Forces acting within the area of atomic contact between surfaces play a central role in friction and adhesion. Such forces are traditionally calculated using continuum contact mechanics, which is known to break down as the contact radius approaches atomic dimensions. Yet contact mechanics is being applied at ever smaller lengths, driven by interest in shrinking devices to nanometre scales, creating nanostructured materials with optimized mechanical properties, and understanding the molecular origins of macroscopic friction and adhesion. Here we use molecular simulations to test the limits of contact mechanics under ideal conditions. Our findings indicate that atomic discreteness within the bulk of the solids does not have a significant effect, but that the atomic-scale surface roughness that is always produced by discrete atoms leads to dramatic deviations from continuum theory. Contact areas and stresses may be changed by a factor of two, whereas friction and lateral contact stiffness change by an order of magnitude. These variations are likely to affect continuum predictions for many macroscopic rough surfaces, where studies show that the total contact area is broken up into many separate regions with very small mean radius.

Extensive all-atom molecular dynamics simulations were performed to characterize the microscopic origin of the force experienced by DNA in a bulk electrolyte and a solid-state nanopore when subject to an external electrostatic field E. The effective screening of the DNA charge was found to originate from the hydrodynamic drag of the electroosmotic flow that is driven by the motion of counterions along the surface of DNA. We show that the effective driving force F in a nanopore obeys the same law as in a bulk electrolyte: F = ξμE, where ξ and μ are the friction coefficient and electrophoretic mobility of DNA, respectively. Using this relationship, we suggest a method for determining the effective driving force on DNA in a nanopore that does not require a direct force measurement.

Recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants (B.1.1.7 and B.1351) have emerged harbouring mutations that make them highly contagious. The N501Y mutation within the receptor-binding domain (RBD) of the spike protein of these SARS-CoV-2 variants may enhance binding to the human angiotensin-converting enzyme 2 (hACE2). However, no molecular explanation for such an enhanced affinity has so far been provided. Here, using all-atom molecular dynamics simulations, we show that Y501 in the mutated RBD can be well-coordinated by Y41 and K353 in hACE2 through hydrophobic interactions, which may increase the overall binding affinity of the RBD for hACE2 by approximately 0.81 kcalÁmol −1 . The binding dynamics revealed in our study may provide a working model to facilitate the design of more effective antibodies.

A hybrid simulation method is introduced and used to study two-dimensional single-asperity and multi-asperity contacts both quasistatically and dynamically. The method combines an atomistic treatment of the interfacial region with a finite-element method description of subsurface deformations. The dynamics in the two regions are coupled through displacement boundary conditions applied at the outer edges of an overlap region. The two solutions are followed concurrently but with different time resolution. The method is benchmarked against full atomistic simulations. Accurate results are obtained for contact areas, pressures, and static and dynamic friction forces. The time saving depends on the fraction of the system treated atomistically and is already more than a factor of 20 for the relatively small systems considered here.

Currently, the new coronavirus disease 2019 (COVID-19) is a global pandemic without any well-calibrated treatment. To inactivate the SARS-CoV-2 virus that causes COVID-19, the main protease (Mpro) that performs key biological functions in the virus has been the focus of extensive studies. With the fastresponse experimental efforts, the crystal structures of Mpro of the SARS-CoV-2 virus have just become available recently. Herein, we theoretically investigated the mechanism of binding between the Mpro's pocket and various marketed drug molecules being tested in clinics to fight COVID-19 that show promising outcomes. By combining the existing experimental results with our computational ones, we revealed an important ligand binding mechanism of the Mpro, demonstrating that the binding stability of a ligand inside the Mpro pocket can be significantly improved if part of the ligand occupies its so-called "anchor" site. Along with the highly potent drugs and/or molecules (such as nelfinavir) revealed in this study, the newly discovered binding mechanism paves the way for further optimizations and designs of Mpro's inhibitors with a high binding affinity.