Related papers: Rebinding kinetics from single-molecule force spec…
The breakage of a polymer chain of segments, coupled by anharmonic bonds with applied constant external tensile force is studied by means of Molecular Dynamics simulation. We show that the mean life time of the chain becomes progressively…
With the help of force spectroscopy, several analytical theories aim at estimating the rate coefficient of folding for various proteins. Nevertheless, a chief bottleneck lies in the fact that there is still no perfect consensus on how does…
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…
We present a statistical mechanics analysis of the finite-size elasticity of biopolymers, consisting of domains which can exhibit transitions between more than one stable state at large applied force. The constant-force (Gibbs) and…
We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the…
Lifetimes of bound states of protein complexes or biomolecule folded states typically decrease when subject to mechanical force. However, a plethora of biological systems exhibit the counter-intuitive phenomenon of catch bonding, where…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
Measurement of the life time of attachments formed by a single microtubule (MT) with a single kinetochore (kt) {\it in-vitro} under force-clamp conditions had earlier revealed a catch-bond-like behavior. In the past the physical origin of…
This thesis develops exact analytical tools to study strongly correlated stochastic systems, with a focus on extreme value statistics, gap statistics, and full counting statistics in multi-particle processes. A central contribution is the…
Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these…
Theories that are used to extract energy-landscape information from single-molecule pulling experiments in biophysics are all invariably based on Kramers' theory of thermally-activated escape rate from a potential well. As is well known,…
Recently experiments showed that some adhesive receptor-ligand complexes increase their lifetimes when they are stretched by mechanical force, while the force increase beyond some thresholds their lifetimes decrease. Several specific…
A variety of high-energy astrophysical phenomena are powered by the release -- via magnetic reconnection -- of the energy stored in oppositely directed fields. Single-fluid resistive magnetohydrodynamic (MHD) simulations with uniform…
To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along which kinetic behavior is presumed to be governed by diffusive…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the…
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 present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by…
Combining simulations and theory I study the interplay between bundle elastic degrees of freedom and crosslink binding propensity. By slowly driving bundles into a deformed configuration, and depending on the mechanical stiffness of the…
We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the…