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ABSTRACT Recently, generative models have become a computationally efficient alternative to physics-based numerical simulations of ground motions. Neural networks can learn from existing ground-motion data to generate unobserved ground-motion data at new source and site locations. A key challenge with generative models is ensuring that predicted ground motions remain within a physically realistic range. For this purpose, we developed an empirical, nonergodic ground-motion model (GMM) for small-magnitude earthquakes in the San Francisco Bay area based on about 5000 recordings per component for Mw ≤ 4 earthquakes. The nonergodic GMM predicts spatially varying median source, site, and path effects for both the Fourier amplitude spectrum (FAS) and the Fourier phase derivative (a proxy for duration), as well as the corresponding epistemic uncertainty for each term. For FAS, our model shows above-average source and site effects in the western part of the region and below-average effects in the eastern part, with regional effects exhibiting larger spatial correlation lengths with increasing frequency. For duration, the source term is negligible for small-magnitude earthquakes, and the site term leads to site-specific variations up to 5 s. Path effects for FAS and duration depend on the source–site pair and are extrapolated spatially using recent methods for path-effect modeling. The aleatory variability of the within-site within-path residuals is similar to the variability found in previous studies for other regions. The nonergodic model provides two key contributions: first, median adjustment terms that are transferable to larger magnitude earthquakes, further reducing aleatory variability in probabilistic seismic hazard analysis; second, region-specific criteria for validating machine learning-based ground-motion generators to evaluate whether synthetic ground motions exhibit physically realistic source, site, and path effects.
Simulations of optical spectra can provide key insights to aid experimental interpretation of electronic excitation phenomena. For chromophores in the condensed phase, these spectra, which incorporate the coupling between electronic excitation and molecular and solvent nuclear motions, can be simulated using excitation energies obtained from molecular dynamics simulations of the chromophore and solvent. Here, we present a hybrid scheme that exploits machine learning and physically informed spectral densities to show that as few as 25 ground and excited state energetic gradient calculations can be used to construct models that accurately predict environment-influenced vibronic coupling in optical spectra. We demonstrate our approach for the green fluorescent protein chromophore in water and the cresyl violet chromophore in methanol. We show that our hybrid approach, employing a machine learning model for the high-frequency spectral density and an ab initio parameterized Debye spectral density for the low-frequency, results in a systematic improvement of the optical absorption lineshape, leading to a simple machine learning scheme that can be used for the simulation of spectral densities and optical spectra.
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An agent-based discrete computational model biologically calibrated to Pseudomonas aeruginosa migration is used to explore the impacts of bacterial reversals and wrap mode on the efficiency of motion in different environments, both with and without chemotaxis. It is first shown that wrap mode increases the exploration of continuous multimodal chemotactic profiles such as those produced by biologically relevant fungal networks. For cells undergoing a run-reverse pattern, it is shown that the bacteria are likely to remain at the first local chemoattractant maximal production site on a hypha they find. However, with wrap mode, the bacteria can more easily escape these local sites to further explore their neighboring environment along the fungi, suggesting that wrap mode may be beneficial for migration along the fungi in liquid. In a different set of simulations of bacterial motion close to an isolated chemotactic source, wrap mode is shown to increase the ability of a bacterium to reorient toward the source while reducing the overall motion required for similar chemotactic efficiency as a run-reverse strategy, suggesting a potential metabolic benefit. In contrast, model simulations show that wrap mode can increase the rate of dispersal of P. aeruginosa in a nonchemotactic environment.
Photosynthesis converts solar energy into chemical energy through coordinated energy transfer between light-harvesting complexes and reaction centers (RCs). Understanding exciton motion, particularly the exciton diffusion length, is essential for optimizing energy efficiency in photosystems. In this work, we combine intensity-cycling transient absorption spectroscopy with kinetic Monte Carlo (kMC) simulation to investigate exciton motion in the C2S2 photosystem II supercomplex of spinach. Using exciton–exciton annihilation, revealed in the fifth-order response, we experimentally estimate an exciton diffusion length of 10.9 nm based on a 3D normal diffusion model, suggesting the ability of excitons to traverse the supercomplex. However, kMC simulations reveal that exciton motion is sub-diffusive because of spatial constraints and the strong RC traps. An anomalous diffusion model analysis of the experimental data yields a diffusion length of 9.7 nm, while the simulated diffusion length is 7.4 nm. The variable exciton residence time across subunits, partly influenced by their connectivity to the trap, indicates inhomogeneous annihilation probability and suggests how plants balance efficient light harvesting with photoprotection. We also explore the influence of specific assumptions in the annihilation simulation, which are challenging to access in more complex environments, such as the thylakoid membrane. Our study provides a framework for studying exciton dynamics using exciton–exciton annihilation, which can be extended to understand the light-harvesting efficiencies of larger, more complex photosynthetic assemblies.
The shape of an aerosol particle strongly influences its mass and momentum transfer cross-sections, charging properties, and other physical properties. Here, we present an explicit time-stepping procedure to simulate the rotational Brownian motion of arbitrary shaped aerosol particles by solving Euler’s equation of rotation. A Langevin formulation of the rotation equations is used, wherein Brownian motion due to thermal collisions between a particle and background gas molecules is represented using a stochastic fluctuating torque and fluid resistance is included as a drag torque. To avoid singularities associated with describing the orientation of a shape with Euler angles, we employ a quaternion formulation that leads to first-order stochastic differential equations to describe the evolution of the angular position and angular velocity of a rigid body. We perform all the rotational dynamics calculations in the body-fixed frame of reference attached to the rotating shape whose basis vectors are the normalized eigenvectors of the inertia tensor of the particle. Numerical solutions to rotation under torque-free conditions, damped rotation without Brownian motion, and stochastic rotation for arbitrary shapes are presented and discussed. The presented method enables time-resolved simulation of Brownian rotation for direct comparison with experimentally measured trajectories or statistical measures. The second order accuracy of the used time-stepping procedure places a severe restriction on the timestep that can be used for obtaining accurate results. Animations of presented simulations are included for visualizing rotational motion at various gas pressures. To aid implementation, MATLAB ® codes are also provided. Extension to include translation Brownian motion is straightforward.
The objective of this research program is to discover and develop new approaches for ab initio computational simulations of molecular motion. Specifically, this program aims to decipher the connection between the underlying electronic structure and the accordant molecular vibrations in reactive ions and radicals for renewable-energy purposes. Recent experimental progress in ion sources and optical spectroscopies has unearthed considerable new inner-sphere detail for these complexes, but the connection between these spectral signatures and mechanistic information often remains elusive, to the continued frustration of experimentalists. For this purpose, new anharmonic vibrational frequency methods, along with a publicly deployed software package, will be developed. Working closely with committed experimental collaborators, this conceptual and computational framework will be used to explain the results of new spectroscopy experiments, focusing specifically on the inner-shell mechanisms of renewable-energy catalysis. The oxidation half of catalytic water-splitting chemistry will be a central focus, along with fundamental studies of the manner in which strong ions and radicals activate solvent as a chemical species. The resulting products of the research program will include openly available software and algorithms for the ab initio simulation of challenging vibrational spectra, as well as critical mechanistic insight into energy-focused catalytic processes that are opaque to other existing analytical techniques.
We propose a new type of energy-efficient multi-bit magnetic memory based on current-driven, field-free, controlled domain wall motion. A meandering domain wall channel with precisely interspersed pinning regions provides the multi-bit capability of a magnetic tunnel junction memory. The magnetic free layer of the memory device has perpendicular magnetic anisotropy (PMA) and interfacial Dzyaloshinskii-Moriya interaction (DMI) so that spin-orbit torques (SOTs) induce efficient domain wall motion. Using micromagnetic simulations, we find two different cell designs: two-way switching and four-way switching. The memory cell design choices and the physics of pinning mechanisms are discussed in detail. Furthermore, we show that switching reliability and speed may be significantly improved by replacing the ferromagnetic free layer with a synthetic antiferromagnetic (SAF) layer. Switching behavior and material choices will be discussed for the two memory implementations.
Abstract A new microphysical treatment that includes aerosol–cloud interactions and secondary ice production (SIP) mechanisms is implemented in the convection scheme of the Community Atmosphere Model, version 6 (CAM6). The approach is to embed a 1D Lagrangian parcel model in the bulk convective plume of the existing deep convection parameterization. Aerosol activation, growth processes including collision/coalescence, and three processes of SIP mechanisms, two of which are normally overlooked in atmospheric models, are represented in this embedded parcel model. These microphysical processes are treated with a hybrid bin/bulk scheme and a high spatial and temporal resolution for the integration of the embedded parcel in 1D, allowing vertical velocity to determine the microphysical evolution following the in-cloud motion during ascent. Simulations of an observed case (Midlatitude Continental Convective Clouds Experiment) of a mesoscale convective system in Oklahoma, United States, with a single-column model (SCAM) version of CAM, are compared with aircraft in situ and ground-based observations of microphysical properties from the convection and precipitation. Results from the validation show the new microphysical scheme has a good representation of the ice initiation in the bulk convective plume, including the known and empirically quantified pathways of primary and secondary initiation, with benefits for the accuracy of properties of its supercooled cloud liquid. The sensitivity simulations and use of tagging tracers for the validated simulation confirm that the newly included SIP mechanisms are of paramount importance for convective microphysics and can be successfully treated in the global model.
The objective of this study is to assess the mechanical robustness of tungsten in first-wall applications for tokamaks. These applications unavoidably involve the challenges of high temperature and radiation damage. Here we report progress on determining the mechanisms governing the mobility of tungsten grain boundaries at high temperature, a key property in the process of recrystallization. The determination of mechanisms enables predictive analytic models of grain boundary response to driving forces like the energy stored in the damaged metal lattice that is released as a grain boundary sweeps through it. In prior work we studied tungsten grain boundary properties such as the energies of boundaries with various orientations and misorientations, including energies of grain boundaries whose high-temperature structure differs from the structure at ambient conditions. We have calculated properties associated with the grain boundary mobility including the response of grain boundaries to applied shear stress. We have also developed methods for direct calculation of the motion of curved grain boundaries at high temperature using molecular dynamics. Here we again utilize molecular dynamics simulation of grain boundary motion and go further to analyze how the defect content in a grain boundary evolves as the boundary moves under the action of a driving force.
A concern in the deployment of large wind turbines on ocean floating platforms is the effect of floating-platform motions on their electrical power generation. Further, it is not clear how floating motions influence waking, which might affect the combined power generation of collections of turbines. We examine the average power output of a single and a collection of NREL 5 MW wind turbines mounted on a tension-leg platform (TLP) under the action of fully developed ocean wave motions, coupling floating motions with the large-eddy simulation (LES) of atmospheric and rotor dynamics. The ocean dynamics enter as fully developed waves derived from the Pierson–Moskowitz spectrum. To assess the influence of ocean motions, we performed simulations over the full range of wind speeds in the operational range of the turbine, reporting comparisons of average power output when the platforms are allowed to move to when they are held rigidly in place. In all simulations, we find that the effects of the TLP floating-platform's induced motions have a minor effect on single and multiple turbine power production and wake deficits. Even when using coherent and large amplitude harmonic-floating-induced perturbations, any significant wake modifications from floating motions are confined to the near-wake region, where downstream turbines are unlikely to be located. The relatively small amplitude of TLP motions relative to pre-existing turbulent fluctuations are the primary reason for low wake and power modifications downstream.
Abstract We compare the dynamical behavior of magnetic skyrmions interacting with square and triangular defect arrays just above commensuration using both atomistic and particle-based models. Under applied drives, the initial motion is a kink traveling through the pinned skyrmion lattice. For the square defect array, both models agree well and show a regime in which the soliton motion is locked along 45°. The atomistic model also produces locking of a soliton along 30°, which is absent in the particle-based model. For the triangular defect array, the atomistic model exhibits 30° soliton motion over a wide region of external current values. In contrast, the particle-based model gives 45° soliton motion over a small range of external driving force values. The difference arises because the nondeforming particle model facilitates meandering skyrmion orbits while the deformable atomistic model enables stronger skyrmion-skyrmion interactions that reduce the meandering. Our results indicate that soliton motion through pinned skyrmion lattices on a periodic substrate is a robust effect.
US Special Operations Command (USSOCOM) was seeking a technological leap in small firearms weapon suppressor technology, because anticipated enemy capabilities are requiring the operators to have smaller detection cross sections to ensure the safe execution of missions. Suppressors have been developed almost exclusively through trial-and-error methods since the time of the original design by Hiram Maxim over one hundred years ago. Consequently USSOCOM deemed it prudent to perform a physicsbased study of weapon suppression to understand performance limits and possibly identify breakthrough technologies. Lawrence Livermore National Laboratory’s (LLNL’s) high performance production level computational tool called ALE3D (Arbitrary Lagrangian-Eulerian 3D and 2D) has unique physics models and numerical algorithms for modeling suppressor dynamics. The flexible and extendable code framework supports fully integrated hydrodynamics, heat transfer, solid and fluid dynamics, and chemistry that can be applied to simulating propellant-driven motion of a bullet down a gun barrel, the transfer of heat from the burning propellant to the barrel and suppressor, the chemistry of muzzle flash, and the shock/acoustic/optical signatures in the near-field. LLNL’s originally anticipated role was to augment ALE3D for this task, by developing the software and analysis methodologies specific to the simulation of blast and muzzle flash phenomena. It was believed that insights provided by our ALE3D simulations in tandem with a coordinated experimental component by our other team members from Oak Ridge National Laboratory (ORNL) and the U. S. Army Armament, Research, Development and Engineering Center (ARDEC), would have excellent prospects of yielding useful suppressor design improvements that could be transitioned to industry and utilized by US Special Operations Command. The three year effort has come to fruition with the development of revolutionary suppressor designs that far outperform any previous or current design by anyone outside this multi-lab team.
Ocean wave energy converters face significant challenges including cost-effectiveness, minimizing maintenance requirements, and withstanding extreme conditions. However, by utilizing smart materials, these converters could overcome these challenges. Such energy harvesters could use dielectric elastomer generators to convert ocean wave energy into electricity through their dynamic straining. Conversely, by applying electricity to these generators, they become actuators - dielectric elastomer actuators - thereby enabling them to alter their stiffness and adapt to the ever-changing ocean energy environments. Such active adaptation could enhance the converter's ability to: reach resonance with ocean waves and protect itself from dangerous waves. This study utilizes numerical analyses through the COMSOL software framework to evaluate the potential energy that could be harvested by a conceptual ocean wave energy converter based upon dielectric elastomer generators/actuators. The converter is composed of an external hull (that is a hollow cylinder), an inertial mass (that is a hollow cylinder and concentric with the hull), and 'spokes' - made of dielectric elastomer generators/actuators - that connect the hull to the inertial mass. Results of the numerical analyses include those outcomes arising from the conceptual converter being simulated via a sinusoidal motion analogous to ocean waves. That motion, therefore, causes relative motion between the converter's hull and inertial mass thereby dynamically stretching the corresponding connecting elastomers. The stretching of the elastomers enables them to 'gain elastic strain energy' and is, therefore, considered to be the theoretical limit of possible electrical energy conversion for the dielectric elastomer generator/actuator spokes. Additionally, the elastomer material properties of the spokes were altered to simulate the actuation of those same elastomers; with overall strain energy being subsequently investigated. Ultimately this is a preliminary study exploring the ability of such smart materials - electricity-generating and self-actuating elastomers - to actively adapt an ocean wave energy converter's structure to address and overcome the aforementioned challenges.
Hydrogen bonds (H-bonds) are central to biomolecular structure and dynamics. Although H-bonds are typically characterized by well-defined proton positions, proton delocalization has been proposed to play a role in facilitating enzyme catalysis and allostery in some systems. Experimentally locating protons is difficult, hampering the study of proton mobility in H-bonds. We used neutron crystallography, atomic resolution X-ray bond length analysis, and large quantum mechanics/molecular mechanics-Born–Oppenheimer molecular dynamics (QM/MM-BOMD) simulations to comprehensively characterize the shared proton/deuteron in a Glu–Asp low-barrier hydrogen bond (LBHB) in the bacterial protein YajL that is a conventional H-bond in the homologous disease-associated human protein DJ-1. X-ray bond length analysis of protiated and perdeuterated DJ-1 and YajL shows no significant effect of deuteron substitution on these carboxylic acid-carboxylate H-bonds but does reveal an effect at the active site glutamic acid near a cysteine thiolate. Residues in an H-bonded network that might favor LBHB formation in YajL were interrogated by the mutation of homologous residues in DJ-1. A distal DJ-1 substitution increases proton delocalization in the Glu–Asp H-bond, demonstrating that mutations within extended H-bond networks can modulate proton transfer barriers in carboxylic acid-carboxylate H-bonds. In addition, proton mobility in the H-bond is correlated with dimer-spanning motions in the QM/MM-BOMD simulations of YajL and DJ-1. Our results show that proton delocalization can be tuned using combined bioinformatic, structural, and computational information, opening the possibility of using engineered proton delocalization as a probe of H-bonding environments and as a tool to test hypotheses about LBHB function.
Conjugated polymers offer unprecedented chemical tunability for modulating energy transfer in a multitude of infrared light applications. In this work, we use a combination of time-resolved spectroscopic experiments and nonadiabatic molecular dynamics calculations to probe the photochemistry and nonradiative transitions in a recently synthesized narrow bandgap donor–acceptor conjugated polymer based on alternating cyclopentadithiophene and electronegative benzothiadiazole heterocycles. Using large-scale semi-empirical nonadiabatic molecular dynamics, which can treat a large 260-atom hexamer, we calculate an S 5 → S 1 lifetime of 34.75 fs, which is consistent with our time-resolved spectroscopic data. Our simulations suggest that vibronic motions of the central carbons in the cyclopentadithiophene functional groups are predominantly involved in the nonradiative transitions, and the excitation becomes more localized on a monomer fragment over time. The combined use of time-resolved experiments and nonadiabatic molecular dynamics calculations in this work provides mechanistic insight into chemical functionalities that can be tuned to enhance energy transfer in other prospective low-bandgap polymer materials.