Related papers: Hidden multiple bond effects in dynamic force spec…
Based on the trajectories of the separation between water molecule pairs from MD simulations, we investigate the bond breakage dynamics in bulk water. From the spectrum of mean first-passage times, the Fokker-Planck equation allows us to…
Over the past decade, advances in super-resolution microscopy and particle-based modeling have driven an intense interest in investigating spatial heterogeneity at the level of single molecules in cells. Remarkably, it is becoming clear…
Chemical bonds are considered in light of correlation of valence electrons that is strengthened when the bond is dissociated. In the framework of the unrestricted Hartree-Fock single-reference version of the configuration interaction…
Realistic modeling of ionic systems necessitates taking explicitly account of many-body effects. In molecular dynamics simulations, it is possible to introduce explicitly these effects through the use of additional degrees of freedom. Here…
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 present a multiple-scattering model for the effective refractive index of an arbitrarily dense suspension of forward-scattering particles. The model provides a very simple formula for the effective refractive index of such a suspension…
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…
Recent work applying multidimentional coherent electronic spectroscopy at dilute samples in the gas phase is reviewed. The development of refined phase-cycling approaches with improved sensitivity has opened-up new opportunities to probe…
Mixtures of linear mixed models are widely used for modelling longitudinal data for which observation times differ between subjects. In typical applications, temporal trends are described using a basis expansion, with basis coefficients…
The question of decoupling and freeze-out is reinvestigated and analysed in terms of transparent semi-classical decoupling formulae, which provide a smooth decoupling in time both, for single and two particle inclusive spectra. They…
Cells and other soft particles are often forced to flow in confined geometries in both laboratory and natural environments, where the elastic deformation induces an additional drag and pressure drop across the particle. In contrast with…
Three problems in the statistical mechanics of models for an assembly of molecular motors interacting with cytoskeletal filaments are reviewed. First, a description of the hydrodynamical behaviour of density-density correlations in…
In this work, a combined modelling approach for crack propagation in defective graphene is presented. Molecular dynamics (MD) simulations are used to obtain material parameters (Young's modulus and Poisson ratio) and to determine the energy…
Model-free knockoffs is a recently proposed technique for identifying covariates that is likely to have an effect on a response variable. The method is an efficient method to control the false discovery rate in hypothesis tests for separate…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
Simple models for ruptures along a heterogeneous earthquake fault zone are studied, focussing on the interplay between the roles of disorder and dynamical effects. A class of models are found to operate naturally at a critical point whose…
Inspired by active shape morphing in developing tissues and biomaterials, we investigate two generic mechanochemical models where the deformations of a thin elastic sheet are driven by, and in turn affect, the concentration gradients of a…
In single-molecule force spectroscopy experiments, the dependence of the mean unfolding force on the loading rate is used for obtaining information about the energetic and dynamic properties of the system under study. However, it is crucial…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
Recently experiments showed that some biological noncovalent bonds increase their lifetimes when they are stretched by an external force, and their lifetimes will decrease when the force increases further. Several specific quantitative…