Related papers: Thermodynamic competition between membrane protein…
Proteins in organisms, rather than act alone, usually form protein complexes to perform cellular functions. We analyze the topological network structure of protein complexes and their component proteins in the budding yeast in terms of the…
Cellular renewing active matter - assemblies of proliferating and apoptotic cells - underlies tissue homeostasis, morphogenesis, and clonal competition. Previous work in one-dimensional periodic systems identified a fitness advantage…
A thermodynamically motivated neural network model is described that self-organizes to transport charge associated with internal and external potentials while in contact with a thermal reservoir. The model integrates techniques for rapid,…
Unravelling the physical mechanisms behind the organisation of lipid domains is a central goal in cell biology and membrane biophysics. Previous studies on cells and model lipid bilayers featuring phase-separated domains found an intricate…
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.…
We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices.…
We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable…
We extend the Saffman theory of membrane hydrodynamics to account for the correlated motion of membrane proteins, along with the effect of protein concentration on that correlation and on the response of the membrane to stresses.…
The architecture of the eukaryotic genome is characterized by a high degree of spatial organization. Chromosomes occupy preferred territories correlated to their state of activity and, yet, displace their genes to interact with remote sites…
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…
The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out many other tasks in the cell. We…
The organization of live cells into tissues and their subsequent biological function involves inter-cell mechanical interactions, which are mediated by their elastic environment. To model this interaction, we consider cells as spherical…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
Hybridization between species is an important mechanism for the origin of novel lineages and adaptation to new environments. Increased allelic variation and modification of the transcriptional network are the two recognized forces currently…
We numerically investigate the hydrodynamics and membrane dynamics of multicomponent vesicles in two strongly confined geometries. This serves as a simplified model for red blood cells undergoing large deformations while traversing narrow…
We present molecular dynamics simulations of a simple model for polymer melts with intramolecular barriers. We investigate structural relaxation as a function of the barrier strength. Dynamic correlators can be consistently analyzed within…
Non-traditional thermodynamics, applied to random behaviour associated with turbulence, mixing and competition, is reviewed and analysed. Competitive mixing represents a general framework for the study of generic properties of competitive…
Recent research has shown that motile cells can adapt their mode of propulsion to the mechanical properties of the environment in which they find themselves--crawling in some environments while swimming in others. The latter can involve…
Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations…