Related papers: Efficient methods for determining folding free ene…
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…
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…
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…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
We analyze the response of molecular adhesion complexes to increasing pulling forces (dynamic force spectroscopy) when dissociation can occur along either one of two alternative trajectories in the underlying multidimensional energy…
In single molecule laser optical tweezer (LOT) pulling experiments a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
Living cells exhibit an important out-of-equilibrium mechanical activity, mainly due to the forces generated by molecular motors. These motor proteins, acting individually or collectively on the cytoskeleton, contribute to the violation of…
We introduce a class of stochastic weakly coupled map lattices, as models for studying heat conduction in solids. Each particle on the lattice evolves according to an internal dynamics that depends on its energy, and exchanges energy with…
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…
Many active materials and biological systems are driven far from equilibrium by embedded agents that spontaneously generate forces and distort the surrounding material. Probing and characterizing these athermal fluctuations is essential for…
Molecular motors drive mechanical motions utilizing the free energy liberated from chemical reactions such as ATP hydrolysis. Although it is essential to know the efficiency of this free energy transduction, it has been a challenge due to…
Starting from a general classical model of many interacting particles we present a well defined step by step procedure to derive the continuum-mechanics equations of nonlinear elasticity theory with fluctuations which describe the…
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We…
Free electron beams such as those employed in electron microscopes have evolved into powerful tools to investigate photonic nanostructures with an unrivaled combination of spatial and spectral precision through the analysis of electron…
Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the…
A new method of accessing information on the symmetry free energy from yields of fragments produced in Fermi-energy heavy-ion collisions is proposed. Furthermore, by means of quantum fluctuation analysis techniques, correlations between…
The equilibrium and fluctuation methods for determining the surface tension, $\sigma$, and bending modulus, $\kappa$, of a bilayer membrane with a fixed projected area are discussed. In the fluctuation method the elastic coefficients…
A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force $f$ acting on it. After equilibration, a switching experiment is performed over the system by…
The information on dynamical fluctuations that can be extracted from the anomalous scaling observed recently in hadron-hadron collision experiments is discussed in some detail. A parameter ``effective fluctuation strength'' is proposed to…