Subodh Tiwari

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.

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...

Acceleration of Dynamic n-Tuple Computations in Many-Body Molecular Dynamics

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.

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.

Energetic Performance of Optically Activated Aluminum/Graphene Oxide Composites

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 efficient additive to improve the energetic performance of micron-sized Al particles, enabling micron-sized Al to be ignited by optical activation and promoting the combustion of Al in air.

Reactivity of Sulfur Molecules on MoO3 (010) Surface

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 precursors for CVD synthesis of MoS2 layers.