Petr Zhilyaev

Experimentally, in the presence of the crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here, we have used molecular dynamics simulations and the “ion binding shells model” of DNA condensation to provide an explanation for the observed variations in condensation of short DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA–DNA attraction, shifting the equilibrium away from the DNA condensed phase.

The liquid–solid phase transition during the confinement of a van der Waals bubble is studied using molecular dynamics simulations. In particular, argon is considered inside a graphene bubble, where the outer membrane is a sheet of graphene, and the substrate is atomically flat graphite. A methodology to avoid metastable states of argon is developed and implemented to derive a melting curve of trapped argon. It is found that in the confinement, the melting curve of argon shifts toward higher temperatures, and the temperature shift is about 10–30 K. The ratio of the height to the radius of the GNB (H/R) decreases with increasing temperature. It also most likely undergoes an abrupt change through the liquid–crystal phase transition. The semi-liquid state of argon was detected in the transition region. At this state, the argon structure stays layered, but the atoms travel distances of several lattice constants.

Additive manufacturing is a modern technique to produce parts with a complex geometry. However, the choice of the printing parameters is a time-consuming and costly process. In this study, the parameter optimization for the laser powder bed fusion process was investigated. Using state-of-the art multi-objective Bayesian optimization, the set of the most-promising process parameters (laser power, scanning speed, hatch distance, etc.), which would yield parts with the desired hardness and porosity, was established. The Gaussian process surrogate model was built on 57 empirical data points, and through efficient sampling in the design space, we were able to obtain three points in the Pareto front in just over six iterations. The produced parts had a hardness ranging from 224–235 HV and a porosity in the range of 0.2–0.37%. The trained model recommended using the following parameters for high-quality parts: 58 W, 257 mm/s, 45 µm, with a scan rotation angle of 131 degrees. The proposed methodology greatly reduces the number of experiments, thus saving time and resources. The candidate process parameters prescribed by the model were experimentally validated and tested.

Kirkpatrick et al . (Reports, 9 December 2021, p. 1385) trained a neural network–based DFT functional, DM21, on fractional-charge (FC) and fractional-spin (FS) systems, and they claim that it has outstanding accuracy for chemical systems exhibiting strong correlation. Here, we show that the ability of DM21 to generalize the behavior of such systems does not follow from the published results and requires revisiting.

The kinetic simulations of plume expansion induced by pulsed laser heating of a copper target in a vacuum or low-pressure argon background gas are performed based on the direct simulation Monte Carlo (DSMC) method and ab initio quantum mechanical calculation of interactions between copper and argon atoms. The potential energy curves (PECs) for Cu–Cu, Ar–Ar, and Ar–Cu interactions are obtained in density functional theory (DFT) calculations with the van der Waals (vdW) correction. The computed Cu–Cu PEC is strikingly different from the Lennard-Jones (LJ) potentials with semi-empirical parameters, which were previously suggested for kinetic simulations of the copper vapor flows. It is found that the Lorentz–Berthelot rule cannot reliably predict the parameters of the LJ potential for cross-species Ar–Cu interaction. The DFT-vdW PECs are fitted by the Morse long-range (MLR) potentials. The MLR potentials are used to compute the outcomes of binary collisions in the DSMC method based on the solution of the classical scattering problem and to parameterize the variable hard sphere (VHS) collision model. The results of the DSMC simulations based on DFT-vdW PECs are compared with the results obtained based on various parameterizations of the VHS model. It is shown that the previously developed parameterizations of the VHS model can either over- or underestimate the plume temperature and density compared to the results obtained based on the DFT-vdW PECs. The simulations also reveal the strong effect of the cross-species collision model parameters on the flow structure in the mixing layer, which is dominated by molecular diffusion.

Herein, the molecular dynamics (MD) simulations of pure Ni crystallites are performed to show the influence of the grain boundary (GB) geometry on the values of the activation energy of GB migration. The considered systems are bicrystal with Σ5[010] tilt plane boundary, spherical grain with initial curvature radius 5 nm, and polycrystalline 30 nm × 30 nm × 30 nm block. The motion of three types of GBs (flat, spherical, and polycrystalline) at constant temperatures and no applied forces is studied. The obtained values of activation energy are 0.45, 0.11, and 0.57 eV for flat, spherical, and polycrystalline types of GBs, respectively. These values are smaller than those that are reported in experimental works, which is a common issue for atomistic simulations of GB migration. Possible sources of such disagreement and ways to overcome it are discussed. The particular part of this work is devoted to the development of the automated analysis of polycrystalline structure. This analysis provides detailed information on grain size distribution and its evolution in time.

Density functional theory (DFT) is one of the most widely used tools to solve the many-body Schrodinger equation. The core uncertainty inside DFT theory is the exchange-correlation (XC) functional, the exact form of which is still unknown. Therefore, the essential part of DFT success is based on the progress in the development of XC approximations. Traditionally, they are built upon analytic solutions in low- and high-density limits and result from quantum Monte Carlo numerical calculations. However, there is no consistent and general scheme of XC interpolation and functional representation. Many different developed parametrizations mainly utilize a number of phenomenological rules to construct a specific XC functional. In contrast, the neural network (NN) approach can provide a general way to parametrize an XC functional without any a priori knowledge of its functional form. In this work, we develop NN XC functionals and prove their applicability to 3-dimensional physical systems. We show that both the local density approximation (LDA) and generalized gradient approximation (GGA) are well reproduced by the NN approach. It is demonstrated that the local environment can be easily considered by changing only the number of neurons in the first layer of the NN. The developed NN XC functionals show good results when applied to systems that are not presented in the training/test data. The generalizability of the formulated NN XC framework leads us to believe that it could give superior results in comparison with traditional XC schemes provided training data from high-level theories such as the quantum Monte Carlo and post-Hartree-Fock methods.

A graphene nanobubble consists of a graphene sheet, an atomically flat substrate, and a substance enclosed between them. Unlike conventional confinement with rigid walls and a fixed volume, the graphene nanobubble has one stretchable wall, which is the graphene sheet, and its volume can be adjusted by changing the shape. In this study, we developed a model of a graphene nanobubble based on classical density functional theory and the elastic theory of membranes. The proposed model takes into account the inhomogeneity of the enclosed substance, the nonrigidity of the wall, and the alternating volume. As an example application, we utilize the developed model to investigate fluid argon inside graphene nanobubbles at room temperature. We observed a constant height-to-radius ratio over the whole range of radii considered, which is in agreement with the results from experiments and molecular dynamics simulations. The developed model provides a theoretical tool to study both the inner structure of the confined substance and the shape of the graphene nanobubble. The model can be easily extended to other types of nonrigid confinement.

Density functional theory (DFT) is one of the most widely used tools to solve the many-body Schrodinger equation. The core uncertainty inside DFT theory is the exchange-correlation (XC) functional, the exact form of which is still unknown. Therefore, the essential part of DFT success is based on the progress in the development of XC approximations. Traditionally, they are built upon analytic solutions in low- and high-density limits and result from quantum Monte Carlo numerical calculations. However, there is no consistent and general scheme of XC interpolation and functional representation. Many different developed parametrizations mainly utilize a number of phenomenological rules to construct a specific XC functional. In contrast, the neural network (NN) approach can provide a general way to parametrize an XC functional without any a priori knowledge of its functional form. In this work, we develop NN XC functionals and prove their applicability to 3-dimensional physical systems. We show that both the local density approximation (LDA) and generalized gradient approximation (GGA) are well reproduced by the NN approach. It is demonstrated that the local environment can be easily considered by changing only the number of neurons in the first layer of the NN. The developed NN XC functionals show good results when applied to systems that are not presented in the training/test data. The generalizability of the formulated NN XC framework leads us to believe that it could give superior results in comparison with traditional XC schemes provided training data from high-level theories such as the quantum Monte Carlo and post-Hartree-Fock methods.

A graphene nanobubble consists of a graphene sheet, an atomically flat substrate and a substance enclosed between them. Unlike conventional confinement with rigid walls and a fixed volume, the graphene nanobubble has one stretchable wall, which is the graphene sheet, and its volume can be adjusted by changing the shape. In this study, we developed a model of a graphene nanobubble based on classical density functional theory and the elastic theory of membranes. The proposed model takes into account the inhomogeneity of the enclosed substance, the nonrigidity of the wall and the alternating volume. As an example application, we utilize the developed model to investigate fluid argon inside graphene nanobubbles at room temperature. We observed a constant height-to-radius ratio over the whole range of radii considered, which is in agreement with the results from experiments and molecular dynamics simulations. The developed model provides a theoretical tool to study both the inner structure of the confined substance and the shape of the graphene nanobubble. The model can be easily extended to other types of nonrigid confinement.