Related papers: Dissecting Ubiquitin Folding Using the Self-Organi…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
Nonequilibrium experiments of single biomolecules such as force-induced unfolding reveal details about a few degrees of freedom of a complex system. Molecular dynamics simulations can provide complementary information, but exploration of…
We study the temperature dependence of the electrical resistivity of interacting two-dimensional metallic systems. We perform a numerical simulation of the nonequilibrium state based on semiclassical Boltzmann transport theory. Through our…
The nonlinear decay of oscillations of a liquid column in a U-shaped tube is investigated within the theoretical framework of the projection method formalized by Bongarzone et al. (2021) [1]. Starting from the full hydrodynamic system…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
Biological adhesion is a critical mechanical function of complex organisms operating at multiple scales. At the cellular scale, cell-cell adhesion is remarkably tunable to enable both cohesion and malleability during development,…
Experiments are conducted in a two-dimensional mono-layer vibrofluidized bed of glass beads, with a goal to understand the transition scenario and the underlying microstructure and dynamics in different patterned-states. At small shaking…
The phase structure of self-avoiding polymerized membranes is studied by extensive Hybrid Monte Carlo simulations. Several folding transitions from the flat to a collapsed state are found. Using a suitable order parameter and finite size…
The folding of the alpha-helice domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKD) complex is studied by the circular dichroism technique in absence of urea. Thermal denaturation is used to…
Computer simulations of contact melting and associated interfacial phenomena in binary eutectic systems were performed on the basis of the standard phase-field model with miscibility gap in solid state. It is shown that the model predicts…
Many processes of scientific importance are characterized by time scales that extend far beyond the reach of standard simulation techniques. To circumvent this impediment a plethora of enhanced sampling methods has been developed. One…
Motivated by the physics of coherently coupled, ultracold atom-molecule mixtures, we investigate a classical model possessing the same symmetry -- namely a $U(1)\times \mathbb{Z}_2$ symmetry, associated with the mass conservation in the…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
Force-clamp spectroscopy reveals the unfolding and disulfide bond rupture times of single protein molecules as a function of the stretching force, point mutations and solvent conditions. The statistics of these times reveal whether the…
We perform the fidelity analysis for Boltzmann-Gibbs-like states in order to investigate whether the topological order of 1D fermionic systems at zero temperature is maintained at finite temperatures. We use quantum walk protocols that are…
Protein biologics hold immense potential in therapeutic applications, but their ephemeral nature has hindered their widespread application. The effects of different stressors on protein folding have long been studied, but whether these…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
We study the deformation of a fluctuating crystalline sheet confined between two flat rigid walls as a simple model for layered solids where bonds among atoms {\it within} the same layer are much stronger than those {\it between} layers.…
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…