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The typical layered transition metal dichalcogenide (TMDC) material, MoS2, is considered a promising candidate for the next-generation electronic device due to its exceptional physical and chemical properties. In chemical vapor deposition synthesis, the sulfurization of MoO3 powders is an essential reaction step in which the MoO3 reactants are converted into MoS2 products. Recent studies have suggested using an H2S/H2 mixture to reduce MoO3 powders in an effective way. However, reaction mechanisms associated with the sulfurization of MoO3 by the H2S/H2 mixture are yet to be fully understood. Here, we perform quantum molecular dynamics (QMD) simulations to investigate the sulfurization of MoO3 flakes using two different gaseous environments: pure H2S precursors and a H2S/H2 mixture. Our QMD results reveal that the H2S/H2 mixture could effectively reduce and sulfurize the MoO3 reactants through additional reactions of H2 and MoO3, thereby providing valuable input for experimental synthesis of higher-quality TMDC materials.

Abstract Transition metal dichalcogenides have shown great potential for next-generation electronic and optoelectronic devices. However, native oxidation remains a major issue in achieving their long-term stability, especially for Zr-containing materials such as ZrS2. Here, we develop a first principles-informed reactive forcefield for Zr/O/S to study oxidation dynamics of ZrS2. Simulation results reveal anisotropic oxidation rates between (210) and (001) surfaces. The oxidation rate is highly dependent on the initial adsorption of oxygen molecules on the surface. Simulation results also provide reaction mechanism for native oxide formation with atomistic details. Graphic Abstract

Phase-change materials are of great interest for low-power high-throughput storage devices in next-generation neuromorphic computing technologies. Their operation is based on the contrasting properties of their amorphous and crystalline phases, which can be switched on the nanosecond time scale. Among the archetypal phase change materials based on Ge-Sb-Te alloys, Sb2Te3 displays a fast and energy-efficient crystallization-amorphization cycle due to its growth-dominated crystallization and low melting point. This growth-dominated crystallization contrasts with the nucleation-dominated crystallization of Ge2Sb2Te5. Here, we show that the energy required for and the time associated with the amorphization process can be further reduced by using a photoexcitation-based nonthermal path. We employ nonadiabatic quantum molecular dynamics simulations to investigate the time evolution of Sb2Te3 with 2.6, 5.2, 7.5, 10.3, and 12.5% photoexcited valence electron-hole carriers. Results reveal that the degree of amorphization increases with excitation, saturating at 10.3% excitation. The rapid amorphization originates from an instantaneous charge transfer from Te-p orbitals to Sb-p orbitals upon photoexcitation. Subsequent evolution of the excited state, within the picosecond time scale, indicates an Sb-Te bonding to antibonding transition. Concurrently, Sb-Sb and Te-Te antibonding decreases, leading to formation of wrong bonds. For photoexcitation of 7.5% valence electrons or larger, the electronic changes destabilize the crystal structure, leading to large atomic diffusion and irreversible loss of long-range order. These results highlight an ultrafast energy-efficient amorphization pathway that could be used to enhance the performance of phase change material-based optoelectronic devices.

A thorough understanding of native oxides is essential for designing semiconductor devices. Here we report a study of the rate and mechanisms of spontaneous oxidation of bulk single crystals of ZrS$_x$Se$_{2-x}$ alloys and MoS$_2$. ZrS$_x$Se$_{2-x}$ alloys oxidize rapidly, and the oxidation rate increases with Se content. Oxidation of basal surfaces is initiated by favorable O$_2$ adsorption and proceeds by a mechanism of Zr-O bond switching, that collapses the van der Waals gaps, and is facilitated by progressive redox transitions of the chalcogen. The rate-limiting process is the formation and out-diffusion of SO$_2$. In contrast, MoS$_2$ basal surfaces are stable due to unfavorable oxygen adsorption. Our results provide insight and quantitative guidance for designing and processing semiconductor devices based on ZrS$_x$Se$_{2-x}$ and MoS$_2$, and identify the atomistic-scale mechanisms of bonding and phase transformations in layered materials with competing anions.

High quality Van der Waals chalcogenides are important for phase change data storage, thermoelectrics, and spintronics. Using a combination of statistical design of experiments and density functional theory, we clarify how the out-of-equilibrium van der Waals epitaxial deposition methods can improve the crystal quality of Sb2Te3 films. We compare films grown by radio frequency sputtering and pulsed laser deposition (PLD). The growth factors that influence the crystal quality for each method are different. For PLD grown films a thin amorphous Sb2Te3 seed layer most significantly influences the crystal quality. In contrast, the crystalline quality of films grown by sputtering is rather sensitive to the deposition temperature and less affected by the presence of a seed layer. This difference is somewhat surprising as both methods are out-of-thermal-equilibrium plasma-based methods. Non-adiabatic quantum molecular dynamics simulations show that this difference originates from the density of excited atoms in the plasma. The PLD plasma is more intense and with higher energy than that used in sputtering, and this increases the electronic temperature of the deposited atoms, which concomitantly increases the adatom diffusion lengths in PLD. In contrast, the adatom diffusivity is dominated by the thermal temperature for sputter grown films. These results explain the wide range of Sb2Te3 and superlattice crystal qualities observed in the literature. These results indicate that, contrary to popular belief, plasma-based deposition methods are suitable for growing high quality crystalline chalcogenides., Comment: 24 pages, 8 figs

Photoexcitation can drastically modify potential energy surfaces of materials, allowing access to hidden phases. SrTiO3 (STO) is an ideal material for photoexcitation studies due to its prevalent use in nanostructured devices and its rich range of functionality-changing lattice motions. Recently, a hidden ferroelectric phase in STO was accessed through weak terahertz excitation of polarization-inducing phonon modes. In contrast, whereas strong laser excitation was shown to induce nanostructures on STO surfaces and control nanopolarization patterns in STO-based heterostructures, the dynamic pathways underlying these optically induced structural changes remain unknown. Here nonadiabatic quantum molecular dynamics reveals picosecond amorphization in photoexcited STO at temperatures as low as 10 K. The three-stage pathway involves photoinduced charge transfer and optical phonon activation followed by nonlinear charge and lattice dynamics that ultimately lead to amorphization. This atomistic understanding could guide not only rational laser nanostructuring of STO but also broader "quantum materials on demand" technologies.

Solid energetic nanocomposites, consisting of reactive metal particles and oxidizers, find broad applications ranging from pyrotechnics to solid rocket propellants and solid ramjet fuels. In particular, nano-aluminum (n-Al) and polyvinylidene fluoride (PVDF) are attractive fuel and oxidizer materials, due to the high energy density of n-Al, and the high oxidizing potential and excellent mechanical properties of PVDF. PVDF is a semi-crystalline polymer and has three common crystalline phases, alpha (α), gamma (γ), and beta (β) phases. Many research works have focused on the chemical reactions between Al and PVDF, yet the effect of PVDF crystallinity on the Al/PVDF reaction is unknown. Here, we experimentally and computationally demonstrate that increasing the mass fraction of β-phase PVDF from 2.5 to 25% in Al/PVDF composites substantially improves peak pressure by 90% (from ~34 to ~64 psi) and pressure rise rates by 300% (from 2.5 psi/ms to 10 psi/ms). This stems from the alignment of F atoms along one side of the β-PVDF polymer chain, making it structurally conducive to reacting with Al particles to form strong Al-F interactions. This strong interaction leads to higher binding energy between, and hence higher reactivity in, β-PVDF and Al. Our research provides a new method for enhancing the reactive performance of Al/PVDF composites by increasing the content of β-PVDF.

The use of artificial neural network (ANN) potentials trained with first-principles calculations has emerged as a promising approach for molecular dynamics (MD) simulations encompassing large space and time scales while retaining first-principles accuracy. To date, however, the application of ANN-MD has been limited to near-equilibrium processes. Here we combine first-principles-trained ANN-MD with multiscale shock theory (MSST) to successfully describe far-from-equilibrium shock phenomena. Our ANN-MSST-MD approach describes shock-wave propagation in solids with first-principles accuracy but a 5000 times shorter computing time. Accordingly, ANN-MD-MSST was able to resolve fine, long-time elastic deformation at low shock speed, which was impossible with first-principles MD because of the high computational cost. This work thus lays a foundation of ANN-MD simulation to study a wide range of far-from-equilibrium processes.

Memristive devices (i.e. memristors) can bring great benefits to many emerging applications that may play important roles in the future generations of electronic systems, such as bio-inspired neuro...

Organic polymers offer many advantages as dielectric materials over their inorganic counterparts because of high flexibility and cost-effective processing, but their application is severely limited by breakdown in the presence of high electric fields. Dielectric breakdown is commonly understood as the result of avalanche processes such as carrier multiplication and defect generation that are triggered by field-accelerated hot carriers (electrons or holes). In stark contrast to inorganic dielectric materials, however, there remains no mechanistic understanding to enable quantitative prediction of the breakdown field in polymers. Here, we perform systematic study of different electric fields on hot carrier dynamics and resulting chemical damage in a slab of archetypal polymer, polyethylene, using nonadiabatic quantum molecular dynamics simulations. We found that high electric fields induce localized electronic states at the slab surface, with a critical transition occurring near the experimentally reported intrinsic breakdown field. This transition in turn facilitates strong polaronic coupling between charge carriers and atoms, which is manifested by severe damping of the time evolution of localized states and the presence of C-H vibrational resonance in the hot-carrier motion leading to rapid carbon-carbon bond breaking on the surface. Such polaronic localization transition may provide a critically missing prediction method for computationally screening dielectric polymers with high breakdown fields.

Ab initio molecular dynamics simulations of shock loading on poly(p-phenylene terephthalamide) (PPTA) reveal stress release mechanisms based on hydrogen bond preserving structural phase transformation (SPT) and planar amorphization. The SPT is triggered by [100] shock-induced coplanarity of phenylene groups and rearrangement of sheet stacking leading to a novel monoclinic phase. Planar amorphization is generated by [010] shock-induced scission of hydrogen bonds leading to disruption of polymer sheets, and trans-to-cis conformational change of polymer chains. In contrast to the latter, the former mechanism preserves the hydrogen bonding and cohesiveness of polymer chains in the identified novel crystalline phase preserving the strength of PPTA. The interplay between hydrogen bond preserving (SPT) and nonpreserving (planar amorphization) shock release mechanisms is critical to understanding the shock performance of aramid fibers.

The typical layered transition metal dichalcogenide (TMDC) material, MoS

Parameterization of interatomic forcefields is a necessary first step in performing molecular dynamics simulations. This is a non-trivial global optimization problem involving quantification of multiple empirical variables against one or more properties. We present EZFF, a lightweight Python library for parameterization of several types of interatomic forcefields implemented in several molecular dynamics engines against multiple objectives using genetic-algorithm-based global optimization methods. The EZFF scheme provides unique functionality such as the parameterization of hybrid forcefields composed of multiple forcefield interactions as well as built-in quantification of uncertainty in forcefield parameters and can be easily extended to other forcefield functional forms as well as MD engines.

Photoexcitation can drastically modify potential energy surfaces of materials, allowing access to hidden phases. SrTiO

Confluence of extreme-scale quantum dynamics simulations (i.e. quantum@scale) and cutting-edge x-ray free-electron laser experiments are revolutionizing materials science. An archetypal example is the exciting concept of using picosecond light pulses to control emergent material properties on demand in atomically-thin layered materials. This paper describes efforts to scale our quantum molecular dynamics engine toward the United States' first exaflop/s computer, under an Aurora Early Science Program project named "Metascalable layered material genome". Key algorithmic and computing techniques incorporated are: (1) globally-scalable and locally-fast solvers within a linear-scaling divide-conquer-recombine algorithmic framework; (2) algebraic 'BLASification' of computational kernels; and (3) data alignment and loop restructuring, along with register and cache blocking, for enhanced vectorization and efficient memory access. The resulting weak-scaling parallel efficiency was 0.93 on 131,072 Intel Xeon Phi cores for a 56.6 million atom (or 169 million valence-electron) system, whereas the various code transformations achieved 5-fold speedup. The optimized simulation engine allowed us for the first time to establish a significant effect of substrate on the dynamics of layered material upon electronic excitation.

Fast deformations in the quartz crystals during shock compression process have been investigated with two time-resolved methods of in-situ diffractions by x-ray free electron laser (XFEL) and large-scale molecular dynamic (MD) simulations in order to get insights in planar deformation feature (PDF) mechanism. PDFs in quartz provide strong evidence for impact and are used to estimate the impact conditions. The present experimental results on X-cut and Y-cut quartz single crystals at pressures below phase transition indicate ideal uniaxial compression and rotation of fractured grains to a direction to heat up locally due to dispersed particle velocity distribution in the dynamic movement. This could explain the observed disordering at given planes, as supported by the MD simulations.

Optical ignition of solid energetic materials, which can rapidly release heat, gas, and thrust, is still challenging due to the limited light absorption and high ignition energy of typical energetic materials (e.g., aluminum, Al). Here, we demonstrated that the optical ignition and combustion properties of micron-sized Al particles were greatly enhanced by adding only 20 wt % of graphene oxide (GO). These enhancements are attributed to the optically activated disproportionation and oxidation reactions of GO, which release heat to initiate the oxidization of Al by air and generate gaseous products to reduce the agglomeration of the composites and promote the pressure rise during combustion. More importantly, compared to conventional additives such as metal oxides nanoparticles (e.g., WO3 and Bi2O3), GO has much lower density and therefore could improve energetic properties without sacrificing Al content. The results from Xe flash ignition and laser-based excitation experiments demonstrate that GO is an eff...

Atomically thin MoS2 layer, a promising transition metal dichalcogenide (TMDC) material, has great potential for application in next-generation electronic and optoelectronic devices. Chemical vapor deposition (CVD) is the most effective technique for the synthesis of high-quality MoS2 layers. During CVD synthesis, monolayered MoS2 is generally synthesized by sulfidation of MoO3. Although qualitative reaction mechanisms for the sulfidation of MoO3 have been investigated by previous studies, the detailed reaction processes, including atomic-scale reaction pathways and growth kinetics, have yet to be fully understood. Here, we present quantum-mechanically informed and validated reactive molecular dynamics simulations of the direct sulfidation of MoO3 surfaces using S2 gas precursors. Our work clarifies the reaction mechanisms and kinetics of the sulfidation of MoO3 surfaces as follows: the reduction and sulfidation of MoO3 surfaces occur primarily at O-termination sites, followed by unsaturated Mo sites; the...

The extreme heat resistance of dormant bacterial spores strongly depends on the extent of protoplast dehydration and the concentration of dipicolinic acid (DPA) and its associated calcium salts (Ca-DPA) in the spore core. Recent experiments have suggested that this heat resistance depends on the properties of confined water molecules in the hydrated Ca-DPA-rich protoplasm, but atomistic details have not been elucidated. In this study, we used reactive molecular dynamics (RMD) simulations to study the dynamics of water in hydrated DPA and Ca-DPA as a function of temperature. The RMD simulations indicate two distinct solid-liquid and liquid-gel transitions for the spore core. Simulation results reveal monotonically decreasing solid-gel-liquid transition temperatures with increasing hydration. Additional calculations on the specific heat and free energy of water molecules in the spore core further support the higher heat resistance of dehydrated spores. These results provide an insight into the experimental trend of moist-heat resistance of bacterial spores and reconciles previous conflicting experimental findings on the state of water in bacterial spores.

Scandium-doped aluminum nitride, Al1-xScxN, represents a new class of displacive ferroelectric materials with high polarization and sharp hysteresis along with high-temperature resilience, facile synthesizability and compatibility with standard CMOS fabrication techniques. The fundamental physics behind the transformation of unswitchable piezoelectric AlN into switchable Al-Sc-N ferroelectrics depends upon important atomic properties such as local structure, dopant distributions and the presence of competing mechanism of polarization switching in the presence of an applied electric-field that have not been understood. We computationally synthesize Al1-xScxN to quantify the inhomogeneity of Sc distribution and phase segregation, and characterize its crystal and electronic structure as a function of Sc-doping. Nudged elastic band calculations of the potential energy surface and quantum molecular dynamics simulations of direct electric-field-driven ferroelectric switching reveal a crossover between two polarization reversal mechanisms-inhomogeneous nucleation-and-growth mechanism originating near Sc-rich regions in the limit of low applied fields and nucleation-limited-switching in the high-field regime. Understanding polarization reversal pathways for these two mechanisms as well as the role of local Sc concentration on activation barriers provides design rules to identify other combinations of dopant elements, such as Zr, Mg etc. to synthesize superior AlN-based ferroelectric materials.

Two-dimensional and layered MoS2 is a promising candidate for next-generation electric devices due to its unique electronic, optical, and chemical properties. Chemical vapor deposition (CVD) is the most effective way to synthesize MoS2 monolayer on a target substrate. During CVD synthesis, sulfidation of MoO3 surface is a critical reaction step, which converts MoO3 to MoS2. However, initial reaction steps for the sulfidation of MoO3 remain to be fully understood. Here, we report first-principles quantum molecular dynamics (QMD) simulations for the initiation dynamics of sulfidation of MoO3 (010) surface using S2 and S8 molecules. We found that S2 molecule is much more reactive on the MoO3 surface than S8 molecule. Furthermore, our QMD simulations revealed that a surface O-vacancy on the MoO3 surface makes the sulfidation process preferable kinetically and thermodynamically. Our work clarifies an essential role of surface defects to initiate and accelerate the reaction of MoO3 and gas-phase sulfur precurso...

Detonation processes probed with atomistic details have remained elusive due to highly complex reactions in heterogeneous shock structures. Here, we provide atomistic details of the initial reaction pathways during shock-induced decomposition of 2,4,6-triamino-1,3,5-trinitrobenzene (TATB) crystal using large reactive molecular dynamics simulations based on reactive force fields. Simulation results reveal the existence of three competing intermolecular pathways for the formation of N2. We also observe the formation of large nitrogen- and oxygen-rich carbon aggregates, which delays the release of final reaction products.

Transition metal dichalcogenides (TMDC) like MoS2 are promising candidates for next-generation electric and optoelectronic devices. These TMDC monolayers are typically synthesized by chemical vapor deposition (CVD). However, despite significant amount of empirical work on this CVD growth of monolayered crystals, neither experiment nor theory has been able to decipher mechanisms of selection rules for different growth scenarios, or make predictions of optimized environmental parameters and growth factors. Here, we present an atomic-scale mechanistic analysis of the initial sulfidation process on MoO3 surfaces using first-principles-informed ReaxFF reactive molecular dynamics (RMD) simulations. We identify a three-step reaction process associated with synthesis of the MoS2 samples from MoO3 and S2 precursors: O2 evolution and self-reduction of the MoO3 surface; SO/SO2 formation and S2-assisted reduction; and sulfidation of the reduced surface and Mo–S bond formation. These atomic processes occurring during ...

Metal combustion reaction is highly exothermic and is used in energetic applications, such as propulsion, pyrotechnics, powering micro- and nano-devices, and nanomaterials synthesis. Aluminum (Al) is attracting great interest in those applications because of its high energy density, earth abundance, and low toxicity. Nevertheless, Al combustion is hard to initiate and progresses slowly and incompletely. On the other hand, ultrathin carbon nanomaterials, such as graphene, graphene oxide (GO), and graphene fluoride (GF), can also undergo exothermic reactions. Herein, we demonstrate that the mixture of GO and GF significantly improves the performance of Al combustion as interactions between GO and GF provide heat and radicals to accelerate Al oxidation. Our experiments and reactive molecular dynamics simulation reveal that GO and GF have strong chemical and thermal couplings through radical reactions and heat released from their oxidation reactions. GO facilitates the dissociation of GF, and GF accelerates the disproportionation and oxidation of GO. When the mixture of GO and GF is added to micron-sized Al particles, their synergistic couplings generate reactive oxidative species, such as CFx and CFxOy, and heat, which greatly accelerates Al combustion. This work demonstrates a new area of using synergistic couplings between ultrathin carbon nanomaterials to accelerate metal combustion and potentially oxidation reactions of other materials.

Dielectric polymers are widely used in electronics and energy technologies, but their performance is severely limited by the electrical breakdown under a high electric field. Dielectric breakdown is commonly understood as an avalanche of processes such as carrier multiplication and defect generation that are triggered by field-accelerated hot electrons and holes. However, how these processes are initiated remains elusive. Here, nonadiabatic quantum molecular dynamics simulations reveal microscopic processes induced by hot electrons and holes in a slab of an archetypal dielectric polymer, polyethylene, under an electric field of 600 MV/m. We found that electronic-excitation energy is rapidly dissipated within tens of femtoseconds because of strong electron-phonon scattering, which is consistent with quantum-mechanical perturbation calculations. This in turn excites other electron-hole pairs to cause carrier multiplication. We also found that the key to chemical damage is localization of holes that travel to a slab surface and weaken carbon-carbon bonds on the surface. Such quantitative information can be incorporated into first-principles-informed, predictive modeling of dielectric breakdown.

QXMD is a scalable, parallel program for Quantum Molecular Dynamics simulations with various eXtensions. Its simulation engine is based on (time-dependent) density functional theory using pseudopotentials and a plane-wave basis set, while extensions include nonadiabatic electron–nuclei dynamics and multiscale shock technique. QXMD serves as a community-development platform for new methods and algorithms, a research platform on high-end parallel supercomputers, and an educational platform for hands-on training. Keywords: Nonadiabatic quantum molecular dynamics, Parallel computing, Hands-on training

Certain bacteria produce iron oxide material assembled with nanoparticles (NPs) that are doped with silicon (Fe:Si ~ 3:1) in ambient environment. Such biogenous iron oxides (BIOX) proved to be an excellent electrode material for lithium-ion batteries, but underlying atomistic mechanisms remain elusive. Here, quantum molecular dynamics simulations, combined with biomimetic synthesis and characterization, show rapid charging and discharging of NP within 100 fs, with associated surface lithiation and delithiation, respectively. The rapid electric response of NP is due to the large fraction of surface atoms. Furthermore, this study reveals an essential role of Si-doping, which reduces the strength of Li-O bonds, thereby achieving more gentle and reversible lithiation culminating in enhanced cyclability of batteries. Combined with recent developments in bio-doping technologies, such fundamental understanding may lead to energy-efficient and environment-friendly synthesis of a wide variety of doped BIOX materials with customized properties.

COVID-19 is a rapidly changing and evolving situation and is extremely challenging to the humankind since it is highly infectious. Around 80% of the COVID-19 patients are asymptomatic but still need special care so that they don’t develop any further serious complications in due course of infection. The aim of present case study was to assess the effect of integrated therapy of yoga and Ayurveda on vital parameters of a COVID-19 positive asymptomatic patient. He was found to be COVID-19 positive with ORF CT value of 29.85. He remained asymptomatic throughout the course of disease. Vital parameters such as body temperature, oxygen saturation, and heart rate remained optimal throughout the course of infection. This was probably due to physical activity such as walking, yoga and Ayurvedic medications which helped in building of immunity. This further prevented progression of the disease to moderate/severe stage and there were no unanticipated events. The patient was rechecked after 8 days and was found to be COVID-19 negative. This implies that Yoga and Ayurveda treatment is effective in controlling symptoms of COVID-19 and prevention of disease progression.

More than 213 countries are effected by the global pandemic of COVID-19, which has caused death of more than 500 thousand people around the world. Even after taking all the precaution, one can still get infected with COVID-19. The whole world is working to find a vacation, where as in alternative system of medicine is focusing on Immunity Boosting helping COVID-19 effected people. The case report shows how Yoga and Ayurveda has helped a COVID-19 positive 84 year’s old man to recover.

Shock-induced detonation simulation provides critical information about high explosive (HE) materials including sensitivity, detonation velocity and reaction pathways. Here, we report a reactive force-field molecular dynamics simulation study of shock-induced decomposition of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) crystal. A flyer acts as mechanical stimuli to induce shock in the system, which initiates chemical reactions. Reaction pathway study reveals that the detonation process of TATB is distinct from those in Octahydro-1,3,5,7-tetranitro-1,3,4,7-terazocine (HMX) and 1,3,5-Trinitro-1,3,5-triazacyclohexane (RDX). Unlike the latter HE materials, N2 production in TATB occurs via three different intermolecular reaction pathways. Being an oxygen deficient HE material, a large carbon rich aggregate remains after the reaction.

Machine learning (ML) is revolutionizing scientific and engineering disciplines owing to its ability to capture hidden patterns in large amounts of data. The recent success of ML can be attributed to increasing amount of data, simulation resources, and improving understanding of statistical inference. For these reasons computational materials science is undergoing a paradigm shift. The main reason is that trial-and-error approach to materials design is inefficient: laboratory trials require a lot of time, and the results of previous trials are not utilized in a systematic fashion. A data-driven approach, which draws upon all relevant data from experiments, and reactive and quantum molecular dynamics simulations, can address these issues. The MAGICS (Materials Genome Innovation for Computational Software) Center develops to aid the synthesis of stacked layered materials by chemical vapor deposition, exfoliation, and intercalation. The identification of different phases is a classification problem and can be solved using ML techniques. We have used feed-forward neural network with three hidden layers to identify the different phases present during computational synthesis of MoSe2. Our goal is to carry out exascale MD simulations using forces for multimillion-atom quantum dynamics simulations from neural networks and deep learning using small QMD simulations.

Reactive molecular dynamics is a powerful simulation method for describing chemical reactions. Here, we introduce a new generalized polarizable reactive force-field (ReaxPQ+) model to significantly improve the accuracy by accommodating the reorganization of surrounding media. The increased computation is accelerated by (1) extended Lagrangian approach to eliminate the speed-limiting charge iteration, (2) shift-collapse computation of many-body renormalized n-tuples, which provably minimizes data transfer, (3) multithreading with round-robin data privatization, and (4) data reordering to reduce computation and allow vectorization. The new code achieves (1) weak-scaling parallel efficiency of 0.989 for 131,072 cores, and (2) eight-fold reduction of time-to-solution (T2S) compared with the original code, on an Intel Knights Landing-based computer. The reduced T2S has for the first time allowed purely computational synthesis of atomically-thin transition metal dichalcogenide layers assisted by machine learning to discover a novel synthetic pathway.

Computation on dynamic n-tuples of particles is ubiquitous in scientific computing, with an archetypal application in many-body molecular dynamics (MD) simulations. We propose a tuple-decomposition (TD) approach that reorders computations according to dynamically created lists of n-tuples. We analyze the performance characteristics of the TD approach on general purpose graphics processing units for MD simulations involving pair (n = 2) and triplet (n = 3) interactions. The results show superior performance of the TD approach over the conventional particle-decomposition (PD) approach. Detailed analyses reveal the register footprint as the key factor that dictates the performance. Furthermore, the TD approach is found to outperform PD for more intensive computations of quadruplet (n = 4) interactions in first principles-informed reactive MD simulations based on the reactive force-field (ReaxFF) method. This work thus demonstrates the viable performance portability of the TD approach across a wide range of applications.

Two-dimensional and layered MoS

Transition metal dichalcogenides (TMDC) like MoS

Wet heat treatments are widely used sterilization techniques for inactivating dangerous and resistant sporulating bacteria. The effectiveness of such treatments depends upon the thermodynamics of water uptake by the spore as well as the kinetics of phase transformations in the hydrated spore core. The mechanism behind these chemical and physical processes remains unknown because the thermodynamic properties of the spore core constituents are not well understood. Here, we use reactive molecular dynamics simulations to calculate the vibrational density of states and specific heat of hydrated calcium dipicolinate as well as the free energy of hydration based on Jarzynski's inequality. These two quantities are used to construct a phase diagram of hydrated calcium dipicolinate, indicating the extent of hydration at different pressures and temperatures, which can be used to identify potential regimes for wet-heat sterilization of bacterial spores.Wet heat treatments are widely used sterilization techniques for inactivating dangerous and resistant sporulating bacteria. The effectiveness of such treatments depends upon the thermodynamics of water uptake by the spore as well as the kinetics of phase transformations in the hydrated spore core. The mechanism behind these chemical and physical processes remains unknown because the thermodynamic properties of the spore core constituents are not well understood. Here, we use reactive molecular dynamics simulations to calculate the vibrational density of states and specific heat of hydrated calcium dipicolinate as well as the free energy of hydration based on Jarzynski's inequality. These two quantities are used to construct a phase diagram of hydrated calcium dipicolinate, indicating the extent of hydration at different pressures and temperatures, which can be used to identify potential regimes for wet-heat sterilization of bacterial spores.

Anisotropic frictional response and corresponding heating in cyclotrimethylene-trinitramine molecular crystals are studied using molecular dynamics simulations. The nature of damage and temperature rise due to frictional forces is monitored along different sliding directions on the primary slip plane, (010), and on non-slip planes, (100) and (001). Correlations between the friction coefficient, deformation, and frictional heating are established. We find that the friction coefficients on slip planes are smaller than those on non-slip planes. In response to sliding on a slip plane, the crystal deforms easily via dislocation generation and shows less heating. On non-slip planes, due to the inability of the crystal to deform via dislocation generation, a large damage zone is formed just below the contact area, accompanied by the change in the molecular ring conformation from chair to boat/half-boat. This in turn leads to a large temperature rise below the contact area.Anisotropic frictional response and corresponding heating in cyclotrimethylene-trinitramine molecular crystals are studied using molecular dynamics simulations. The nature of damage and temperature rise due to frictional forces is monitored along different sliding directions on the primary slip plane, (010), and on non-slip planes, (100) and (001). Correlations between the friction coefficient, deformation, and frictional heating are established. We find that the friction coefficients on slip planes are smaller than those on non-slip planes. In response to sliding on a slip plane, the crystal deforms easily via dislocation generation and shows less heating. On non-slip planes, due to the inability of the crystal to deform via dislocation generation, a large damage zone is formed just below the contact area, accompanied by the change in the molecular ring conformation from chair to boat/half-boat. This in turn leads to a large temperature rise below the contact area.

The mineralization of dipicolinic acid (DPA) molecules in bacterial spore cores with Ca2+ ions to form Ca-DPA is critical to the wet-heat resistance of spores. This resistance to “wet-heat” also depends on the physical properties of water and DPA in the hydrated Ca-DPA-rich protoplasm. Using reactive molecular dynamics simulations, we have determined the phase diagram of hydrated Ca-DPA as a function of temperature and water concentration, which shows the existence of a gel phase along with distinct solid-gel and gel-liquid phase transitions. Simulations reveal monotonically decreasing solid-gel-liquid transition temperatures with increasing hydration, which explains the experimental trend of wet-heat resistance of bacterial spores. Our observation of different phases of water also reconciles previous conflicting experimental findings on the state of water in bacterial spores. Further comparison with an unmineralized hydrated DPA system allows us to quantify the importance of Ca mineralization in decreasi...

The excited-state hydride release from 10-methyl-9-phenyl-9,10-dihydroacridine (PhAcrH) was investigated using steady-state and time-resolved UV/vis absorption spectroscopy. Upon excitation, PhAcrH is oxidized to the corresponding iminium ion (PhAcr(+)), while the solvent (acetonitrile/water mixture) is reduced (52% of PhAcr(+) and 2.5% of hydrogen is formed). The hydride release occurs from the triplet excited state by a stepwise electron/hydrogen-atom transfer mechanism. To facilitate the search for improved organic photohydrides that exhibit a concerted mechanism, a computational methodology is presented that evaluates the thermodynamic parameters for the hydride ion, hydrogen atom, and electron release from organic hydrides.

The redox properties of model chromophores from the green fluorescent protein family are characterized computationally using density functional theory with a long-range corrected functional, the equation-of-motion coupled-cluster method, and implicit solvation models. The analysis of electron-donating abilities of the chromophores reveals an intricate interplay between the size of the chromophore, conjugation, resonance stabilization, presence of heteroatoms, and solvent effects. Our best estimates of the gas-phase vertical/adiabatic detachment energies of the deprotonated (i.e., anionic) model red, green, and blue chromophores are 3.27/3.15, 2.79/2.67, and 2.75/2.35 eV, respectively. Vertical/adiabatic ionization energies of the respective protonated (i.e., neutral) species are 7.64/7.35, 7.38/7.15, and 7.70/7.32 eV, respectively. The standard reduction potentials (E(red)(0)) of the anionic (Chr•/Chr–) and neutral (Chr+•/Chr) model chromophores in acetonitrile are 0.34/1.40 V (red), 0.22/1.24 V (green), and −0.12/1.02 V (blue), suggesting, counterintuitively, that the red chromophore is more difficult to oxidize than the green and blue ones (in both neutral and deprotonated forms). The respective redox potentials in water follow a similar trend but are more positive than the acetonitrile values.