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We describe the random motion of a particle immersed in a thermally fluctuating medium and harmonically trapped at a certain distance from a wall. The medium, modeled by a Gaussian field with a tunable correlation length $\xi$, is linearly…
Diffusion in a multidimensional energy surface with minima and barriers is a problem of importance in statistical mechanics and also has wide applications, such as protein folding. To understand it in such a system, we carry out theory and…
Reversible switching of the complex network dynamics of proteins is mimicked in selected network glasses and compacted small carbohydrate molecules. Protein transitions occur on long time scales ~ us -ms, evocative of the exponentially…
A model for diffusion in liquids that couples the dynamics of tracer particles to a fluctuating Stokes equation for the fluid is investigated in the limit of large Schmidt number. In this limit, the concentration of tracers is shown to…
Why reaction rate constants for enzymatic reactions are typically inversely proportional to fractional power exponents of solvent viscosity remains to be already a thirty years old puzzle. Available interpretations of the phenomenon invoke…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
Semi-analytical expressions are suggested for the temperature dependence of those combinations of transport coefficients which govern the fission process. This is based on experience with numerical calculations within the linear response…
We report the results of molecular dynamics simulations of the protein myosin carried out with an elastic network model. Quenching the system, we observe glassy behavior of a density correlation function and a density response function that…
In the vicinity of a phase transition, the order parameter starts fluctuating before vanishing at the critical point. The fluctuation regime, i.e. the way the ordered phase disappears, is a characteristics of a transition, and determines…
Single molecule chemical reactions yield new insight into fluctuation phenomena which are obscured in measurement of ensemble of molecules. Kramers escape problem is investigated here in a framework suitable for single molecule reactions.…
Electrons can organize themselves into charge-ordered states to minimize the effects of long-ranged Coulomb interactions. In the presence of a lattice, commensurability constraints lead to the emergence of incompressible Wigner-Mott…
A known limitation of time-dependent mean-field approaches is a lack of quantum tunneling for collective motions such as in sub-barrier fusion reactions. As a first step toward a solution, a time-dependent model is considered using a…
Understanding the nature of glass transition, as well as precise estimation of the glass transition temperature for polymeric materials, remain open questions in both experimental and theoretical polymer sciences. We propose a data-driven…
`Gating' is a widely observed phenomenon in biochemistry that describes the transition between the activated (or open) and deactivated (or closed) states of an ion-channel, which makes transport through that channel highly selective. In…
The fluctuations exhibited by the cross-sections generated in a compound-nucleus reaction or, more generally, in a quantum-chaotic scattering process, when varying the excitation energy or another external parameter, are characterized by…
A simple fluid, described by point-like particles interacting via the Lennard-Jones potential, is considered under confinement in a slit geometry between two walls at distance Lz apart for densities inside the vapor-liquid coexistence…
We propose a simple dynamical model for a glass transition. The dynamics is described by a Langevin equation in a piecewise parabolic free energy landscape, modulated by a temperature dependent overall curvature. The zero-curvature point…
The change from the diffusion-limited to the reaction-limited cooperative behaviour in reaction-diffusion systems is analysed by comparing the universal long-time behaviour of the coagulation-diffusion process on a chain and on the Bethe…
The glassy dynamics of soft harmonic spheres is often mapped onto the dynamics of hard spheres by considering an effective diameter for the soft particles and therefore an effective packing fraction. While in this approach the thermal…
As it is well known there may arise situations when an interaction between electrons is attractive. A weak attraction should manifest itself strongly in 1D systems, since it can create two-electron bound states. This paper interprets the…