Related papers: Rebinding kinetics from single-molecule force spec…
The strength of a simple soft bond under constant loading rate is studied theoretically. We find a scaling regime where rebinding is negligible and the rupture force of the bond scales as $const. + (\ln (kv))^{2/3}$, where $kv$ is the…
The mechanics of single-chain stretching and rupture are central to understanding the resilience of biological polymers and designing strong and tough soft materials such as double-network gels and multi-network elastomers. In this work, we…
Causality implies that by measuring an absorption spectrum, the time-dependent linear response function can be retrieved. Recent experiments suggest a link between the shape of spectral lines observed in absorption spectroscopy with the…
A coarse-grained molecular simulation approach originally developed for entangled polymeric liquids is extended to model the mechanical behavior of long-fiber networks. The model, based on the slip-link picture of chain entanglements,…
Single-molecule mechanical manipulation has enabled the quantitative understanding of the kinetics of bond ruptures as well as protein unfolding mechanism. Single-molecule experiments with theoretical models have allowed one to gain insight…
Time-dependent density functional theory, proposed recently in the context of atomic diffusion and non-equilibrium processes in solids, is tested against Monte Carlo simulation. In order to assess the basic approximation of that theory, the…
We study theoretically ultracold collisions in quasi one-dimensional optical traps for bosonic and fermionic reactive molecules in the presence of a periodic potential along the trap axis. Elastic, reactive, and umklapp processes due to…
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four…
Event reconstruction is a central step in many particle physics experiments, turning detector observables into parameter estimates; for example estimating the energy of an interaction given the sensor readout of a detector. A corresponding…
Bell inequalities or Bell-like experiments are supposed to test hidden variable theories based on three intuitive assumptions: determinism, locality and measurement independence. If one of the assumptions of Bell inequality is properly…
We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach,…
We present a detailed analysis of two-state trajectories obtained from force-clamp spectroscopy (FCS) of reversibly bonded systems. FCS offers the unique possibility to vary the equilibrium constant in two-state kinetics, for instance the…
Protein-ligand (un)binding simulations are a recent focus of biased molecular dynamics simulations. Such binding and unbinding can occur via different pathways in and out of a binding site. We here present a theoretical framework how to…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
Thermodynamic bulk measurements of binding reactions critically rely on the validity of the law of mass action and the assumption of a dilute solution. Yet important biological systems such as allosteric ligand-receptor binding,…
Quantifying the irreversibility and dissipation of non-equilibrium processes is crucial to understanding their behavior, assessing their possible capabilities, and characterizing their efficiency. We introduce a physical quantity that…
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…
We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand complexes. By integrating Kramers' theory with Bell's equation,…