Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “dynamic 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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,441 records · Page 80
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The effect of protein mutations on drug binding suggests ensuing personalised drug selection

The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied 50 breast cancer patients belonging to a population-cohort in the state of Qatar. From Sanger sequencing, we identified several new deleterious mutations in the estrogen receptor 1 gene (ESR1). The effect of these mutations on drug treatment in the protein target encoded by ESR1, namely the estrogen receptor, was achieved via rapid and accurate protein–ligand binding affinity interaction studies which were performed for the selected drugs and the natural ligand estrogen. Four nonsynonymous mutations in the ligand-binding domain were subjected to molecular dynamics simulation using absolute and relative binding free energy methods, leading to the ranking of the efficacy of six selected drugs for patients with the mutations. Our study shows that a personalised clinical decision system can be created by integrating an individual patient’s genomic data at the molecular level within a computational pipeline which ranks the efficacy of binding of particular drugs to variant proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Computational approaches to model X-ray photon correlation spectroscopy from molecular dynamics

X-ray photon correlation spectroscopy (XPCS) allows for the resolution of dynamic processes within a material across a wide range of length and time scales. X-ray speckle visibility spectroscopy (XSVS) is a related method that uses a single diffraction pattern to probe ultrafast dynamics. Interpretation of the XPCS and XSVS data in terms of underlying physical processes is necessary to establish the connection between the macroscopic responses and the microstructural dynamics. To aid the interpretation of the XPCS and XSVS data, we present a computational framework to model these experiments by computing the X-ray scattering intensity directly from the atomic positions obtained from molecular dynamics simulations. We compare the efficiency and accuracy of two alternative computational methods: the direct method computing the intensity at each diffraction vector separately, and a method based on fast Fourier transform that computes the intensities at all diffraction vectors at once. Furthermore, the computed X-ray speckle patterns capture the density fluctuations over a range of length and time scales and are shown to reproduce the known properties and relations of experimental XPCS and XSVS for liquids.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Broadening of the drumhead-mode spectrum due to in-plane thermal fluctuations of two-dimensional trapped ion crystals in a Penning trap

Two-dimensional crystals of ions stored in Penning traps are a leading platform for quantum simulation and sensing experiments. For small amplitudes, the out-of-plane motion of such crystals can be described by a discrete set of normal modes called the drumhead modes, which can be used to implement a range of quantum information protocols. However, experimental observations of crystals with Doppler-cooled and even nearground- state-cooled drumhead modes reveal an unresolved drumhead-mode spectrum. In this work, we establish in-plane thermal fluctuations in ion positions as a major contributor to the broadening of the drumhead-mode spectrum. In the process, we demonstrate how the confining magnetic field leads to unconventional in-plane normal modes, whose average potential and kinetic energies are not equal. This property, in turn, has implications for the sampling procedure required to choose the in-plane initial conditions for molecular-dynamics simulations. Further, for current operating conditions of the NIST Penning trap, our study suggests that the two-dimensional crystals produced in this trap undergo in-plane potential-energy fluctuations of the order of 10mK. Our study therefore motivates the need for designing improved techniques to cool the in-plane degrees of freedom.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Polarizable Water Potential Derived from a Model Electron Density

A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Plasma hydrodynamics from mean force kinetic theory

Mean force kinetic theory is used to evaluate the electrical conductivity, thermal conductivity, electrothermal coefficient, thermoelectric coefficient, and shear viscosity of a two-component plasma. The results are compared with molecular dynamics simulations. These simulations are made possible by assuming a repulsive Coulomb force for all interactions. Good agreement is found for all coefficients up to a Coulomb coupling strength of Γ ≈ 20. This is over 100-times larger than the coupling strength at which traditional theories break down. It is concluded that mean force kinetic theory is a promising framework for extending hydrodynamics to dense plasmas.

Electrical conductivity↗
DOE OSTI2025

Ferroelectric phase transition in group-IV monochalcogenides from an equivariant machine learned force field

Group-IV monochalcogenides are a class of layered ferroelectric semiconductors that have demonstrated spontaneous intrinsic polarization above room temperature. Here, in this study, we use the multi-atomic cluster expansion (MACE) machine learning architecture to train and test a force field capable of modeling the structural properties and second-order ferroelectric-to-paraelectric phase transition in a Group-IV monochalcogenide, GeSe. The model captures the double-well potential energy surface associated with the onset of macroscopic polarization in bulk GeSe within 12.5 meV/atom, as well as near-equilibrium properties like the phonon dispersion. The development of this quantitatively accurate force field enables long-time molecular dynamics simulations, which predict the critical temperature of the ferroelectric-to-paraelectric phase transition in bulk GeSe to be T c = 600 K. This study demonstrates the capabilities of equivariant force-fields to accurately describe phenomena associated with structural symmetry breaking.

ferroelectricity↗
DOE OSTI2024

Neutrons in Structural Biology: Challenges and Opportunities (Workshop Report)

Gaining a thorough understanding of biological systems requires building our knowledge about biological processes from the level of atoms and electrons, and up to whole organisms. Such comprehensive knowledge will allow for a predictive understanding of complex biological systems behavior. It will guide us in the design and development of novel therapeutics and vaccines to tackle existing health threats and to prepare for future pandemics, and it will provide information necessary to create new biomaterials and bio-inspired technologies through manipulation of biological macromolecules, their assemblies, single cells and even microorganisms. Reaching these goals will require a synergistic combination of multiple experimental techniques with molecular calculations and predictive simulations, and the design and development of new techniques and capabilities that bridge current knowledge and technology gaps. Neutron scattering provides unique information about the biomacromolecular structure and function and can play a major role in achieving these goals. A workshop was held to engage the scientific community in identifying pressing challenges in biochemistry, structural biology, enzymology and structure-guided drug design not solved with the current neutron scattering technologies or utilizing other structural biology techniques such as X-ray crystallography, NMR, and cryo-EM. The workshop brought together structural biology, biochemistry and computational experts, as well as early career researchers and students, creating a forum for discussing scientific advancement and collaboration. The workshop included a one-day satellite training workshop where graduate students and postdoctoral researchers were educated in the application of neutron crystallography and small-angle scattering in structural biology. Furthermore, the Instrument Scientific Advisory Board (ISAB) for the development of a macromolecular neutron diffractometer at ORNL’s Second Target Station was introduced at the workshop. The major outcome was that neutrons can provide atomic-level understanding of biomacromolecular structure, function and dynamics which is of paramount importance for addressing the identified challenges. Neutron crystallography, in particular, can resolve long-standing biochemical issues regarding enzyme function by delineating the underlying chemistry and can have a major impact on the design of small-molecule therapeutics, especially in combination with molecular computation (quantum chemistry and molecular dynamics simulations) and the emerging artificial intelligence (AI)-assisted drug design technologies. The unique properties of neutrons, including their high sensitivity to hydrogen and their non-destructive nature, make them ideal probes of biological matter. There is a palpable need in the scientific community to expand and enhance the impact of neutron sciences on biology. Neutron crystallography is the only structural biology method capable of determining positions of all hydrogen atoms in proteins, nucleic acids and their complexes at near-physiological temperatures and of unstable species at cryogenic temperatures. Moreover, neutron analysis is non-ionizing, non-destructive and does not perturb the structure or redox chemistry of active site metal centers and clusters in proteins, which can be invaluable for studying radiation-sensitive metalloprotein complexes. Further, neutron energies used in scattering applications are similar to atomic motions, permitting neutron spectroscopies to characterize the dynamics of biomacromolecules on the picosecond to microsecond timescales. The different sensitivities of neutrons to protium (H) and deuterium (D) isotopes of hydrogen allow enhanced visibility of specific parts of biological complexes through isotopic labeling. The impact of neutrons will be most powerful when neutron scattering is combined with complementary experimental techniques that use photons and electrons, and with high-performance computing. The interconnection and mutuality of the experimental and theoretical capabilities will drive discoveries in biological and health sciences to generate more complete picture of complex biological systems. The major limitation in the field of biological neutron crystallography has been signal-to-noise, demanding large samples that are difficult to produce for the majority of biomacromolecules and limiting the applicability of this technique in biological sciences. A neutron crystallography instrument at the Second Target Station will revolutionize biological science with neutrons by engaging a large scientific community of structural biologists, enabling successful neutron diffraction experiments from radically smaller biomacromolecular crystals, resolving unanswered biochemical questions, and meaningfully contributing to rational drug design. The meeting highlighted 10 grand challenges that will be addressed with this advanced capability over the next decade and beyond, and the recommendations required to help address them are given below.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A molecular dynamics study of collisional heat transfer to nanoclusters in the gas phase

Nanoclusters in the gas phase grow by condensation and coagulation, which heat up nanoclusters, creating thermal non-equilibrium with the surrounding gas. The extent of non-equilibrium for nanoclusters is dependent upon the rate of heating relative to the rate of cooling brought about by nanocluster-gas molecule collisions, hence the latter process plays an important role in nanocluster energy evolution during growth. We apply molecular dynamics simulations to investigate heat transfer between metal nanoclusters and gas molecules relevant to high temperature aerosol systems. In analysis, we first define a thermal reemission coefficient (TRC), which is a correction factor for the portion of energy possessed by reemitted gas molecules after collision. Here, the TRC differs from the thermal accommodation coefficient (TAC), which is a correction factor for the maximum possible energy transfer rate from nanoclusters to gas molecules based on the diffusive collision model. We find the TRC is insensitive to nanocluster size but is affected by the nanocluster to gas temperature ratio and the nanocluster to gas atomic mass ratio. Comparison to the traditionally-defined TAC shows that the TAC is insensitive to temperature, a phenomenon that has been widely indicated in literature but not quantitatively explained. We show how the temperature insensitivity of the TAC arises because of the manner in which TRCs vary with both nanocluster and gas temperature, i.e. the manner in which the reemitted gas molecule energy from a surface varies with the temperature of that surface relative to that of the gas. In addition, while calculations ultimately reveal temperature insensitive TACs and justify their continued use in modeling gas-phase heat transfer, we argue that the TRC is more appropriate to calculate a priori in analyzing simulations; it is physically more realistic to first introduce a correction factor solely for the energy of reemitted gas molecules after a collision (as TRCs) instead of a correction factor applying to both the reemission energy and the initial energy (as TACs), as the latter is exactly calculable and independent of nanocluster properties. In line with prior work, for monoatomic gases we find the TAC decreases as the nanocluster to gas atomic mass increases, approaching 0.08 for gold nanoclusters in helium.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Unveiling mechanisms and onset threshold of humping in high-speed laser welding

The fabrication of fuel cells relies on a rapid laser welding process. However, challenges arise with the occurrence of humping when the welding speed surpasses a critical threshold, which poses difficulties in achieving a smooth surface finish and a consistent weld strength. This study aims to elucidate the humping mechanisms by analyzing the morphology of molten pool and the characteristics of melt flow at varying welding speeds via in situ synchrotron high-speed X-ray imaging and computational fluid dynamics simulations. Our findings indicate that the short keyhole rear wall, the high backward melt velocity, and the prolonged tail of molten pool are the primary factors contributing to the onset of humping. Furthermore, a dimensionless humping index (π h ) was introduced, which successfully captured the onset threshold of humping across different literatures. This index not only provides a quantitative description of the humping formation tendency but also serves as a valuable tool for optimizing the laser welding process.

42 ENGINEERING↗
DOE OSTI2022

On the mechanisms of ion adsorption to aqueous interfaces: air-water vs. oil-water

The adsorption of ions to water-hydrophobe interfaces influences a wide range of phenomena, including chemical reaction rates, ion transport across biological membranes, and electrochemical and many catalytic processes; hence, developing a detailed understanding of the behavior of ions at water-hydrophobe interfaces is of central interest. Here, we characterize the adsorption of the chaotropic thiocyanate anion (SCN − ) to two prototypical liquid hydrophobic surfaces, water-toluene and water-decane, by surface-sensitive nonlinear spectroscopy and compare the results against our previous studies of SCN − adsorption to the air-water interface. For these systems, we observe no spectral shift in the charge transfer to solvent spectrum of SCN − , and the Gibb’s free energies of adsorption for these three different interfaces all agree within error. We employed molecular dynamics simulations to develop a molecular-level understanding of the adsorption mechanism and found that the adsorption for SCN − to both water-toluene and water-decane interfaces is driven by an increase in entropy, with very little enthalpic contribution. This is a qualitatively different mechanism than reported for SCN − adsorption to the air-water and graphene-water interfaces, wherein a favorable enthalpy change was the main driving force, against an unfavorable entropy change.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Comparing ab initio and quantum-kinetic approaches to electron transport in warm dense matter

Accurate knowledge of the electronic transport properties of warm dense matter is one of the main concerns of research in high-energy-density physics. Three modern approaches with vastly different levels of fidelity are reviewed and compared: the Kubo–Greenwood (KG) approach based on density-functional-theory molecular dynamics simulations (QMD), quantum kinetic theory based on average-atom models, and time-dependent density functional theory. Throughout, emphasis is placed on the connection between static properties of the electrons (e.g., density of states) and transport properties. Overall, it is found that whenever the conduction electrons can be modeled as being nearly free, fair to excellent agreement is found between QMD and kinetic theory approaches. Such a circumstance is required for modeling warm dense matter as a plasma of ions and free electrons, which is assumed in most kinetic theory approaches. The sensitivity of transport properties to the electronic structure is further highlighted by comparing different exchange–correlation approximations in QMD and KG calculations. It is found that the inclusion of exact exchange via thermal hybrid functionals can make a pronounced impact on electrical and thermal conduction in warm dense matter. We also investigate dynamic screening physics via kinetic theory and time-dependent density functional theory calculations of the mean free path of an electron in a hot dense plasma. In sum, we identify three axes along which to make progress in predicting electron transport in warm dense matter.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Negative capacitance regime in ferroelectrics demystified from nonequilibrium molecular dynamics

Negative capacitance regime in ferroelectrics is associated with the negative slope in the dependence of the polarization on electric field and is prohibited by the laws of equilibrium thermodynamics. Very recently, it developed into a controversial but very productive area with a promise for next generation low-power transistors. At least, in part, the controversies arise from the lack of direct experimental insight into the mechanism for such phenomena. Although the experimental insight is, indeed, challenging at present, we probe the effect in ferroelectric PbTiO 3 bulk and a thin film with realistic first-principles-based nonequilibrium molecular dynamics simulations which model most closely experimental conditions. Here, the following insights emerge from the simulations: (i) the ferroelectric never enters the thermodynamically forbidden region even under extreme rates of electric-field application; (ii) the negative slope naturally arises when the compensating charge is either scarce or slowed down by the external circuitry; (iii) the negative slope is well controlled by the interplay between the applied step pulse field and the amount of the screening charge. The latter can be used to design the negative capacitance regime.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

RELAP-7 Application and Enhancement for FLEX Strategies and ATF Behavior under Extended Loss of AC Power Conditions

This report summarizes the results of a three-year research project sponsored by the U.S. Department of Energy (DOE) Nuclear Energy University Program (NEUP) to enhance and apply the RELAP-7 code by adding and improving several important components (e.g., a mechanistic Reactor Core Isolation Cooling (RCIC) system model) for thermal hydraulic studies of LWRs under ELAP conditions and evaluating the time available for transition to portable FLEX equipment. The project team included University of Massachusetts–Lowell, The Ohio State University, Texas A&M University, Idaho National Laboratory and Oak Ridge National Laboratory. In the Fukushima accident, it was found that the RCIC system played a crucial role in delaying core meltdown by almost three days in Fukushima Daiichi Unit 2, because of self-regulated operation of the steam driven RCIC turbine-pump injection system. Steam flow in the convergent-divergent nozzles of the RCIC Terry turbine is two-phase non-equilibrium transonic flow with homogenous nucleation condensation. To more accurately predict the dynamic process and behavior of the transonic compressible steam flow, a one-dimensional transient two-phase analytical model is presented. A simplified four-fluid model was employed in the present work with the consideration of four separate fluid fields: vapor, liquid film, entrained droplets and condensed droplets. The mass, momentum and energy interactions between the fluids were considered and modeled. An extended seven-equation non-equilibrium critical flow model was developed to obtain the critical pressure and velocities of each phase at the nozzle throat. To predict the wetness in the divergent section, a mechanistic nucleation condensation model was integrated in the nozzle analysis model, considering the generation and consequent growth of droplets. The governing differential equations on a staggered grid were discretized using the second-order Lax-Wendroff scheme with a flux limiter, and the Semi-Implicit Method for Pressure-Linked Equation (SIMPLE) algorithm was employed to solve the discrete linear system. To demonstrate the predictability and reliability of the physical models and the numerical method proposed in the present work, three representative nozzles were modeled and simulated. The results show good agreement with the available experimental data, even for condensation shock. Then, the 1D nozzle model was employed to obtain nozzle flow tables of the Terry turbine nozzle for different working pressures which can cover the operation pressure range of the RCIC system. A mechanistic RCIC turbine-pump system model was developed and implemented in the system code TRACE to simulate dynamic responses of the RCIC system under Beyond Design Basis Accident (BDBA) conditions. The turbine-pump governing equations are based on the control volume approach of the angular momentum balance. The physics based mechanistic RCIC model was developed using the TRACE control system components (i.e., signal variables, control blocks, and tables), and incorporated into a TRACE boiling water reactor (BWR) model. The TRACE model in this report has a detailed nodalization of the reactor pressure vessel (RPV), and all of the major flow paths and system components, including the safety relief valves (SRVs) and the containment suppression pool and drywell. Based on the nozzle flow tables generated from the 1D nozzle model developed, the turbine drive torque can be calculated from table lookup. Since the detailed specifications of the RCIC pump are unavailable, the homologous curves for a Bingham pump were used in the current pump component. A station black-out (SBO) accident test problem was selected to demonstrate the TRACE RCIC model. The short-term SBO simulations were performed for two cladding materials: Zircaloy and FeCrAl, to demonstrate the effect of the accident tolerant fuel cladding on fuel heat-up under BDBA accident conditions. The wetwell plays a vital safety role in SBO and other BWR accident scenarios in that it can reduce containment pressure and supply additional core make-up water. The suppression pool temperature distribution has a very large impact on both RPV and containment pressure. Thus, another novel contribution of the project comes mainly from an improved, systems-level wetwell model which can capture buoyancy-induced thermal stratification effects due to steam injection and condensation. A two-zone stratified wetwell model has been implemented in RELAP-7 and some results from that model are presented. This wetwell model is capable of simulating thermal stratification due to a low steam mass injection rate. With a low mass flow rate, the model assumes that all the steam condenses within the pipe and the resulting plume can be approximated with a purely buoyant, heat-source driven model. The wetwell model developed with these assumptions is adequate to simulate slow transients such as extended SBO transients.

42 ENGINEERING↗
DOE OSTI2022

Correlations for the specific heat capacity of ( U x Pu 1 - x ) 1 - y Gd y O 2 - z derived from molecular dynamics

We report UO 2 is the primary conventional fuel used in most nuclear reactors with Gd 2 O 3 commonly added as a burnable absorber to produce a more level power distribution in the reactor core at the beginning of operation. It can also be mixed with other actinide oxides to produce mixed oxide (MOx) fuel. In this study, molecular dynamics simulations were used to predict the specific heat capacity of Gd-doped PuO 2 , UO 2 and (U, Pu)O 2 MOx accommodating Gd 3+ substituted at cation sites via two charge compensation mechanisms - oxygen vacancy formation and the oxidation of U 4+ to U 5+ . The specific heat capacity values for PuO 2 and UO 2 are in good agreement with other studies showing a distinct peak at high temperatures - above 1800 K. As Gd 3+ is added, the peak height reduces for each composition considered. An analytical fit was applied to the data where Gd 3+ was fully charge compensated by either oxygen vacancies or U 5+ . The expression was then validated by predicting the specific heat capacity for three compositions of (Ux Pu 1-x ) 1-y Gd y O 2-z containing both oxygen vacancies and U 5+ , and compared to molecular dynamics data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Structural Characterization and Dynamics of AdhE Ultrastructures from Clostridium thermocellum Show a Containment Strategy for Toxic Intermediates

Clostridium thermocellum, a cellulolytic thermophilic anaerobe, is considered by many to be a prime candidate for the realization of consolidated bioprocessing (CBP) and is known as an industry standard for biofuel production. C. thermocellum is among the best biomass degraders identified to date in nature and produces ethanol as one of its main products. Many studies have helped increase ethanol titers in this microbe; however, ethanol production using C. thermocellum is still not economically viable. Therefore, a better understanding of its ethanol synthesis pathway is required. The main pathway for ethanol production in C. thermocellum involves the bifunctional aldehyde-alcohol dehydrogenase (AdhE). To better understand the function of the C. thermocellum AdhE, we used cryo-electron microscopy (cryo-EM) to obtain a 3.28 A structure of the AdhE complex. This high-resolution structure, in combination with molecular dynamics simulations, provides insight into the substrate channeling of the toxic intermediate acetaldehyde, indicates the potential role of C. thermocellum AdhE to regulate activity and cofactor pools, and establishes a basis for future engineering studies. The containment strategy found in this enzyme offers a template that could be replicated in other systems where toxic intermediates need to be sequestered to increase the production of valuable biochemicals.

09 BIOMASS FUELS↗
DOE OSTI2026

Molecular dynamics based study on the effects of cation size on the local structure and diffusion in polymerized ionic liquids

We have used coarse-grained molecular dynamics simulations to understand the effect of cation size on ion diffusion in polymerized ionic liquids at temperatures well above the glass transition temperature of the polymers. We investigated dependencies of the diffusion constant on the cation radius and static dielectric constant and interpreted these results in terms of underlying structural changes, and decoupling phenomenon. We have found non-monotonic effects of the cation radius on the diffusion constant, with a maximum at an intermediate radius resulting from two different size dependent effects. Changes in the radial distribution functions characterizing spatial distribution of cations with respect to anions result in a monotonic increase in the coordination number. This yields an increase in the effective interaction energy as a function of cation radius, which can explain the decrease in the diffusion constant. This increase is counteracted at small cation radii by a corresponding increase in decoupling of cation and anion dynamics. In addition, the diffusion constant is found to increase on increasing the static dielectric constant for all radii of the cations. These results highlight the significant role of decoupling in designing polymerized ionic liquids with an enhanced diffusion constant of cations.

Gillespie, Colin [ORNL] (ORCID:0000000320287080)↗
DOE OSTI2023

Molecular dynamics study of grain boundary and radiation effects on tritium population and diffusion in zirconium

Tritium population thermodynamics and transport kinetics critically define the tritium storage performance of zirconium tritides that can be used for a variety of nuclear applications including tritium-producing burnable absorber rods. Both thermodynamic and kinetic properties can be sensitive to grain sizes of materials and can be significantly altered by irradiated defects during operation under the reactor environments. A thorough experimental characterization of how these properties evolve under different reactor conditions and different initial grain structures is extremely challenging. Here molecular dynamics simulations are used to investigate tritium population and diffusion in zirconium with and without different planar symmetric and asymmetric tilt grain boundaries and irradiated defects. Here, we found that in addition to trapping tritium, the most significant effect of planar grain boundaries is to increase tritium diffusivity on the boundary plane. Furthermore, fine grain structures are found to mitigate the change of tritium diffusivity due to irradiated point defects as these point defects are likely to migrate to and sink at grain boundaries.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP

YiiP is a secondary transporter that couples Zn 2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn 2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn 2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn 2+ . To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn 2+ and validated its performance with known Zn 2+ -binding proteins. Using these tools, we find that, in the presence of Zn 2+ , YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn 2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn 2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn 2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗