Related papers: Unfolding protein with an atomic force microscope:…

The use of machine learning to estimate the energy of a group of atoms, and the forces that drive them to more stable configurations, has revolutionized the fields of computational chemistry and materials discovery. In this domain, rigorous…

Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…

We experimentally investigate the distribution of the non-equilibrium work done by an external force on a mesoscopic system with many coupled degrees of freedom: a colloidal monolayer mechanically driven across a periodic light field. Since…

How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…

We study the non-contact friction between an atomic force microscope tip and a metal substrate in the presence of bias voltage. The friction is due to energy losses in the sample created by the electromagnetic field from the oscillating…

Using a tight-binding atomistic simulation, we simulate the recent atomic-force microscopy experiments probing the slipperiness of graphene flakes made slide against a graphite surface. Compared to previous theoretical models, where the…

The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…

Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…

As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…

We study the dynamic structure factor of fluctuating elastic thin sheets subject to conservative (athermal) random forcing. In Steinbock, Katzav & Boudaoud, Phys. Rev. Research 4, 033096 (2022), the static structure factor of such a sheet…

Both classical and quantum electrodynamics predict the existence of dipole-dipole long-range electrodynamic intermolecular forces; however, these have never been hitherto experimentally observed. The discovery of completely new and…

The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin…

Critical fluctuations of some order parameter describing a fluid generates long-range forces between boundaries. Here, we discuss fluctuation-induced forces associated to a disordered Landau-Ginzburg model defined in a $d$-dimensional slab…

High moments of multiplicity distributions of conserved quantities are predicted to be sensitive to critical fluctuations. To understand the effect of the complicated non-critical physics backgrounds on the proposed observable, we have…

This is an archival document; the work contains theoretical development to be used in new publications and to stimulate further development. Here, we develop a statistical mechanical treatment of a braid formed of two molecules subject to…

We find a general formula for the distribution of time averaged observables for weakly non-ergodic systems. Such type of ergodicity breaking is known to describe certain systems which exhibit anomalous fluctuations, e.g. blinking quantum…

The breakage of a polymer chain of segments, coupled by anharmonic bonds with applied constant external tensile force is studied by means of Molecular Dynamics simulation. We show that the mean life time of the chain becomes progressively…

The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…

Diffusion processes are widespread in biological and chemical systems, where they play a fundamental role in the exchange of substances at the cellular level and in determining the rate of chemical reactions. Recently, the classical picture…

We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…