Related papers: Functional State Dependence of Picosecond Protein …
A fully atomistic modelling of biological macromolecules at relevant length- and time-scales is often cumbersome or not even desirable, both in terms of computational effort required and it a posteriori analysis. This difficulty can be…
We used an optical reflection method to measure the temperature-dependence of the piezoelectricity, electrostriction and time constant of a morphotropic phase boundary (MPB) thin film. We obtained the piezoelectric constant and the…
We study the steady state of a stochastic particle system on a two-dimensional lattice, with particle influx, diffusion and desorption, and the formation of a dimer when particles meet. Surface processes are thermally activated, with…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
Cytoskeletal filaments are capable of self-assembly in the absence of externally supplied chemical energy, but the rapid turnover rates essential for their biological function require a constant flux of ATP or GTP hydrolysis. The same is…
The mechanisms of solid-state electron transport (ETp) via a monolayer of immobilized Azurin (Az) was examined by conducting probe atomic force microscopy (CP-AFM), both as function of temperature (248 - 373K) and of applied tip force (6-12…
We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or…
The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…
We using differential scanning calorimetry of the unfolding process to identify conditions in which the pseudo two-state refolding of thermally denatured lysozyme can be observed to occur on time scales of hours, in solutions that approach…
The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use quasi-elastic neutron…
We present the self-dynamics of protein amino acids of hydrated lysozyme powder around the physiological temperature by means of molecular dynamics (MD) simulations. The self-intermediate scattering functions (SISF) of the amino acid…
We have proposed a model to analyze the growth kinetics of lysozyme crystals/aggregates under non-isothermal conditions. The model was formulated through an analysis of the entropy production of the growth process which was obtained by…
There has been renewed interest in the frequency dependent specific heat of supercooled liquids in recent years with computer simulation studies exploring the whole frequency range of relaxation. The simulation studies can thus supplement…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
Direct, all-atom calculations of the free energy of hydration of aqueous deca-alanine structures --- holistically including backbone and side-chain interactions together --- show that attractive interactions and the thermal expansion of the…
In order to elucidate the role of the native state topology and the stability of subdomains in protein folding, we investigate free energy landscape of human lysozyme, which is composed of two subdomains, by Monte Carlo simulations. A…
The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric G\=o-like models with a coarse-grained C$_\alpha$ chain representation. We…
We present a temperature dependence study on the gas phase reactions of the C$_2$({\it a}$^3Pi_u$) radical with a selected series of saturated alkanes (C$_2$H$_6$, C$_3$H$_8$, n-C$_4$H$_10$, i-C$_4$H$_10$, and n-C$_6$H$_14$) by means of…
The theory describing action of medicines explored in this paper is based on assumption that vital activity of the cell may be described in terms of the model of two states: resting state and excitation. According to available physiological…
We have exactly solved the relaxational dynamics of a model protein which possesses a kinetically perfect funnel-like energy landscape. We find that the dependence of the relaxation time, $\tau$, on the density of states (DOS) and the…