相关论文: Role of pulling direction in understanding the ene…

We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…

Protein biologics hold immense potential in therapeutic applications, but their ephemeral nature has hindered their widespread application. The effects of different stressors on protein folding have long been studied, but whether these…

We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…

Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…

Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…

We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…

Energy landscape theory describes how a full-length protein can attain its native fold after sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the…

The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…

The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…

A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…

Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…

The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…

We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and…

Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…

Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…

The unfolding of a polymer below the $\theta$ point when pulled by an external force is studied both in d=2 on the lattice and in $d=3$ off lattice. A ground state analysis of finite length chains shows that the globule unfolds via multiple…

Single-molecule mechanical manipulation has enabled the quantitative understanding of the kinetics of bond ruptures as well as protein unfolding mechanism. Single-molecule experiments with theoretical models have allowed one to gain insight…

Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…

We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe…

We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…