Related papers: Solvent-quality dependent contact formation dynami…
Intrachain contact formation rates, fundamental to the dynamics of biopolymer self-organization such as protein folding, can be monitored in the laboratory through fluorescence quenching measurements. The common approximations for the…
Experiments measuring contact formation between a probe and quencher in disordered chains provide information on the fundamental dynamical timescales relevant to protein folding, but their interpretation usually relies on simplified…
We study the kinetics of protein folding via statistical energy landscape theory. We concentrate on the local-connectivity case, where the configurational changes can only occur among neighboring states, with the folding progress described…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
In this paper, we develop an encounter-based model of partial surface adsorption for fractional diffusion in a bounded domain. We take the probability of adsorption to depend on the amount of particle-surface contact time, as specified by a…
We systematically studied the dynamics of Fermi polarons driven by time-dependent scattering length using a time-dependent variational method. Starting from the non-interacting initial state, we calculated the evolution behavior of the…
The control of energy dissipation in non-spherical particle contact remains an unresolved problem. Unlike spherical contact, where the interaction reduces to a one-dimensional normal oscillator, both the effective inertia and the effective…
We use molecular dynamics computer simulations to study the relaxation dynamics of a viscous melt of silica. The coherent and incoherent intermediate scattering functions, F_d(q,t) and F_s(q,t), show a crossover from a nearly exponential…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
The three-phase contact line of a droplet on a smooth surface can be characterized by the Young-Dupr\'e equation. It relates the interfacial energies with the macroscopic contact angle $\theta_e$. On the mesoscale, wettability is modeled by…
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,…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
The formation of correlations due to collisions in an interacting nucleonic system is investigated. Results from one-time kinetic equations are compared with the Kadanoff and Baym two-time equation with collisions included in Born…
We suggest that the $\gamma p \to \phi \eta p$ reaction cross section, in the kinematics where the $\eta p$ invariant mass in the final state lies between the threshold value (m$_p$+m$_\eta$) and the N*(1535) resonance mass, is largely…
Normal contact behaviour between non adhesive fractal rough particles is studied using a finite element method (FEM). A series of spherical grain surfaces with distinguished roughness features are generated by means of Spherical Harmonics.…
Classes of two-nucleon ($2N$) contact interactions are developed in configuration space at leading order (LO), next-to-leading order (NLO), and next-to-next-to-next-to-leading order (N3LO) by fitting the experimental singlet $np$ scattering…
Using molecular dynamics simulation, we calculate fluctuations and response for steadily sheared hard spheres over a wide range of packing fractions $\phi$ and shear strain rates $\gamma$, using two different methods to dissipate energy. To…
A self-consistent mode coupling theory (MCT) with microscopic inputs of equilibrium pair correlation functions is developed to analyze electrolyte dynamics. We apply the theory to calculate concentration dependence of (i) time dependent ion…
We study the reaction kinetics of end-functionalized polymer chains dispersed in an unreactive polymer melt. Starting from an infinite hierarchy of coupled equations for many-chain correlation functions, a closed equation is derived for the…
The recently-developed non-equilibrium extension of the self-consistent generalized Langevin equation theory of irreversible relaxation [Phys. Rev. E (2010) 82, 061503; ibid. 061504] is applied to the description of the irreversible process…