相关论文: Extracting folding landscape characteristics of bi…

Single-molecule force spectroscopy experiments, as well as a number of other physical systems, are governed by thermally activated transitions out of a metastable state under the action of a steadily increasing external force. The main…

Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…

Mechanical single molecule experiments probe the energy profile of biomolecules. We show that in the case of a profile with two minima (like folded/unfolded) periodic driving leads to a stochastic resonance-like phenomenon. We demonstrate…

Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level…

Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…

In comparing the behavior of an energy spectrum to the predictions of random matrix theory one must transform the spectrum such that the averaged level spacing is constant, a procedure known as unfolding. Once energy spectrums belong to an…

A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…

We study the temperature dependence of the single particle spectral function as well as of the dynamical spin and charge structure factors for the one-dimensional Hubbard model using the finite temperature auxiliary field quantum Monte…

We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…

The electronic band structure, describing the periodic dependence of electronic quantum states on lattice momentum in reciprocal space, is a fundamental concept in solid-state physics. However, it's only well-defined for static nuclei. To…

Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…

Single-molecule force spectroscopy has proven to be a powerful tool for studying the kinetic behavior of biomolecules. Through application of an external force, conformational states with small or transient populations can be stabilized,…

Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…

We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We obtain…

Many problems in physics, material sciences, chemistry and biology can be abstractly formulated as a system that navigates over a complex energy landscape of high or infinite dimensions. Well-known examples include phase transitions of…

Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…

The structural dynamics of a biopolymer is governed by a process of diffusion through its conformational energy landscape. In pulling experiments using optical tweezers, features of the energy landscape can be extracted from the probability…

In single-molecule force spectroscopy experiments, a biomolecule is attached to a force probe via polymer linkers, and the total extension -- of molecule plus apparatus -- is monitored as a function of time. In a typical unfolding…

We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape…

The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…