Related papers: Force-induced Unbinding Dynamics in a Multidimensi…
The lifetime of protein domains and ligand-receptor complexes under force is crucial for mechanosensitive functions, while many aspects of how force affects the lifetime still remain poorly understood. Here, we report a new analytical…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
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…
As a prototype of systems bearing a localization-delocalization transition, the strand-separation (melting) process in a double-stranded biopolymer is studied by a mapping to a quantum-mechanical problem with short-ranged potentials. Both…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
We consider self-avoiding lattice polygons, in the hypercubic lattice, as a model of a ring polymer adsorbed at a surface and either being desorbed by the action of a force, or pushed towards the surface. We show that, when there is no…
By analyzing hot-wire velocity data taken in an open channel flow, an unambiguous definition of surface-layer thickness is here provided in terms of the cross-over scale between backward and forward energy fluxes. It is shown that the…
We study the forced rupture of adhesive contacts between monomers that are not covalently linked in a Rouse chain. When the applied force ($f$) to the chain end is less than the critical force for rupture ($f_c$), the {\it reversible}…
We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex ($P_1$$P_2$). The joint distribution $P(\tau_1,\tau_2)$ of unbinding lifetimes $\tau_1$ and $\tau_2$ measurable in…
The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is…
Although the stretching of polymers and biomolecules is important in numerous settings, their response when confined to two-dimensions is relatively poorly-studied. In this paper, we derive closed-form analytical expressions for the…
We study the steady state of a stochastic particle system on a two-dimensional lattice, with particle influx, diffusion and desorption, and the formation of a dimer when particles meet. Surface processes are thermally activated, with…
We consider reversible breaking of adhesion bonds or folding of proteins under the influence of a constant external force. We discuss the stochastic properties of the unbinding/rebinding events and analyze their mean number and their…
We study the dependence of the surface tension of a fluid interface on the density profile of a third suspended phase. By means of an approximated model for the binary mixture and of a perturbative approach we derive close formulas for the…
Rebinding kinetics of molecular ligands plays a critical role in biomachinery, from regulatory networks to protein transcription, and is also a key factor for designing drugs and high-precision biosensors.In this study, we investigate…
Biological organisms swimming at low Reynolds number are often influenced by the presence of rigid boundaries and soft interfaces. In this paper we present an analysis of locomotion near a free surface with surface tension. Using a…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined…
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the…