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At least 919 records · Page 51

Unraveling Hydrogen Induced Geochemical Reaction Mechanisms through Coupled Geochemical Modeling and Machine Learning

Underground hydrogen storage (UHS) provides a promising large-scale, long-term energy storage solution. A reasonable recovery of stored hydrogen is critical for a successful storage scheme. However, in subsurface reservoirs hydrogen is subject to active geochemical reactions that might result in hydrogen loss. In this study, we implemented a geochemical modeling approach coupled with an unsupervised machine learning technique called non-negative matrix factorization (NMF) to unravel the complex brine-rock-H 2 geochemical processes responsible for hydrogen losses, with particular focus on sulfate reduction reactions. NMF is applied to modeled mineral evolution and fluid component profiles to retrieve profiles that can be interpreted to more easily assess competing processes. NMF decouples simulated competing equilibrium reactions. This facilitates separation of overlapping reaction profiles from redox processes, dissolution fronts, and secondary precipitation while considering the effects of simulation parameters such as salinity, temperature, and total H 2 pressure. NMF successfully discriminates these competing effects in nonlinear ways, allowing robust interpretation. In addition, NMF reveals subtle coupled mineral associations and reaction fronts that are invisible to conventional model analysis. This integrated approach strengthens the conceptual understanding of complex nonlinear hydrogen-brine-rock interactions and advances geochemical research on UHS systems to resolve complexities in modeled geochemical systems without the need for direct experiments or prior knowledge. Furthermore, this study highlights the efficacy of combining geochemical modeling with machine learning techniques to enhance the interpretability of the intricate geochemical simulation output through deciphering the overlapping reaction path that cannot be achieved only using conventional analysis of geochemical models alone.

08 HYDROGEN↗

Bioenergy pathways within United States net-zero CO 2 emissions scenarios in the Energy Modeling Forum 37 study

The Energy Modeling Forum 37 study is organized around carbon dioxide (CO 2 ) mitigation scenarios reaching net-zero CO 2 emissions by 2050 in the United States. Here, this paper summarizes the potential contribution of bioenergy use in the electric power, transportation, industrial, and buildings sectors toward meeting that target based on model results. Thirteen modeling teams reported bioenergy consumption in the Reference and Net Zero scenarios. Consumption of bioenergy increased over time in the Reference scenario, from an average across models of 3.2 exajoules (EJ) in 2020 to 3.8 EJ in 2050. Average bioenergy consumption in 2050 increased further to 7.3 EJ in the Net Zero scenario. All scenarios that reach net-zero emissions required some form of carbon dioxide removal to offset emissions that are difficult to reduce. Carbon dioxide removal using bioenergy with CO 2 capture and storage (BECCS) varies widely across models, up to 1000 Mt CO 2 in 2050. Some models rely instead on direct air carbon capture and storage (DACCS), up to 2200 Mt CO 2 , and others use a combination of BECCS and DACCS. Model results show a strong inverse relationship between the amounts of BECCS and DACCS deployed. All modeling teams assumed a carbon sink from land use, land use change, and forestry, further offsetting a portion of emissions from fossil fuels and industry that are expensive to eliminate. Bioenergy consumption in 2050 decreased by an average of 1.5 EJ across eight models in a Net Zero+ scenario relative to the Net Zero scenario, due in part to a lower equilibrium carbon price resulting from optimistic cost assumptions for all energy technologies.

09 BIOMASS FUELS↗

Modeling wiggler with hard edge dipoles

Wigglers and undulators are used as devices for generating synchrotron radiation. They are also used for modification of various beam properties circulating in a storage ring. Basic ‘dumping wiggler’ is used for change of the damping time, equilibrium emittance, and energy spread. In damping wigglers are used to increase the damping rate of the energy spread induced by the beam-beam interaction. The commonly used MAD and Elegant software has only simplified planar wiggler configuration and no model for a helical wiggler.

43 PARTICLE ACCELERATORS↗

Modeling Nanosecond-Pulsed Spark Discharge and Flame Kernel Evolution

Dilute combustion, either using exhaust gas recirculation or with excess air, is considered a promising strategy to improve the thermal efficiency of internal combustion engines. However, the dilute air-fuel mixture, especially under intensified turbulence and high-pressure conditions, poses significant challenges for ignitability and combustion stability, which may limit the attainable efficiency benefits. In-depth knowledge of the flame kernel evolution to stabilize ignition and combustion in a challenging environment is crucial for effective engine development and optimization. To date, a comprehensive understanding of ignition processes that result in the development of fully predictive ignition models usable by the automotive industry does not yet exist. Spark-ignition consists of a wide range of physics that includes electrical discharge, plasma evolution, joule-heating of gas, and flame kernel initiation and growth into a self-sustainable flame. In this study, an advanced approach is proposed to model spark-ignition energy deposition and flame kernel growth. To decouple the flame kernel growth from the electrical discharge, a nanosecond-pulsed high-voltage discharge is used to trigger spark-ignition in an optically accessible small ignition test vessel with a quiescent mixture of air and methane. Initial conditions for the flame kernel, including its thermodynamic state and species composition, are derived from a plasma-chemical equilibrium calculation. The geometric shape and dimension of the kernel are characterized using a multi-dimensional thermal plasma solver. Here, the proposed modeling approach is evaluated using a high-fidelity computational fluid dynamics procedure to compare the simulated flame kernel evolution against flame boundaries from companion Schlieren images.

42 ENGINEERING↗

The role of cellular structure, non-equilibrium eutectic phases and precipitates on quasi-static strengthening mechanisms of as-built AlSi10Mg parts 3D printed via laser powder bed fusion

The quasi-static loading strengthening mechanism in the as-built state of an AlSi10Mg alloy 3D-printed via Laser Powder Bed Fusion (LPBF) was thoroughly identified and quantified using state-of-the-art electron microscopy and synchrotron X-ray diffraction techniques. The yield strength was comprehensively modelled through an in-depth characterization and quantification of the microstructural features as well as their effective volumes for strengthening. In particular, the non-equilibrium eutectic network was characterized with a two-fold structure: cell boundary particles as well as intracellular lamellar/fibrous networks, each consisting of discrete phases exhibiting a thru-thickness compositional gradient, a semi-coherent interface with the matrix and an abundance of crystal defects such as nano-sized sub-grains, microstrains and stacking faults. Further, these altogether made the eutectic phase the most potent contributor to the yield strength accounting for ~30–40% of the estimated value (i.e., cell boundary and eutectic network strengthening combined). Precipitates strengthening was identified as the second most potent mechanism via a shearing process only. Moreover, the presented methodology was able to capture the effect of LPBF processing variables on the individual strengthening contributions, e.g., the effect of a lower laser scanning speed on increasing the cell size as well as the mean precipitate size, which are shown to exhibit opposing impacts on strengthening.

36 MATERIALS SCIENCE↗

Mesoscale Modeling of Dislocation Cell Structure Evolution and Radiation-Induced Segregation in Additively Manufactured Austenitic Stainless Steel

Structural alloys under irradiation develop radiation-induced segregation (RIS) at point defect sinks, which lead to undesired changes in the alloy's properties. Additively manufactured austenitic stainless steels are expected to yield a distinct response to irradiation damage owing to their unique as-printed dislocation cell structure. In this talk, we present the development of a mesoscale model for dislocation cell structure evolution coupled with RIS using the MOOSE framework. The evolution of network dislocations within spatially distinct cells and cell walls are modeled using climb-mediated edge annihilation and generation processes. Starting with initial microstructures of as-printed non-equilibrium segregations at dislocation cell walls, our 2D and 3D simulations explore the effects of irradiation temperature, dose rate, dislocation sink bias, and specimen thickness on microstructure evolution. The results will be compared against experimental characterizations of in-situ and ex-situ ion-irradiated samples, and the implications of evolving cell structure on irradiation damage response will be discussed.

additive manufacturing↗

Semi-empirical model for Henry’s law constant of noble gases in molten salts

Henry’s law constant, which describes the proportionality of dissolved gas to partial pressure of free gas in liquid–gas equilibrium systems, can also be applied to mass transport applications. In this work, we investigated an approach for determining the solubility of noble gases in a molten salt liquid utilizing the equilibrium concept of Henry’s gas constant. Henry’s gas constant is described as a mathematical function dependent on the van der Waals radius of the noble gas and the temperature of the molten salt. The alteration in Gibbs free energy encompasses contributions from both surface and volume energies. Enthalpy and entropy are deduced from these surface and volume energies in the Gibbs free energy formulation. A comparative analysis was conducted between the conventional method and our proposed model. Moreover, useful chemical properties can be determined from examination of surface and volume energies. Our findings provide an accurate and general theory of Gibbs free energy that can be validated experimentally based on the model proposed herein. This work unifies the prediction of Henry gas constant and subsequently the entropy and enthalpy calculation for noble gases in a molten salt solution to a single functional form using van der Waals radius of the gas and temperature of the system. This functional form is then used to perform a multiple regression method to find two parameters corresponding to the surface energy and volume energy. These two parameters are consistent between all combinations of noble gas and molten salt.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Zonally dominated dynamics and Dimits threshold in curvature-driven ITG turbulence

The saturated state of turbulence driven by the ion-temperature-gradient instability is investigated using a two-dimensional long-wavelength fluid model that describes the perturbed electrostatic potential and perturbed ion temperature in a magnetic field with constant curvature (a $Z$ -pinch) and an equilibrium temperature gradient. Numerical simulations reveal a well-defined transition between a finite-amplitude saturated state dominated by strong zonal-flow and zonal temperature perturbations, and a blow-up state that fails to saturate on a box-independent scale. We argue that this transition is equivalent to the Dimits transition from a low-transport to a high-transport state seen in gyrokinetic numerical simulations (Dimits et al. , Phys. Plasmas , vol. 7, 2000, 969). A quasi-static staircase-like structure of the temperature gradient intertwined with zonal flows, which have patch-wise constant shear, emerges near the Dimits threshold. The turbulent heat flux in the low-collisionality near-marginal state is dominated by turbulent bursts, triggered by coherent long-lived structures closely resembling those found in gyrokinetic simulations with imposed equilibrium flow shear (van Wyk et al. , J. Plasma Phys. , vol. 82, 2016, 905820609). The breakup of the low-transport Dimits regime is linked to a competition between the two different sources of poloidal momentum in the system – the Reynolds stress and the advection of the diamagnetic flow by the $\boldsymbol {E}\times \boldsymbol {B}$ flow. By analysing the linear ion-temperature-gradient modes, we obtain a semi-analytic model for the Dimits threshold at large collisionality.

Physics↗

Modeling of deformation of battery cells using thick shell element formulation

Here, we describe a new approach for modeling nonlinear deformation and stress distribution of battery cells using a new thick shell finite element formulation with a through-thickness calculation of stresses and strains that satisfy equilibrium conditions. Battery cells are transversely layered materials that contain numerous thin layers in a repeating sequence. The layers are made of materials with significantly different mechanical responses. Explicit discretization of the layers is computationally impractical except for very small domains, while homogenized material models cannot account for stress and strain variations and partition through the thickness. The new formulation allows for calculation of the transverse and interlayer stresses based on the material properties of the individual cell layers. The application to problems where the transverse stresses have strong influence is also possible.

25 ENERGY STORAGE↗

Model for the Solid–Liquid Interfacial Free Energy at High Pressures

The free energy involved in the formation of an interface between two phases (e.g., a solid–liquid interface) is referred to as the interfacial free energy. For the case of solidification, the interfacial free energy dictates the height of the energy barrier required to nucleate stable clusters of the newly forming solid phase and is essential for producing an accurate solidification kinetics model using classical nucleation theory (CNT)-based methods. While various methods have been proposed for modeling the interfacial free energy for solid–liquid interfaces in prior literature, many of these formulations involve making restrictive assumptions or approximations, such as the system being at or near equilibrium (i.e., the system temperature is approximately equal to the melt temperature) or that the system is at pressures close to atmospheric. However, these approximations and assumptions may break down in highly non-equilibrium situations, such as in dynamic-compression experiments where metastable liquids that are undercooled by hundreds of kelvin or over-pressurized by several gigapascals or more are formed before eventually solidifying. We derive a solid–liquid interfacial free-energy model for such high-pressure conditions by considering the enthalpies of interactions between pairs of atoms or molecules. We also consider the contribution of interface roughness (disordering) by incorporating a multilayer interface model known as the Temkin n-layer model. Our formulation is applicable to a diverse variety of materials, and we demonstrate it by developing models specifically for two different materials: water and gallium. We apply our interfacial free-energy formulation to CNT-based kinetics simulations of several suites of dynamic-compression experiments that cause liquid water to solidify to the high-pressure solid polymorph ice VII and have found good agreement to the observed kinetics with only minor empirical fitting.

36 MATERIALS SCIENCE↗

Thermal conductivity of a laser plasma

Here, we present a model of the electron thermal conductivity of a laser-produced plasma. The model, supported by Vlasov–Fokker–Planck simulations, predicts that laser absorption reduces conductivity by forcing electrons out of a Maxwell–Boltzmann equilibrium, which results in depletion of both low-velocity bulk electrons and high-velocity tail electrons. We show that both the bulk and tail electrons approximately follow super-Gaussian distributions, but with distinct exponents that each depend on the laser intensity and wavelength through the parameter a = Zv$^{2}_{E}$/v$^{2}_{T}$. For a value of a = 0.5, tail depletion reduces the thermal conductivity to half its zero-intensity value. We present our results as simple analytic fits that can be readily implemented in any radiation-hydrodynamics code or used to correct the local limit of non-local conduction models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

OC6 project Phase IV: validation of numerical models for novel floating offshore wind support structures

Abstract. This paper provides a summary of the work done within Phase IV of the Offshore Code Comparison Collaboration, Continued with Correlation and unCertainty (OC6) project, under International Energy Agency Wind Technology Collaboration Programme Task 30. This phase focused on validating the loading on and motion of a novel floating offshore wind system. Numerical models of a 3.6 MW horizontal-axis wind turbine atop the TetraSpar floating support structure were compared using measurement data from a 1:43-Froude-scale test performed in the University of Maine's Alfond Wind–Wave (W2) Ocean Engineering Laboratory. Participants in the project ran a series of simulations, including system equilibrium, surge offsets, free-decay tests, wind-only conditions, wave-only conditions, and a combination of wind and wave conditions. Validation of the models was performed by comparing the aerodynamic loading, floating support structure motion, tower base loading, mooring line tensions, and keel line tensions. The results show a relatively good estimation of the aerodynamic loading and a reasonable estimation of the platform motion and tower base fore–aft bending moment. However, there is a significant dispersion in the dynamic loading for the upwind mooring line. Very good agreement was observed between most of the numerical models and the experiment for the keel line tensions.

17 WIND ENERGY↗

Assessment of Physics Models for Phase Transition Kinetics

The time dependence of phase diagrams and how to model rate dependent transitions remains one of the key unanswered questions in physics. When a material is loaded dynamically through equilibrium phase boundaries, it is the kinetics that determines the real time expression of a phase transition. Here we report the atomic and nanosecond-scale quantification of kinetics of shock-driven phase transition in multiple materials. We uniquely make use of a both a simple shock as well as shock-and-hold loading pathways compress different crystalline solids and induce structural phase transitions below melt. Coupling shock loading with time-resolved synchrotron x-ray diffraction (DXRD), we probe the structural transformations of these solids in the short-lived high pressure and temperature states generated. The novelty and power of using DXRD for the assessment of kinetics of phase transitions lies in the ability to discover and identify new phases and to examine kinetics without prior knowledge of a material's phase diagram. Our results provide a quantified expression and a physics model of kinetics of formation of high-pressure phases under shock loading: transition incubation time, evolution, completion time and crystallization rate.

36 MATERIALS SCIENCE↗

Dissociation-induced depletion of high-energy reactant molecules as a mechanism for pressure-dependent rate constants for bimolecular reactions

In 1922, Lindemann proposed the now-well-known mechanism for pressure-dependent rate constants for unimolecular reactions: reactant molecules with sufficiently high energies dissociate more quickly than collisions can reestablish the Boltzmann distribution of the internal energies of the molecule during its dissociation at low pressures – yielding pressure-dependent rate constants for unimolecular reactions due to the preferential depletion of the high energy states capable of dissociation. In the last century, incredible progress has been made in achieving a far greater understanding of and quantitative predictions for unimolecular and association reactions. In the modern era, pressure-dependent phenomenological rate constants are now nearly universally used to describe the rates of unimolecular and associative reactions in phenomenological kinetic modeling. However, there is a second, more indirect, implication of Lindemann’s mechanism that relates to how these dissociation-induced non-equilibrium distributions impact bimolecular reactions, including non-associative bimolecular reactions – which are generally not considered to have pressure-dependent rate constants. Yet, as we show herein, the same high energy states depleted due to dissociation would otherwise react most rapidly in high-activation-energy bimolecular reactions – yielding a mechanism for pressure-dependent rate constants for bimolecular reactions (including non-associative reactions). Here, we present results from a case study for CH 2 O dissociation, isomerization, and bimolecular reaction with O2 to explore this question. Results from our master equation calculations indicate that the effect of dissociation-induced non-equilibrium distributions on bimolecular reactions can be substantial – even when chemical timescales are well separated from internal energy relaxational timescales (i.e. when the traditional rate constant description would be thought to apply). This effect is found to be more pronounced – and more complex – for bimolecular reactions involving molecular entities whose chemical timescales are merged with the internal energy relaxational timescales. Lastly, we present some ideas for discussion regarding what should be considered as “chemical species” in phenomenological kinetic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transition Core Planning and Safety Analyses in Support of LEU Fuel Conversion of the University of Missouri Research Reactor (MURR)

The University of Missouri Research Reactor (MURR®) is one of six U.S. High Performance Research Reactors (USHPRR), including one critical facility, that is working with the National Nuclear Security Administration (NNSA) Office of Material Management and Minimization (M3) Reactor Conversion Program to convert from highly enriched uranium (HEU) to low-enriched uranium (LEU) fuel. The M3 Reactor Conversion USHPRR Project objectives include the development of LEU fuel element designs that will ensure safe reactor operations and to maintain the existing experimental performance of each facility. The work is being conducted through many inter-related activities being completed by four Project Pillars: Fuel Qualification (FQ), Fuel Fabrication (FF), Reactor Conversion (RC), and Cross Cutting (CC). A new type of LEU fuel based on an alloy of uranium-10 wt% molybdenum (U-10Mo) is expected to allow the conversion of those USHPRR, like MURR, requiring higher density fuels. The very-high-density LEU U-10Mo monolithic fuel is currently undergoing irradiation testing and post-irradiation examination under a planned and documented fuel qualification effort. The FQ Pillar will document fuel property and fuel performance data and qualify the fuel for use in these reactors. The FF Pillar is fabricating fuel for ongoing and future irradiation tests, as well as conducting fabrication demonstrations to validate or update preliminary fabrication assumptions. The FF Pillar is also working to develop and install commercial manufacturing capacity with the U-10Mo monolithic fuel to produce prototypic fuel. Working with the RC Pillar at Argonne, MURR has progressed through a preliminary fuel element design using preliminary data for the proposed monolithic alloy of U-10Mo. Analyses were completed in previous work that found for typical equilibrium operations with the preliminary LEU fuel element design, in conjunction with a power uprate to 12 MW and appropriate changes to the MURR Limiting safety system settings (LSSS), MURR will have adequate margins to safety for steady-state operations and postulated transient accidents and will have experimental performance in key locations that meets or exceeds current operations with HEU fuel. The purpose of this work is to develop a sequence of transition cycles that will enable MURR to transition from operation with the reactor core loaded with fresh LEU fuel elements only to typical equilibrium operations with mixed-burnup cores following conversion while meeting operational requirements on safety and experimental performance. It is expected that the use of fresh LEU fuel at conversion and subsequent low burnup of the LEU fuel elements that will initially be available for use following conversion will result in critical control blade positions that will substantially change the axial power distribution in the core and the neutron flux available in key experimental locations relative to equilibrium LEU operations. Given the constraints of MURR safety margins, operational practices, and production and research, a novel method has been developed to identify a transition sequence that minimizes the time MURR operates atypically compared to the current prototypic cycles using HEU fuel. The proposed transition sequence moves quickly to the same sort of equilibrium cycles for the LEU fuel that have already been evaluated in documented preliminary safety analyses. Although shifting the neutron flux peak to the lower half of the core during initial cycles with LEU at 12 MW reduces the experiment performance in some key locations relative to current HEU operations at 10 MW, all LEU cores provide an average performance that meets or exceeds that of HEU. An LEU cycle is reached that meets or exceeds the level of experimental performance predicted for current HEU and equilibrium LEU operations in more than 450 key locations identified by a reactor specialist at MURR by the 23rd cycle following conversion and that afterwards will enable MURR to consistently meet its experimental performance requirements. The proposed transition sequence only requires the fabrication of 34 fresh LEU elements in the first year of operation and does not exceed the anticipated availability of fresh elements that can be produced by the fuel fabricator. By the third year after conversion, 22 fresh LEU elements will be required each year, which is the same as expected for equilibrium LEU operations and the same as current operations with HEU fuel. The proposed transition sequence thus combines a relatively short time period before equilibrium burnup is achieved, a temporary increase of fuel elements needed annually relative to typical operations that are within the production capabilities of the fuel fabricator, and demonstrates comparable experimental performance of the LEU cores relative to current HEU operations. Further measures may be taken to reduce any initial experimental performance penalty even further, where possible, by repositioning certain experiments to leverage the increased performance in the lower axial experimental positions in the initial cycles following conversion or leaving the experiments in the irradiation facilities longer in order to achieve the required neutron fluence. This analysis may require refinement depending on the experimental facilities in use at the time of conversion. Nonetheless, the results presented here, including the experimental performance, core burnup, and critical control blade positions throughout the transition cycles, show that the proposed transition cycle fuel management patterns are consistent with what is expected and desired for MURR operation with LEU U-10Mo fuel. Detailed core power distributions from the neutronics models were also used to evaluate safety margins during steady-state operations for the selected transition cycles and the equilibrium LEU core. It is shown that there are adequate safety margins for both steady-state operations and postulated accident scenarios. For the steady-state operations with the preliminary LEU fuel element design the analysis predicts at least 2.49 MW margin to the onset of flow instability at the LSSS power of 15 MW. Considering the LSSS power is 125% of full license power, the margin to OFI is sufficient. In addition, the critical heat flux ratio at LSSS power is well above the requirement of CHFR > 2.0 from NUREG-1537 for all considered cases. For postulated transient accidents, the minimum margin to the fuel temperature safety limit is at least 109 °C. In summary, the proposed sequence of core loadings for MURR operations following conversion to LEU fuel and a power uprate to 12 MW provides sufficient safety margins for both steady-state operations and postulated transient accidents during a proposed sequence of transition cycles to equilibrium operations. Analysis has shown that there are some local experimental performance penalties during the initial cycles. Although there are local shifts in the experimental performance, on average all LEU cores at 12 MW have equal or higher performance than HEU at 10 MW. Temporary adjustments are being planned that will produce suitable experimental performance during these cycles. The results indicate that for the equilibrium LEU core the experimental performance exceeds that of current HEU operations in all key locations while also demonstrating sufficient safety margins.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Revising the dynamic energy budget theory with a new reserve mobilization rule and three example applications to bacterial growth

Dynamic energy budget (DEB) theory has been applied to model a wide range of organisms, including microbes. In the standard DEB model, biomass is partitioned into reserve and structural compartments, where reserve biomass is mobilized in a pseudolinear manner (while the reserve biomass density, defined as the ratio between reserve and structural biomass, decays linearly) to drive maintenance and the growth of structural biomass (and extracellular enzyme production if it is considered). However, the linear dynamics of the reserve biomass density makes the standard DEB model incapable of explaining the slowdown of microbial growth at high reserve density that is caused by macromolecular crowding effect which reduces biochemical reaction rates (a typical situation occurs when microbes are experiencing severe moisture stress) and is inconsistent with the observation that intracellular enzymatic reactions generally follow non-linear kinetics. By partitioning biomass into reserve, kinetic, and structural compartments, we show here that the Equilibrium Chemistry Approximation (ECA) kinetics can be used to represent enzymatically catalyzed reserve biomass mobilization that can then drive the kinetic and structural biomass synthesis. This revised DEB model better represents the tradeoff in ribosome allocation for structural growth and internal enzyme production, is structurally compatible with metabolic models of cell individuals, and includes the standard DEB model and the popular compromise model as special cases for representing population growth. We then applied the revised DEB model to interpret components of bacterial respiration, their dependence on substrate availability, and emergent microbial carbon use efficiency dynamics for an exponentially growing population. We found that the revised DEB model enables a better understanding of bacterial substrates use (carbon in our examples) than that can be derived from a few other models in the literature. In particular, the revised DEB model explains why carbon use efficiency may first increase, then plateau, and finally decrease with growth rate (and substrate uptake rate), as a function of proteomics. Additionally, the revised DEB model explains why the kinetic biomass compartment needs to be divided to reasonably incorporate proteomic control of microbial growth.

59 BASIC BIOLOGICAL SCIENCES↗

Incorporating dynamic recrystallization into a crystal plasticity model for high-temperature deformation of Ti-6Al-4V

During hot deformation of (α + β) titanium alloys, the simultaneous action of strain and temperature in the (α + β) regime facilitates dynamic recovery, dynamic recrystallization (DRX), and phase transformations via non-equilibrium paths. DRX is manifested in the form of fine recrystallized α or β grains. Here, in the present study, a two-phase crystal plasticity finite element framework (CP-DRX) has been developed which incorporates DRX kinetics into the crystal plasticity (CP) model to predict the flow characteristics of Ti-6Al-4V alloys during thermo-mechanical processing. The CP slip system parameters, as well as elastic properties from both α and β phases of Ti, are calibrated for different strain rate conditions. An EBSD-informed two-phase microstructure representation has been utilized in the CP-DRX framework to explore the time-dependent evolution of DRX microstructure and crystal orientation for different strain rate conditions. The proposed CP-DRX can capture the evolution of crystal orientation and plastic flow stress–strain response of polycrystalline Ti-6Al-4V during the deformation process. Furthermore, the proposed model is able to capture the softening behavior, observed in average stress–strain response from experiments performed using a Gleeble thermomechanical simulator and predict the recrystallization texture.

(α+ β)-Titanium (Ti) Alloys↗

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗