Multimillion-atom Molecular Dynamics Research Articles

Unexpected Observation of Disorder and Multiple Phase-Transition Pathways in Shock-Compressed Zr.

The response of materials under dynamic compression involves a complex interplay of various deformation mechanisms aimed at relieving shear stresses, yielding a remarkable diversity in material behavior. In this Letter, we utilize femtosecond x-ray diffraction coupled with nanosecond laser compression to reveal an intricate competition between multiple shear-relieving mechanisms within an elemental metal. Our observations in shocked-compressed single-crystal Zr indicate a disorder-mediated shear relaxation at lower pressures. Above the phase-transition pressure, we observe the increasing contribution of structural phase transition in relieving shear stress. We detect not one but three concurrent pathways during the transition from the hcp to a hex-3 structure. These complex dynamics are partially corroborated through multimillion-atom molecular dynamics simulations employing a machine-learned interatomic potential. Our observation of multiple concurrent pathways and disorder during shock compression underscore the far greater intricacies in the dynamic response of metals than previously assumed.

From Molecular Constraints to Macroscopic Dynamics in Associative Networks Formed by Ionizable Polymers: A Neutron Spin Echo and Molecular Dynamics Simulations Study.

The association of ionizable polymers strongly affects their motion in solutions, where the constraints arising from clustering of the ionizable groups alter the macroscopic dynamics. The interrelation between the motion on multiple length and time scales is fundamental to a broad range of complex fluids including physical networks, gels, and polymer-nanoparticle complexes where long-lived associations control their structure and dynamics. Using neutron spin echo and fully atomistic, multimillion atom molecular dynamics (MD) simulations carried out to times comparable to that of chain segmental motion, the current study resolves the dynamics of networks formed by suflonated polystryene solutions for sulfonation fractions 0 ≤ f ≤ 0.09 across time and length scales. The experimental dynamic structure factors were measured and compared with computational ones, calculated from MD simulations, and analyzed in terms of a sum of two exponential functions, providing two distinctive time scales. These time constants capture confined motion of the network and fast dynamics of the highly solvated segments. A unique relationship between the polymer dynamics and the size and distribution of the ionic clusters was established and correlated with the number of polymer chains that participate in each cluster. The correlation of dynamics in associative complex fluids across time and length scales, enabled by combining the understanding attained from reciprocal space through neutron spin echo and real space, through large scale MD studies, addresses a fundamental long-standing challenge that underline the behavior of soft materials and affect their potential uses.

Extreme Metastability of Diamond and its Transformation to the BC8 Post-Diamond Phase of Carbon.

Diamond possesses exceptional physical properties due to its remarkably strong carbon-carbon bonding, leading to significant resilience to structural transformations at very high pressures and temperatures. Despite several experimental attempts, synthesis and recovery of the theoretically predicted post-diamond BC8 phase remains elusive. Through quantum-accurate multimillion atom molecular dynamics (MD) simulations, we have uncovered the extreme metastability of diamond at very high pressures, significantly exceeding its range of thermodynamic stability. We predict the post-diamond BC8 phase to be experimentally accessible only within a narrow high pressure-temperature region of the carbon phase diagram. The diamond to BC8 transformation proceeds through premelting followed by BC8 nucleation and growth in the metastable carbon liquid. We propose a double-shock compression pathway for BC8 synthesis, which is currently being explored in experiments at the National Ignition Facility.

Supersonic Impact Response of Polymer Thin Films via Large-Scale Atomistic Simulations.

Recent nanoscale ballistic tests have shown the applicability of nanomaterials for ballistic protection but have raised questions regarding the nanoscale structure-property relationships that contribute to the ballistic response. Herein, we report on multimillion-atom reactive molecular dynamics simulations of the supersonic impact, penetration, and failure of polyethylene (PE) and polystyrene (PS) ultrathin films. The simulated specific penetration energy (Ep*) versus impact velocity predicts to within 15% the experimentally determined Ep* for PS. For impact velocities less than 1 km s-1, a crazing/petalling failure mode is observed due to chain disentanglement, transitioning to fragmentation coupled with large amounts of adiabatic heating at velocities greater than 1 km s-1. Interestingly, the high entanglement density of PE provides enhanced penetration resistance at low velocities, whereas increased adiabatic heating in PS promotes greater penetration resistance at elevated velocities. By understanding nanoscale mechanisms of energy absorption, nanomaterials can be designed to provide superior penetration resistance.

Defect Healing in Layered Materials: A Machine Learning-Assisted Characterization of MoS2 Crystal Phases.

Monolayer MoS2 is an outstanding candidate for a next-generation semiconducting material because of its exceptional physical, chemical, and mechanical properties. To make this promising layered material applicable to nanostructured electronic applications, synthesis of a highly crystalline MoS2 monolayer is vitally important. Among different types of synthesis methods, chemical vapor deposition (CVD) is the most practical way to synthesize few- or mono-layer MoS2 on the target substrate owing to its simplicity and scalability. However, synthesis of a highly crystalline MoS2 layer remains elusive. This is because of the number of grains and defects unavoidably generated during CVD synthesis. Here, we perform multimillion-atom reactive molecular dynamics (RMD) simulations to identify an origin of the grain growth, migration, and defect healing process on a CVD-grown MoS2 monolayer. RMD results reveal that grain boundaries could be successfully repaired by multiple heat treatments. Our work proposes a new way of controlling the grain growth and migration on a CVD-grown MoS2 monolayer.

Molecular Simulation of MoS2 Exfoliation

A wide variety of two-dimensional layered materials are synthesized by liquid-phase exfoliation. Here we examine exfoliation of MoS2 into nanosheets in a mixture of water and isopropanol (IPA) containing cavitation bubbles. Using force fields optimized with experimental data on interfacial energies between MoS2 and the solvent, multimillion-atom molecular dynamics simulations are performed in conjunction with experiments to examine shock-induced collapse of cavitation bubbles and the resulting exfoliation of MoS2. The collapse of cavitation bubbles generates high-speed nanojets and shock waves in the solvent. Large shear stresses due to the nanojet impact on MoS2 surfaces initiate exfoliation, and shock waves reflected from MoS2 surfaces enhance exfoliation. Structural correlations in the solvent indicate that shock induces an ice VII like motif in the first solvation shell of water.

Parallel Large-Scale Molecular Dynamics Simulation Opens New Perspective to Clarify the Effect of a Porous Structure on the Sintering Process of Ni/YSZ Multiparticles.

Ni sintering in the Ni/YSZ porous anode of a solid oxide fuel cell changes the porous structure, leading to degradation. Preventing sintering and degradation during operation is a great challenge. Usually, a sintering molecular dynamics (MD) simulation model consisting of two particles on a substrate is used; however, the model cannot reflect the porous structure effect on sintering. In our previous study, a multi-nanoparticle sintering modeling method with tens of thousands of atoms revealed the effect of the particle framework and porosity on sintering. However, the method cannot reveal the effect of the particle size on sintering and the effect of sintering on the change in the porous structure. In the present study, we report a strategy to reveal them in the porous structure by using our multi-nanoparticle modeling method and a parallel large-scale multimillion-atom MD simulator. We used this method to investigate the effect of YSZ particle size and tortuosity on sintering and degradation in the Ni/YSZ anodes. Our parallel large-scale MD simulation showed that the sintering degree decreased as the YSZ particle size decreased. The gas fuel diffusion path, which reflects the overpotential, was blocked by pore coalescence during sintering. The degradation of gas diffusion performance increased as the YSZ particle size increased. Furthermore, the gas diffusion performance was quantified by a tortuosity parameter and an optimal YSZ particle size, which is equal to that of Ni, was found for good diffusion after sintering. These findings cannot be obtained by previous MD sintering studies with tens of thousands of atoms. The present parallel large-scale multimillion-atom MD simulation makes it possible to clarify the effects of the particle size and tortuosity on sintering and degradation.

Integrating Ultrafast Coherent Diffractive Imaging and Atomistic Simulations to Investigate Externally Stimulated Metallic Nanocrystals

Despite the increasing role of nanomaterials in technology, the mechanical and dynamical properties of single nanoparticles at picosecond timescales are not well understood. In particular, core-shell nanocrystals are an important class of nanoparticles for catalysis, biomedical and energy applications. The effect of the nanoscale interface between the core and shell material on coherent lattice vibrations (phonons) is yet to be investigated in detail. Understanding the temporal behavior of such nanomaterials under conditions of external thermal stimulation is crucially important for energy research. In addition, observing ultrafast lattice distortions can provide key insights into the behavior of nanomaterials and nanoscale interfaces. Recently, experimental techniques have evolved to conduct time-dependent lattice dynamics measurements in nanomaterials. In particular, Bragg Coherent Diffraction Imaging (BCDI) in conjunction with optical pump-probe experiments via ultrafast x-ray lasers has been used to directly image the generation and subsequent evolution of coherent acoustic phonons within nanocrystals. In particular, experiments on bimetal (Au/Al) core-shell nanocrystals have revealed inhomogeneous effects in the lattice breathing upon heating with femtosecond x-ray lasers. Conventional theoretical models cannot be used to explain the physics of the phenomena in such non-equilibrium environments that involve extreme heat fluxes and temperature gradients. Atomistic molecular dynamics (MD) simulation is an appropriate technique to investigate lattice dynamics in such environments, particularly in core-shell structures where interfacial effects can play an important role in phonon scattering. With the convergence of time and length scales accessible by both experiments and simulations, we are now able to integrate experimental observations with multi-million atom MD simulations to enhance the fundamental understanding of materials behavior under external stimulation. In this talk, we demonstrate the workflow to integrate ultrafast time-resolved coherent diffractive imaging with large-scale atomistic molecular dynamics simulations to investigate lattice dynamics in externally stimulated core-shell bimetallic nanocrystals. We will focus, primarily, on the MD simulations performed on core-shell bimetallic nanocrystals under the influence of extreme heat fluxes. We explore the vibrational modes that dominate lattice breathing and look into the effect the nanoparticle size and shape have on the same. In addition, we attempt to identify the origin of the inhomogeneous effects, observed experimentally, in the lattice breathing of core-shell structures. Figure 1

Quantum Molecular Dynamics Validation of Nanocarbon Synthesis by High-Temperature Oxidation of Nanoparticles

ABSTRACTThis study uses ab initio quantum molecular dynamics (QMD) simulations to validate multimillion-atom reactive molecular dynamics (RMD) simulations, and predicts unexpected condensation of carbon atoms during high-temperature oxidation of silicon-carbide nanoparticles (nSiC). For the validation process, a small nSiC in oxygen environment is chosen to perform QMD simulation. The QMD results provide the number of Si-O and C-O bonds as a function of time. RMD simulation is then performed under the identical condition. The time evolutions of different bonds are compared between the QMD and RMD simulations. We observe the condensation of large number of C-cluster nuclei into larger C clusters in both simulations, thereby validating RMD. Furthermore, we use the QMD simulation results as an input to a multi-objective genetic algorithm to train the RMD force-field parameters. The resulting force field far better reproduces the ground-truth QMD simulation results.

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.

Role of grain size on the martensitic transformation and ultra-fast superelasticity in shape memory alloys

We use multi-million-atom molecular dynamics (MD) simulations with an embedded atom model potential parameterized for NiAl to study temperature- and stress-induced martensitic phase transformations in nanocrystalline shape memory alloys. Nucleation of the martensite phase occurs in the grain interiors and grows outward up to the point where further transformation is hindered by the constraints imposed by neighboring grains. Decreasing grain size inhibits the transformation process and the temperature-induced transformation is completely suppressed for samples with average grain sizes of 7.5nm and less. Interestingly, mechanical loads can induce the martensitic transformation in samples with ultra-fine grains and, quite surprisingly, the sample with 7.5nm grain size exhibits improved, ultra-fast, superelasticity as compared with its coarser grain counterparts. The simulations provide a picture of the processes that govern the performance and fundamental limits of nanocrystalline shape memory alloys with atomistic resolution.

Combined Hydrodynamic and Diffraction Simulations of Femtosecond X-ray Scattering from Laser-Shocked Crystals

We describe a simple hydrocode based on a two-step integration scheme that models the evolution of elastic and plastic strains in crystals subject to rapid laser-shock loading. By monitoring the elastic strains during plastic flow we track the rotation and spacing of lattice planes within the polycrystalline sample, and can thus predict the signal that would be produced by x-ray diffraction in a variety of experimental geometries. By employing a simple Taylor-Orowan dislocation model we simulate diffraction patterns in a Debye-Scherrer geometry to track the orthogonal strain states within a laser-shocked sample. The yielding rate is approximately matched to those observed in multi-million atom molecular dynamics (MD) simulations, allowing movies to be made of the diffraction images that would be seen in a real experimental geometry, and illustrating the pertinent experimental requirements, including target texture. Judicious choice of geometry allows clear demarcation of the initial elastic response of the target to be made from the subsequent plastic relaxation. We discuss the simulations in the context of the novel experimental capabilities that have recently become available with the advent of 4th generation light sources, which allow single-shot diffraction with sub-100-fsec resolution.

Size effect on the oxidation of aluminum nanoparticle: Multimillion-atom reactive molecular dynamics simulations

The size effect in the oxidation of aluminum nanoparticles (Al-NPs) has been observed experimentally; however, the mechano-chemistry and the atomistic mechanism of the oxidation dynamics remain elusive. We have performed multimillion atom reactive molecular dynamics simulations to investigate the oxidation dynamics of Al-NPs (diameters, D = 26, 36, and 46 nm) with the same shell thickness (3 nm). Analysis of alumina shell structure reveals that the shell of Al-NPs does not break or shatter, but only deforms during the oxidation process. The deformation depends slightly on the size of Al-NP. This reaction from the oxidation heats the Al-NP to a temperature of T > 5000 K. Ejection of Al atoms from shell starts earlier in small Al-NPs—at t0 = 0.18, 0.28 and 0.42 ns for D = 26, 36 and 46 nm, when they all have the same shell temperature of 2900 K. As the oxidation dynamics proceeds, the total system temperature (including the environmental oxygen) increases monotonically; however, the time derivative of the total temperature, (dTsystem/dt), reaches a maximum at t1 = 0.20, 0.32 and 0.51 ns for D = 26, 36 and 46 nm. At this peak value of (dTsystem/dt), the shell temperature for the three Al-NPs are 3100 K, 3300 K, and 3500 K, respectively. The time lag between t1 and t0 is 0.02, 0.04 and 0.09 ns for D = 26, 36 and 46 nm clearly indicates the size effect.

Nanoindentation response of substrate-attached and freestanding single-crystalline Fe7Pd3 ferromagnetic shape memory thin films around the martensite transition: The impact of constraints and beyond

Ferromagnetic shape memory alloys offer great potential in the fields of engineering and medical sciences as integrated actuators or sensors. However, their physical properties, when miniaturized and connected to a substrate or mounted as active elements, are still insufficiently understood. The present work explores the impact of miniaturization and external boundaries on one of the most central features, namely twin boundary mobility. By measuring the nanoindentation response of substrate-attached films and freestanding foils around the austenite↔martensite transformation temperature in classical indentation, as well as dynamical quasi-continuous stiffness-measurement mode, dramatic softening and increasing recovery after film lift-off are discovered. The atomistics of these findings are explored with the help of classical multimillion-atom molecular dynamics simulations on indentation into martensite and austenite films on rigid or flexible substrates, as well as freestanding or mounted thin foils. They clearly demonstrate how substrate or lateral constrains hinder twin boundary motion, while complete untwinning only prevails in the presence of a flexible substrate or completely free foils. Experimentally observed pop-in events can be rationalized as local austenite→martensite transitions. Surface softness, which is observed by low indentation moduli, when compared to predictions from the bulk elastic constants, might indicate a more fundamental scenario close to the martensite transformation.

Collective oxidation behavior of aluminum nanoparticle aggregate

Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. The calculated speed of penetration is 54 m/s, which is within the range of experimentally measured flame propagation rates.

Poration of Lipid Bilayers by Shock-Induced Nanobubble Collapse

Sonoporation is a promising noninvasive drug- and gene-delivery approach, in which cavitation bubbles generated by ultrasound are used to enhance the cell membrane permeability. We have performed multimillion-atom molecular dynamics (MD) simulations to study the impact of shock waves on nanobubbles in the vicinity of a dipalmitoylphosphatidylcholine (DPPC) bilayer. The MD simulations reveal that the nanojet impact generates shear flow of water on bilayer leaflets and pressure gradients across them, which transiently enhance the bilayer permeability by creating nanopores and water molecules translocation across the bilayer. Effects of nanobubble size and temperature on the porosity of lipid bilayers will be discussed.Fig.: Nanojet (blue, green and red are velocity streamlines) impact deforming the lipid membrane (yellow). The nanopore created in the membrane (blue) is shown in the bottom inset. The top inset shows the time evolution of lateral flow on the lipid membrane surface.View Large Image | View Hi-Res Image | Download PowerPoint Slide

Molecular Dynamics Study of Size Dependence of Combustion of Aluminum Nanoparticles

ABSTRACTOxidation dynamics of three different sizes (26, 36 and 46 nm) of single aluminum nanoparticle (ANP) in oxygen environment are studied using multimillion-atom reactive molecular dynamics simulations. In the simulation, each aluminum nanoparticle is coated with an amorphous alumina shell of the same thickness (3 nm), and is ignited by heating the nanoparticle to 1100 K. The metallic aluminum and ceramic alumina are modeled by the Voter- Chen embedded atom model and the interatomic potential by Vashishta et al., respectively. Energy release rate and atomistic-level details of combustion of these single aluminum nanoparticles are investigated, along with the effect of nanoparticle size. The onset temperature of shell Al ejection is found to be independent of the ANP size, whereas the onset time of ejection and the time delay to the highest temperature change rate dT/dt depend on the size.

Poration of lipid bilayers by shock-induced nanobubble collapse

We investigate molecular mechanisms of poration in lipid bilayers due to shock-induced collapse of nanobubbles. Our multimillion-atom molecular dynamics simulations reveal dynamics of nanobubble shrinkage and collapse, leading to the formation and penetration of nanojets into lipid bilayers. The nanojet impact generates shear flow of water on bilayer leaflets and pressure gradients across them, which transiently enhance the bilayer permeability by creating nanopores through which water molecules translocate rapidly across the bilayer. Effects of nanobubble size and temperature on the porosity of lipid bilayers are examined.

Effects of oxide-shell structures on the dynamics of oxidation of Al nanoparticles

Effects of the crystalline and amorphous structure of alumina shells on the dynamics of oxidation of an aluminum nanoparticle (ANP) are studied using multimillion-atom molecular dynamics simulations. With an amorphous shell, formation of oxidized nanocluster fragments produced by the shattering of the shell, combined with the fragmentation and dispersion of the nanoparticle, catalyzes faster oxidation reactions. Consequently, the energy release rate of an ANP with an amorphous shell is much higher than that with a crystalline shell. Analysis on the formation of oxygen-rich fragments further confirms an enhanced reaction rate with an amorphous shell.

Towards a Computational Model of Lignocellulose: Molecular Simulation of Lignin

Atomic-detailed computational models of lignocellulose can complement experiments in understanding its structure and dynamics. Here, we present results of Molecular Dynamics simulation of the plant cell wall polymer lignin. Polymer theory is employed to interpret these results. Finally the steps towards a realistic model of lignocellulose are discussed.1. L. Petridis and J.C. Smith (2009); A molecular mechanics force field for lignin; Journal of Computational Chemistry 30 457-4672. R. Shulz, B. Lindner, L. Petridis and J.C. Smith (in print); Scaling of Multimillion-atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer; DOI: 10.1021/ct900292r