Related papers: Selection originating from protein foldability: I.…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
We simulate the electrical properties of a device realized by a G protein coupled receptor (GPCR), embedded in its membrane and in contact with two metallic electrodes through which an external voltage is applied. To this purpose, recently,…
The glass transition temperature and its connection to statistical properties of confined and free-standing polymer films of varying thickness containing unentangled to highly entangled bead-spring chains are studied by molecular dynamics…
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching…
A statistical thermodynamic approach of moving particles forming an elastic body is presented which leads to reveal molecular-mechanical properties of classical and nonextensive dynamical systems. We derive the Boltzmann-Gibbs (BG) entropy…
A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions.…
Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been…
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…
The continuous random energy model (CREM) is a toy model of spin glasses on $\{0,1\}^N$ that, in the limit, exhibits an infinitely hierarchical correlation structure. We give two polynomial-time algorithms to approximately sample from the…
The apparent thermalization of the particles produced in hadronic collisions can be obtained by quantum entanglement of the partons of the initial state once a fast hard collision is produced. The scale of the hard collision is related to…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
Self Consistent Normal Mode Analysis (SCNMA) is applied to heme c type cytochrome f to study temperature dependent protein motion. Classical Normal Mode Analysis (NMA) assumes harmonic behavior and the protein Mean Square Displacement (MSD)…
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…
We study the abundance of a particle species in a thermalized plasma by introducing a quantum kinetic description based on the non-equilibrium effective action. A stochastic interpretation of quantum kinetics in terms of a Langevin equation…
The dynamic properties of liquid phase-change materials (PCMs), such as viscosity $\eta$ and atomic self-diffusion coefficients D, play an essential role in ultrafast phase switching behavior of novel non-volatile phase-change memory…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
We study a stochastic model of gene expression, in which protein production has a form of random bursts whose size distribution is arbitrary, whereas protein decay is a first-order reaction. We find exact analytical expressions for the time…
In this paper we develop a generalized formalism for equilibrium thermodynamic systems when an information is shared between the system and the reservoir. The information results in a correction to the entropy of the system. This extension…
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in…
In Proteomics, only the de novo peptide sequencing approach allows a partial amino acid sequence of a peptide to be found from a MS/MS spectrum. In this article a preliminary work is presented to discover a complete protein sequence from…