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At least 217 records · Page 12

Technical note: A modified formulation of dynamic energy budget theory for faster computation of biological growth

Abstract. The mass conservation equation in the presence of boundary fluxes and chemical reactions from non-equilibrium thermodynamics is used to derive a modified dynamic energy budget (mDEB) model. Compared to the standard dynamic energy budget (sDEB) model (Kooijman, 2009), this modified formulation does not place the dilution effect in the mobilization kinetics of reserve biomass, and it maintains the partition principle for reserve mobilization dynamics for both linear and non-linear kinetics. Overall, the mDEB model shares most features with the sDEB model. However, for biological growth that requires multiple nutrients, the mDEB model is computationally much more efficient by not requiring numerical iterations for obtaining the specific growth rate. In an example of modeling the growth of Thalassiosira weissflogii in a nitrogen-limiting chemostat, the mDEB model was found to have almost the same accuracy as the sDEB model while requiring almost half of the computing time of the sDEB model. Since the sDEB model has been successfully applied in numerous studies, we believe that the mDEB model can help improve the modeling of biological growth and the associated ecosystem processes in various contexts.

Tang, Jinyun↗

Non-equilibrium rate theory for polariton relaxation dynamics

We derive an analytic expression of the non-equilibrium Fermi’s golden rule (NE-FGR) expression for a Holstein–Tavis–Cumming Hamiltonian, a universal model for many molecules collectively coupled to the optical cavity. These NE-FGR expressions capture the full-time-dependent behavior of the rate constant for transitions from polariton states to dark states. The rate is shown to be reduced to the well-known frequency domain-based equilibrium Fermi’s golden rule (E-FGR) expression in the equilibrium and collective limit and is shown to retain the same scaling with the number of sites in non-equilibrium and non-collective cases. We use these NE-FGR to perform population dynamics with a time-non-local and time-local quantum master equation and obtain accurate population dynamics from the initially occupied upper or lower polariton states. Furthermore, NE-FGR significantly improves the accuracy of the population dynamics when starting from the lower polariton compared to the E-FGR theory, highlighting the importance of the non-Markovian behavior and the short-time transient behavior in the transition rate constant.

Chemical dynamics↗

0D Modeling of Reactor Networks Within Zuzax

We report on progress in developing macroscopic balance equations for combustion and electrochemistry systems. A steady state solution capability is described for the macroscopic reactor network, with an associated steady state continuation method and solution storage capability added in. An example is provided of continuation of a hydrogen flame versus the equivalence ratio. The reactor modeling capability is extended to charged fluid systems, with a description of the new ChargedFluidReactor, SubstrateElement, and MetalCurrentElement reactor classes and novel setup of unknowns within these reactors that preserve charge neutrality. Zuzax's setup for electrochemistry is explained including the specification of the electron chemical potential and the adherence to the SHE Reference electrode specification. The description of the different ways to enter electrochemical reaction rates are described, contrasted, and their derivations with respect to one another are derived. An example of using the ChargedFluidReactor within corrosion problems is provided. We present a description of calculations to understand the phenomena of corrosion of copper from a micron sized droplet of NaCl water droplet, where secondary spreading occurs. An analysis of the discrepancies with experiment is carried out, demonstrating that macroscopic balances can be an important tool for understanding what major factors need to be addressed for a better understanding of a physical system.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

A multi-region approach for the analysis of porous materials and gas-solid reactions using USAXS-SAXS-WAXS: application to CaO carbonation

The reaction rate of gas-solid non-catalytic reactions is typically investigated using reactant conversion data over time and ex-situ measurements of the porous solid reactant textural properties; these data enable the experimental estimation of the initial intrinsic reaction rate, whereas the evolution of the textural properties and the reaction rate over time are evaluated theoretically using reaction models. In this work, a different methodology is presented, based on: a) in-situ time-resolved USAXS-SAXS-WAXS measurements of the solid sample, and b) a multi-region modeling approach; this methodology allows for the estimation of the textural properties and the intrinsic reaction rate at any time during the reaction. Referring to a reaction in which a solid product is obtained from a solid reactant and a gaseous reactant, the porous particle is described as consisting of several distinct regions with different microstructural properties, and both a gas-solid reaction model and a SAXS model are derived and applied to the carbonation of porous CaO. The proposed reaction model highlights the role of the inaccessible reactant and accurately predicts the solid reactant conversion versus time profile. The SAXS model accurately predicts the measured linear trends of the Porod invariant and of the pre-factor of the power law scattering profile versus CaO mass fraction; in the absence of chemical reactions, the proposed equations extend classical SAXS theory to porous materials containing macropores and nonporous solid phases in addition to standard nanoscale inhomogeneous regions.

CO2 solid sorbents↗

Numerical simulations of the Los Alamos gapstick experiment

The gapstick is a high explosive (HE) sensitivity test recently developed at Los Alamos. The experiment design was motivated by the traditional gap test and consists of a series of HE and inert pellets in a rate stick configuration. The inert pellets are made increasingly longer so that eventually the attenuated shock is unable to initiate the next HE pellet. While the gapstick is a mechanically simple experiment it poses several challenges for numerical simulation. In particular, accurately modeling the HE initiation and detonation phenomena requires a reactive burn model with sufficient mesh resolution to capture the reaction scales. In this work, the Scaled Uniform Reactive Front (SURF) and Arrhenius Wescott-Stewart-Davis (AWSD) burn models are used for simulations of a PBX 9501 (95 wt% HMX, 5% binder) gapstick. Furthermore, the material model for the inert pellet material, Polyvinylidene Fluoride (PVDF), has a direct influence on the shock propagation and a new equation of state (EOS) calibration for PVDF is developed using available Hugoniot data. Despite some challenges, the simulations are able to reasonably predict shock transit velocities and detonation failure in the gapstick.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Opportunities and challenges in process modeling and simulation of electrochemical systems

Electrochemical technologies have garnered intense interest in both academic research and industrial applications due to their potential to increase energy efficiency and reduce carbon footprint. However, electrochemical process fundamentals have been absent from the chemical process simulators available to millions of chemical engineers worldwide. To expedite process research and development of electrochemical technologies in the chemical industry, it is imperative that essential electrochemical process fundamentals be incorporated into process simulators to support modeling and simulation of electrochemical processes. Here, this study examines three process fundamentals key to the research and development of electrochemical processes: electrochemical reaction kinetics, electrolyte thermodynamics, and heat and mass transfer. It further illustrates application of these process fundamentals with a case study modeling an electrochemical process for the conversion of acrylonitrile to adiponitrile. The modeling example highlights the roles of applied voltage on reaction rates, and electron flow rates on the performance of electrochemical processes. It suggests that the applied voltage and electron flow rates are two unique concepts that should be included in simulators for electrochemical processes.

09 BIOMASS FUELS↗

Fluid-Kinetic Coupling: Advanced Discretizations for Simulations on Emerging Heterogeneous Architectures (LDRD FY20-0643)

Plasma physics simulations are vital for a host of Sandia mission concerns, for fundamental science, and for clean energy in the form of fusion power. Sandia's most mature plasma physics simulation capabilities come in the form of particle-in-cell (PIC) models and magnetohydrodynamics (MHD) models. MHD models for a plasma work well in denser plasma regimes when there is enough material that the plasma approximates a fluid. PIC models, on the other hand, work well in lower-density regimes, in which there is not too much to simulate; error in PIC scales as the square root of the number of particles, making high-accuracy simulations expensive. Real-world applications, however, almost always involve a transition region between the high-density regimes where MHD is appropriate, and the low-density regimes for PIC. In such a transition region, a direct discretization of Vlasov is appropriate. Such discretizations come with their own computational costs, however; the phase-space mesh for Vlasov can involve up to six dimensions (seven if time is included), and to apply appropriate homogeneous boundary conditions in velocity space requires meshing a substantial padding region to ensure that the distribution remains sufficiently close to zero at the velocity boundaries. Moreover, for collisional plasmas, the right-hand side of the Vlasov equation is a collision operator, which is non-local in velocity space, and which may dominate the cost of the Vlasov solver. The present LDRD project endeavors to develop modern, foundational tools for the development of continuum-kinetic Vlasov solvers, using the discontinuous Petrov-Galerkin (DPG) methodology, for discretization of Vlasov, and machine-learning (ML) models to enable efficient evaluation of collision operators. DPG affords several key advantages. First, it has a built-in, robust error indicator, allowing us to adapt the mesh in a very natural way, enabling a coarse velocity-space mesh near the homogeneous boundaries, and a fine mesh where the solution has fine features. Second, it is an inherently high-order, high-intensity method, requiring extra local computations to determine so-called optimal test functions, which makes it particularly suited to modern hardware in which floating-point throughput is increasing at a faster rate than memory bandwidth. Finally, DPG is a residual-minimizing method, which enables high-accuracy computation: in typical cases, the method delivers something very close to the $L^2$ projection of the exact solution. Meanwhile, the ML-based collision model we adopt affords a cost structure that scales as the square root of a standard direct evaluation. Moreover, we design our model to conserve mass, momentum, and energy by construction, and our approach to training is highly flexible, in that it can incorporate not only synthetic data from direct-simulation Monte Carlo (DSMC) codes, but also experimental data. We have developed two DPG formulations for Vlasov-Poisson: a time-marching, backward-Euler discretization and a space-time discretization. We have conducted a number of numerical experiments to verify the approach in a 1D1V setting. In this report, we detail these formulations and experiments. We also summarize some new theoretical results developed as part of this project (published as papers previously): some new analysis of DPG for the convection-reaction problem (of which the Vlasov equation is an instance), a new exponential integrator for DPG, and some numerical exploration of various DPG-based time-marching approaches to the heat equation. As part of this work, we have contributed extensively to the Camellia open-source library; we also describe the new capabilities and their usage. We have also developed a well-documented methodology for single-species collision operators, which we applied to argon and demonstrated with numerical experiments. We summarize those results here, as well as describing at a high level a design extending the methodology to multi-species operators. We have released a new open-source library, MLC, under a BSD license; we include a summary of its capabilities as well.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Hydro-chemo-mechanical phase field formulation for corrosion induced cracking in reinforced concrete

Steel corrosion induced cracking in reinforced concrete structures is often caused by volumetric straining at the steel-concrete interface. This volumetric strain is mainly controlled by the rate of generation of corrosion product, which depends on the diffusion of Cl{sup −} and dissolved O{sub 2} as well as the chemical reaction at the steel-concrete interface. While many numerical modeling techniques have been proposed to tackle this complex phenomenon, most have been limited to using staggered solution schemes, where the diffusion, chemical reaction, mechanical strain, and crack fields are solved for separately. Unfortunately, such approaches introduce numerical errors that can lead to unrealistic predictions. Therefore, a coupled solution, is needed to remove the formulation induced errors and understand this complex phenomenon. To provide a unifying solution framework for corrosion induced cracking in reinforced concrete, a phase field formulation is presented and implemented with FEM algorithms. The governing equations are derived from the system's free energy and Fick's law of diffusion. The proposed formulation was first validated in 1D by comparing the modeling results with the semi-analytical solution approximated via Laurent series to avoid singularities in the complex domain. 2D plane strain solutions to the embedded rebar undergoing corrosion induced cracking with pre-cracks are also presented and compared with the approximated solutions from linear elastic fracture mechanics theory (LEFM). The modeling of crack propagation enabled by the proposed formulation is also presented along with parametric studies to reveal the roles of the fracture toughness and permeability of the concrete on the corrosion induced cracking. A case study was also conducted on H-pile steel with concrete jackets to demonstrate the feasibility of modeling corrosion induced fracture in reinforced concrete structures with complex steel-concrete interfaces.

36 MATERIALS SCIENCE↗

Automated theoretical chemical kinetics: Predicting the kinetics for the initial stages of pyrolysis

Large scale implementation of high level computational theoretical chemical kinetics offers the prospect for dramatically improving the fidelity of combustion chemical modeling. To facilitate such efforts, we have developed a suite of codes, collectively referred to as AutoMech, that allow for the automatic prediction of the kinetics for large sets of reactions via ab initio transition-state-theory based master-equation calculations. The primary input is simply the mechanism, a dictionary relating chemically identifiable species descriptors (e.g., SMILES or InChIs) to species labels in the mechanism, and a specification of the electronic structure and transition state theory models to be implemented. Here we illustrate the current utility of AutoMech through a study of the initial stages of pyrolysis for 3 sets of fuels: sequences of alkanes, alcohols, and aldehydes. For simplicity, the analysis focuses on abstractions from the fuel by H, CH 3 , and OH, and the decomposition of the resulting radicals. Altogether, there are a total of 166 input channels in these sets (more than 363 forward reactions when expanded to the full set of elementary reactions). The code successfully produces high quality rate estimates (with apparent uncertainties less than a factor of two in limited comparisons with experiment) for > 95% of these. For the radical decomposition reactions, the analysis includes predictions for the pressure dependence of the kinetics. This wide-ranging exploration illustrates (i) the effect of different levels of prediction on the expected accuracy, (ii) the branching between abstractions at different sites for different abstractors, (iii) the dependence of the rates on the chemical structure, and (iv) the variation in radical stabilities across chemical families. These results, as well as the demonstrated feasibility of the methodology, should find further utility in the development of accurate rate expressions for arbitrary fuels. (c) 2020 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Elliott, Sarah N.↗

Investigating shock-induced chemical reactions in Ni+Al multilayers: A continuum-based mesoscale approach with Arrhenius kinetics and artificial thermal conduction

A new continuum-based mesoscale modeling approach for shock-induced chemical reactions (SICRs) in Ni+Al multilayers is demonstrated in Sandia’s shock physics hydrocode, CTH. The approach utilizes Arrhenius-type kinetics and artificial thermal conduction. Our work builds upon previous efforts to parameterize equations of state for Ni x Al y [J. Appl. Phys. 137, 075102 (2025)], as well as simulations of inert shocks in realistic 2D microstructures [J. Appl. Phys. 137, 225301 (2025)]. To calibrate the reaction kinetics, pairs of the reaction coordinate, R′, vs time are extracted from the molecular dynamics (MD) literature. Here, the MD-informed kinetics are used to simulate the dynamic evolution of pressure and temperature in 2D mesoscale simulations. Overall, the MD-informed kinetics obtained for planar interfaces are too slow, as initial reaction is not observed on a nanosecond time scale. Even with quasi-periodic shock focusing leading to the formation of so-called “hot-spots,” the hot spots are unable to grow and coalesce using the fitted Arrhenius rate constants. However, by increasing the rate constants by two orders of magnitude, SICRs are observed at a shock pressure near 30 GPa, which is supported by experiments. Consequently, these mesoscale simulations suggest that unresolved shear-based mechanical mixing might possibly account for the discrepancies in kinetic rates, with shock-generated intense perturbations, interfacial vortical flows, and elevated temperatures serving as favorable reaction conditions. Future work will calibrate a shear-dependent reaction rate from the MD simulations with realistic interfaces that are wavy, diffuse, and disordered.

Kittell, David E. [Sandia National Laboratories (S↗

Addressing Limitations of the Endpoint Slippage Analysis

Some rate of oxidation and reduction side-reactions will inevitably coexist in most rechargeable batteries. While parasitic reduction traps electrons, parasitic oxidation donates electrons to the cell’s inventory and may cause temporary capacity gain. Consequently, capacity measurements can provide unreliable information about the total extent of side-reactions occurring in the cell. The most widely used method to determine the rate of both these parasitic processes involves analyzing the slippage of endpoints, which consists in tracking the termination of cell charge and discharge when data is represented along a cumulative capacity axis. Here, we argue that this approach could lead to inaccuracies when applied to certain systems, which includes Si electrodes in Li-ion batteries and hard carbon in Na-ion batteries. This inaccuracy originates from the smooth nature of the voltage profiles of these materials at low and high alkali-ion content, causing the termination of charge and discharge to be dictated by voltage changes at both the positive and negative electrodes. We analyze this issue in quantitative terms and propose equations that can provide true rates of parasitic processes from experimental endpoint slippage data. This work shows that, in battery science, well-established analytical approaches may not be directly transferrable to new electrode systems.

25 ENERGY STORAGE↗

Robustness of neutron star merger simulations to changes in neutrino transport and neutrino-matter interactions

Binary neutron star mergers play an important role in nuclear astrophysics: Their gravitational wave and electromagnetic signals carry information about the equation of state of cold matter above nuclear saturation density, and they may be one of the main sources of r-process elements in the Universe. Neutrino-matter interactions during and after merger impact the properties of these electromagnetic signals and the relative abundances of the produced r-process elements. Existing merger simulations are, however, limited in their ability to realistically model neutrino transport and neutrino-matter interactions. Here, we perform a comparison of the impact of the use of state-of-the art two-moment or Monte Carlo transport schemes on the outcome of merger simulations, for a single binary neutron star system with a short-lived neutron star remnant [(5–10) ms]. We also investigate the use of different reaction rates in the simulations. While the best transport schemes generally agree well on the qualitative impact of neutrinos on the system, differences in the behavior of the high-density regions can significantly impact the collapse time and the properties of the hot tidal arms in this metastable merger remnant. The chosen interaction rates and transport algorithm as well as recent improvements by Radice et al. to the two-moment algorithms can all contribute to changes at the (10–30)% level in the global properties of the merger remnant and outflows. Furthermore, the limitations of previous moment schemes fixed by Radice et al. also appear sufficient to explain the large difference that we observed in the production of heavy-lepton neutrinos in a previous comparison of Monte Carlo and moment schemes in the context of a low-mass binary neutron star system.

79 ASTRONOMY AND ASTROPHYSICS↗

Probing reaction channels via reinforcement learning

Abstract Chemical reactions are dynamical processes involving the correlated reorganization of atomic configurations, driving the conversion of an initial reactant into a result product. By virtue of the metastability of both the reactants and products, chemical reactions are rare events, proceeding fleetingly. Reaction pathways can be modelled probabilistically by using the notion of reactive density in the phase space of the molecular system. Such density is related to a function known as the committor function, which describes the likelihood of a configuration evolving to one of the nearby metastable regions. In theory, the committor function can be obtained by solving the backward Kolmogorov equation (BKE), which is a partial differential equation (PDE) defined in the full dimensional phase space. However, using traditional methods to solve this problem is not practical for high dimensional systems. In this work, we propose a reinforcement learning based method to identify important configurations that connect reactant and product states along chemical reaction paths. By shooting multiple trajectories from these configurations, we can generate an ensemble of states that concentrate on the transition path ensemble. This configuration ensemble can be effectively employed in a neural network-based PDE solver to obtain an approximation solution of a restricted BKE, even when the dimension of the problem is very high. The resulting solution provides an approximation for the committor function that encodes mechanistic information for the reaction, paving a new way for understanding of complex chemical reactions and evaluation of reaction rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Real-Time Observation of the Diffusion Mechanism Progression from Liquid to Solid State of Transition Metal Complexes

Copper complexes have recently shown remarkable performance upon conversion from liquid-based to solid-state hole transport materials (HTMs) in mesoscopic solar cells; however, the diffusion mechanism is not clear. Here, we apply an in situ solidification analysis of the charge diffusion and find that the dominant mechanism of [Cu(dmbpy) 2 ] 2+/+ (dmbpy = 6,6'-dimethyl-2,2'-bipyridine) changes from ionic to electronic diffusion. Through use of the modified Dahms–Luff equation, a fast self-exchange rate constant of hole-hopping in the HTM of 8.3 × 10 8 (±5 × 10 7 ) M –1 s –1 is calculated, which indicates a small reorganization energy of 0.47 eV. These findings present a new methodology to analyze the transport mechanism of solids, reveal the mechanism of charge transport in molecular-based HTMs, and offer insight into ways to control the flow of charge in optoelectronic systems

14 SOLAR ENERGY↗

The role of collisional energy transfer in the thermal and prompt dissociation of 1-methyl allyl

Collisional energy transfer plays a pivotal role in a-priori calculations of the pressure-dependent rate constants obtained from a master equation. However, accurate determinations of collisional energy transfer parameters are rare and so most kinetic studies rely on best-fits of these parameters to experimental measurements (if available) or estimates guided from literature studies. In this work, we have quantified the effect of the uncertainty in energy transfer parameters on the thermal and prompt dissociation kinetics of a resonance stabilized radical, 1-methyl allyl (1MA), of relevance to the combustion of 1- and 2-butene isomers. Simulations using literature kinetics models were performed to assess the impact of these uncertainties on flame propagation and speciation data in laminar flames of 1- and 2-butene. Analyses of the uncertainty propagated by the energy transfer parameters for 1MA dissociation to the flame simulations, in particular the laminar flame speed, indicate an intricate coupling between the kinetics of 1MA dissociation (chain propagation) and its reaction with H-atoms (chain-termination). Ab-initio based theoretical calculations were also performed to obtain pressure-dependent kinetics for the reaction of 1MA with H-atoms. Lastly, theoretically calculated energy transfer parameters were used to best characterize the kinetics and branching between the chain propagating 1MA dissociation and the chain-terminating reaction 1MA + H.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The role of energy transfer and competing bimolecular reactions in characterizing the unimolecular dissociations of allylic radicals

Resonantly stabilized radicals (RSR's) such as allylic radicals typically have bond energies exceeding 45 kcal/mol and are therefore reasonably long-lived up to quite high temperatures. Consequently, kinetics of the unimolecular dissociations and bimolecular reactions of these long-lived RSR's assume significance in high temperature chemically reacting systems such as in flames. Our recent analyses (J. Cho et al., Proc. Comb. Inst., 2022) of the uncertainty propagated by the energy transfer parameters for 1-methylallyl (1MA) dissociation to the laminar flame speed, indicates an intricate coupling between the kinetics of 1MA dissociation (chain propagation) and its reaction with H-atoms (chain-termination). Here, this work extends such analyses to other C 3 – C 5 allylic radicals: allyl, 2-methylallyl, 1,1-dimethylallyl, 1,2-dimethylallyl, and 1,3-dimethylallyl. Theoretical kinetics for the C 3 – C 4 allylic radicals were taken from prior literature studies (J.A. Miller et al., J. Phys. Chem., 2008; J. Cho et al., Proc. Comb. Inst., 2022; R.S. Tranter et al., Proc. Comb. Inst., 2017). Potential energy surfaces were newly computed for the dissociations of the larger C5 allylic radicals and the reactions of these radicals with H-atoms. These PES's were then used to calculate rate constants for the relevant unimolecular and bimolecular reactions. Energy transfer has a crucial role to play in these pressure-dependent reactions and therefore the present kinetics calculations relied on a-priori predictions of collisional energy transfer parameters to best characterize the branching between chain propagating unimolecular dissociations of these allylic radicals and chain terminating bimolecular reactions of these RSR's with H-atoms. Prompt dissociations are now established to be a universal feature of free radical dissociations. Here we have also characterized the propensity for prompt dissociations in these more-stable allylic RSR's and their role in combustion simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mixed quantum–classical approach to model non-adiabatic electron–nuclear dynamics: Detailed balance and improved surface hopping method

We develop a density matrix formalism to describe coupled electron–nuclear dynamics. To this end, we introduce an effective Hamiltonian formalism that describes electronic transitions and small (quantum) nuclear fluctuations along a classical trajectory of the nuclei. Using this Hamiltonian, we derive equations of motion for the electronic occupation numbers and for the nuclear coordinates and momenta. We show that, in the limit, when the number of nuclear degrees of freedom coupled to a given electronic transition is sufficiently high (i.e., the strong decoherence limit), the equations of motion for the electronic occupation numbers become Markovian. Furthermore, the transition rates in these (rate) equations are asymmetric with respect to the lower-to-higher energy transitions and vice versa. In thermal equilibrium, such asymmetry corresponds to the detailed balance condition. We also study the equations for the electronic occupations in the non-Markovian regime and develop a surface hopping algorithm based on our formalism. To treat the decoherence effects, we introduce additional “virtual” nuclear wave packets whose interference with the “real” (physical) wave packets leads to the reduction in coupling between the electronic states (i.e., decoherence) as well as to the phase shifts that improve the accuracy of the numerical approach. Remarkably, the same phase shifts lead to the detailed balance condition in the strong decoherence limit.

74 ATOMIC AND MOLECULAR PHYSICS↗