The SARS‐CoV‐2 virus is responsible for the COVID‐19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike (...) protein at the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants. (shrink)

This paper considers the relationship between continuum hydrodynamics and discrete molecular dynamics in the context of explaining the behavior of breaking droplets. It is argued that the idealization of a fluid as a continuum is actually essential for a full explanation of the drop breaking phenomenon and that, therefore, the less "fundamental," emergent hydrodynamical theory plays an ineliminable role in our understanding.

A molecular dynamics (MD) approach which determines automatically the complex magnetic structures in itinerant electron systems is applied to Fe-Cr alloys with use of 250 atoms in a MD unit cell (5×5×5 bcc lattice). It is demonstrated that the Fe-Cr alloys show various complex magnetic structures due to competing interactions: the collinear ferromagnetism (F) of matrix Fe with antiparallel Cr moments beyond 80 at.% Fe, the coexistence of non-collinear structure of Cr and collinear F of Fe between 50 (...) and 75 at.% Fe, the coexistence of broken antiferromagnetism (AF) of Cr and the F of Fe between 25 and 45 at.% Fe, the coexistence of F of Fe and antiferromagnetic long-range order of Cr around 20 at.% Fe, the AF of Cr matrix with non-collinear Fe moments (spin-glass like structure) between 5 and 15 at.% Fe, and the AF below 5 at.% Fe. In the concentration region between 5 and 20 at.% Fe, ferromagnetic Fe pairs which are stabilized with different amplitudes of local moments are found. The magnetic phase diagram and calculated magnetic moments are shown to be consistent with the neutron, Mössbauer, and photoemission experiments. (shrink)

This paper concerns the scale related decoupling of the physics of breaking drops and considers the phenomenon from the point of view of both hydrodynamics and molecular dynamics at the nanolevel. It takes the shape of droplets at breakup to be an example of a genuinely emergent phenomenon---one whose explanation depends essentially on the phenomenological (non-fundamental) theory of Navier-Stokes. Certain conclusions about the nature of "fundamental" theory are drawn.

An in-situ transmission electron microscopy straining technique has been used to investigate the dynamics of dislocation-defect interactions in ion-irradiated copper and the subsequent formation of defect-free channels. Defect removal frequently required interaction with multiple dislocations, although screw dislocations were more efficient at annihilating defects than edge dislocations were. The defect pinning strength was determined from the dislocation curvature prior to breakaway and exhibited values ranging from 15 to 175 MPa. Pre-existing dislocations percolated through the defect field but did not (...) show long-range motion, indicating that they are not responsible for creating the defect-free channels and have a limited contribution to the total plasticity. Defect-free channels were associated with the movement of many dislocations, which originated from grain boundaries or regions of high stress concentration such as at a crack tip. These experimental results are compared with atomistic simulations of the interaction of partial dislocations with defects in copper and a dispersed-barrier-hardening crystal plasticity model to correlate the observations to bulk mechanical properties. (shrink)

This paper combines naturalized metaphysics and a philosophical reflection on a recently evolving interdisciplinary branch of quantum chemistry, ab initio molecular dynamics. Bridging the gaps among chemistry, physics, and computer science, this cutting-edge research field explores the structure and dynamics of complex molecular many-body systems through computer simulations. These simulations are allegedly crafted solely by the laws of fundamental physics, and are explicitly designed to capture nature as closely as possible. The models and algorithms employed, however, (...) involve many approximations and significant degrees of idealization of their target systems. Therefore, for philosophers of science the pivotal question of whether relying only on the fundamental laws of physics supports a reductionist or realist stance arises. One conceivable answer to this question is that the irreducible approximations and idealizations support rather anti-realist positions. After reviewing an influential attitude in the philosophy of computer simulations and the debate concerning scientific realism, I offer a fair interpretation of such ab initio modelling in quantum chemistry within a naturalistic metaphysical framework that gives rise to a specific type of ontic structural realism. (shrink)