Related papers: The dynamical transition in proteins and non-Gauss…
Static and dynamical properties of elastic phase transitions under the influence of short--range defects, which locally increase the transition temperature, are investigated. Our approach is based on a Ginzburg--Landau theory for…
We study heat conduction in a one-dimensional chain of particles with longitudinal as well as transverse motions. The particles are connected by two-dimensional harmonic springs together with bending angle interactions. The problem is…
An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied using two theoretical approaches. One is the equilibrium simulation approach with quantum…
A stochastic theory is developed to predict the spectral signature of proton-transfer processes and applied to infrared spectra computed from ab initio molecular-dynamics simulations of a single H$_5$O$_2{}^{+}$ cation. By constraining the…
A low-power stable tunnel diode oscillator with non-traditional single-layer flat pick-up coil is an excellent MHz-range instrument with which one may study weakly expressed peculiarities of the superconductive (SC) state in tiny plate-like…
Understanding the molecular vibrations underlying each of the unknown infrared emission (UIE) bands (such as those found at 3.3, 3.4, 3.5, 6.2, 6.9, 7.7, 11.3, 15.8, 16.4, 18.9 mm) observed in or towards astronomical objects is a vital link…
The dynamics of short 1D nonlinear Hamiltonian chains is analyzed numerically at different temperatures (energy per particle). The boundary temperature $T_b$ separating the regular (quasiperiodic) and the stochastic (chaotic) chain motion…
Symmetry-breaking phases in many-fermion systems are characterized by anomalous functions that represent transient processes during which some properties of free particles, such as spin or charge, are not conserved. Connecting the…
We study a stochastic version of the one-dimensional discrete nonlinear Schr{\"o}dinger equation (DNSE), which is derived from first principles, and thus possesses all the properties required by statistical mechanics, such as detailed…
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule…
First-principles dynamical CPA (Coherent-Potential Approximation) for electron correlations has been developed further by taking into account higher-order dynamical corrections with use of the asymptotic approximation. The theory is applied…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
We outline a kinetic theory of non-thermal fixed points for the example of a dilute Bose gas, partially reviewing results obtained earlier, thereby extending, complementing, generalizing and straightening them out. We study universal…
The building blocks of Nature, namely atoms and elementary particles, are described by quantum mechanics. This fundamental theory is the ground on which physicists have built their major mathematical models [1]. Today, the unique features…
We consider a vectorial, confining SU(N) gauge theory with a variable number, $N_f$, of massless fermions transforming according to the fundamental representation. Using the Schwinger-Dyson and Bethe-Salpeter equations, we calculate the $S$…
The Ludwig-Soret effect, the migration of a species due to a temperature gradient, has been extensively studied without a complete picture of its cause emerging. Here we investigate the dynamics of DNA and spherical particles sub jected to…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
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…
The equilibration of sinusoidally modulated distribution of the kinetic temperature is analyzed in the $\beta$-Fermi-Pasta-Ulam-Tsingou chain with different degrees of nonlinearity and for different wavelengths of temperature modulation.…
We study nonequilibrium dynamics of the quantum Ising chain at zero temperature when the transverse field is varied stochastically. In the equivalent fermion representation, the equation of motion of Majorana operators is derived in the…