相关论文: Dominant Folding Pathways of a WW Domain

This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…

Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…

We have combined a custom implementation of the fast multiple-time-stepping LN integrator with parallel tempering to explore folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this…

Using the Helmholtz decomposition of the vector field of folding fluxes in a two-dimensional space of collective variables, a potential of the driving force for protein folding is introduced. The potential has two components. One component…

Motivated by the need for a robust policy in the face of environment shifts between training and deployment, we contribute to the theoretical foundation of distributionally robust reinforcement learning (DRRL). This is accomplished through…

Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…

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…

We represent the results of micromagnetic modeling and experimental magnetic force microscopy investigations of domain wall (DW) pinning-depinning effects in the hybrid systems consisting of ferromagnetic nanowire (NW) and two ferromagnetic…

These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…

The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to…

Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…

We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…

We provide the exact solution of several variants of simple models of the zipping transition of two bound polymers, such as occurs in DNA/RNA, in two and three dimensions using pairs of directed lattice paths. In three dimensions the…

We have applied a simple statistical-mechanics G$\bar{\text{o}}$-like model to the analysis of the PIN1 WW domain, resorting to Mean Field and Monte Carlo techniques to characterize its thermodynamics, and comparing the results with the…

Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…

Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…

Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for…

Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $\beta$-hairpin, motivated by the fact that folding of a…

We present a new computational approach, Action-CSA, to sample multiple reaction pathways with fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing method. This…

Determinantal point processes (DPPs) are random point processes well-suited for modeling repulsion. In machine learning, the focus of DPP-based models has been on diverse subset selection from a discrete and finite base set. This discrete…