Data-driven molecular modeling with the generalized Langevin equation
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Grogan, Francesca↗
SEARCH · Engineering Papers
Results for “system simulation”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Matlab implementation of a novel semi-structured kinetic model for methanotroph-photoautotroph cocultures
This paper presents the MatLab implementation details of a novel semi-structured kinetic model for methanotroph-photoautotroph cocultures. This includes the parameterization of the modeling equations, and the initialization of the simulation based on experimental conditions. More importantly, it provides details on how the differential equations governing mass balances in both gas and liquid phases are integrated together to simulate the system dynamics over time. The semi-structured kinetic model for methanotroph-photoautotroph coculture is validated using a wide range of experimental conditions. The model: Accurate predicts both the coculture growth in liquid phase and the gas composition changes in head space over time; Explicitly models the exchange of in situ produced O 2 and CO 2 within the coculture; Considers the self-shading effect on the growth of photoautotroph.
42 ENGINEERING↗
Nuclear safety Enhanced: A Deep dive into current and future RAVEN applications
As the horizon of nuclear energy expands with the advent of small modular reactors, IV generation reactors, and fusion reactors, there is a growing perspective that the licensing process could benefit from a more comprehensive approach. Moving beyond traditional deterministic and PRA analysis might pave the way for a novel safety analysis paradigm propelled by the increasing computational power at our disposal. This paper explores different methodologies that can improve the outcomes of nuclear safety analysis. These range from uncertainty quantification techniques, aimed at enhancing the precision of safety margins, to deploying dynamic event trees by driving system code simulations, capturing the potential evolutions of severe accidents. These methodologies introduce innovative dimensions to safety analysis, considering the consequences of postulated events and the dynamics of accident sequences. However, they also bring forth challenges, especially in managing the complexity and sheer volume of potential scenarios. The paper touches upon some strategies to counter these challenges, emphasizing the importance of adaptability and continuous evolution in the face of emerging nuclear safety concerns. Additionally, the paper sheds light on the need for advanced tools to apply these methodologies. Among these tools is RAVEN, an open-source software designed for parametric and probabilistic analyses. Its core components, including distribution, sampler, and reduced order model, enable various applications, from risk assessment and mitigation to dynamic learning and plant control logic simulations.
97 - MATHEMATICS AND COMPUTING↗
Thermalization of nuclear matter in heavy-ion collisions at Fermi energies
We analyze the time evolution of the kinetic properties of nuclear matter produced in heavy-ion collisions at Fermi energies. The collision system is simulated using Constrained Molecular Dynamics (CoMD) transport calculations whose output is the isospin, position, and momentum of the nucleons. Focusing on central 35 A·MeV 40 Ca+ 40 Ca collisions we utilize this information to extract localized momentum distributions in volume elements of 8 fm 3 and time steps of 5 fm/$c$. We then parameterize the single-particle momentum distributions with thermally motivated fit functions in the local rest frame of each cell. While the transverse-momentum distributions are well reproduced by thermal ones, the longitudinal ones carry a marked imprint of the initial nuclear motion which we capture by introducing a centroid motion into our fit functions. In particular, we find that Fermi distributions yield significantly better fits than Boltzmann ones, a consequence of the Pauli blocking implemented in CoMD. From the fits we extract the time dependence of the thermodynamic and collective properties of the excited nuclear medium. We find that the transverse temperature gradually rises to about 6 MeV, which is accompanied by a dissipation of the initial centroid motion of the incoming nuclei which vanishes at about 100 fm/c after initial impact. In conclusion, we are therefore able to track the transition of beam energy into random kinetic energy for nucleons, suggesting a three-dimensional equilibration of energy in the late stages of the collision.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Scalable self attraction and loading calculations for unstructured ocean tide models
Self attraction and earth-loading effects are important for accurately modeling global tides. A common approach of handling this forcing is to expand mass anomalies into spherical harmonics, which are scaled by load Love numbers to account for elastic earth deformation. We investigate two different approaches to perform these calculations for ocean models that employ unstructured meshes and distributed memory parallelization. The first approach leverages a highly efficient spherical harmonics library, but requires all-to-one and one-to-all communications and interpolation operations between the unstructured and a structured mesh. This approach is compared to a parallel algorithm that computes the spherical harmonic transformations directly on the unstructured mesh with an all-reduce communication. Here, our results show that although the unstructured mesh calculations are more expensive, the scalability of the unstructured mesh approach allows for more efficient spherical harmonics transforms for high-resolution meshes and large processor counts. This methodology enables the efficient inclusion of tidal dynamics large-scale Earth system model simulations.
54 ENVIRONMENTAL SCIENCES↗
Bio-inspired bistable piezoelectric energy harvester for powering animal telemetry tags: Conceptual design and preliminary experimental validation
Here, this paper presents the conceptual design, preliminary experimental validation, and performance evaluation of a novel bio-inspired bi-stable piezoelectric energy harvester for self-powered animal telemetry tags. The overall conceptual design, which includes a bio-inspired attachment and a bi-stable piezoelectric energy harvester, is introduced firstly with a specific application example of marine fish tracking. The self-powered telemetry tag can be externally deployed on fish (dorsal fin) to monitor fish habitats, population, and underwater environment. Inspired by the Venus flytrap's rapid shape transition, a bi-stable piezoelectric energy harvester is developed to scavenge energy from fish maneuvering and the surrounding fluid flow for a sustainable power supply. The bistability of the harvester is characterized by the measured force-displacement curve and double potential wells. A bluff body is integrated to the free end of the bistable piezoelectric energy harvester to enhance the structure-fluid interaction for the large-amplitude snap-through vibrations and higher voltage output. Controlled laboratory experiments are conducted in a water tank on the bio-inspired bi-stable piezoelectric energy harvester using a servo motor system to simulate fish swing motion at various conditions to evaluate the power generation performance. The preliminary underwater experimental results demonstrated that the proposed bio-inspired bi-stable piezoelectric energy harvester could effectively convert fish swing motions into electricity. The device collected 17.25 mJ of energy over 130 s under a peak-to-peak swing angle of 30° at 1.5 Hz in the capacitor charging experiments.
Animal tracking↗
Theoretical Advances in Polariton Chemistry and Molecular Cavity Quantum Electrodynamics
When molecules are coupled to an optical cavity, new light–matter hybrid states, so-called polaritons, are formed due to quantum light–matter interactions. With the experimental demonstrations of modifying chemical reactivities by forming polaritons under strong light–matter interactions, theorists have been encouraged to develop new methods to simulate these systems and discover new strategies to tune and control reactions. This review summarizes some of these exciting theoretical advances in polariton chemistry, in methods ranging from the fundamental framework to computational techniques and applications spanning from photochemistry to vibrational strong coupling. Even though the theory of quantum light–matter interactions goes back to the midtwentieth century, the gaps in the knowledge of molecular quantum electrodynamics (QED) have only recently been filled. We review recent advances made in resolving gauge ambiguities, the correct form of different QED Hamiltonians under different gauges, and their connections to various quantum optics models. Then, we review recently developed ab initio QED approaches which can accurately describe polariton states in a realistic molecule–cavity hybrid system. We then discuss applications using these method advancements. We review advancements in polariton photochemistry where the cavity is made resonant to electronic transitions to control molecular nonadiabatic excited state dynamics and enable new photochemical reactivities. When the cavity resonance is tuned to the molecular vibrations instead, ground-state chemical reaction modifications have been demonstrated experimentally, though its mechanistic principle remains unclear. We present some recent theoretical progress in resolving this mystery. Finally, we review the recent advances in understanding the collective coupling regime between light and matter, where many molecules can collectively couple to a single cavity mode or many cavity modes. We also lay out the current challenges in theory to explain the observed experimental results. We hope that this review will serve as a useful document for anyone who wants to become familiar with the context of polariton chemistry and molecular cavity QED and thus significantly benefit the entire community.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking
A critical step in structure-based drug discovery is predicting whether and how a candidate molecule binds to a model of a therapeutic target. However, substantial protein side chain movements prevent current screening methods, such as docking, from accurately predicting the ligand conformations and require expensive refinements to produce viable candidates. Here, we present the development of a high-throughput and flexible ligand pose refinement workflow, called “tinyIFD”. The main features of the workflow include the use of specialized high-throughput, small-system MD simulation code mdgx.cuda and an actively learning model zoo approach. We show the application of this workflow on a large test set of diverse protein targets, achieving 66% and 76% success rates for finding a crystal-like pose within the top-2 and top-5 poses, respectively. We also applied this workflow to the SARS-CoV-2 main protease (M pro ) inhibitors, where we demonstrate the benefit of the active learning aspect in this workflow.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Importance of Nuclear Quantum Effects on Aqueous Electrolyte Transport under Confinement in Ti 3 C 2 MXenes
Protons display a high chemical activity and strongly affect the charge storage capability in confined interlayer spaces of two-dimensional (2D) materials. As such, an accurate representation of proton dynamics under confinement is important for understanding and predicting charge storage dynamics in these materials. While often ignored in atomistic-scale simulations, nuclear quantum effects (NQEs), e.g., tunneling, can be significant under confinement even at room temperature. Here, using the thermostatted ring polymer molecular dynamics implementation of path integral molecular dynamics (PIMD) in conjunction with the ReaxFF force field, density functional tight binding (DFTB), and NequIP neural network potential simulations, we investigate the role of NQEs on proton and water transport in bulk water and aqueous electrolytes under confinement in Ti 3 C 2 MXenes. Although overall NQEs are relatively small, especially in bulk, we find that they can alter both quantitative values and qualitative trends on both proton transport and water self-diffusion under confinement relative to classical MD predictions. Therefore, our results suggest the need for NQEs to be considered to simulate aqueous systems under confinement for both qualitative and quantitative accuracy.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Determining the Ensemble N -Representability of Reduced Density Matrices
The N-representability problem for reduced density matrices remains a fundamental challenge in electronic structure theory. Following our previous work that employs a unitary-evolution algorithm based on an adaptive derivative-assembled pseudo-Trotter variational quantum algorithm to probe pure-state N-representability of reduced density matrices [J. Chem. Theory Comput. 2024, 20, 9968], in this work we propose a practical framework for determining the ensemble N-representability of a p-body matrix. This is accomplished using a purification strategy that embeds an ensemble state into a pure state defined on an extended Hilbert space, such that the reduced density matrices of the purified state reproduce those of the original ensemble. By iteratively applying variational unitaries to an initial purified state, the proposed algorithm minimizes the Hilbert-Schmidt distance between its p-body reduced density matrix and a specified target p-body matrix, which serves as a measure of the N-representability of the target. This methodology facilitates both error correction of defective ensemble reduced density matrices and quantum-state reconstruction on a quantum computer, offering a route for density-matrix refinement. We validate the algorithm with numerical simulations on systems of two, three, and four electrons in both simple models as well as molecular systems at finite temperature, demonstrating its robustness.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Thermal Shape Stability of fcc Metal Nanocrystals Synthesized with Faceted Nonequilibrium Shapes
Highly refined capabilities of the shape-controlled solution-phase synthesis of metal nanocrystals (NCs) allow the generation of NCs with faceted nonequilibrium shapes, which optimize properties for target applications such as catalysis and plasmonics. Often, for such applications and also for TEM analysis, the NCs are removed from the solution-phase environment. We explore the postsynthesis evolution of these metastable NCs in a high-vacuum TEM environment. Specifically, here we analyze their reshaping toward the equilibrium Wulff shapes mediated by surface diffusion, where such reshaping degrades the above-mentioned optimized properties. Typical sizes for these NCs range from 5 to 30 nm or 10 3 –10 6 atoms, and reshaping often occurs on the time scale of minutes for temperatures around, say, 400 °C. We discuss the development of predictive stochastic atomistic-level models for NC evolution with a realistic description of surface diffusion. These models, in contrast to Molecular Dynamics, can naturally address the relevant time and length scales for these systems. KMC simulation results for the stochastic models are described, focusing on the reshaping of slightly elongated nanorods and of mildly truncated octahedra and nanocubes. In addition, we review appropriate theoretical formulations for reshaping, which involves the nucleation and growth on 2D islands or layers on outer facets of the NC. We note the limitations of classical nucleation theory in some scenarios and demonstrate the successes of a more fundamental and general master equation-based analysis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Viscoelastic Response of Dispersed Entangled Polymer Melts
Any polymer synthesis routes result in molecular weight dispersity DAI, depending on the polymerization mechanism. The lowest dispersity polymers are those made by anionic and atom-transfer radical polymerization, which exhibit relatively narrow distributions DM=g,„1A172 — 1.02-1.04. This small divergence from monodispersity results in significant number of molecules that differ in their molecular weight from the average and their impact on the viscoelastic response remains an open question. Here the effects of low dispersity on stress relaxation and shear viscosity of entangled melts are studied using a coarse-grained model for polyethylene. Polymer melts with chain length dispersity set to follow a Schulz-Zimm distribution of Dm = 1.0 — 1.16 for an entangled polyethylene melt using molecular dynamic simulations. The systems were studied to times up to 800 ,us which is beyond the terminal time. These systems are compared to those with binary and ternary distributions. The stress relaxation functions were extracted from the Green-Kubo relation and from stress-strain relaxation following a uniaxial extension. We find on the entanglement time scale, both the mean squared displacement and the stress relaxation are independent of D m . The tube diameter and the rubbery plateau for entangled dynamics do not depend on D m . At longer times, the terminal relaxation time decreases as the faster motion of the shorter chains results in constraint release for the longer chains. Probing this low dispersity regime opens the way to evaluate the degree of dispersity that affects mechanical properties.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural and Dynamical Roles of Bound Polymer Chains in Rubber Reinforcement
The addition of nanofillers to rubber matrices is a powerful route to improve the mechanical properties. Here, we focus on a molecular understanding of basic mechanisms that are important for the reinforcement in rubbers. The key role in this process is ascribed to bound rubber (BR) that engages with the matrix as well as with adjacent nanofillers. To date, this understanding has been impeded by the lack of experimental tools to directly probe the BR chains buried in a polymer matrix composed of the same polymer. To tackle this challenge, we combine neutron scattering/spectroscopy techniques with isotope-labeling and molecular dynamics simulations. The system is a simplified carbon-black-filled polybutadiene. The combined experimental and computational results provide new insights into the local structural and dynamical heterogeneities of BR chains and their interactions with the matrix polymer, highlighting (i) the structural partition of the bound chains into three components (i.e., trains, loops, and tails) and their fractions; (ii) their dynamical hierarchies, i.e., the trains that remain immobile on the filler surface, the loops that are fairly large and hence allow the interdigitation of matrix chains, and the tails with their unique characteristics to reach far out into the matrix and entangle with matrix chains. These multiple roles of the constituent components of the BR chains promote the formation of a well-developed adhesive polymer–filler interface, enhancing the elastic property of a filled rubber. Finally, the comprehensive understanding derived and validated by the model rubber will be translatable to many other polymer nanocomposites.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Investigation of the Self-Assembly Behavior of Statistical Bottlebrush Copolymers via Self-Consistent Field Theory Simulations
Bottlebrush copolymers, a class of high-density side-chain-grafted copolymers with high molecular weights, have recently attracted extensive research attention due to the dramatic reduction of chain entanglement in these copolymers, unique self-assembly behaviors, and distinctive physical properties. In this study, we employ self-consistent field theory simulations to systemically investigate the phase behavior of statistical bottlebrush copolymers A-stat-B, an intriguing subclass of bottlebrush copolymers with random or alternating sequences of A and B side chains. We find that a broader variety of ordered mesophases can be stabilized in the melts of these copolymers relative to the more extensively studied bottlebrush block copolymers. In particular, we observe that these statistical copolymers can stabilize sphere phases over a larger range of species volume fractions than their diblock and tetrablock counterparts but require much higher segregation strength to achieve this. The sphere and hexagonally packed cylinder phases formed by conformationally symmetric statistical bottlebrush copolymers possess interesting discrete core–shell structures with the backbone and lower volume fraction side-chain species forming shells and cores, respectively. Moreover, we uncover a new strategy of stabilizing the Frank–Kasper phase A15 by introducing conformational asymmetry through different side-chain lengths and also observe deflection of order–order phase boundaries and significant mixing between the backbones and short side chains as conformational asymmetry is introduced.
36 MATERIALS SCIENCE↗
Assessing the Accuracy of Property Model Predictions for Cost Optimization of Desalination Technologies
Accurate modeling of seawater thermophysical and thermodynamic properties is critical for optimizing desalination processes. This study compares three seawater property models, a Reaktoro multicomponent model, the thermophysical seawater properties library from the Massachusetts Institute of Technology, and a simplified sodium chloride model, in the context of levelized cost of water (LCOW) minimization for reverse osmosis (RO) and mechanical vapor compression systems. Process simulations and cost optimizations reveal that although all three models yield comparable LCOW and specific energy consumption (SEC) estimates under baseline conditions, deviations among their predictions increase with salinity. Relative differences in LCOW and SEC reach up to 6% and 8%, respectively. RO results show greater variability due to differences in osmotic pressure predictions, which affect pressure constraints at high recoveries. Computational performance varies substantially; specifically, Reaktoro simulations are up to 28 times slower than empirical models due to their detailed equilibrium calculations. These results suggest that empirical models offer acceptable accuracy for routine desalination process design, while Reaktoro provides advantages in scenarios requiring detailed speciation, such as scaling or pH adjustment studies. These findings underscore the importance of selecting appropriate property models based on the modeling objective of desalination applications and motivate future work integrating thermodynamic rigor with empirical efficiency.
Physical and chemical properties↗
The Climate Response to Emissions Reductions Due to COVID-19: Initial Results From CovidMIP
Many nations responded to the COVID-19 pandemic by restricting travel and other activities during 2020, resulting in temporarily reduced emissions of CO 2 , other greenhouse gases and ozone and aerosol precursors. We perform a coordinated Intercomparison, CovidMIP, of Earth System model simulations to assess the impact on climate of these emissions reductions. Eleven models performed multiple initial-condition ensembles to produce over 280 simulations spanning both initial condition and model structural uncertainty. We find model consensus on reduced aerosol amounts (particularly over East Asia) and associated increases in surface shortwave radiation levels. However, any impact on near-surface temperature or rainfall during 2020-2024 is extremely small and is not detectable in this initial analysis. Regional analyses on a finer scale, and closer attention to extremes (especially linked to changes in atmospheric composition and air quality) are required to test the impact of COVID-19-related emission reductions on near-term climate.
54 ENVIRONMENTAL SCIENCES↗
Contribution of the Two Types of Ekman Pumping Induced Eddy Heat Flux to the Total Vertical Eddy Heat Flux
Based on eddy-rich (0.1° horizontal resolution for ocean) Community Earth System Model simulations, we compute the Ekman pumping induced vertical eddy heat flux using two formulations: the classical and the Stern-Ekman pumping. The two mechanisms yield similar patterns in the eddy-induced vertical heat flux, showing strong upward heat flux in ocean frontal regions such as the western boundary current regions. Using the Gulf Stream Extension region as an example, we estimate (1) the Stern-Ekman pumping induced eddy heat flux is 23% and 12% of the total vertical eddy heat flux at 50 m depth during summer and winter, respectively; (2) the classical Ekman pumping accounts for 82% and 88% of the Stern-Ekman pumping induced eddy heat flux at 50 m during summer and winter, respectively. The second finding indicates eddy current feedback on wind stress is the primary cause for the upward eddy heat flux generated by Ekman pumping.
58 GEOSCIENCES↗
The Potential of Stratospheric Aerosol Injection to Reduce the Climatic Risks of Explosive Volcanic Eruptions
Sulfur-rich volcanic eruptions happen sporadically. If Stratospheric Aerosol Injection (SAI) were to be deployed, it is likely that explosive volcanic eruptions would happen during such a deployment. Here we use an ensemble of Earth System Model simulations to show how changing the injection strategy post-eruption could be used to reduce the climate risks of a large volcanic eruption; the risks are also modified even without any change to the strategy. For a medium-size eruption (10 Tg-SO 2 ) comparable to the SAI injection rate, the volcanic-induced cooling would be reduced if it occurs under SAI, especially if artificial sulfur dioxide injections were immediately suspended. Alternatively, suspending injection only in the eruption hemisphere and continuing injection in the opposite would reduce shifts in precipitation in the tropical belt and thus mitigate eruption-induced drought. Finally, we show that for eruptions much larger than the SAI deployment, changes in SAI strategy would have minimal effect.
54 ENVIRONMENTAL SCIENCES↗