Pankaj Rajak

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations.

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10(6)-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.

Nanoscopic mechanisms of singlet fission in amorphous molecular solid

Fission of a spin-singlet exciton into two triplet excitons, if realized in disordered organic solid, could revolutionize low-cost fabrication of efficient solar cells. Here, a divide-conquer-recombine approach involving nonadiabatic quantum molecular dynamics and kinetic Monte Carlo simulations identifies the key molecular geometry and exciton-flow-network topology for singlet-fission “hot spots” in amorphous diphenyl tetracene, where fission occurs preferentially. The simulation reveals the molecular origin of experimentally observed two time scales in exciton population dynamics and may pave a way to nanostructural design of efficient solar cells from first principles.

Computational Synthesis of MoS2 Layers by Reactive Molecular Dynamics Simulations: Initial Sulfidation of MoO3 Surfaces

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 early stage MoS2 synthesis, which are consistent with experimental observations and existing theoretical literature, provide valuable input for guided rational synthesis of MoS2 and other TMDC crystals by the CVD process.

Nanocarbon synthesis by high-temperature oxidation of nanoparticles

High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp2 carbons with pentagonal and heptagonal defects. This work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites.

Interfacial design for reducing charge recombination in photovoltaics

Key to high power conversion efficiency of organic solar cells is to minimize charge recombination (CR) at electron donor/acceptor interfaces. Here, nonadiabatic quantum molecular dynamics simulation shows how the interfacial structure can be controlled by molecular design at acene/C60 interfaces to suppress CR. Orders-of-magnitude reduction of the CR rate is achieved through drastic modification of interfacial structure by attaching phenyl groups to tetracene. This finding confirms a molecular design principle for efficient organic photovoltaics underlying a recent experimental study.

Structural Phase Transformation in Strained Monolayer MoWSe2 Alloy

Two-dimensional (2D) materials exhibit different mechanical properties from their bulk counterparts owing to their monolayer atomic thickness. Here, we have examined the mechanical behavior of 2D molybdenum tungsten diselenide (MoWSe2) precipitation alloy grown using chemical vapor deposition and composed of numerous nanoscopic MoSe2 and WSe2 regions. Applying a bending strain blue-shifted the MoSe2 and WSe2 A1g Raman modes with the stress concentrated near the precipitate interfaces predominantly affecting the WSe2 modes. In situ local Raman measurements suggested that the crack propagated primarily thorough MoSe2-rich regions in the monolayer alloy. Molecular dynamics (MD) simulations were performed to study crack propagation in an MoSe2 monolayer containing nanoscopic WSe2 regions akin to the experiment. Raman spectra calculated from MD trajectories of crack propagation confirmed the emergence of intermediate peaks in the strained monolayer alloy, mirroring experimental results. The simulations revealed that the stress buildup around the crack tip caused an irreversible structural transformation from the 2H to 1T phase both in the MoSe2 matrix and WSe2 patches. This was corroborated by high-angle annular dark-field images. Crack branching and subsequent healing of a crack branch were also observed in WSe2, indicating the increased toughness and crack propagation resistance of the alloyed 2D MoWSe2 over the unalloyed counterparts.

Gel phase in hydrated calcium dipicolinate

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...

Multiobjective genetic training and uncertainty quantification of reactive force fields

The ReaxFF reactive force-field approach has significantly extended the applicability of reactive molecular dynamics simulations to a wide range of material properties and processes. ReaxFF parameters are commonly trained to fit a predefined set of quantum-mechanical data, but it remains uncertain how accurately the quantities of interest are described when applied to complex chemical reactions. Here, we present a dynamic approach based on multiobjective genetic algorithm for the training of ReaxFF parameters and uncertainty quantification of simulated quantities of interest. ReaxFF parameters are trained by directly fitting reactive molecular dynamics trajectories against quantum molecular dynamics trajectories on the fly, where the Pareto optimal front for the multiple quantities of interest provides an ensemble of ReaxFF models for uncertainty quantification. Our in situ multiobjective genetic algorithm workflow achieves scalability by eliminating the file I/O bottleneck using interprocess communications. The in situ multiobjective genetic algorithm workflow has been applied to high-temperature sulfidation of MoO3 by H2S precursor, which is an essential reaction step for chemical vapor deposition synthesis of MoS2 layers. Our work suggests a new reactive molecular dynamics simulation approach for far-from-equilibrium chemical processes, which quantitatively reproduces quantum molecular dynamics simulations while providing error bars.Molecular dynamics: multi-objective genetic algorithms for training and uncertainty quantificationMulti-objective genetic algorithms allow training and uncertainty quantification of force-field parameters with minimal modifications of molecular dynamics codes. A team led by Aiichiro Nakano at University of Southern California used an algorithm based on reactive molecular dynamics (RMD) simulations for the training of reactive force-field parameters and uncertainty quantification of simulated quantities of interest. Chemical vapor deposition synthesis of MoS2 monolayer was set as a specific example, and force-field parameters were trained against quantum molecular dynamics (QMD) simulations. Starting from a 128-atom MoO3–H2S system, the reaction dynamics were investigated by estimating the numbers of H–S, Mo–O, and Mo–S bonds as a function of time during the QMD simulations. By comparing these quantities of interest with those obtained in the RMD simulations, it was found that RMD can quantitatively reproduce QMD within an error bar.

Free energy of hydration and heat capacity of calcium dipicolinate in Bacillus spore cores

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 Jarzynskis 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 Jarzynskis 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 heating and defect generation in cyclotrimethylene-trinitramine molecular crystals

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.