Related papers: Force-induced Unbinding Dynamics in a Multidimensi…
Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here, we study a general model…
The effect of a diffusivity edge is studied in a system of scalar active matter confined by a periodic potential and driven by an externally applied force. We find that this system shows qualitatively distinct stationary regimes depending…
We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting…
We consider membranes adhered through specific receptor-ligand bonds. Thermal undulations of the membrane induce effective interactions between adhesion sites. We derive an upper bound to the free energy that is independent of interaction…
Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of…
This work extends the results of the recently developed theory of a rather complete thermodynamic formalism for discrete-state, continuous-time Markov processes with and without detailed balance. We aim at investigating the question that…
We present Molecular Dynamics simulations of a single stranded unprotonated DNA i-motif in explicit solvent. Our results indicate that the native structure in non-acidic solution at 300 K is unstable and completely vanishes on a time scale…
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…
Although known that single domain proteins fold and unfold by parallel pathways, demonstration of this expectation has been difficult to establish in experiments. Unfolding rate, $k_\mathrm{u}(f)$, as a function of force $f$, obtained in…
Biological adhesion often involves several pairs of specific receptor-ligand molecules. Using rate equations, we study theoretically the rupture of such multiple parallel bonds under dynamic loading assisted by thermal activation. For a…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
Interface free energy is the contribution to the free energy of a system due to the presence of an interface separating two coexisting phases at equilibrium. It is also called surface tension. The content of the paper is 1) the definition…
The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is…
In living cells, protein-rich condensates can wet the cell membrane and surfaces of membrane-bound organelles. Interestingly, many phase-separating proteins also bind to membranes leading to a molecular layer of bound molecules. Here we…
A fiber bundle model in $(1+1)$-dimensions for the breaking of fibrous composite matrix is introduced. The model consists of $N$ parallel fibers fixed in two plates. When one of the plates is pulled in the direction parallel to the fibers,…
We derive the energy of the surface between the normal and superfluid components of a mixed phase of a system composed of two particle species with different densities. The surface energy is obtained by the integration of the free energy…
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…
We show that the force generated by active enzyme molecules are strong enough to influence the dynamics of their surroundings under artificial crowded environments. We measured the behavior of polymer microparticles in a…
The conditions under which biological cells switch from a static to a motile state are fundamental to the understanding of many healthy and pathological processes. In this paper, we show that even in the presence of a fully symmetric…
The momentum space zero-range model is used to investigate universal properties of three interacting particles confined to two dimensions. The pertinent equations are first formulated for a system of two identical and one distinct particle…