相关论文: Molecular origin of constant m-values, denatured s…
A dynamical study of the decay of a metastable state by quantum tunneling through an anisotropic, non separable, two-dimensional potential barrier is performed by the numerical solution of the time-dependent Schrodinger equation. Initial…
A growth model which describes the deposition of particles (or the growth of a rigid crystal) on a disordered substrate is investigated. The dynamic renormalization group is applied to the stochastic growth equation using the Martin, Sigga,…
We present a systematic analysis of diffusion-controlled evolution and collapse of two identical spatially separated $d$-dimensional $A$-particle islands in the $B$-particle sea at propagation of the sharp reaction front $A+B\to 0$ at equal…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
In this work, we present an efficient framework that combines machine learning potential (MLP) and metadynamics to explore multi-dimensional free energy surfaces for investigating solid-solid phase transition. Based on the spectral…
We explore the possibility for the native state of a protein being inherently a multi-conformation state in an ab initio coarse-grained model. Based on the Wang-Landau algorithm, the complete free energy landscape for the designed sequence…
The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native…
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…
An ever growing number of observational and theoretical evidence suggests that the deuterated fraction (column density ratio between a species containing D and its hydrogenated counterpart, Dfrac) is an evolutionary indicator both in the…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
A probable model of the liquid-liquid (L-L) type phase transitions in water-salt dispersions of native (N*, N) globular proteins in the temperature range between thermal (D*) and cold (D) denaturation has been proposed. Protein…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Phi-values are experimental measures of the effects of mutations on the folding kinetics of a protein. A central question is which structural information Phi-values contain about the transition state of folding. Traditionally, a Phi-value…
A comprehensive study of various ground-state properties of neutron-rich and neutron-deficient Mg isotopes with $A$=20-36 is performed in the framework of the self-consistent deformed Skyrme-Hartree-Fock plus BCS method. The correlation…
In conventional glassformers at sufficiently short times and low enough temperatures, molecules are mutually caged by the intermolecular potential. The fluctuation and dissipation from motion of caged molecules when observed by elastic…
Continuum dislocation dynamics (CDD) represents the evolution of systems of curved and connected dislocation lines in terms of density-like field variables which include the volume density of loops (or 'curvature density') as an additional…
We analyze recently-measured total reaction cross sections for 24-38Mg isotopes incident on 12C targets at 240 MeV/nucleon by using the folding model and antisymmetrized molecular dynamics(AMD). The folding model well reproduces the…