Related papers: Confinement Effects on the Kinetics and Thermodyna…
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…
The formation of (bio)molecular condensates via liquid-liquid phase separation in cells has received increasing attention, as these coacervates play important functional and regulatory roles within biological systems. However, the majority…
In cellular environment, confinement and macromulecular crowding play an important role on thermal stability and folding kinetics of a protein. We have resorted to a generalized version of the Wako-Saito-Munoz-Eaton model for protein…
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,…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
Living cells are characterized by the micrometric confinement of various macromolecules at high concentrations. Using droplets containing binary polymer blends as artificial cells, we previously showed that cell-sized confinement causes…
Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of…
Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of…
The spreading of bacterial populations is central to processes in agriculture, the environment, and medicine. However, existing models of spreading typically focus on cells in unconfined settings--despite the fact that many bacteria inhabit…
Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, consisting of…
We study structural properties of a ring polymeric melt confined in a film in comparison to a linear counterpart using molecular dynamics simulations. Local structure orderings of ring and linear polymers in the vicinity of the surface are…
The diffusion of small molecular penetrants through polymeric materials represents an important fundamental problem, relevant to the design of materials for applications such as coatings and membranes. Polymer networks hold promise in these…
Modifications of Casimir-Polder interactions due to confinement inside a cylindrical cavity and due to curvature in- and outside the cavity are studied. We consider a perfectly conducting cylindrical shell with a single particle (atom or…
Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
Bacterial colonies are a well-known example of living active matter, exhibiting collective behaviors such as nematic alignment and collective motion that play an important role in the spread of microbial infections. While the underlying…
We examine the effects of confinement on the dynamics of premelted films driven by thermomolecular pressure gradients. Our approach is to modify a well-studied setting in which the thermomolecular pressure gradient is driven by a…
We study the dynamics of a single chain polymer confined to a two dimensional cell. We introduce a kinetically constrained lattice gas model that preserves the connectivity of the chain, and we use this kinetically constrained model to…