Related papers: Temperature dependence of normal mode reconstructi…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
The sensitivity of the native states of protein-like heteropolymers to mutations modelled as perturbations in the interaction potential between amino acids is studied. The stability threshold against mutations is shown to be zero for random…
We investigate the transport of proteins inside the proteasome and propose an active transport mechanism based on a spatially asymmetric interaction potential of peptide chains. The transport is driven by fluctuations which are always…
We propose a detailed investigation of the schematic mode-coupling approach to experimental data, a method based on the use of simple mode-coupling equations to analyze the dynamics of supercooled liquids. Our aim here is to clarify…
Molecular transport maintains cellular structures and functions. For example, lipid and protein diffusion sculpts the dynamic shapes and structures on the cell membrane that perform essential cellular functions, such as cell signaling.…
Production of heat shock proteins are induced when a living cell is exposed to a rise in temperature. The heat shock response of protein DnaK synthesis in E.coli for temperature shifts from temperature T to T plus 7 degrees, respectively to…
We derive an analytic expression for site-specific stationary distributions of amino acids from the Structurally Constrained Neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that…
Analysis of experimental kinetic dependences and results of the computer modeling of pairwise interactions in the heterogeneous system have shown that a character of its fractal property variation in the evolution process would be different…
The temperature dependence of the solid-liquid interfacial free energy, {\gamma}, is investigated for Al and Ni at the undercooled temperature regime based on a recently developed persistent-embryo method. The atomistic description of the…
Gibbs and Boltzmann definitions of temperature agree only in the macroscopic limit. The ambiguity in identifying the equilibrium temperature of a finite sized `small' system exchanging energy with a bath is usually understood as a…
We study the equilibrium statistical properties of the potential energy landscape of several glass models in a temperature regime so far inaccessible to computer simulations. We show that unstable modes of the stationary points undergo a…
Using two extremely different models of glass formers in two and three dimensions we demonstrate how to encode the subtle changes in the geometric rearrangement of particles during the scenario of the glass transition. We construct a…
Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant that accounts for…
The instantaneous normal modes corresponding to base pair vibrations (radial modes) and twist angle fluctuations (angular modes) of a DNA molecule model at ambient temperature are theoretically investigated. Due to thermal disorder, normal…
The expression for the higher temperature dependence of the mean squared displacement in proteins is obtained. The quantum multi-well model explains the dynamic transitions of the proteins and minimizes the amount of parameters to a single…
We present an ab-initio study of the temperature dependent elastic constants of BAs, a semiconductor that exhibits ultra-high thermal conductivity and is under investigation for thermal management in electronics. We test the consistency of…