相关论文: Polymer uncrossing and knotting in protein folding…

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…

The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the…

We study the {\em min-cost chain-constrained spanning-tree} (abbreviated \mcst) problem: find a min-cost spanning tree in a graph subject to degree constraints on a nested family of node sets. We devise the {\em first} polytime algorithm…

The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…

In the first part of the paper, we present an (1+\mu)-approximation algorithm to the minimum-spanning tree of points in a planar arrangement of lines, where the metric is the number of crossings between the spanning tree and the lines. The…

An increasing number of proteins are being discovered with a remarkable and somewhat surprising feature, a knot in their native structures. How the polypeptide chain is able to knot itself during the folding process to form these highly…

We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…

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…

In this paper we present a selfcontained analysis and description of the novel {\it ab initio} folding algorithm {\sf cross}, which generates the minimum free energy (mfe), 3-noncrossing, $\sigma$-canonical RNA structure. Here an RNA…

We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…

Self-avoiding random walks were performed on protein residue networks. Compared with protein residue networks with randomized links, the probability of a walk being successful is lower and the length of successful walks shorter in…

Proteins can sometimes be knotted, and for many reasons the study of knotted proteins is rapidly becoming very important. For example, it has been proposed that a knot increases the stability of a protein. Knots may also alter enzymatic…

We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…

A protein is a linear chain containing a set of amino acids, which folds on itself to create a specific native structure, also called the minimum energy conformation. It is the native structure that determines the functionality of each…

Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…

Short spanning trees subject to additional constraints are important building blocks in various approximation algorithms. Especially in the context of the Traveling Salesman Problem (TSP), new techniques for finding spanning trees with…

The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…

We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nano-channels and under periodic compression. We…

Deep unrolling, or unfolding, is an emerging learning-to-optimize method that unrolls a truncated iterative algorithm in the layers of a trainable neural network. However, the convergence guarantees and generalizability of the unrolled…

The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…