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Structural superlubricity, one of the most important concepts in modern tribology, has attracted lots of interest in both fundamental research and practical applications. However, the underlying model, known as the Prandtl-Tomlinson (PT)…
Small mechanical forces play important functional roles in many crucial cellular processes, including in the dynamical behavior of the cytoskeleton and in the regulation of osmotic pressure through membrane-bound proteins. Molecular…
Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
Atmospheric systems incorporating thermal dynamics must be stable with respect to both energy and entropy. While energy conservation can be enforced via the preservation of the skew-symmetric structure of the Hamiltonian form of the…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
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…
We address the problem of predicting the solvation free energy and equilibrium solvent density profile in fews minutes from the molecular density functional theory beyond the usual hypernetted-chain approximation. We introduce a bridge…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
Biological macromolecules have complex and non-trivial energy landscapes, endowing them a unique conformational adaptability and diversity in function. Hence, understanding the processes of elasticity and dissipation at the nanoscale is…
A harmonically trapped active Brownian particle exhibits two types of positional distributions -- one has a single peak, the other has a single well -- that signify steady-state dynamics with low and high activity, respectively. Adding…
For over 30 years, mode-coupling theory (MCT) has been the de facto theoretic description of dense fluids and the liquid-glass transition. MCT, however, is limited by its ad hoc construction and lacks a mechanism to institute corrections.…
We numerically study the entanglement dynamics of free fermions on a cubic lattice with potential disorder following a quantum quench. We focus, in particular, on the metal-insulator transition at a critical disorder strength and compare…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
The electrical conductance of molecular junctions may strongly depend on the temperature, and weakly on molecular length, under two distinct mechanisms: phase-coherent resonant conduction, with charges proceeding via delocalized molecular…
When pulling a particle in a driven granular fluid with constant force $F_{ex}$, the probe particle approaches a steady-state average velocity $v$. This velocity and the corresponding friction coefficient of the probe $\zeta=F_{ex}/v$ are…
Frictional forces are a key ingredient of any physical description of the macroscopic world, as they account for the phenomena causing transformation of mechanical energy into heat. They are ubiquitous in nature, and a wide range of…
A non-hydrostatic depth-averaged model for dry granular flows is proposed, taking into account vertical acceleration. A variable friction coefficient based on the $\mu(I)$ rheology is considered. The model is obtained from an asymptotic…
A thermodynamically related model is developed for describing elastic rubber-like behavior of amorphous and crystallizing polymers and demonstrated on example of simple extension. Both the “entropic” and “energetic”…