduce details of the diffusion process in a medium in which direct…

The interplay of phase separation and dynamical arrest can lead to the formation of gels and glasses, which is relevant for such diverse fields as hard and soft condensed matter physics, materials science, food engineering and…

Eukaryote cells have a flexible shape, which dynamically changes according to the function performed by the cell. One mechanism for deforming the cell membrane into the desired shape is through the expression of curved membrane proteins.…

Bacterial growth and division generally occur by the process known as binary fission, in which the cells grow polarly until they divide into two daughter cells. Although this process is affected by factors that introduce stochastic…

Biofilms are ubiquitous macro-colonies of bacteria that develop at various interfaces (solid-liquid, solid-gas or liquid-gas). The formation of biofilms starts with the attachment of individual bacteria to an interface, where they…

In this article, we study in details the fluid dynamics system proposed in Clarelli et al (2013) to model the formation of cyanobacteria biofilms. After analyzing the linear stability of the unique non trivial equilibrium of the system, we…

We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric and thermal forces. As three model systems with distinctly different properties we consider the pairs…

A dissipative particle dynamics (DPD) model for the quantitative simulation of biofilm growth controlled by substrate (nutrient) consumption, advective and diffusive substrate transport, and hydrodynamic interactions with fluid flow…

Controlling thin film formation is technologically challenging. The knowledge of physical properties of the film and of the atoms in the surface vicinity can help improve control over the film growth. We investigate the use of the…

Bacteria generally live in complicated structures called biofilms, consisting of communicating bacterial colonies and extracellular polymeric substance (EPS). Since biofilms are related to detrimental effects such as infection or antibiotic…

In this paper we derive a pore-scale model for permeable biofilm formation in a two-dimensional pore. The pore is divided in two phases: water and biofilm. The biofilm is assumed to consist of four components: water, extracellular polymeric…

A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…

We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…

This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an…

We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…

Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…

The high-pressure compaction of three dimensional granular packings is simulated using a bonded particle model (BPM) to capture linear elastic deformation. In the model, grains are represented by a collection of point particles connected by…