Related papers: Kinetic energy flows in activated dynamics of biom…
The elliptic flow for $Z\le2$ particles in heavy ion collisions at energies from several tens to several hundreds MeV per nucleon is investigated by means of transport model,i.e. a new version of the Improved Quantum Molecular Dynamics…
Kinetic energy functionals of the electronic density are used to model large systems in the context of density functional theory, without the need to obtain electronic wavefunctions. We discuss the problems associated with the application…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Conventional kinesin is a dimeric motor protein that transports membranous organelles toward the plus-end of microtubules (MTs). Individual kinesin dimers show steadfast directionality and hundreds of consecutive steps, yetthe detailed…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
Using the Helmholtz decomposition of the vector field of folding fluxes in a two-dimensional space of collective variables, a potential of the driving force for protein folding is introduced. The potential has two components. One component…
A system containing a pre-steady state standard (non-autocatalytic) reaction, with multiple paths, evolves toward a kinetic state with the minimum attainable activation free energy. Displacement of the path frequency distribution in this…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
The detailed analysis of excitation function of elliptical flow by taking into account the nature of equation of state, nucleon-nucleon cross sections as well as momentum dependent interactions is performed within Quantum Molecular Dynamics…
The adsorption at the interface between an aqueous solution of several surface-active agents and another fluid (air or oil) phase is addressed theoretically. We derive the kinetic equations from a variation of the interfacial free energy,…
The transfer of kinetic energy from large to small scales is a hallmark of turbulent flows. Yet, a precise mechanistic description of this transfer, which is expected to occur via an energy cascade, is still missing. Several conceptually…
Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating 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…
Fluid dynamics in intrinsically curved geometries is encountered in many physical systems in nature, ranging from microscopic bio-membranes all the way up to general relativity at cosmological scales. Despite the diversity of applications,…
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,…
Modeling of process for reaction kinetics is a fashionable subject of publications. The meaning of both the mortality and fertility terms are mathematically analyzed in details involving variation of their power exponents. We developed an…
A non-Newtonian flow of a polymer melt is discussed. The description of the exponential decrease of the apparent viscosity by the well-known Eyring formula with an activation energy reduction proportional to the shear stress does not take…
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…
Active filaments, such as microtubules with attached cargo-carrying motor proteins, are important dynamic structures for fluid transport in and around living cells. The mathematical models of active filaments appearing in the literature…