Related papers: Rebinding kinetics from single-molecule force spec…
We point out that in the first order time-dependent perturbation theory, the transition probability may behave nonsmoothly in time and have kinks periodically. Moreover, the detailed temporal evolution can be sensitive to the exact…
In this work, we study in the framework of the so-called driven tight-binding chain (TBC) the issue of quantum unitary dynamics interspersed at random times with stochastic resets mimicking non-unitary evolution due to interactions with the…
Receptor-ligand interactions are essential for biological function and their binding strength is commonly explained in terms of static lock-and-key models based on molecular complementarity. However, detailed information of the full…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
We have studied the aging effect on the dynamics of unbinding of a double stranded directed polymer in a random medium. By using the Monte Carlo dynamics of a lattice model in two dimensions, for which disorder is known to be relevant, the…
We show that the failure of the real-space RG method in the 1D tight-binding model is not intrinsic to the method as considered so far but depends on the choice of boundary conditions. For fixed BC's the failure does happen. For free BC's…
Curvatures in the most probable rupture force ($f^*$) versus log-loading rate ($\log{r_f}$) observed in dynamic force spectroscopy (DFS) on biomolecular complexes are interpreted using a one-dimensional free energy profile with multiple…
Analytical relations for the mechanical response of single polymer chains are valuable for modeling purposes, on both the molecular and the continuum scale. These relations can be obtained using statistical thermodynamics and an idealized…
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force…
We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using…
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…
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,…
Theoretical considerations of Bell-inequality experiments usually assume identically prepared and independent pairs of particles. Here we consider pairs that exhibit both intra- and inter-pair entanglement. The pairs are taken from a large…
Binding kinetic parameters can be correlated with drug efficacy, which led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms in recent…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…
Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most phenomenological models of the unfolding process are two-state and/or one dimensional, with the details of the…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
This work focuses on a theoretical analysis of a well-known inertia demonstration, which uses a weight suspended by a string with an extra string that hangs below the weight. The point in question is which string, the upper or lower, will…
One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active…
Solid state physics deals with systems composed of atoms with strongly bound electrons. The tunneling probability of each electron is determined by interactions that typically extend to neighboring sites, as their corresponding wave…