Related papers: Protein conformational dynamics and electronic str…
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
We consider continuum dielectric models as minimal models to understand the effect of a surrounding globular protein and solvent on the quantum dynamics of electronic excitations in a biological chromophore. We derive expressions for the…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
The paper is devoted to a systematic account of the theory of conformational dynamics of protein molecules. As an example of application of this theory, we provide a complete analytical description of experiments on the kinetics of CO…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
Chromatin is a complex of DNA and specific proteins forming an intermediary level of organization of eukaryotic genomes, between double-stranded DNA and chromosome. Within a generic modeling of the chromatin assembly, we investigate the…
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure…
The soft condensed matter of biological organisms exhibits atomic motions whose properties depend strongly on temperature and hydration conditions. Due to the superposition of rapidly fluctuating alternative motions at both very low…
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…
We study various derivations of Hawking radiation in conformally rescaled metrics. We focus on two important properties, the location of the horizon under a conformal transformation and its associated temperature. We find that the…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
Heat fluctuations of a harmonic oscillator in contact with a thermostat and driven out of equilibrium by an external deterministic force are studied experimentally and theoretically within the context of Fluctuation Theorems. We consider…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…
Prompted by results that showed that a simple protein model, the frustrated G\=o model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
We present force-clamp data on the collapse of ubiquitin polyproteins in response to a quench in the force. These nonequilibrium trajectories are analyzed using a general method based on a diffusive assumption of the end-to-end length to…