相关论文: The Relative Diffusivities of Bound and Unbound Pr…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
The flow of motor proteins on a filamental track is modelled within the the framework of lattice driven diffusive systems. Motors, considered as hopping particles, perform a highly biased asymmetric exclusion process when bound to the…
Accurate measurements of kinetic rate constants for interacting biomolecules is crucial for understanding the mechanisms underlying intracellular signalling pathways. The magnitude of binding rates plays a very important molecular…
We obtain lower and upper bounds on the skewness and kurtosis associated with the cycle completion time of unicyclic enzymatic reaction schemes. Analogous to a well known lower bound on the randomness parameter, the lower bounds on skewness…
Bacteria often traverse confined spaces to perform critical functions in symbiosis, infection, drug delivery, and soil bioremediation. While the canonical run-and-tumble strategy enables exploration, its reliance on constant sensing and…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such…
Chemotaxis, the directional locomotion of cells towards a source of a chemical gradient, is an integral part of many biological processes - for example, bacteria motion, single-cell or multicellular organisms development, immune response,…
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…
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…
Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…
By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
The biological properties of proteins are uniquely determined by their structure and dynamics. A protein in solution populates a structural ensemble of metastable configurations around the global fold. From overall rotation to local…
An analysis on the discrete versus continuous views of kinetics of macromolecules is presented. It is shown that the discrete approach traditional to biochemistry is insufficient for understanding the dynamics of protein molecules in…
We develop a theory of reversible diffusion-controlled reactions with generalized binding/unbinding kinetics. In this framework, a diffusing particle can bind to the reactive substrate after a random number of arrivals onto it, with a given…
Plasma membranes appear as deformable systems wherein molecules are free to move and diffuse giving rise to condensed microdomains (composed of ordered lipids, transmembrane proteins and cholesterol) surrounded by disordered lipid…
The usual Kramers theory of reaction rates in a condensed medium predict the rate to have an $\eta^{-1}$ dependence, $\eta$ being the viscosity of the medium. However, experiments on ligand binding to proteins performed long ago, showed the…
An Ising--like model of proteins is used to investigate the mechanical unfolding of the Green Fluorescent Protein along different directions. When the protein is pulled from its ends, we recover the major and minor unfolding pathways…
A discrete chemotactic predator-prey model is proposed in which the prey secrets a diffusing chemical which is sensed by the predator and vice versa. Two dynamical states corresponding to catching and escaping are identified and it is shown…