相关论文: Pre-transition effects mediate forces of assembly …
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 study the phase behaviour of a fluid composed of particles which interact via a pair potential that is repulsive for large inter-particle distances, is attractive at intermediate distances and is strongly repulsive at short distances…
We investigate the role of order/disorder transitions in alchemical simulations of protein-ligand absolute binding free energies. We show, in the context of a potential of mean force description, that for a benchmarking system (the complex…
This article summarizes a variety of physical mechanisms proposed in the literature, which can generate micro- and nanodomains in multicomponent lipid bilayers and biomembranes. It mainly focusses on lipid-driven mechanisms that do not…
We consider a stiff polymer chain in poor solvent and apply a force at one end of the chain. We find that by varying the stiffness parameter, polymer undergoes a transition from the globule state to the folded like state. The conformation…
We study lipid translocation ("flip-flop") between the leaflets of a planar lipid bilayer with transition path sampling (TPS). Rare flip-flops compete with biological machineries that actively establish asymmetric lipid compositions.…
Premelting at the ice-polymer interfaces, in which a quasi-liquid layer (QLL) forms below the melting point, is strongly influenced by polymer surface chemistry; however, the molecular-scale mechanisms underlying these effects remain poorly…
Diffusive transport of small molecules within the internal structures of biological and synthetic material systems is complex because the crowded environment presents chemical and physical barriers to mobility. We explored this mobility…
The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…
One-dimensional model of a system where first-order phase transition occurs is examined in the present paper. It is shown that basic properties of the phenomenon, such as a well defined temperature of transition, are caused both by…
Deformable colloids and macromolecules adsorb at interfaces, as they decrease the interfacial energy between the two media. The deformability, or softness, of these particles plays a pivotal role in the properties of the interface. In this…
Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behaviour of single cells, we use extensive Monte Carlo simulations to predict non-trivial…
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
The effect of increasing structural disorder on the distribution of contact forces P(f), inside three dimensional particle assemblies is systematically studied using computer simulations of model granular packings. Starting from a…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
Recent experimental and computational studies of vibrated thin layers of identical spheres have shown transitions to ordered phases similar to those seen in equilibrium systems. Motivated by these results, we carry out simulations of hard…
Biological active matter like the cytoskeleton or tissues are characterized by their ability to transform chemical energy into mechanical stress. In addition, it often exhibits orientational order, which is essential for many cellular and…
Protein aggregation in the form of amyloid fibrils has important biological and technological implications. Although the self-assembly process is highly efficient, aggregates not in the fibrillar form would also occur and it is important to…
Fusion of lipid bilayers in membranes is important in processes from vesicle-cell interactions (as in drug delivery) to exosome-cell signaling, while transient transmembrane electric fields are known to occur spontaneously. Two contacting…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…