Related papers: Temperature Dependence of Protein Folding Deduced …
In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…
A microscopic model for thermal excitation of vibrational ground state of a molecule interacting with a condensed medium is developed. The master equation for evolution of occupancies of the vibrational levels is derived. The rate constant…
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 resistivity around the ferromagnetic transition temperature in the double exchange model is studied by the Schwinger boson approach. The spatial spin correlation responsible for scattering of conduction electrons are taken into account…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
We analyze electron transport through a quantum shuttle for the applied voltage below the instability threshold. We obtain current-voltage characteristics of this system and show that at low temperature they exhibit pronounced steps. The…
A quantum model on the chemically and physically induced pluripotency in stem cells is proposed. Based on the conformational Hamiltonian and the idea of slow variables (molecular torsions) slaving fast ones the conversion from the…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Transmission through a quantum point contact (QPC) in the quantum Hall regime usually exhibits multiple resonances as a function of gate voltage and high nonlinearity in bias. Such behavior is unpredictable and changes sample by sample.…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go models we show that DeltaT/T_F ~ N^-1, where T_F is the folding transition…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
In this thesis the finite temperature transition between confined and deconfined matter is studied at zero and nonzero quark densities. The findings are relevant for the understanding of the evolution of the early Universe and contemporary…
We study fragmentation of small atomistic clusters via molecular dynamics. We calculate the time scales related to fragment formation and emission. We also show that some degree of thermalization is achieved during the expansion process,…
We investigate the spin-squeezing behavior under thermal effects in a one-dimensional transverse field XY model with spin-1/2. The exact solution of the model helps us to compute the spin-squeezing parameter as a function of temperature and…
We discuss how the thermalization of an elementary quantum system is modified when the system is placed in an environment out of thermal equilibrium. To this aim we provide a detailed investigation of the dynamics of an atomic system placed…
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…
A simple extension of the thermodynamic dislocation theory to non-uniform plastic deformations is proposed for an analysis of high-temperature torsion of aluminum bars. Employing a small set of physics-based parameters, which we expect to…
We have developed a theoretical formalism to introduce temperature as a parameter into the framework of non-relativistic quantum mechanics using the laws of classical thermodynamics and the canonical ensemble scheme of statistical…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…