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We combine on-the-fly trajectory surface hopping simulations and the doorway–window representation of nonlinear optical response functions to create an efficient protocol for the evaluation of time- and frequency-resolved fluorescence (TFRF) spectra and anisotropies of the realistic polyatomic systems. This approach gives the effective description of the proper (e.g., experimental) pulse envelopes, laser field polarizations, and the proper orientational averaging of TFRF signals directly from the well-established on-the-fly nonadiabatic dynamic simulations without extra computational cost. To discuss the implementation details of the developed protocol, we chose cis-azobenzene as a prototype to simulate the time evolution of the TFRF spectra governed by its nonadiabatic dynamics. The results show that the TFRF is determined by the interplay of several key factors, i.e., decays of excited-state populations, evolution of the transition dipole moments along with the dynamic propagation, and scaling factor of the TFRF signals associated with the cube of emission frequency. This work not only provides an efficient and effective approach to simulate the TFRF and anisotropies of realistic polyatomic systems but also discusses the important relationship between the TFRF signals and the underlining nonadiabatic dynamics. [ABSTRACT FROM AUTHOR]

This article presents methodological advances in the state-of-the-art for making time-dependent, thermochemical measurements within kilogram-scale explosive post-detonation fireballs utilizing tunable laser absorption spectroscopy. This measurement capability is critical for validating multi-scale, multi-physics models of post-detonation dynamics. The technique is based on hardened gauges built around rapidly-tunable lasers and custom post-processing algorithms that provide quantitative thermochemical data interior to large and opaque explosive fireballs. The authors present a holistic overview of the technique including gauge design, the laser absorption diagnostic, and the custom data processing algorithms. Additionally, fielding high-bandwidth laser absorption probes at stand-off ranges presents new challenges in data processing that must compensate for long distance signal transmission effects. We highlight representative data from a hardened gauge measurement at 0.81 m stand-off from a 2.78 kg LX-14 explosive charge detonated in an outdoor test arena. We discuss progress in all-optical measurement of temperature, pressure, and water vapor number density at a 100 kHz repetition rate during the first 10 ms of the fireball evolution. We conclude the article with a brief discussion on our current approach for comparing hardened gauge measurements with computational fluid dynamic simulations. [ABSTRACT FROM AUTHOR]

Modelling of many real-world processes, such as drug delivery, wastewater treatment, and pharmaceutical production, requires accurate descriptions of the dynamics of hard particles confined in complicated domains. In particular, when modelling sedimentation processes or systems with driven flows, it is important to accurately capture volume exclusion effects. This work applies Dynamic Density Functional Theory to the evolution of a particle density under diffusion, external forces, particle–particle interaction, and volume exclusion. Using a spectral element framework, for the first time it is possible to include all of these effects in dynamic simulations on complex domains. Moreover, this allows one to apply complicated no-flux, and other non-local, non-linear, boundary conditions. The methodology is also extended to control problems, addressing questions of how to enhance production set-up in industrially-motivated processes. In this work the relevant models are introduced, numerical methods are discussed, and several example problems are solved to demonstrate the methods' versatility. It is shown that incorporating volume exclusion is crucial for simulation accuracy and we illustrate that the choice of boundary conditions significantly impacts the dynamics. [ABSTRACT FROM AUTHOR]

Parkinson's disease is accompanied by the presence of amyloids in the brain that are formed of α-synuclein chains. The correlation between COVID-19 and the onset of Parkinson's disease led to the idea that amyloidogenic segments in SARS-COV-2 proteins can induce aggregation of α-synuclein. Using molecular dynamic simulations, we show that the fragment FKNIDGYFKI of the spike protein, which is unique for SARS-COV-2, preferentially shifts the ensemble of α-synuclein monomer toward rod-like fibril seeding conformations and, at the same time, differentially stabilizes this polymorph over the competing twister-like structure. Our results are compared with earlier work relying on a different protein fragment that is not specific for SARS-COV-2. [ABSTRACT FROM AUTHOR]

In this work, we investigate the water capture process for functionalized carbon nanocones (CNCs) through molecular dynamic simulations in the following three scenarios: a single CNC in contact with a reservoir containing liquid water, a single CNC in contact with a water vapor reservoir, and a combination of more than one CNC in contact with vapor. We found that water flows through the nanocones when in contact with the liquid reservoir if the nanocone tip presents hydrophilic functionalization. In contact with steam, we observed the formation of droplets at the base of the nanocone only when hydrophilic functionalization is present. Then, water flows through in a linear manner, a process that is more efficient than that in the liquid reservoir regime. The scalability of the process is tested by analyzing the water flow through more than one nanocone. The results suggest that the distance between the nanocones is a fundamental ingredient for the efficiency of water harvesting. [ABSTRACT FROM AUTHOR]

In this paper, we investigate the ejection production from twice-shocked Sn using molecular dynamic simulations in regimes where the metal undergoes complete shock melting after the first shock. A new description form of a bubble shape is proposed to fit the interface during the whole stage, which overcomes the inapplicability of the flycut profile in later stages. We then explore the ejection on second shock with the dimensionless intervals of ∼3.8 and ∼96 between the two shocks. Surprisingly, the results show that the ejecta model can well predict the second ejecta mass with a shock interval of ∼3.8 while far underestimated that with a shock interval of ∼96. We find that in the presence of the first ejecta, the high-speed secondary interface interacts with the low-speed first ejecta, resulting in the movement of liquid metals to the secondary ejecta, thereby promoting the increase of secondary ejecta mass. These findings are further validated by our smoothed particle hydrodynamics simulations at a macroscale. [ABSTRACT FROM AUTHOR]

Large-scale nonequilibrium molecular dynamics simulation is used to study the effect of grain size and Cr segregation at the twin boundary (TB) on the spalling fracture mechanism of nickel based alloys. In particular, loading waves are designed so that the maximum tensile stress first appears in the grain interior for all the crystals with different grain sizes. In contrast to traditional understandings, no monotonous relationship between the spall strength and the grain size appears in our results. The spall strength is found to depend on the wave attenuation distance measured from the first maximum tensile stress position to the spalled TB as well as the accompanied microstructure evolutions. The number of spalling plane increases with the increase of TB or the decrease of the grain size. As the grain size continues to decrease, a greater impact strength is required to cause spallation fracture at multiple TBs. In this case, the spall strength becomes insensitive to the first maximum tensile stress position. With the increment of solute atom concentration, the number of the spalling plane increases when the solution is segregated. But it decreases when the solution is uniformly distributed. Such a result is explained by segregation-enhanced energy dissipation and interactions between the waves and the microstructures nearby TBs. In particular, the shock wave would induce a local lattice reorientation nearby the TB depending on its segregation degree and the lattice reorientation would modify the slip manner of stacking faults and, thus, affect void nucleation and growth. The lattice reorientation would also contribute to the generation of sub-grain boundaries inside the grains in terms of the movement of stacking faults. Void nucleation at the sub-GB is the main cause of fracture at the grain interior. [ABSTRACT FROM AUTHOR]

In the current study, a dynamic layer freeze desalination system is simulated numerically. The computational domain is a two-dimensional rectangular channel which contains inlet and outlet flows, and the simulation is performed using computational fluid dynamics. A pre-concentrated mixture is considered as the feed solution with an initial temperature and concentration of 257 K and 0.2 kg/kg, respectively. In this work, since the simulation parameters such as temperature and species mass fraction have high importance across the entire domain, the k–ω shear stress transport turbulence model was selected. A parametric study on the effect of the heat flux of the cold wall on the ice salinity and desalination rate is performed using three cases with heat fluxes of − 1000 , − 1500 , and − 3000 W m − 2 . It is observed that the ice generation speed in the case with a heat flux of − 3000 W m − 2 is 3.28 times greater compared to the case with − 1000 W m − 2 and its desalination rate is only 2.59 % lower. The effect of the inlet velocity on the mentioned parameters is also investigated. It is observed that the cases with turbulent flow have approximately 19 % and 23 % lower ice salinity compared to the case with laminar flow. [ABSTRACT FROM AUTHOR]

Investigating immiscible displacement in fractured porous media is essential for understanding the two-phase flow behavior within pores and fractures. In this work, a three-dimensional pore-fracture network model was developed to address the influence of fracture on flow patterns and to characterize fracture-matrix crossflow under different flow conditions. Sensitivity studies at a wide range of viscosity ratios and capillary numbers underscored that fracture significantly influenced flow patterns in the capillary fingering zone. Fracture with an advantageous path effect in the displacement direction caused a shift in the boundary of capillary fingering zone toward an increase in capillary numbers. As fracture aperture decreased and aspect ratio increased, there was a discernible decline in the crossflow rate. When fracture aperture equaled average matrix throat diameter, fracture lose advantageous path effect in compact displacement zone but retained it in viscous fingering and capillary fingering zones. Distinct matrix-fracture crossflow development processes were observed in different zones: in cross zone, following displacement breakthrough, the crossflow underwent a "long-term" process to attain stability. Viscous fingering zone promptly achieved stability post-breakthrough, whereas both capillary fingering and compact displacement zones had already reached a stable state before breakthrough. Nonlinear variations in breakthrough saturation were observed in the cross zone between compact displacement and capillary fingering zones. The control process of immiscible displacement exhibited variability under different flow conditions: compact displacement zone was characterized by matrix dominance, viscous fingering zone was jointly controlled by matrix displacement and fracture-matrix crossflow, and capillary fingering zone was primarily governed by fracture-matrix crossflow. These findings enhance scholarly comprehension of immiscible displacement behavior in fractured porous media. [ABSTRACT FROM AUTHOR]

Capillary wicking characteristics play an important role in two-phase thermal management devices including heat pipes and vapor chambers, yet three-dimensional (3D) pore-scale simulations of the dynamic capillary wicking process on various micro-structured surfaces have been rare. In this paper, we conduct 3D pore-scale simulations of capillary wicking on three commonly used micro-structured wicks including micro-pillar array, micro-channel, and sintered particles. The micro-scale liquid propagation dynamics and the "stick-slip" behavior of the propagating liquid front are captured using a 3D pseudo-potential multiple-relaxation-time lattice Boltzmann method. Based on the Lucus–Washburn approach and a work-energy approach, we theoretically analyze wickabilities of different micro-structured wicks. Effects of wick geometry and structural parameters on the capillary wicking characteristics are discussed. We demonstrate that an optimal pillar pitch distance exists, which maximizes the wickability of the micro-pillar array. We show that when the porosity is relatively low, the wickability of the micro-channel is higher than that of the micro-pillar array and the sintered particles. When the porosity is large, however, the sintered particles exhibit higher wickability than the micro-pillar array and the micro-channel. We also demonstrate that the capillary pressure of the sintered particles is always higher than that of the micro-pillar array and the micro-channel throughout the porosity range investigated. The numerical simulation results are compared with theoretical predictions. Findings in this work provide guidelines for the designs of porous wick in various two-phase thermal management systems for high heat flux devices. [ABSTRACT FROM AUTHOR]

Rotational–translational decoupling in systems near Tg, in which translational diffusion is apparently enhanced relative to rotation, has been observed in ensemble and single molecule experiments and has been linked to dynamic heterogeneity. Here, simulations of single molecules experiencing homogeneous diffusion and static and dynamic heterogeneous diffusion are performed to clarify the contributions of heterogeneity to such enhanced translational diffusion. Results show that time-limited trajectories broaden the distribution of diffusion coefficients in the presence of homogeneous diffusion but not when physically reasonable degrees of static heterogeneity are present. When dynamic heterogeneity is introduced, measured diffusion coefficients uniformly increase relative to input diffusion coefficients, and the widths of output distributions decrease, providing support for the idea that dynamic heterogeneity can drive apparent translational enhancement. Among simulations with dynamic heterogeneity, when the frequency of dynamic exchange is correlated with the initial diffusion coefficient, the measured diffusion coefficient behavior as a function of observation time matches that seen experimentally, the only set of simulations explored in which this occurs. Taken together with experimental results, this suggests that enhanced translational diffusion in glassy systems occurs through dynamic exchange consistent with wide underlying distributions of diffusion coefficients and exchange coupled to local spatiotemporal dynamics. [ABSTRACT FROM AUTHOR]

The science and engineering communities have significant interest in experimental platforms to evaluate and improve models for dynamic material deformation. While well-developed platforms exist, there are still gaps to fill for strain and strain rate conditions accessed during impact and other high-rate loading scenarios. To fill one such gap for strength measurements, a platform was recently developed that accesses high strain rate (≥ 10 5 / s) and large strain (≥ 50 %) conditions by measuring the transient closure of a cylindrical hole using in situ x-ray imaging. In the work reported here, further refinement of the platform is performed to reduce the potential effects of porosity and anelasticity on the measurement. This helps us to isolate the strength effects that are the focus of the experiment. The updated experimental configuration employs a two-layer flyer design and elongated target to reduce the magnitude of the tensile excursions associated with rarefaction wave interactions. This allows for a more direct assessment of strength models commonly used for dynamic simulations of metals. We apply the new technique to well-characterized tantalum material, allowing for a robust connection to other experimental techniques. Deformation localization can be a concern in large strain experiments, and to help inform future use of the experimental platform, we use simulations with a sub-zone treatment of shear banding to explore potential localization behavior. Overall, we develop and utilize an experimental configuration with improved isolation of strength effects that can be applied to an expanded range of materials. [ABSTRACT FROM AUTHOR]

Though jamming transitions are long studied in condensed matter physics and granular systems, much less is known about active jamming (or unjamming), which commonly takes place in living materials. In this paper, we explore, by molecular dynamic simulations, the jamming–unjamming transition in a dense system of active semiflexible filaments. In particular, we characterize the distinct impact of polar vs nematic driving for different filament rigidities and at varying densities. Our results show that high densities of dynamic active filaments can be achieved by only changing the nature of the active force, nematic or polar. Interestingly, while polar driving is more effective at unjamming the system at high densities below confluency, we find that at even higher densities, nematic driving enhances unjamming compared to its polar counterpart. The effect of varying the rigidity of filaments is also significantly different in the two cases: While for nematic driving, lowering the bending rigidity unjams the system, we find an intriguing reentrant jamming–unjamming–jamming transition for polar driving as the filament rigidity is lowered. While the first transition (unjamming) is driven by softening due to reduced rigidity, the second transition (jamming) is a cooperative effect of ordering and coincides with the emergence of nematic order in the system. Together, through a generic model of self-propelled flexible filaments, our results demonstrate how tuning the nature of self-propulsion and flexibility can be employed by active materials to achieve high densities without getting jammed. [ABSTRACT FROM AUTHOR]

In modern high-fidelity computational fluid dynamic simulations, the primary vortex system in hover often breaks down into secondary vortices. The sources of numerical error influencing the prediction of the vortex system were studied by performing high-fidelity simulations of the wake of a two-bladed rotor and comparing the predictions to stereoscopic particle image velocimetry measurements in different measurement planes. Various numerical inputs, including sub-iteration convergence, blade pitch offset, and grid resolution, were varied to resolve discrepancies between the measured and predicted vortex characteristics from a previous study done by the authors. A parametric study on near- and off-body solver sub-iteration convergence demonstrated that although the secondary vortex characteristics converged as the sub-iteration convergence of both solvers increased, a large discrepancy in the number of secondary vortices remained. This discrepancy was investigated by varying the thrust, where it was found that the breakdown of the primary vortex is directly linked to the number of secondary vortices. Dissimilarities in the blade pitch angle, which could not be avoided in the experiment, were modeled by intentionally using an offset in the blade pitch angle of the two blades. It was shown that as blade pitch angle offset increases, vortex pairing becomes more distinct. When vortex pairing occurred in both the experiment and simulation, the decay of secondary vortices in the experiment and simulation agreed best. To better match the experimental resolution, grid resolution was increased and comparing the two simulations, the finer mesh simulation agreed best with the measured primary and secondary vortex characteristics. [ABSTRACT FROM AUTHOR]

The size dependence of the surface tension of critical bubbles in a superheated (stretched) Lennard–Jones solution with complete solubility of the components is considered. Two approaches are used to determine this dependence. The first one is based on the van der Waals gradient theory, and the second one is based on molecular dynamic simulation results of nucleation in a solution. It is established that, unlike in a one-component liquid, where the surface tension of the equilibrium bubble is less than that for the flat interface, in solution, it can exceed the flat limit. The ranges of temperatures, pressures, and mixture compositions, where this effect occurs, are determined. The asymptotic behavior of the surface tension of vapor phase nuclei within the limits of zero and infinitely large curvature of the dividing surface is analyzed. [ABSTRACT FROM AUTHOR]

The bimolecular reaction between OH− and CH3F is not just a prototypical SN2 process, but it has three other product channels. Here, we develop an accurate full-dimensional potential energy surface (PES) based on 191 193 points calculated at the level CCSD(T)-F12a/aug-cc-pVTZ. A detailed dynamics and mechanism analysis was carried out on this potential energy surface using the quasi-classical trajectory approach. It is verified that the trajectories do not follow the minimum energy path (MEP), but directly dissociate to F− and CH3OH. In addition, a new transition state for proton exchange and a new product complex CH2F−⋯H2O for proton abstraction were discovered. The trajectories avoid the transition state or this complex, instead dissociate to H2O and CH2F− directly through the ridge regions of the minimum energy path before the transition state. These non-MEP dynamics become more pronounced at high collision energies. Detailed dynamic simulations provide new insights into the atomic-level mechanisms of the title reaction, thanks to the new chemically accurate PES, with the aid of machine learning. [ABSTRACT FROM AUTHOR]

Static and dynamic fluid–structure interaction of a flexible plate behind a stationary cylinder in uniform flow is explored for a body-to-fluid mass ratio of 10. Steady flow-structure computations for Re = 150, based on the diameter of cylinder and free-stream speed, reveal four regimes with respect to increasing flexibility of the plate. The plate does not undergo any lateral deflection in regime 1 beyond which it undergoes a symmetry-breaking bifurcation causing it to spontaneously deflect laterally. The curvature is of the same sign along the entire length of plate in regime 2 while it changes sign along the plate in regime 3. The lateral deflection, however, is still maximum at the plate tip. The location of maximum deflection moves away from the plate tip in regime 4. The evolution of flow structures including the strength of various standing vortices, with flexibility, is studied. The role of reattachment of flow on the surface of the plate and the modification of the pressure distribution is explored. The critical Re, beyond which the splitter plate spontaneously achieves a deflected shape, decreases with increase in flexibility. It is estimated to be Re = 122.33 for the limiting case of an infinitely flexible plate. Computations for dynamic fluid–structure interaction reveal several regimes of lock-in with different natural vibration modes of the plate and related hysteresis. No lateral bias in the time-averaged deflection is found during lock-in; it occurs in the desynchronization regime that precedes the lock-in regime with second mode. For the mass ratio considered, the bias in the static and dynamic simulations start at the same flexibility. [ABSTRACT FROM AUTHOR]

Multi-stage centrifugal pumps with floating impellers provide a convenient means of adjustment to meet diverse head requirements. These pumps utilize sealing gaskets to minimize leakage losses and restrict impeller axial motion. However, the impact of sealing gasket breakage on hydraulic performance and internal flow remains uncertain. To investigate this, a novel dynamic mesh simulation method is proposed to enable simultaneous axial motion and rotation of the impeller. Validation of numerical simulations with experiments is performed. Transient hydraulic performance is influenced by impeller axial motion, with a lagging flow field response. Head coefficient and efficiency curves exhibit asymmetric triangular functions with higher fluctuations compared to impeller with fixed axial position. At the design condition, with the impeller floating, the head coefficient ranges from 0.7 to 1.9, while the efficiency ranges from 29.7% to 60.1%. Among the various loss ratios, the hydraulic loss ratio exhibits the highest magnitude, followed by the leakage loss ratio, with the shroud friction loss ratio being the smallest. Entropy production reveals the significant influence of impeller oscillation on local flow loss. The axial motion of the impeller causes drastic velocity and pressure fluctuations in both time and space. [ABSTRACT FROM AUTHOR]

In this paper, we investigate the three-dimensional nature of dynamic stall. Conducting the investigation, the flow around a harmonically pitching National Advisory Committee for Aeronautics (NACA) 0012 airfoil is numerically simulated using Unsteady-Reynolds-Averaged Navier–Stokes (URANS) and multiple detached eddy simulation (DES) solvers: the Delayed-DES (DDES) and the Improved-DDES (IDDES). Two- and three-dimensional simulations are performed for each solver, and the results are compared against experimental measurements in the literature. The results showed that three-dimensional simulations surpass two-dimensional ones in capturing the stages of dynamic stall and predicting the lift coefficient values, with a distinguished performance of the DES solvers over the URANS ones. For instance, the IDDES simulations, as an inherently three-dimensional solver, predicted the necessary cascaded amalgamation process of vortices to form the adequate strength of the dynamic stall vortex. This vortex size and timing provided accurate and sufficient suction that resulted in identical matching of the numerical and experimental lift coefficients at the peak value. Hence, the hypothesis that dynamic stall has a three-dimensional nature is supported by the superiority of the three-dimensional simulation in all aspects. In conclusion, it is found that dynamic stall is intrinsically a three-dimensional phenomenon. [ABSTRACT FROM AUTHOR]

To mitigate climate change, the share of renewable energies in power production needs to be increased. Renewables introduce new challenges to power grids regarding the dynamic stability due to decentralization, reduced inertia, and volatility in production. Since dynamic stability simulations are intractable and exceedingly expensive for large grids, graph neural networks (GNNs) are a promising method to reduce the computational effort of analyzing the dynamic stability of power grids. As a testbed for GNN models, we generate new, large datasets of dynamic stability of synthetic power grids and provide them as an open-source resource to the research community. We find that GNNs are surprisingly effective at predicting the highly non-linear targets from topological information only. For the first time, performance that is suitable for practical use cases is achieved. Furthermore, we demonstrate the ability of these models to accurately identify particular vulnerable nodes in power grids, so-called troublemakers. Last, we find that GNNs trained on small grids generate accurate predictions on a large synthetic model of the Texan power grid, which illustrates the potential for real-world applications. [ABSTRACT FROM AUTHOR]

One of the most intriguing phenomena in active matter has been the gas–liquid-like motility-induced phase separation (MIPS) observed in repulsive active particles. However, experimentally, no particle can be a perfect sphere, and the asymmetric shape, mass distribution, or catalysis coating can induce an active torque on the particle, which makes it a chiral active particle. Here, using computer simulations and dynamic mean-field theory, we demonstrate that the large enough torque of circle active Brownian particles in two dimensions generates a dynamical clustering state interrupting the conventional MIPS. Multiple clusters arise from the combination of the conventional MIPS cohesion, and the circulating current caused disintegration. The nonvanishing current in non-equilibrium steady states microscopically originates from the motility "relieved" by automatic rotation, which breaks the detailed balance at the continuum level. This suggests that no equilibrium-like phase separation theory can be constructed for chiral active colloids even with tiny active torque, in which no visible collective motion exists. This mechanism also sheds light on the understanding of dynamic clusters observed in a variety of active matter systems. [ABSTRACT FROM AUTHOR]

Inter-anion hydrogen and halogen bonds have emerged as counterintuitive linkers and inspired us to expand the range of this unconventional bonding pattern. Here, the inter-anion chalcogen bond (IAChB) was proposed and theoretically analyzed in a series of complexes formed by negatively charged bidentate chalcogen bond donors with chloride anions. The kinetic stability of IAChB was evidenced by the minima on binding energy profiles and further supported by ab initio molecular dynamic simulations. The block-localized wave function (BLW) method and its subsequent energy decomposition (BLW-ED) approach were employed to elucidate the physical origin of IAChB. While all other energy components vary monotonically as anions get together, the electrostatic interaction behaves exceptionally as it experiences a Coulombic repulsion barrier. Before reaching the barrier, the electrostatic repulsion increases with the shortening Ch⋯Cl− distance as expected from classical electrostatics. However, after passing the barrier, the electrostatic repulsion decreases with the Ch⋯Cl− distance shortening and subsequently turns into the most favorable trend among all energy terms at short ranges, representing a dominating force for the kinetic stability of inter-anions. For comparison, all energy components exhibit the same trends and vary monotonically in the conventional counterparts where donors are neutral. By comparing inter-anions and their conventional counterparts, we found that only the electrostatic energy term is affected by the extra negative charge. Remarkably, the distinctive (nonmonotonic) electrostatic energy profiles were reproduced using quantum mechanical-based atomic multipoles, suggesting that the crucial electrostatic interaction in IAChB can be rationalized within the classical electrostatic theory just like conventional non-covalent interactions. [ABSTRACT FROM AUTHOR]

This work introduces a new permutation-symmetry-adapted machine learning diabatization procedure, termed the diabatization by equivariant neural network (DENN). In this approach, the permutation symmetric and anti-symmetric elements in diabatic potential energy metrics (DPEMs) were simultaneously simulated by the equivariant neural network. The diabatization by deep neural network scheme was adopted for machine learning diabatization, and non-zero diabatic coupling was included to increase accuracy in the near degenerate region. Based on DENN, the global DPEMs for 11A′ and 21A′ states of MgH2 have been constructed. To the best of our knowledge, these are the first global DPEMs for the MgH2 system. The root-mean-square-errors (RMSEs) for diagonal elements (H11 and H22) and the off-diagonal element (H12) around the conical intersection region were 5.824, 5.307, and 5.796 meV, respectively. The RMSEs of global adiabatic energies for two adiabatic states were 4.613 and 12.755 meV, respectively. The spectroscopic calculations of the 11A′ state in the linear HMgH region are in good agreement with the experiment and previous theoretical results. The differences between calculated frequencies and corresponding experiment values are 1.38 and 1.08 cm−1 for anti-symmetric stretching fundamental vibrational frequency and first overtone. The global DPEMs obtained in this work should be useful for further quantum mechanics dynamic simulations on the MgH2 system. [ABSTRACT FROM AUTHOR]

Shock-induced micro-jets and micro-spalls on metal surfaces and the subsequent mixing with surrounding gas are of interest for a wide range of applications, such as inertial-confinement fusion and armor design. This study interprets the mixing of micro-spalled metal with gas as the permeation of gas into the evolving porous structure created by micro-spalled liquid debris. A technical route is established based on the combination of fluid mechanics in porous media and shock dynamics. The topology of the porous metal is studied through molecular dynamic simulation, which captures the major characters of a micro-spalling process driven by shock loading. Pore-network modeling is applied to convert the porous structure of the micro-spalled metal into an assembly of pores and throats. Accordingly, the main porous characteristics of the micro-spalled metal are described by five nondimensional parameters, including porosity, specific area, coordination number, ratio of pore to throat radius, and tortuosity. In addition, the permeability of the micro-spalled metal, characterizing its gas-transport capacity, is also determined by directly simulating a single-phase flow throughout the pore network. The evolution of both porous structure and permeability of the micro-spalled metal subjected to various shock conditions is systematically analyzed. Moreover, the dependence of permeability on porous structure is clarified via a sensitivity analysis, which builds a cross-scale connection between the micro-void morphology and gas permeation at continuum level. The results and conclusions of this study could serve as useful references for both the characterization and design of porous samples in future experimental studies on micro-spalled metal-gas mixing. [ABSTRACT FROM AUTHOR]

Molecular dynamic simulation was performed to study the correlation between atomic packing and shear transformation under compressive deformation in apparent elastic regime in CuZr metallic glass. The packing feature of atomic structures was characterized in terms of cavities in metallic glass. It is found that while atoms surrounded by larger cavity volumes, i.e., loosely packed regions, show very small nonaffine displacements, some atoms surrounded by very small cavities, i.e., densely packed regions, undergo very large nonaffine displacement and form cooperative shear transformations with large scale in space. The size of shear transformation zones monotonically increases with decreasing cavity volume. However, shear transformations rarely occur in either densely packed or loosely packed regions with very small probability. In addition, metallic glasses are revealed to possess characteristic cavity volumes around which atoms have more probability to undergo relatively larger nonaffine displacements. It is found that more neighboring atoms together with these central atoms experience cooperative shear transformations. These findings are general in different metallic glasses and provide a general underlying structural basis for different sizes of shear transformation zones observed in previous studies. [ABSTRACT FROM AUTHOR]

The applicability of deep eutectic solvents is determined by their physicochemical properties. In turn, the properties of eutectic mixtures are the result of the components' molar ratio and chemical composition. Owing to the relatively low viscosities displayed by alcohol-based deep eutectic solvents (DESs), their application in industry is more appealing. Modeling the composition–property relationships established in polyalcohol-based mixtures is crucial for both understanding and predicting their behavior. In this work, a physicochemical property–structure comparison study is made between four choline chloride polyalcohol-based DESs, namely, ethaline, propeline, propaneline, and glyceline. Physicochemical properties obtained from molecular dynamic simulations are compared to experimental data, whenever possible. The simulations cover the temperature range from 298.15 to 348.15 K. The simulated and literature experimental data are generally in good agreement for all the studied DESs. Structural properties, such as radial and spatial distribution functions, coordination numbers, hydrogen bond donor (HBD)–HBD aggregate formation, and hydrogen bonding are analyzed in detail. The higher prevalence of HBD:HBD and HBD:anion hydrogen bonds is likely to be the major reason for the relatively high density and viscosity of glyceline as well as for lower DES self-diffusions. [ABSTRACT FROM AUTHOR]

Using molecular dynamics simulation, we studied thermodynamic effects of a nanobubble's collapse-induced erosion occurring at different ambient temperatures. We analyzed the dynamics of a single nanobubble collapsing near an aluminum (Al) solid boundary immersed in water at temperatures ranging 10–60 °C (283 – 333 K). We used a momentum mirror protocol to investigate the nanobubble's collapse-induced shock wave as the associated nanojet formed and moved toward the solid boundary. The results showed that the nanojet was formed during the collapse process after the collision of the nanobubble with the shock wave. On the aluminum surface, the erosion at lower ambient temperatures was greater than at higher ambient temperatures. [ABSTRACT FROM AUTHOR]

In this article, the structures and energies of CF3COCl in the low-lying electronic states have been determined by SA-2-CAS(8,7)/6-31G* and SA-2-MSPT2(8,7)/6-31G* calculations, which include equilibrium geometries, transition states, and three minimum-energy conical intersections (CI-1, CI-2, and CI-3) between S0 and S1 states. The AIMS method was used to carry out non-adiabatic dynamic simulations with the ab initio calculation performed at the SA-2-CAS(8,7)/6-31G* level. Upon irradiation to the S1 state, CF3COCl first relaxes to S1 minimum and then overcomes the ∼10 kcal/mol (TSS1_CCl) or ∼30 kcal/mol (TSS1_CO) barrier to the conical intersection region CI-1 or CI-3 (minor), with the S1 → S0 transition probability of 63:1. After non-adiabatic transition to the S0 state through CI-1, trajectories mainly distribute to three different reaction pathways, with one going back to S0 minimum through shortening of the C–Cl bond, the other forming CF3CO and Cl radicals by continuous elongation of the C–Cl distance, and another dissociating into CF3 + CO + Cl and running into the CI-3 region through elongation of C–C and C–Cl distances. Moreover, we found that the trajectories would recross to the S1 state with the recrossing probability of 13.9% through the CI-3 region due to the extremely sloped topographic character of CI-3. On the basis of time evolution of wavefunctions simulated here, the product ratio of CF3 + CO + Cl and CF3CO + Cl is 53.5%:18.4%, which is consistent with the experimental value of 3:1. We further explain the photo-dissociation wavelength dependence of CF3COCl, and the product ratio of CF3 + CO + Cl increases with the increase in total energy. [ABSTRACT FROM AUTHOR]

The energy landscape of ZrO2-doped amorphous Ta2O5 is explored in this work. With models corresponding to experimental concentrations of 50% Zr and 50% Ta cations, we search for, gather, and analyze two-level systems (TLSs) from molecular dynamic simulations. The mechanical loss function is calculated for each TLS individually. The results show that TLS with low asymmetry and large elastic coupling constants contribute the most to mechanical loss. We identify these as "bad actors." The higher barriers relate to the mechanical loss at higher temperatures. The concept of the oxygen cage that describes the local structural environment surrounding a metal ion is introduced. The existence of a drastic change in local environment, or a cage-breaking process, enables us to understand the double peaks present in the asymmetry distribution and provides a pictorial interpretation to distinguish two types of TLS. Quantitatively, a cage-breaking event is related to at least one large distance change in an atom–atom pair, and non-cage-breaking transitions have only small rearrangements. The majority of TLSs are cage-breaking transitions, but non-cage-breaking TLS transitions show higher average mechanical loss in ZrO2-doped Ta2O5. By decomposing the contributions to mechanical loss, we find that the low temperature loss peak near 40 K mainly comes from non-cage-breaking TLS transitions and the second loss peak near 120 K originates from cage-breaking TLS transitions. This finding is important for understanding the interplay between the atomic structure of TLS and mechanical loss. [ABSTRACT FROM AUTHOR]

Molecular dynamic (MD) simulation techniques are increasingly being adopted as efficient computational tools to design novel and exotic classes of materials for which traditional methods of synthesis and prototyping are either too costly, unsafe, and time-consuming in laboratory settings. Of such class of materials are liquid crystalline elastomers (LCEs) with favorable shape memory characteristics. These materials exhibit some distinct properties, including stimuli responsiveness to heat or UV and appropriate molecular structure for shape memory behaviors. In this work, the MD simulations were employed to compare and assess the leading force fields currently available for modeling the behavior of a typical LCE system. Three force fields, including Dreiding, PCFF, and SciPCFF, were separately assigned to model the LCE system, and their suitability was validated through experimental results. Among these selected force fields, the SciPCFF produced the best agreement with the experimentally measured thermal and viscoelastic properties compared to those of simulated steady-state density, transition temperature, and viscoelastic characteristics. Next, shape fixity (Rf) and shape recovery (Rr) of LCEs were estimated using this force field. A four-step simulated shape memory procedure proceeded under a tensile mode. The changes in molecular conformations were calculated for Rf and Rr after the unloading step and the reheating step. The results revealed that the model LCE system exhibits characteristic behaviors of Rf and Rr over the thermomechanical shape memory process, confirming the suitability of selected force field for use in the design and prediction of properties of typical LCE class of polymers. [ABSTRACT FROM AUTHOR]

Solid-state nanopores are a promising platform for characterizing proteins. In order to improve their lifetime and prevent fouling, Polyethylene Glycol (PEG) grafting is one of the most efficient and low-cost solutions. Different models to calculate the PEG thickness do not consider their interaction with the nanopore inner surface nor the effect of confinement. Here, we investigate by molecular dynamic simulation the PEG conformation inside a nanopore in the case of hydrophobic and hydrophilic nanopores. Our results reveal that the nanopore inner surface plays a role in the PEG organization and, thus, in the speed of the salt constituent. The resulting pair interaction between PEG and its environment clearly shows a more important affinity for K+ compared to Li+ cations. [ABSTRACT FROM AUTHOR]

The non-radiative relaxation process within the Q-bands of chlorophylls represents a crucial preliminary step during the photosynthetic mechanism. Despite several experimental and theoretical efforts performed in order to clarify the complex dynamics characterizing this stage, a complete understanding of this mechanism is still far to be reached. In this study, non-adiabatic excited-state molecular dynamic simulations have been performed to model the non-radiative process within the Q-bands for a model system of chlorophylls. This system has been considered in the gas phase and then, to have a more representative picture of the environment, with implicit and mixed implicit–explicit solvation models. In the first part of this analysis, absorption spectra have been simulated for each model in order to guide the setup for the non-adiabatic excited-state molecular dynamic simulations. Then, non-adiabatic excited-state molecular dynamic simulations have been performed on a large set of independent trajectories and the population of the Qx and Qy states has been computed as the average of all the trajectories, estimating the rate constant for the process. Finally, with the aim of investigating the possible role played by the solvent in the Qx–Qy crossing mechanism, an essential dynamic analysis has been performed on the generated data, allowing one to find the most important motions during the simulated dynamics. [ABSTRACT FROM AUTHOR]

This paper presents a study on the relationship between transport properties and geometric free volume for a hard sphere (HS) system in a dense fluid region. First, a generic free volume distribution function is proposed based on recent simulation results on the HS geometric free volume by Maiti and Sastry [J. Chem. Phys. 141(4), 044510 (2014)] and Maiti et al. [Eur. Phys. J. E 36(1), 5 (2013)]. Combining the new distribution function with a local particle transportation model, we obtain a power law for the HS transport properties. Then, a relation between the geometric free volume and thermodynamic free volume is established, which makes it possible to use well-developed equations of state (EoS) for the expressions of the geometric free volume. The new power law models are tested with molecular dynamic simulation results for HS viscosity, diffusivity and thermal conductivity, respectively, and the results are very satisfactory. Moreover, using the power law, we are able to reproduce several equations obtained from different approaches, such as the entropy scaling laws [Bell et al., J. Phys. Chem. B 123(29), 6345–6363 (2019]), mode coupling theory [Barrat et al., J. Phys. Condens. Matter 1, 7163–7170 (1989)], or empirical correlations [Sigurgeirsson and Heyes, J. Mol. Phys. 101(3), 469–482 (2003)]. In particular, a long-standing controversy regarding the well-known Cohen–Turnbull–Doolittle free volume model [Cohen and Turnbull, J. Chem. Phys. 31(3), 1164–1169 (1959); Doolittle, J. Appl. Phys. 22(12), 1471–1475 (1951)] is resolved by using the power law combined with the Heyes and Woodcock EoS [Heyes and Woodcock, Mol. Phys. 59(6), 1369–1388 (1986)]. [ABSTRACT FROM AUTHOR]

Intracerebral hemorrhage (ICH) is a common and severe brain disease associated with high mortality and morbidity. Accurate measurement of the ICH area is an essential indicator for doctors to determine whether a surgical operation is necessary. However, although currently used clinical detection methods, such as computed tomography (CT) and magnetic resonance imaging (MRI), provide high-quality images, they may have limitations such as high costs, large equipment size, and radiation exposure to the human body in the case of CT. It makes long-term bedside monitoring infeasible. This paper presents a dynamic monitoring method for ICH areas based on magnetic induction. This study investigates the influence of the bleeding area and the position of ICH on the phase difference at the detection point near the area to be measured. The study applies a neural network algorithm to predict the bleeding area using the phase difference data received by the detection coil as the network input and the bleeding area as the network output. The relative error between the predicted and actual values of the neural network is calculated, and the error of each group of data is less than 4%, which confirms the feasibility of this method for detecting and even trend monitoring of the ICH area. [ABSTRACT FROM AUTHOR]

The rapid development of new energy sources has brought a certain impact on the original power grid structure, accelerated the wear of unit equipment, and affected the stability, safety, and economy of thermal power unit operation, so it is proposed to add an energy storage system to solve the above problems. To analyze the secondary frequency regulation effect of thermal power units assisted by a flywheel energy storage system, a mathematical model of the control strategy on both sides of the boiler, steam turbine, and flywheel permanent magnet synchronous motor is proposed, and a two-regional power grid model is built through MATLAB/Simulink to simulate the frequency regulation effect of units with or without energy storage participation through step disturbance and continuous disturbance, which are 0.045 and 0.023 p.u. MW. Under step disturbance, the frequency fluctuation of the coupled energy storage system changed by 0.025 228 p.u. Hz, the time for the system to return to a steady state was shortened by 5.85 s, the maximum change of the frequency of the system in Region 2 was reduced by 0.025 579 p.u. Hz, and under continuous disturbance, the fluctuation of the output power of the steam turbine in Region 1 was reduced by 0.022 982 p.u. MW. In summary, under the same disturbance conditions in the outside world, the use of flywheel energy storage to assist the frequency regulation of thermal power units can effectively reduce the frequency fluctuation of the system, reduce the fluctuation of the output power of the steam turbine, reduce the loss of mechanical equipment, and extend the service life of the unit to a certain extent. [ABSTRACT FROM AUTHOR]

In this article, we implement a recently developed non-equilibrium chemical kinetics model [N. Singh and T. Schwartzentruber, J. Chem. Phys. 152, 224302 (2020)] based on ab initio simulation data and perform verification studies. Direct molecular simulation data are used to verify the predictive capabilities of the model. Using the model, dominant physics, such as the need for a rotational energy equation, and the quantitative role of non-Boltzmann effects are identified. Based on the analysis and reasonable assumptions, a simplified model for implementation into large-scale computational fluid dynamic simulations is proposed. Without incurring additional computational cost, the model can be used in existing flow solvers to analyze hypersonic flows. [ABSTRACT FROM AUTHOR]

The transport behavior of ionic liquids (ILs) is pivotal for a variety of applications, especially when ILs are used as electrolytes. Many aspects of the transport dynamics of ILs remain to be understood. Here, a common ionic liquid, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimNTf2), was studied with molecular dynamics simulations. The results show that BmimNTf2 displays typical structural relaxation, subdiffusive behavior, and a breakdown of the Stokes-Einstein diffusion relation as in glass-forming liquids. In addition, the simulations show that the translational dynamics, reorientation dynamics, and structural relaxation dynamics are well described by the Vogel-Fulcher-Tammann equation like fragile glass forming liquids. Building on previous work that employed ion cage models, it was found that the diffusion dynamics of the cations and anions were well described by a hopping process random walk where the step time is the ion cage lifetime obtained from the cage correlation function. Detailed analysis of the ion cage structures indicated that the electrostatic potential energy of the ion cage dominates the diffusion dynamics of the caged ion. The ion orientational relaxation dynamics showed that ion reorientation is a necessary step for ion cage restructuring. The dynamic ion cage model description of ion diffusion presented here may have implications for designing ILs to control their transport behavior. [ABSTRACT FROM AUTHOR]

An Fe-W potential has been constructed by means of the embedded-atom method and has proven to be more realistic than the three published Fe-W potentials in the literature. Based on the constructed Fe-W potential, molecular dynamic simulation has been used to reveal structural stability, thermodynamic properties, and mechanical properties of BCC Fe-W solid solutions within the entire composition range. It is found that the Fe-W interaction in BCC Fe-W solid solutions should be weak and attractive with small and negative heats of formation, which agree well with those from the thermodynamic Miedema model and could clarify the controversy regarding heats of formation of Fe-W solid solutions in the literature. In addition, the derived coefficient of thermal expansion, heat capacity, elastic constants, and elastic moduli of Fe-W solid solutions from the present Fe-W potential are in good agreement with the corresponding data from ab initio calculation or experiments in the literature. [ABSTRACT FROM AUTHOR]

Modern particle-based simulations increasingly incorporate polarization charges arising from spatially nonuniform permittivity. For complex dielectric geometries, calculation of these induced many-body effects typically requires numerical solvers based upon boundary-element methods, which very significantly increase the required computational effort. For the special case of dielectric spheres, such as colloids or nanoparticles, we recently proposed a semianalytical spectrally accurate hybrid method that combines the method of moments, the image-charge method, and the fast multipole method. The hybrid method is efficient and accurate even when dielectric spheres are closely packed. Here, we extend the method to the evaluation of direct and induced electrostatic forces and demonstrate how this can be incorporated in molecular dynamics simulations. The choice of the relevant numerical parameters for molecular dynamics simulations is discussed in detail, as well as comparisons to the boundary-element method. As a concrete example, we examine the challenging case of binary crystal structures composed of close-packed dielectric colloidal spheres. [ABSTRACT FROM AUTHOR]

The purpose of this study is to investigate deep dynamic stall over a pitching National Advisory Committee for Aeronautics 0015 airfoil and its control with an alternating current dielectric barrier discharge (AC-DBD) plasma actuator by means of large eddy simulation. The airfoil oscillates at a reduced frequency of k = 0.08 with the angle of attack (AoA) varying between 5° and 25°. The chord-based Reynolds number is Re = 7.6 × 104. Rich fluid dynamics and physics involved in the dynamic stall are resolved by large eddy simulation. It is found that the dynamic stall under consideration initiates with the onset of a leading edge vortex (LEV). The deep dynamic stall is characterized and dominated by four successive LEVs at high angles of attack. The control of dynamic stall with AC-DBD plasma actuation is investigated in depth. At low AoAs, the plasma forcing can delay the laminar-to-turbulent transition of the attached flow over the suction surface of the airfoil. Although the formation of the first LEV is delayed by the plasma actuation, the first three LEVs cannot be effectively suppressed in high AoAs beyond 20°. The impact of the AC-DBD on the flow becomes increasingly pronounced in the downstroke phase, and at the intermediate angles of attack, the flow separation can be effectively controlled. Substantial gain from the flow control is obtained. The area of the lift hysteresis loop and drag force are appreciably reduced, and the nose-down pitch moment is alleviated notably. Finally, the influence of forcing frequency on flow control is examined. [ABSTRACT FROM AUTHOR]

This study investigates and quantifies the electromagnetic effects of vibration and noise in high-speed, permanent magnet motors. In particular, the effects of carrier harmonics generated in the electromagnetic excitation source by the pulse width modulation method are derived based on dynamic simulations. Noise, vibration, and harshness responses are then analyzed and compared to assess their induced effects on motors during actual operations. [ABSTRACT FROM AUTHOR]

In the current research, we studied the collapse mechanism of the nanobubble under mirror and real wall protocols using molecular dynamics simulation. Moreover, we analyzed reactive properties of the real wall during the collapse process. Towards this aim, an aluminum (Al) slab has been considered as a real wall, and its behavior after the formation of a nanojet has been investigated. The obtained results indicated that the dynamics of nanobubble collapse under the mirror and real protocols are similar. The collision between the shock wave and the nanobubble leads to the collapse of nanobubble, and the nanojet was formed during this collapse process. However, the nanobubble can collapse sooner when the Al slab is used as a real wall. Moreover, the surface roughness of the Al slab during the shock propagation and nanobubble collapse was increased due to the formation of the chemical reaction between Al and water under the real wall protocol, while the mirror wall has a roughness-free surface from the beginning to the end. The chemical reaction 2Al + H 2 O → AlOH + AlH creates the amorphous layer containing the AlOH and AlH species on the surface of the Al slab. This layer grows semi-smoothly during bubble shrinkage and collapse process, while the growth type was changed to an island shape after the complete collapsing. The island shape on the Al slab was formed behind the nanojet due to the water vortices that are formed after the nanobubble collapse. [ABSTRACT FROM AUTHOR]

A monocopter, which is a biology-inspired aircraft based on the samara, has been proved to have passive flight stability. However, due to the asymmetry of its configurations and the constant rotation during flight, its flight dynamics equation is complex. In this paper, the longitudinal stability of a monocopter is systematically analyzed. The longitudinal motion of the monocopter is used as the main research object in this paper. By transforming the body axis coordinate frame to the semi-body axis coordinate frame, its longitudinal dynamics equation is greatly simplified. Then, a fourth-order state space matrix of the longitudinal motion of the monocopter is established, and its longitudinal stability is analyzed at different pitch angles of the wing. Furthermore, the fourth-order state space matrix is simplified into a third-order matrix, and the Rouse criterion is used to analyze the stability of the simplified state space. A set of sufficient conditions is obtained as the criterion for longitudinal stability. Based on this criterion, it is found that the product of inertia I y z b is a very important factor affecting the stability. Then, the inertial parameters of the aircraft are modified, which greatly expands the range of the pitch angle that maintains longitudinal stability. Finally, the six-degree-of-freedom nonlinear flight dynamic simulation is performed to verify the rationality of the longitudinal stability criterion. [ABSTRACT FROM AUTHOR]

To alleviate the deterioration in wind turbine performance caused by dynamic stall, the flow control of a pitching NACA0012 airfoil is investigated through numerical simulation of an alternating current dielectric barrier discharge (AC-DBD) plasma actuator at a Reynolds number Re = 135 000. To avoid the harmonic oscillations of aerodynamic force caused by unsteady DBD actuation, this work focuses on improving the control potential for steady actuation. The control mechanisms of actuators at various positions are investigated using five groups of actuators mounted at 0%, 3%, 10%, 45%, and 80% chord lengths c above the upper surface of an airfoil. The actuator at 80%c performs more efficiently in terms of lift enhancement in the initial upstroke and the final downstroke. The actuator at 0%c suppresses the growth of the leading-edge vortex and maintains the suction of the dynamic stall vortex (DSV). After the shedding of the DSV, it suppresses the secondary separation to delay the onset of dynamic stall. At the flow reattachment stage, the actuators at 3%c and 10%c accelerate the boundary layer reattachment by momentum injection. From these results, a multi-DBD control strategy is proposed. The scheme selects the optimal actuator in operation at a certain stage of dynamic stall and takes advantage of actuators at different positions to enhance the average and maximum aerodynamic force, delay the onset of dynamic stall, accelerate flow reattachment, and avoid excessive energy consumption. [ABSTRACT FROM AUTHOR]

Here, we present an implicit-solvent model for dynamic simulations of hard-rod and rod-polymer suspensions. Individual rods are represented by a rigid linear chain consisting of overlapping spheres which interact through a pseudohard-core potential based on the cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). In the rod-polymer suspensions, the polymers are modeled as freely interpenetrable spheres with respect to each other, while there is the pseudohard-core repulsion between the polymer and rod spheres. Dynamic simulations with this model are carried out with a dissipative particle dynamics (DPD) thermostat—each sphere is put in a larger DPD sphere and thus interacts with others via additional pairwise frictional and random forces—which captures the effects of Brownian forces due to the solvent while conserving local momentum. The phase behavior of these models, obtained from continuous compression and expansion simulations, reproduces previous predictions based on theoretical calculations and Monte Carlo simulations. Our method is suited to study dynamic processes in these suspensions, including nucleation and self-assembly, and can be readily extended to colloidal particles of different shapes and chemistry. [ABSTRACT FROM AUTHOR]

A single sheet of Si nanoclusters with an average diameter of about 2 nm has been formed in a 30 nm Si/7 nm SiO2/Si layer stack by 50 and 60 keV Si+ ion-beam mixing at room temperature and fluences between 8.5 ⋅ 1015 and 2.6 ⋅ 1016 ions/cm2 and by subsequent thermal annealing at a temperature above 1000 °C. Computer modeling of the process is accomplished by TRIDYN dynamic ballistic simulation of ion mixing and subsequent lattice kinetic Monte Carlo simulation of the phase decomposition of substoichiometric silicon oxide into Si nanoclusters in a SiO2 matrix. The simulation algorithms are briefly described with special emphasis on the choice of governing parameters for the present system. In comparison to the experimental results, it is concluded that the predicted ion mixing profiles overestimate the interface broadening. This discrepancy is attributed to the neglect of chemical driving forces in connection with thermal-spike induced diffusion, which tends to reconstitute the Si/SiO2 interfaces. With a corresponding correction and a suitable number of Monte Carlo steps, the experimentally obtained areal densities and average diameters of the nanoclusters are successfully reproduced. [ABSTRACT FROM AUTHOR]

The dynamic behavior of bundles of actin filaments growing against a loaded obstacle is investigated through a generalized version of the standard multifilament Brownian Ratchet model in which the (de)polymerizing filaments are treated not as rigid rods but as semiflexible discrete wormlike chains with a realistic value of the persistence length. By stochastic dynamic simulations, we study the relaxation of a bundle of Nf filaments with a staggered seed arrangement against a harmonic trap load in supercritical conditions. Thanks to the time scale separation between the wall motion and the filament size relaxation, mimicking realistic conditions, this setup allows us to extract a full load-velocity curve from a single experiment over the trap force/size range explored. We observe a systematic evolution of steady nonequilibrium states over three regimes of bundle lengths L. A first threshold length Λ marks the transition between the rigid dynamic regime (L < Λ), characterized by the usual rigid filament load-velocity relationship V(F), and the flexible dynamic regime (L > Λ), where the velocity V(F, L) is an increasing function of the bundle length L at a fixed load F, the enhancement being the result of an improved level of work sharing among the filaments induced by flexibility. A second critical length corresponds to the beginning of an unstable regime characterized by a high probability to develop escaping filaments which start growing laterally and thus do not participate anymore in the generation of the polymerization force. This phenomenon prevents the bundle from reaching at this critical length the limit behavior corresponding to perfect load sharing. [ABSTRACT FROM AUTHOR]

We use molecular dynamic simulations to investigate the motion of a folding molecular motor inside soft matter. Purcell's scallop theorem forbids the displacement of the motor due to time symmetrical hydrodynamic laws at low Reynolds numbers whatever the asymmetry of the folding and unfolding rates. However, the fluctuation theorems imply a violation of the time symmetry of the motor's trajectories due to the entropy generated by the motor, suggesting a breakdown of the scallop theorem at the nanoscale. To clarify this picture, we study the predicted violation of time reversibility of the motor's trajectories, using two reverse asymmetric folding mechanisms. We actually observe this violation of time reversibility of the motor's trajectories. We also observe the previously reported fluidization of the medium induced by the motor's folding, but find that this induced diffusion is not enough to explain the increase of the motor's displacement. As a result, the motor is not carried by the medium in our system but moves by its own, in violation of the scallop theorem. The observed violation of the scallop theorem opens a route to create very simple molecular motors moving in soft matter environments. [ABSTRACT FROM AUTHOR]

The presence of small hydrocarbons is known to reduce the interfacial tension of the gas-water interface, and this phenomenon can affect the formation of the clathrate hydrates of these gases. In this work, the interfacial behavior of the pure methane-, ethane-, and propane-water, and the ternary 90:7:3 mol. % gas mixture of (methane + ethane + propane)-water were studied with molecular dynamics simulations. The interfacial tension, γ, and z-density profiles for the gases and water from simulations of the gas-water systems were determined at the temperatures of 275.15 and 298.15 K, and pressures up to 10 MPa for methane and up to near the experimental saturation pressures of ethane and propane. The goal is to accurately calculate the interfacial tension for the hydrocarbon/water systems and to analyze the molecular behaviors at the interfaces which lead to the observed trends. At the same hydrostatic gas phase pressure, propane, ethane, and methane reduce the gas-water interfacial tension in that order. The local density of the gas molecules at the interface is enhanced relative to the bulk gas, and it was determined that about 13%-20%, 33%-40%, and 54%-59% of the gas molecules in the simulation congregated at the interfaces for the CH4-, C2H6-, and C3H8-water systems, respectively, at the different simulated hydrostatic pressure ranges. For all gases in the pressure range studied, a complete monolayer of gas had not formed at the water interface. Furthermore, a dynamic equilibrium with fast exchange between molecules at the interface and in the gas phase was observed. For the gas mixture, deviations were observed between total calculated interfacial tension, γmix, and the "ideal mixture" value, ∑xiγi,pure, calculated from the interfacial tensions of the pure gases, where xi is the mole fraction of each substance in the simulation. Some possible implications of the results on the mechanism of clathrate hydrate formation are discussed. [ABSTRACT FROM AUTHOR]

Experiments have shown that cholesterol influences the membrane permeability of small molecules, amino acids, and cell-penetrating peptides. However, their exact translocation mechanisms under the influence of cholesterol remain poorly understood. Given the practical importance of cell-penetrating peptides and the existence of varied cholesterol contents in different cell types, it is necessary to examine the permeation of amino acids in cholesterol-containing membranes at atomic level of details. Here, bias-exchange metadynamics simulations were employed to investigate the molecular mechanism of the membrane permeation of two amino acids Arg and Trp important for cell-penetrating peptides in the presence of different concentrations of cholesterol. We found that the free energy barrier of Arg+ (the protonated form) permeation increased linearly as the cholesterol concentration increased, whereas the barrier of Trp permeation had a rapid increase from 0 mol. % to 20 mol. % cholesterol-containing membranes and nearly unchanged from 20 mol. % to 40 mol. % cholesterol-containing membranes. Arg0 becomes slightly more stable than Arg+ at the center of the dipalmitoylphosphatidylcholine (DPPC) membrane with 40 mol. % cholesterol concentrations. As a result, Arg+ has a similar permeability as Trp at 0 mol. % and 20 mol. % cholesterol, but a significantly lower permeability than Trp at 40 mol. % cholesterol. This difference is caused by the gradual reduction of water defects for Arg+ as the cholesterol concentration increases but lack of water defects for Trp in cholesterol-containing membranes. Strong but different orientation dependence between Arg+ and Trp permeations is observed. These results provide an improved microscopic understanding of amino-acid permeation through cholesterol-containing DPPC membrane systems. [ABSTRACT FROM AUTHOR]