相关论文: Reliable extraction of energy landscape properties…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
Forced detachment of a single polymer chain, strongly-adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
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 problem of diffusive bond-dissociation in a double well potential under application of an external force is scrutinized. We compute the probability distribution of rupture forces and present a detailed discussion of the influence of…
Motivated by the experiments on DNA under torsion, we consider the problem of pulling a polymer out of a potential well by a force applied to one of its ends. If the force is less than a critical value, then the process is activated and has…
We investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
We use Newtonian and overdamped Langevin dynamics to study long flexible polymers dragged by an external force at a constant velocity $v$. The work $W$ by that force depends on the initial state of the polymer and the details of the…
Rugged (or, rough) energy landscape (REL) with spatially distributed maxima and minima are often employed in applications of physics, chemistry and biology (enzyme kinetics, protein folding, diffusion in disordered solids, transport in…
Using theoretical arguments and extensive Monte Carlo (MC) simulations of a coarse-grained three-dimensional off-lattice model of a \beta-hairpin, we demonstrate that the equilibrium critical force, $F_c$, needed to unfold the biopolymer…
Taking into account the nonequivalence of fixed-force and fixed-length ensembles in the weak-force regime, equations of state are derived that describe the equilibrium extension or compression of an ideal Gaussian polymer chain in response…
Rugged energy landscapes find wide applications in diverse fields ranging from astrophysics to protein folding. We study the dependence of diffusion coefficient $(D)$ of a Brownian particle on the distribution width $(\varepsilon)$ of…
Energy landscape theory describes how a full-length protein can attain its native fold by sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome,…
We examine challenges to sampling from Boltzmann distributions associated with multiscale energy landscapes. The multiscale features, or "roughness," corresponds to highly oscillatory, but bounded, perturbations of a smooth landscape.…
Macroscopic mechanical properties of polymers are determined by their microscopic molecular chain distribution. Due to randomness of these molecular chains, probability theory has been used to find their micro-states and energy…
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the…
Force-clamp spectroscopy reveals the unfolding and disulfide bond rupture times of single protein molecules as a function of the stretching force, point mutations and solvent conditions. The statistics of these times reveal whether the…
We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching…