相关论文: Realistic protein-protein association rates from a…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
Rugged energy landscapes find wide applications in diverse fields ranging from astrophysics to protein folding. We study the dependence of diffusion coefficient $(D)$ of a Brownian particle on the distribution width $(\varepsilon)$ of…
The transport equation of active motion is generalised to consider time-fractional dynamics for describing the anomalous diffusion of self-propelled particles observed in many different systems. In the present study, we consider an…
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…
Diffusion models have achieved remarkable success in generative modeling, yet how to effectively adapt large pretrained models to new tasks remains challenging. We revisit the reconstruction behavior of diffusion models during denoising to…
We study the diffusion of a Brownian particle quadratically coupled to a thermally fluctuating field. In the weak coupling limit, a path-integral formulation allows to compute the effective diffusion coefficient in the cases of an active…
A methodology to calculate the friction coefficient of an aggregate in the continuum regime is proposed. The friction coefficient and the monomer shielding factors, aggregate-average or individual, are related to the molecule-aggregate…
Energy barriers for different moves of a single Rh adatom in the vicinity of steps on Rh(111) surface are studied with molecular statics. Interatomic interactions are modeled by the semi-empirical many-body Rosato-Guillope-Legrand…
Describing the diffusion of particles through crowded, confined environments with which they can interact is of considerable biological and technological interest. Under conditions where the confinement dimensions become comparable to the…
We investigate the dynamics of two interacting diffusing particles in an infinite effectively one dimensional system; the particles interact through a step-like potential of width b and height phi_0 and are allowed to pass one another. By…
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature…
Extensive molecular dynamics simulation studies of particles interacting via a short ranged attractive square-well (SW) potential are reported. The calculated loci of constant diffusion coefficient $D$ in the temperature-packing fraction…
The interaction cutoff contribution to the ruggedness of protein-protein energy landscape (the artificial ruggedness) is studied in terms of relative energy fluctuations for 1/r^n potentials based on a simplistic model of a protein complex.…
Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…
We systematically check explicit and implicit assumptions of Persson's contact mechanics theory. It casts the evolution of the pressure distribution ${\rm Pr}(p)$ with increasing resolution of surface roughness as a diffusive process, in…
From the exact single step evolution equation of the two-point correlation function of a particle distribution subjected to a stochastic displacement field $\bu(\bx)$, we derive different dynamical regimes when $\bu(\bx)$ is iterated to…
The usual Kramers theory of reaction rates in a condensed medium predict the rate to have an $\eta^{-1}$ dependence, $\eta$ being the viscosity of the medium. However, experiments on ligand binding to proteins performed long ago, showed the…
I investigate a disordered version of a simplified model of protein folding, with binary degrees of freedom, applied to an ideal beta-hairpin structure. Disorder is introduced by assuming that the contact energies are independent and…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…