相关论文: Medium effects on the selection of sequences foldi…
We show that the interplay between excluded volume effects, hydrophobicity, and hydrogen bonding of a tube-like representation of a polypeptide chain gives rise to free energy landscapes that exhibit a small number of metastable minima…
A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from…
At low pressure, free surfaces play a crucial role in the melting transition. Under pressure, the surface of the sample is acted upon by some pressure transmitting medium. To examine the effect of this medium on melting, we performed Monte…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein's sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral…
The some dynamic properties of a random heteropolymer in the condensed state are studied in the mode coupling approximation. In agreement with recent report a dynamic friction increasing is predicted for the random heteropolymer with…
Understanding protein structure is of crucial importance in science, medicine and biotechnology. For about two decades, knowledge based potentials based on pairwise distances -- so-called "potentials of mean force" (PMFs) -- have been…
Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic…
The hydrophobic/polar HP model on the square lattice has been widely used to investigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states) were enumerated without restrictions on the…
As is well known, the sound-speed profile has significant effects on underwater acoustic sound propagation. These effects can be quantified by normal-mode models, for example. The basic case is a laterally homogeneous medium, for which the…
We study structural properties of a ring polymeric melt confined in a film in comparison to a linear counterpart using molecular dynamics simulations. Local structure orderings of ring and linear polymers in the vicinity of the surface are…
Based on the isospin-dependent Boltzmann-Uehling-Uhlenbeck transport model, we systematically investigate the in-medium effects of nucleon-nucleon ($NN$) cross sections on nucleonic and pionic observables in heavy-ion collisions, employing…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
The entropic effects of anchored polymers on biomembranes are studied using simulations of a meshless membrane model combined with anchored linear polymer chains. The bending rigidity and spontaneous curvature are investigated for anchored…
We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between inter and…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…
Random media introduce large degrees of freedom in device design and can thus address challenges in manipulating optical waves. Wave shaping with metasurfaces has mainly utilized periodic or quasi-periodic grids, and, the potential of…
The structural properties of a linear polymer and its evolution in time have a strong bearing on its anisotropic stress response. The mean-square bond length and mean bond angle are the critical parameters that influence the time-varying…
We study the non-Markovian folding dynamics of the $\alpha$3D protein under low- and neutral-pH conditions. Recently published all-atom simulations of $\alpha$3D by the Shaw group reveal that lowering the pH significantly reduces both…
Autoregressive models have transformed protein engineering by enabling the generation of novel protein sequences beyond those found in nature. However, their sequential inference introduces significant latency, limiting their utility in…