Related papers: Kinetic energy flows in activated dynamics of biom…
Understanding electron energy dynamics in low-temperature plasmas such as capacitively coupled plasmas (CCPs), including energy absorption, conversion, transport, and dissipation, is essential for interpreting discharge physics and process…
In the derivation of the thermodynamics of overdamped systems, one ignores the kinetic energy contribution, since the velocity is a slow variable. In this paper, we show that the kinetic energy needs to be present in the calculation of the…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We explore the classical dynamics of two interacting rotating dipoles that are fixed in the space and exposed to an external homogeneous electric field. Kinetic energy transfer mechanisms between the dipoles are investigated varying both…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
The elliptical flow of fragments is studied for different systems at incident energies between 50 and 1000 MeV/nucleon using the isospin-dependent quantum molecular dynamics (IQMD) model. Our findings reveal that elliptical flow shows a…
In classical thermodynamics energy always flows from the hotter system to the colder one. However, if these systems are initially correlated, the energy flow can reverse, making the cold system colder and the hot system hotter. This…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
Previously, using an incompressible von K\'arm\'an-Howarth formalism, the behavior of cross-scale energy transfer in magnetic reconnection and turbulence was found to be essentially identical to each other, independent of an external…
With the formal construction of a thermodynamic spring, I describe the mechanics, energetics, entropy, and kinetics of a binary mechanical model system. A protein that transitions between two metastable structural states behaves as a…
Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions…
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…
We analyze the probability distribution for entropy production rates of trajectories evolving on a class of out-of-equilibrium kinetic networks. These networks can serve as simple models for driven dynamical systems, which are of particular…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Two equations are constructed which reflect, for fermions moving independently in a spherical harmonic potential, a differential virial theorem and a relation between the turning points of kinetic energy and particle densities. These…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding…
Conventional kinesin is a two-headed homodimeric motor protein, which is able to walk along microtubules processively by hydrolyzing ATP. Its neck linkers, which connect the two motor domains and can undergo a docking/undocking transition,…
In this paper we report, clarify and broaden various recent efforts to complement the chemistry-centered models of force generation in muscles by mechanics-centered models. The physical mechanisms of interest can be grouped into two…
In the present paper we give a brief summary of some recent theoretical advances in the treatment of inhomogeneous fluids and methods which have applications in the study of dynamical properties of liquids in situations of extreme…