相关论文: Non-Gaussian dynamics from a simulation of a short…
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…
The mean time of contact formation between two ends of a protein chain shows power law dependence with respect to the number of residues, $\tau_{CF} \sim N^{\alpha}$. Fluorescence quenching measurements based on triplet-triplet energy…
Molecular dynamics simulations are carried out to investigate the diffusion behavior of penetrable-sphere model fluids characterized by a finite energy barrier $\epsilon$. The self-diffusion coefficient is evaluated from the time-dependent…
We present a systematic study of the self-diffusion coefficient for a fluid of particles interacting via the square-well pair potential by means of molecular dynamics simulations in the canonical (N,V,T) ensemble. The discrete nature of the…
Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using…
We present simulation results for a model polymer melt, consisting of short, nonentangled chains, in the supercooled state. The analysis focuses on the monomer dynamics, which is monitored by the incoherent intermediate scattering function.…
Short polymer chains exhibit clear deviations from Gaussian end-to-end distance statistics, yet the molecular mechanism by which Gaussian behavior is recovered in long chains remains unestablished. Atomistic molecular dynamics simulations…
We investigate the kinetics of loop formation in flexible ideal polymer chains (Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the…
Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…
We calculate the inelastic scattering rates and the hot electron inelastic mean free paths for both monolayer and bilayer graphene on a polar substrate. We study the quasiparticle self-energy by taking into account both electron-electron…
We report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute which has a concentration gradient, and…
We report on a comprehensive theory-simulation-experimental study of collective and self-diffusion in suspensions of charge-stabilized colloidal spheres. In simulation and theory, the spheres interact by a hard-core plus screened Coulomb…
We report results of molecular-dynamics simulations of a model polymer melt consisting of short non-entangled chains in the supercooled state above the critical temperature of mode-coupling theory (MCT). To analyse the dynamics of the…
Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
Dilute or semi-dilute solutions of non-intersecting self-avoiding walk (SAW) polymer chains are mapped onto a fluid of ``soft'' particles interacting via an effective pair potential between their centers of mass. This mapping is achieved by…
A theory of diffusion-controlled intramolecular reactions of polymer chain in dilute solution is formulated. Our model is based on the widely used diffusion-reaction formalism of Wilemski and Fixman (J. Chem. Phys. 60, 866 (1974). Our model…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
We develop Monte Carlo simulations for uniformly charged polymers and machine learning algorithm to interpret the intra-polymer structure factor of the charged polymer system, which can be obtained from small-angle scattering experiments.…
Presenting theoretical arguments and numerical results we demonstrate long-range intrachain correlations in concentrated solutions and melts of long flexible polymers which cause a systematic swelling of short chain segments. They can be…