We develop a sublinear-scaling method, referred to as MacroDFT, for the study of crystal defects using ab-initio Density Functional Theory (DFT). The sublinear scaling is achieved using a combination of the Linear Scaling Spectral Gauss Quadrature method (LSSGQ) and a Coarse-Graining approach (CG) based on the quasi-continuum method. LSSGQ reformulates DFT and evaluates the electron density without computing individual orbitals. This direct evaluation is possible by recourse to Gaussian quadrature over the spectrum of the linearized Hamiltonian operator. Furthermore, the nodes and weights of the quadrature can be computed independently for each point in the domain. This property is exploited in CG, where fields of interest are computed at selected nodes and interpolated elsewhere. In this paper, we present the MacroDFT method, its parallel implementation and an assessment of convergence and performance by means of test cases concerned with point defects in magnesium.1 physical understanding of the exponential decay properties of the density matrix -especially in conductors -remains unavailable and, therefore, the development of linear scaling methods for metallic systems has long been considered an open problem [17].An additional challenge is encountered in the study of crystal defects. Defects determine critical properties of crystalline materials despite occurring at relatively low concentrations. Defects intimately couple phenomena at multiple scales, including the chemistry and atomic structure of the core and the attendant long-range elastic fields. In particular, the slow decay of the elastic fields of defects necessitates the use of exceedingly large unit cells in order to achieve convergence with respect to cell size [18,19]. The need to simultaneously resolve the electronic structure and the long-range elastic fields of defects poses a severe technical challenge. A number of multiscale approaches have been proposed that consist of patching together heterogeneous models at different scales, from DFT to continuum elasticity. The coupling between the various models varies from simple parameter passing to hybrid Hamiltonians (e. g., [20,21,22,23,24,25]). Since these methods bring together distinct models that embody different physics and differing mathematical formulations, they typically assume separation of scales (as in parameter passing) or additional physics or constraints at the interface (as in hybrid Hamiltonians). Often, the models need to be adjusted or calibrated to the particular phenomenon under consideration, which ultimately detracts from the predictiveness and fundamental nature of first-principles calculations.The present work differs from the 'patched'-model approach crucially in that we strive to formulate a computational scheme scalable to large representative material samples with DFT as its sole input. In particular, in the resulting scheme, coarse-graining is strictly the result of approximation theory and, consequently, is ansatz-free and does not introduce spurious physics or uncontr...

a b s t r a c tWe study dynamic nanovoid growth in copper single crystals under prescribed volumetric strain rates ranging from moderate ( _ ¼ 10 5 s À1 ) to high ( _ ¼ 10 10 s À1 ). We gain access to lower strain rates by accounting for thermal vibrations in an entropic sense within the framework of maximum-entropy non-equilibrium statistical mechanics. We additionally account for heat conduction by means of empirical atomic-level kinetic laws. The resulting mean trajectories of the atoms are smooth and can be integrated implicitly using large time steps, greatly in excess of those required by molecular dynamics. We also gain access to large computational cells by means of spatial coarse-graining using the quasicontinuum method. On this basis, we identify a transition, somewhere between 10 7 and 10 8 s À1 , between two regimes: a quasistatic regime characterized by nearly isothermal behavior and low dislocation velocities; and a dynamic regime characterized by nearly adiabatic conditions and high dislocation velocities. We also elucidate the precise mechanisms underlying dislocation emission from the nanovoids during cavitation. We additionally investigate the sensitivity of the results of the analysis to the choice of interatomic potential by comparing two EAM-type potentials.

The binding affinity and adhesive strength between the spike (S) glycoproteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the human angiotensin-converting enzyme 2 (ACE2) receptor is computed using molecular dynamics (MD) simulations. The calculations indicate that the binding affinity is $$e_{RS}= 12.6 \pm 1$$ e RS = 12.6 ± 1 $$\hbox {kCal}{\cdot }\hbox {mol}^{-1}$$ kCal · mol - 1 with a maximum adhesive force of $$\sim 102$$ ∼ 102 pN. Our analysis suggests that only 27 (13 in S-protein, 14 in ACE2) residues are active during the initial fusion process between the S-protein and ACE2 receptor. With these insights, we investigated the effect of possible therapeutics in the size and wrapping time of virus particles by reducing the binding energy. Our analysis indicates that this energy has to be reduced significantly, around 50% or more, to block SARS-CoV-2 particles with radius in the order of $$R\le 60$$ R ≤ 60 nm. Our study provides concise target residues and target binding energy reduction between S-proteins and receptors for the development of new therapeutics treatments for COVID-19 guided by computational design.

We report diffusive molecular dynamics simulations concerned with the lithiation of Si nano-pillars, i. e., nano-sized Si rods held at both ends by rigid supports. The duration of the lithiation process is of the order of miliseconds, well outside the range of molecular dynamics but readily accessible to diffusive molecular dynamics. The simulations predict an alloy Li 15 Si 4 at the fully lithiated phase, exceedingly large and transient volume increments up to 300% due to the weakening of Si-Si iterations, a crystalline-to-amorphous-tolithiation phase transition governed by interface kinetics, high misfit strains and residual stresses resulting in surface cracks and severe structural degradation in the form of extensive porosity, among other effects.

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