Related papers: Changing the mechanical unfolding pathway of FnIII…
Deviations from linearity in the dependence of the logarithm of protein unfolding rates, $\log k_u(f)$, as a function of mechanical force, $f$, measurable in single molecule experiments, can arise for many reasons. In particular, upward…
Folding of Ubiquitin (Ub) is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained Self-Organized-Polymer model with side chains. The calculated radius of gyration, showing dramatic variations…
Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central…
We report on a computational study of the statics and dynamics of long flexible linear polymers that spontaneously knot and unknot. Specifically, the equilibrium self-entanglement properties, such as the knotting probability, knot length…
We explore manganite interface magnetism in epitaxially grown La0.7Sr0.3MnO3(LSMO)/SrTiO3 ultrathin superlattices (SL) along (110) orientation. we show that robust ferromagnetism persists down to four monolayers LSMO(MLs) (~1.1 nm in…
A variety of emergent phenomena has been enabled by interface engineering in the complex oxides heterostructures. While extensive attention has been attracted to LaMnO3 (LMO) thin films for observing the control of functionalities at its…
We investigate the work dissipated during the irreversible unfolding of single molecules by mechanical force, using the simplest model necessary to represent experimental data. The model consists of two levels (folded and unfolded states)…
We summarize the recent simulation progress of micromanipulation experiments on RNAs. Our work mainly consults with two important small RNAs unfolding experiments carried out by Bustamante group. Our results show that, in contrast to…
In the experiments on stress-induced phase transitions in SMA strips, several interesting instability phenomena have been observed, including a necking-type instability, a shear-type instability and an orientation instability. By using the…
Motivated by results from an earlier Brownian Dynamics (BD) simulation for the collapse of a single, stiff polymer in a poor solvent [B. Schnurr, F. C. MacKintosh, and D. R. M. Williams, Europhys. Lett. 51 (3), 279 (2000)] we calculate the…
Experimental observations suggest that proteins follow different pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the SH3 domain over a broad range of temperatures, and identify…
The competition between spin-orbit coupling, bandwidth ($W$) and electron-electron interaction ($U$) makes iridates highly susceptible to small external perturbations, which can trigger the onset of novel types of electronic and magnetic…
We monitored isotropic spreading of mouse embryonic fibroblasts on fibronectin-coated substrates. Cell adhesion area versus time was measured via total internal reflection fluorescence microscopy. Spreading proceeds in well-defined phases.…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
We use numerical simulations to investigate the hydrodynamic behavior of the interface between nematic (N) and isotropic (I) phases of a confined active liquid crystal. At low activities, a stable interface with constant shape and velocity…
The ability to control the magnetic state provides a powerful means to tune the underlying band topology, enabling transitions between distinct electronic phases and the emergence of novel quantum phenomena. In this work, we address the…
We introduce a phenomenological continuum model for mode III dynamic fracture that is based on the phase-field methodology used extensively to model interfacial pattern formation. We couple a scalar field, which distinguishes between…
In this paper we report, clarify and broaden various recent efforts to complement the chemistry-centered models of force generation in muscles by mechanics-centered models. The physical mechanisms of interest can be grouped into two…
The overall structure of the transition state and intermediate ensembles experimentally observed for Dihydrofolate Reductase and Interleukin-1beta can be obtained utilizing simplified models which have almost no energetic frustration. The…
Interfacial charge transfer in oxide heterostructures gives rise to a rich variety of electronic and magnetic phenomena. Designing heterostructures where one of the thin-film components exhibits a metal-insulator transition opens a…