相关论文: Solvent-quality dependent contact formation dynami…

A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…

We examine the nanoscale behavior of an equilibrium three-phase contact line in the presence of long-ranged intermolecular forces by employing a statistical mechanics of fluids approach, namely density functional theory (DFT) together with…

The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…

Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…

We calculate the temperature dependence of the weak localization correction in a two dimensional system at arbitrary relation between temperature, $T$ and the elastic mean free time. We describe the crossover in the dephasing time…

Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…

The extinction transition in the presence of a localized quenched defect is studied numerically. When the bulk is at criticality, the correlation length diverges and even an infinite system cannot "decouple" from the defect. The results…

We study the mass dependence of various quantities (like the average and maximum density, collision rate, participant-spectator matter, temperature as well as time zones for higher density) by simulating the reactions at the energy of…

We present an exact calculation of the mean first-passage time to a small target on the surface of a 2D or 3D spherical domain, for a molecule performing surface-mediated diffusion. This minimal model of interfacial reactions, which…

We study a lattice model describing the non-equilibrium dynamics emerging from the pulling of a tracer particle through a disordered medium occupied by randomly placed obstacles. The model is considered in a restricted geometry pertinent…

We present theoretical models for the time-dependent voltage of an electrochemical cell in response to a current step, including effects of diffuse charge (or "space charge") near the electrodes on Faradaic reaction kinetics. The full model…

We show that the defect density $n$, for a slow non-linear power-law quench with a rate $\tau^{-1}$ and an exponent $\alpha>0$, which takes the system through a critical point characterized by correlation length and dynamical critical…

We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…

Steric or attractive interactions among reactants or between reactants and inert crowders can substantially influence the total rate of a diffusion-influenced reaction in the liquid phase. However, the role of the product species, that has…

The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy…

A sharp change in apparent mobility at a characteristic temperature that depends on the observation time has been reported in experiments and simulations of hydrated proteins. Such behavior is often discussed in the context of the protein…

We investigate an intermittent stochastic process, in which the diffusive motion with time-dependent diffusion coefficient $D(t)\sim t^{\alpha-1}$, $\alpha>0$ (scaled Brownian motion), is stochastically reset to its initial position and…

According to time-dependent density functional theory, the exact exchange-correlation kernel f$_{xc}$(n, q, $\omega$) determines not only the ground-state energy but also the excited-state energies/lifetimes and time-dependent linear…

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…

We investigate a class of diffusion-controlled reactions that are initiated at the time instance when a prescribed number $K$ among $N$ particles independently diffusing in a solvent are simultaneously bound to a target region. In the…