Coarse grained simulation and dynamic bridging for turbulent mixing predictions
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Grinstein, Fernando F. (ORCID:0000000304427936)↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase
We report a molecular dynamics investigation of the structure, function, and inhibition of geranylgeranyl diphosphate synthase (GGPPS), a potential drug target, from the malaria parasite Plasmodium vivax. During this work, we discovered several GGPPS inhibitors, benzoic acids, and determined their structures crystallographically. We then used molecular dynamics simulations to investigate the dynamics of three such inhibitors and two bisphosphonate inhibitors, zoledronate and a lipophilic analogue of zoledronate, as well as the enzyme’s product, GGPP. We were able to identify the main motions that govern substrate binding and product release as well as the molecular features required for GGPPS inhibition by both classes of inhibitor. The results are of broad general interest because they represent the first detailed investigation of the mechanism of action, and inhibition, of an important antimalarial drug target, geranylgeranyl diphosphate synthase, and may help guide the development of other, novel inhibitors as new drug leads.
59 BASIC BIOLOGICAL SCIENCES↗
Oxalic Acid Adsorption on Rutile: Experiments and Surface Complexation Modeling to 150 °C
Here, we characterize oxalate adsorption by rutile in NaCl media (0.03 and 0.30 m) and between pH 3 and 10 over a wide temperature range which includes the near hydrothermal regime (10–150 °C). Oxalate adsorption increases with decreasing pH (as is typical for anion binding by metal oxides), but systematic trends with respect to ionic strength or temperature are absent. Surface complexation modeling (SCM) following the CD-MUSIC formalism, and as constrained by molecular modeling simulations and IR spectroscopic results from the literature, is used to interpret the adsorption data. The molecular modeling simulations, which include molecular dynamics simulations supported by free-energy and ab initio calculations, reveal that oxalate binding is outer-sphere, albeit via strong hydrogen bonds. Conversely, previous IR spectroscopic results conclude that various types of inner-sphere complexes often predominate. SCMs constrained by both the molecular modeling results and the IR spectroscopic data were developed, and both fit the adsorption data equally well. We conjecture that the discrepancy between the molecular simulation and IR spectroscopic results is due to the nature of the rutile surfaces investigated, that is, the perfect (110) crystal faces for the molecular simulations and various rutile powders for the IR spectroscopy studies. Although the (110) surface plane is most often dominant for rutile powders, a variety of steps, kinks, and other types of surface defects are also invariably present. Hence, we speculate that surface defect sites may be primarily responsible for inner-sphere oxalate adsorption, although further study is necessary to prove or disprove this hypothesis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Water Dynamics in Gyroid Phases of Self-Assembled Gemini Surfactants
Water-mediated ion transport through functional nanoporous materials depends on the dynamics of water confined within a given nanostructured morphology. In this study, we investigate hydrogen-bonding dynamics of interfacial water within a ‘normal’ (Type I) lyotropic gyroid phase formed by a gemini dicarboxylate surfactant self-assembly using a combina- tion of 2DIR spectroscopy and molecular dynamics simulations. Experiments and simulations demonstrate that water dynamics in the normal gyroid phase is one order of magnitude slower than that in bulk water, due to specific interactions between water, the ionic surfactant headgroups, and counterions. However, the dynamics of water in the normal gyroid phase are faster than those of water confined in a reverse spherical micelle of a sulfonate surfactant, given that the water pool in the reverse micelle and the water pore in the gyroid phase have roughly the same diameters. This difference in confined water dynamics likely arises from the significantly reduced curvature- induced frustration at the convex interfaces of the normal gyroid, as compared to the concave interfaces of a reverse spherical micelle. These detailed insights into confined water dynamics may guide the future design of artificial membranes that rapidly transport protons and other ions.
36 MATERIALS SCIENCE↗
The hydrogen-bond collective dynamics in liquid methanol
The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HB dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Failure of molecular dynamics to provide appropriate structures for quantum mechanical description of the aqueous chloride ion charge-transfer-to-solvent ultraviolet spectrum
The lowest band in the charge-transfer-to-solvent ultraviolet absorption spectrum of aqueous chloride ion is studied by experiment and computation. Interestingly, the experiments indicate that at concentrations up to at least 0.25 M, where calculations indicate ion pairing to be significant, there is no notable effect of ionic strength on the spectrum. The experimental spectra are fitted to aid comparison with computations. Classical molecular dynamic simulations are carried out on dilute aqueous Cl - , Na + , and NaCl, producing radial distribution functions in reasonable agreement with experiment and, for NaCl, clear evidence of ion pairing. Clusters are extracted from the simulations for quantum mechanical excited state calculations. Accurate ab initio coupled-cluster benchmark calculations on a small number of representative clusters are carried out and used to identify and validate an efficient protocol based on time-dependent density functional theory. The latter is used to carry out quantum mechanical calculations on thousands of clusters. The resulting computed spectrum is in excellent agreement with experiment for the peak position, with little influence from ion pairing, but is in qualitative disagreement on the width, being only about half as wide. It is concluded that simulation by classical molecular dynamics fails to provide an adequate variety of structures to explain the experimental CTTS spectrum of aqueous Cl - .
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A generalized Ewald decomposition for screened Coulomb interactions
Medium-range interactions occur in a wide range of systems, including charged-particle systems with varying screening lengths. We generalize the Ewald method to charged systems described by interactions involving an arbitrary dielectric response function ϵ(𝐤). We provide an error estimate and optimize the generalization to find the break-even parameters that separate a neighbor list-only algorithm from the particle-particle particle-mesh algorithm. We examine the implications of different choices of the screening length for the computational cost of computing the dynamic structure factor. We then use our new method in molecular dynamics simulations to compute the dynamic structure factor for a model plasma system and examine the wave-dispersion properties of this system.
Dharuman, Gautham↗
Dynamic and weak electric double layers in ultrathin nanopores
The unique properties of aqueous electrolytes in ultrathin nanopores have drawn a great deal of attention in a variety of applications, such as power generation, water desalination, and disease diagnosis. Inside the nanopore, at the interface, properties of ions differ from those predicted by the classical ionic layering models (e.g., Gouy–Chapman electric double layer) when the thickness of the nanopore approaches the size of a single atom (e.g., nanopores in a single-layer graphene membrane). Here, using extensive molecular dynamics simulations, the structure and dynamics of aqueous ions inside nanopores are studied for different thicknesses, diameters, and surface charge densities of carbon-based nanopores [ultrathin graphene and finite-thickness carbon nanotubes (CNTs)]. The ion concentration and diffusion coefficient in ultrathin nanopores show no indication of the formation of a Stern layer (an immobile counter-ionic layer) as the counter-ions and nanopore atoms are weakly correlated in time compared to the strong correlation observed in thick nanopores. The weak correlation observed in ultrathin nanopores is indicative of a weak adsorption of counter-ions onto the surface compared to that of thick pores. The vanishing counter-ion adsorption (ion–wall correlation) in ultrathin nanopores leads to several orders of magnitude shorter ionic residence times (picoseconds) compared to the residence times in thick CNTs (seconds). The results of this study will help better understand the structure and dynamics of aqueous ions in ultrathin nanopores.
2D materials↗
Development of a deep machine learning interatomic potential for metalloid-containing Pd-Si compounds
Interatomic potentials based on neural-network machine learning (ML) approach to address the long-standing challenge of accuracy versus efficiency in molecular-dynamics simulations have recently attracted a great deal of interest. In this work, utilizing Pd-Si system as a prototype, we extend the development of neural-network ML potentials to compounds exhibiting various types of bonding characteristics. The ML potential is trained by fitting to the energies and forces of both liquid and crystal structures first-principles calculations based on density-functional theory (DFT). We show that the generated ML potential captures the structural features and motifs in Pd 82 Si 18 and Pd 75 Si 25 liquids more accurately than the existing interatomic potential based on embedded-atom method (EAM). The ML potential also describes the solid-liquid interface of these systems very well. Moreover, while the existing EAM potential fails to describe the relative energies of various crystalline structures and predict wrong ground-state structures at Pd 3 Si and Pd 9 Si 2 composition, the developed ML potential predicts correctly the ground-state structures from genetic algorithm search. The efficient ML potential with DFT accuracy from our study will provide a promising scheme for accurate atomistic simulations of structures and dynamics of complex Pd-Si system.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Spin dynamics of the antiferromagnetic Heisenberg model on a kagome bilayer
We research the spin dynamics of a classical Heisenberg antiferromagnet with nearest-neighbor interactions on a quasi-two-dimensional kagome bilayer. This geometrically frustrated lattice consists of two kagome layers connected by a triangular-lattice linking layer. By combining Monte Carlo with precessional spin dynamics simulations, we compute the dynamical structure factor of the classical spin liquid in the kagome bilayer and investigate the thermal and dilution effects. While the low-frequency and long-wavelength dynamics of the cooperative paramagnetic phase is dominated by spin diffusion, weak magnon excitations persist at higher energies, giving rise to the half-moon pattern in the dynamical structure factor. In the presence of spin vacancies, the dynamical properties of the diluted system can be understood within the two-population picture. The spin diffusion of the “correlated” spin clusters is mainly driven by the zero-energy weather-vane modes, giving rise to an autocorrelation function that decays exponentially with time. On the other hand, the diffusive dynamics of the quasifree “orphan” spins leads to a distinctive longer-time power-law tail in the autocorrelation function. We discuss the implications of our work for the glassy behaviors observed in the archetypal frustrated magnet SrCr 9p Ga 12-9 pO 19 (SCGO).
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Nonequilibrium study of the chiral magnetic effect from real-time simulations with dynamical fermions
We show a real-time lattice approach to study the nonequilibrium dynamics of vector and axial charges in S U ( N ) × U ( 1 ) gauge theories. Based on a classical description of the non-Abelian and Abelian gauge fields, we include dynamical fermions and develop operator definitions for (improved) Wilson and overlap fermions that allow us to study real-time manifestations of the axial anomaly from first principles. We present a first application of this approach to anomalous transport phenomena such as the chiral magnetic effect (CME) and the chiral separation effect (CSE) by studying the dynamics of fermions during and after a S U ( N ) sphaleron transition in the presence of a U ( 1 ) magnetic field. We investigate the fermion mass and magnetic field dependence of the suggested signatures of the CME and the CSE and point out some important aspects which need to be accounted for in the macroscopic description of anomalous transport phenomena.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Controlling Strain Bursts and Avalanches at the Nano- to Micrometer Scale
We demonstrate, through three-dimensional discrete dislocation dynamics simulations, that the complex dynamical response of nano- and microcrystals to external constraints can be tuned. Under load rate control, strain bursts are shown to exhibit scale-free avalanche statistics, similar to critical phenomena in many physical systems. For the other extreme of displacement rate control, strain burst response transitions to quasiperiodic oscillations, similar to stick-slip earthquakes. External load mode control is shown to enable a qualitative transition in the complex collective dynamics of dislocations from self-organized criticality to quasiperiodic oscillations.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Dynamic Neutron Scattering by Biological Systems
Dynamic neutron scattering directly probes motions in biological systems on femtosecond to microsecond timescales. When combined with molecular dynamics simulation and normal mode analysis, detailed descriptions of the forms and frequencies of motions can be derived. We examine vibrations in proteins, the temperature dependence of protein motions, and concepts describing the rich variety of motions detectable using neutrons in biological systems at physiological temperatures. In conclusion, new techniques for deriving information on collective motions using coherent scattering are also reviewed.
59 BASIC BIOLOGICAL SCIENCES↗
CASTELO: clustered atom subtypes aided lead optimization—a combined machine learning and molecular modeling method
Background: Drug discovery is a multi-stage process that comprises two costly major steps: pre-clinical research and clinical trials. Among its stages, lead optimization easily consumes more than half of the pre-clinical budget. We propose a combined machine learning and molecular modeling approach that partially automates lead optimization workflow in silico, providing suggestions for modification hot spots. Results: The initial data collection is achieved with physics-based molecular dynamics simulation. Contact matrices are calculated as the preliminary features extracted from the simulations. To take advantage of the temporal information from the simulations, we enhanced contact matrices data with temporal dynamism representation, which are then modeled with unsupervised convolutional variational autoencoder (CVAE). Finally, conventional and CVAE-based clustering methods are compared with metrics to rank the submolecular structures and propose potential candidates for lead optimization. Conclusion: With no need for extensive structure-activity data, our method provides new hints for drug modification hotspots which can be used to improve drug potency and reduce the lead optimization time. It can potentially become a valuable tool for medicinal chemists.
59 BASIC BIOLOGICAL SCIENCES↗
Dynamic System Simulation of the KRUSTY Experiment
The proposed KRUSTY experiment is a demonstration of a reactor operating at power. The planned experimental configuration includes a highly enriched uranium (HEU) reflected core, cooled by multiple heat pipes leading to Stirling engines for primary heat rejection. Operating power is expected to be approximately four (4) to five (5) kilowatts with a core temperature above 1,000 K. No data is available on any historical reactor employing HEU metal that operated over the temperature range required for the KRUSTY experiment. Further, no reactor has operated with heat pipes as the primary cooling mechanism. Historic power reactors have employed either natural or forced convection so data on their operation is not directly applicable to the KRUSTY experiment. The primary purpose of the system model once developed and refined by data from these component experiments, will be used to plan the KRUSTY experiment. This planning will include expected behavior of the reactor from start-up, through various transient conditions where cooling begins to become present and effective, and finally establishment of steady-state. In addition, the model can provide indicators of anticipated off-normal events and appropriate operator response to those conditions. This information can be used to develop specific experiment operating procedures and aids to guide the operators in conduct of the experiment.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Surface Engineering by Simultaneous Action of Multiple External Fields (Final Technical Report)
This research project aims at enabling surface engineering strategies based on the fundamental understanding and predictive modeling of the surface morphological response of solid materials subjected to the combined action of multiple external forces. Surface morphological response to mismatch strain in strained-layer heterostructures also is analyzed. Our research focuses on the surface morphological evolution and stability of electrically conducting (metallic, such as Cu) and semiconducting (such as Si) solids under the simultaneous application of mechanical stresses, electric fields, and temperature gradients. We emphasize on identifying the conditions under which the multiply driven surface morphology is stable and on exploring the complexity of the corresponding various morphologically stable surface patterns. We also emphasize on the driven evolution of nanoscale features aiming at stabilizing and controlling nanoscale patterns on surfaces by their manipulation through simultaneously applied multiple external forces. Specifically, we address systematically the morphological response to the combined action of multiple external forces of bulk solid surfaces, surfaces of thin films grown epitaxially on thick or thin substrates, as well as nanoscale surface features such as coherently strained islands grown epitaxially on substrate surfaces. The research is based on a modeling approach that combines theoretical analyses of surface morphological stability with self-consistent dynamical simulations of surface evolution based on properly parameterized continuum and multiscale surface transport models.
36 MATERIALS SCIENCE↗
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