Related papers: Changing the mechanical unfolding pathway of FnIII…
Emergent magnetic states at oxide interfaces arise from the interplay of charge transfer, orbital reconstruction, and dimensional confinement, offering a route to engineered correlated-electron behavior in nanoscale spintronic materials.…
We propose a general multiscale approach for the mechanical behavior of three-dimensional networks of macromolecules undergoing strain-induced unfolding. Starting from a (statistically based) energetic analysis of the macromolecule…
Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
Transition metal oxides hold great potential for the development of new device paradigms because of the field-tunable functionalities driven by their strong electronic correlations, combined with their earth abundance and environmental…
We investigate clean mutilayered structures of the SFS and SFSFS type, (where the S layer is intrinsically superconducting and the F layer is ferromagnetic) through numerical solution of the self-consistent Bogoliubov-de Gennes equations…
The flow field in a two-dimensional three-ramp hypersonic mixed-compression inlet in a freestream Mach number of $M_\infty=5$ is numerically solved to understand the unsteady throttling dynamics. Throttling conditions are simulated by…
Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally…
Mechanical instabilities in thin solids offer a powerful route to engineer nonlinear responses, yet their controlled use in functional crystalline oxides has remained largely unexplored. Notably, by changing the aspect ratio of solids, the…
The dynamic behavior of bundles of actin filaments growing against a loaded obstacle is investigated through a generalized version of the standard multi filaments Brownian Ratchet model in which the (de)polymerizing filaments are treated…
A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…
Protein folding is an indispensable process for the majority of proteins after their synthesis from ribosomes in the cell. Most in vitro protein folding studies have focused on single-domain proteins. Hence, it is important to understand…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and unwinding from it. This dynamics is of interest in several problems in biology and constitutes a fundamental instance of polymer relaxation from…
The process of magnetic reconnection when studied in Nature or when modeled in 3D simulations differs in one key way from the standard 2D paradigmatic cartoon: it is accompanied by much fluctuations in the electromagnetic fields and plasma…
We study the free energy of the worm-like-chain model, in the constant-extension ensemble, as a function of the stiffness for finite chains of length L. We find that the polymer properties obtained in this ensemble are "qualitatively"…
Mixing in numerous medical and chemical applications, involving overly long microchannels, can be enhanced by inducing flow instabilities. The channel length, is thus shortened in the inertial microfluidics regime due to the enhanced…
The interior of cells is crowded thus making it important to assess the effects of macromolecules on the folding of proteins. Using the Self-Organized Polymer (SOP) model, which is a coarse-grained representation of polypeptide chains, we…
The nonequilibrium dynamics of a cycling three-state Potts model is studied on a square lattice using Monte Carlo simulations and continuum theory. This model is relevant to chemical reactions on a catalytic surface and to molecular…