Thermodynamic Coupling Function Analysis of Allosteric Mechanisms in the Human Dopamine Transporter
Not Available
LeVine, Michael V.↗
SEARCH · Search NASA
Results for “thermodynamic coupling”
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.
Performance of a Kilowatt-Class Stirling Power Conversion System in a Thermodynamically Coupled Configuration
A pair of 1-kWe free-piston Stirling power convertors has been modified into a thermodynamically coupled configuration, and performance map testing has been completed. This is the same configuration planned for the full-scale 12-kWe power conversion unit (PCU) that will be used in the Fission Power System Technology Demonstration Unit (TDU). The 1-kWe convertors were operated over a range of conditions to evaluate the effects of thermodynamic coupling on convertor performance and to identify any possible control challenges. The thermodynamically coupled convertor showed no measureable difference in performance from the baseline data collected when the engines were separate, and no major control issues were encountered during operation. The results of this test are guiding controller development and instrumentation selection for the TDU.
Geng, Steven M.↗
3D Radiative MHD Modeling of Thermodynamical Coupling From Subsurface Layers of the Sun to Corona
Explore the source record for details and available documents.
SMD↗
Coupling computational thermodynamics with density-function-theory based calculations to design L12 precipitates in Fe Ni based alloys
Achieving a high-volume fraction of thermodynamically stable L12-type precipitates that are resistant to coarsening is of great importance for the development of low-cost FeNi based austenitic steels. With the aid of computational thermodynamics, this work designed two model alloys: Fe-37.4Ni-6.1Al-2.9Ti (FNAT) and Fe-45.2Ni-5.9Al-8.5Si (FNAS). Both alloys were designed to contain a similar amount of L1 2 precipitate in Fe-Ni matrix without forming other precipitates. Density-Function-Theory (DFT) calculation was coupled with computational thermodynamics to predict the critical radius at which the precipitates change shape from spherical to cuboidal. The calculation results suggest that critical radius for the FNAT alloy is about two orders of magnitude larger than that for the FeNiAlSi alloy. Phase stability and morphology of the L1 2 precipitates in these two alloys were experimentally investigated through X-ray diffraction, atom probe tomography, and scanning and transmission electron microscopy. The L1 2 precipitates in the FeNiAlSi system were found to be cuboidal and rod shaped, with much larger size than the spherical ones in the FeNiAlTi system, agreeing with the calculation results. This work suggested that coupling computational thermodynamics with DFT calculations can be reliably used to design L1 2 precipitates in FeNi based alloys.
36 MATERIALS SCIENCE↗
Methodology for Thermodynamic Analysis Coupled with Computational Fluid Dynamics Modeling for Casting a Novel Aluminum–Cerium Alloy
In this paper, we present the results of computational fluid dynamics (CFD) analysis to assess castability, porosity, molten metal fluidity and other technological properties of a new Al-Ce alloy. A thermodynamic analysis of a new Al-Ce alloy is done to obtain the physical properties as a function of temperature across both solid and liquid phases. These properties are then used to build the CFD of model the full casting process from initial pouring through to final solidification of the part, here an example of a heavy duty mor mount is used. While several excellent commercial CFD codes exists this process shows that CFD can be used to assess the capability of the alloy to properly fill the mold, as well as give predictions where scattered porosity or large-scale defects may occur in the casting. Further, unlike the commercially available software (e.g., ProCAST, SOLIDCast , MAGMASOFT®) the complex 3D-analysis of the stress / strain fields in cast parts is not performed at this time. However, the availability of free software for assessing the required thermodynamic / thermo-physical properties of new alloys (OpenCALPHAD) and CFD codes such as OpenFOAM® makes the developed option attractive and economical, especially for the analysis of new Al-Ce alloys, for which the available data does not exist.
36 MATERIALS SCIENCE↗
Acceleration of Solvation Free Energy Calculation via Thermodynamic Integration Coupled with Gaussian Process Regression and Improved Gelman–Rubin Convergence Diagnostics
The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are powerful tools for computing this critical parameter. Nevertheless, the accurate and efficient calculation of the solvation free energy becomes a formidable endeavor when dealing with complex systems characterized by potent Coulombic interactions and sluggish ion dynamics and, consequently, slow transition across various metastable states. Here, in the present study, we expose limitations stemming from the conventional calculation of the statistical inefficiency g in the thermodynamic integration method, a factor that can hinder the determination of convergence of the solvation free energy and its associated uncertainty. Instead, we propose a robust scheme based on Gelman–Rubin convergence diagnostics. We leverage this improved estimation of uncertainties to introduce an innovative accelerated thermodynamic integration method based on the Gaussian Process regression. This methodology is applied to the calculation of the solvation free energy of trivalent rare-earth elements immersed in ionic liquids, a scenario in which the aforementioned challenges render standard approaches ineffective. The proposed method proves to be effective in computing solvation free energy in situations where traditional thermodynamic integration methods fall short.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis
We report that replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD algorithm for ligand binding, in which replicas along the alchemical thermodynamic coupling axis λ were expanded as a series of Hamiltonian boosted replicas along a second axis to form a two-dimensional (2D) replica-exchange exchange map [Jiang, W.; Roux, B., J. Chem. Theory Comput. 2010, 6 (9), 2559-2565]. Aiming to achieve a similar performance at a lower computational cost, we propose here a modified version of this algorithm in which only the end-states along the alchemical axis are augmented by boosted replicas. The reduced FEP/(λ,H)-REMD method with one-dimensional (1D) unbiased alchemical thermodynamic coupling axis λ is implemented on the basis of generic multiple copy algorithm (MCA) module of the biomolecular simulation program NAMD. The flexible MCA framework of NAMD enables a user to design customized replica-exchange patterns through Tcl scripting in the context of a highly parallelized simulation program without touching the source code. Two Hamiltonian tempering boosting scheme were examined with the new algorithm: a first one based on potential energy rescaling of a pre-identified “solute”, and a second one via the introduction of flattening torsional free energy barriers. As two illustrative examples with reliable experiment data, the absolute binding free energies of pxylene and n-butylbenzene to the nonpolar cavity of the L99A mutant of T4 lysozyme were calculated. Lastly, the tests demonstrate that the new protocol efficiently enhances the sampling of torsional motions for backbone and side chains around the binding pocket and accelerates the convergence of the free energy computations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
On computing the evolution of temperature for materials under dynamic loading
Modeling and simulation of the dynamic response of materials is important to many applications including the development of armor systems, understanding the safety of explosives, and assessing the crashworthiness of vehicles. Within such applications it is often critical to accurately compute the evolution of the temperature because it is a state variable that affects the kinetics of competing active processes within the material (e.g., dislocation motion, phase transformation, decomposition). Depending on the selection of an independent state variable, e.g. temperature or entropy, the approach for computing temperature is well understood based on the thermodynamic framework attributed to Coleman and Noll. However, different computational codes used for modeling the dynamic response of materials adopt different independent state variables. In this work, two thermodynamically consistent strategies for computing the temperature of a coupled thermodynamic state are compared and implemented into two different Lagrangian computational codes. The equivalence of these two approaches is established through the numerical solutions of several test problems. Finally, the implication of various approximations made to each of these approaches within the literature are assessed in the context of uniaxial stress conditions (split Hopkinson pressure bar experiments) and uniaxial strain conditions (plate impact experiments). Here, it is shown that the temperature rate or energy partition approaches are equivalent when implemented in their complete forms, but that several common simplifying assumptions, that are warranted in the case of uniaxial stress, lead to significant errors in the resulting Hugoniot state for plate impact.
36 MATERIALS SCIENCE↗
Black hole accretion disks - Electrodynamic coupling of accretion-disk coronae and the partitioning of soft and hard X-ray emission
It is demonstrated that the observed large ratio of hard to soft X-ray emission and the bimodel behavior of black hole accreting X-ray sources such as Cygnus X-1 can be described in terms of a magnetically structured accretion disk corona which is electrodynamically coupled to the disk turbulent motions while the disk is thermodynamically coupled to the corona as described by a feedback parameter delta. The observed ratio of hard to soft X-ray emission is independent of the disk thickness, and weakly dependent of the disk parameter alpha relating the disk viscous stresses to the total pressure. Observed values of the luminosity ratio point towards strong differences of the feedback of the low state compared to the high state, in the sense that low state means small feedback (delta less than 0.2) and high state means strong feedback delta of about 0.5.
Kuperus, M.↗
Differential Ligation Alters Electronic State and Coupling Signals of Iron-Sulfur Clusters in Flavin-Based Electron Bifurcation
Flavin-based electron bifurcation (FBEB) is employed by microorganisms for controlling pools of redox equivalents by reversibly splitting electron pairs into high- and low-energy levels from an initial midpoint potential. Our ability to harness this phenomenon is crucial for biocatalytic design which is limited by our understanding of energy coupling in the bifurcation system. In Pyrococcus furiosus, FBEB is carried out by the NADH-dependent ferredoxin:NADP+-oxidoreductase (NfnSL), coupling the uphill reduction of ferredoxin in NfnL to the downhill reduction of NAD+ in NfnS from oxidation of NADPH. Flanking the bifurcating flavin are two site-differentiated iron-sulfur clusters; the nearest is a glutamate-ligated [4Fe-4S] cluster in NfnL. Recent biochemical experiments substituting the native glutamate with cysteine led to loss of coupling between the uphill and downhill pathways, in contrast to the tight thermodynamic coupling in the native system. To understand how this decoupling is biochemically manifested by the cysteine-substituted [4Fe-4S] in NfnL, we employed electron paramagnetic resonance (EPR) spectroscopy to identify changes in electronic architecture and square wave voltammetry (SWV) to probe thermodynamic shifts produced by the substitution. We observed notable g-value shifts in the EPR for the cysteine-substituted iron-sulfur cluster in addition to significant downward shifts in the redox potential, as well as the disappearance of several low-field signals observed in the native NfnSL complex. These results suggest the site-differentiated glutamate residue facilitates higher spin states in the [4Fesingle bond4S] cluster to bridge energetic gaps in electron transfer to the bifurcating flavin in the native complex, preventing unwanted short-circuiting seen in the cysteine-substituted complex.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A path towards single molecule vibrational strong coupling in a Fabry–Pérot microcavity
Few-molecule vibrational strong coupling in a microcavity using cavity optomechanics and its application as cavity-mediated thermodynamic coupling of chemical reactions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Mechanistic implications of excited high-spin states, spin–spin coupling, and differential [2Fe–2S] + cluster temperature relaxations in the electron-bifurcating NfnABC from Thermococcus sibiricus
Electron bifurcation (EB) is a mechanism of biological energy transduction in which multiple oxidation–reduction (redox) reactions are thermodynamically coupled within a single enzyme, enabling the enzyme to harness the excess free energy from an exergonic process to drive an endergonic process. Because of this unprecedented chemistry, there is interest to translate EB principles to artificial and bioengineered systems, but a hurdle is that knowledge pertaining to the fundamental design principles of EB enzymes remains scarce. Here, we investigated the fundamental physical and electronic properties of electron transfer sites in a spectroscopically uncharacterized member of the BfuABC family of EB enzymes, the NADH-dependent reduced-ferredoxin:NADP + oxidoreductase from Thermococcus sibiricus (Tsi NfnABC). Cryo-EM structures of Tsi NfnABC previously demonstrated that it contains twelve redox cofactors: two flavins (one FAD and one FMN), eight [4Fe–4S] clusters, and two [2Fe–2S] clusters. The FMN, one [4Fe–4S] cluster, and one [2Fe–2S] cluster comprise the bifurcating active site termed the electron-bifurcating flavobicluster (BF-FBC), which is found in all BfuABC family members. By using electron paramagnetic resonance spectroscopy, we identified spectral signatures originating from interactions between the FMN radical and [4Fe–4S] + cluster in the BF-FBC and observed temperature dependent behavior of the BF-FBC's [2Fe–2S] + cluster indicative of moderately slow spin–lattice relaxation. Additionally, we uncovered numerous spectral features corresponding to half-integer, S > ½ spin states of [4Fe–4S] + clusters, including one attributable to the consequences of lysine-ligation of a [4Fe–4S] cluster unique to NfnABC. We contextualize these findings to electron transfer theory and NfnABC's structure. Our insights further the understanding of how enzymes are designed to exert control over electron transfer to conduct thermodynamically challenging reactions.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
A coupled dynamic-thermodynamic model of an ice-ocean system in the marginal ice zone
Thermodynamics are incorporated into a coupled ice-ocean model in order to investigate wind-driven ice-ocean processes in the marginal zone. Upswelling at the ice edge which is generated by the difference in the ice-air and air-water surface stresses is found to give rise to a strong entrainment by drawing the pycnocline closer to the surface. Entrainment is shown to be negligible outside the areas affected by the ice edge upswelling. If cooling at the top is included in the model, the heat and salt exchanges are further enhanced in the upswelling areas. It is noted that new ice formation occurs in the region not affected by ice edge upswelling, and it is suggested that the high-salinity mixed layer regions (with a scale of a few Rossby radii of deformation) will overturn due to cooling, possibly contributing to the formation of deep water.
Hakkinen, Sirpa↗
Phase-field modeling of radiation-induced segregation for multicomponent alloys
Structural alloys under irradiation are known to undergo radiation-induced solute redistribution (RIS) at grain boundaries, leading to detrimental effects such as intergranular corrosion and stress-assisted cracking. To better understand the phenomenon, improved models of RIS applicable to concentrated, multicomponent alloys, and mesoscale microstructures are needed. In this talk, we present a novel grand-potential-based phase-field model to account for the complete set of multicomponent kinetic and thermodynamic couplings between atoms and point defects in the Onsager transport equations. We demonstrate multiscale modeling capability by deriving the Onsager coefficient matrix from atomistic-based Kinetic Monte Carlo simulations. Model predictions and validations of RIS and the effect of defect production, grain boundary sink strength and density are demonstrated for a model FCC FeCrNi system. We also demonstrate the novel capability to describe RIS in the presence of equilibrium segregation described using a density-based CALPHAD thermodynamic framework. This modeling approach overcomes certain limitations in conventional RIS models and provides a step closer towards multiscale modeling.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
ARCLITE: the Arctic Lidar Technology Facility at Sondre Stromfjord, Greenland
SRI International is presently developing an Arctic lidar (ARCLITE) facility at the incoherent-scatter radar site in Sondre Stromfjord, Greenland (67.0 degrees N, 209.2 degrees W). The project, funded by NSF through the CEDAR (Coupling Energetics and Dynamics of Atmospheric Regions) initiative, is to perform high-altitude molecular/aerosol backscatter measurements in the Arctic covering the stratosphere/mesosphere region during nighttime and daytime conditions. The lidar system employs an injection seeded, high-energy GCR-5 Spectra Physics Nd:YAG laser for primary operation at 532 nm (550 mJ per pulse at 30 Hz). The receiver system is designed around a 36-inch Cassegrainian telescope of astronomical quality with receiver components and photon-counting electronics for day and night operations. The Rayleigh backscatter measurements will conduct investigations concerning long-term studies of the basic density and temperature structure of the Arctic stratosphere/mesosphere region; effects of stratospheric warming on the structure of the stratosphere/mesosphere region; occurrence and properties of polar stratospheric clouds; occurrence of noctilucent clouds and their properties at high latitudes; and dynamic and thermodynamic coupling between the stratosphere/mesosphere region and the lower thermosphere.
Thayer, J. P.↗
Design for Highly Piezoelectric and Visible/Near-Infrared Photoresponsive Perovskite Oxides
Defect–engineered perovskite oxides that exhibit ferroelectric and photovoltaic properties are promising multifunctional materials. Though introducing gap states by transition metal doping on the perovskite B–site can obtain low bandgap (i.e., 1.1–3.8 eV), the electrically leaky perovskite oxides generally lose piezoelectricity mainly due to oxygen vacancies. Therefore, the development of highly piezoelectric ferroelectric semiconductor remains challenging. Here, inspired by point–defect–mediated large piezoelectricity in ferroelectrics especially at the morphotropic phase boundary (MPB) region, an efficient strategy is proposed by judiciously introducing the gap states at the MPB where defect–induced local polar heterogeneities are thermodynamically coupled with the host polarization to simultaneously achieve high piezoelectricity and low bandgap. A concrete example, Ni 2+ –mediated (1– x )Na 0.5 Bi 0.5 TiO 3– x Ba(Ti 0.5 Ni 0.5 )O 3–δ ( x = 0.02–0.08) composition is presented, which can show excellent piezoelectricity and unprecedented visible/near–infrared light absorption with a lowest ever bandgap ≈0.9 eV at room temperature. In particular, the MPB composition x = 0.05 shows the best ferroelectricity/piezoelectricity ( d 33 = 151 pC N –1 , P r = 31.2 μC cm –2 ) and a largely enhanced photocurrent density approximately two orders of magnitude higher compared with classic ferroelectric (Pb,La)(Zr,Ti)O 3 . Furthermore, this research provides a new paradigm for designing highly piezoelectric and visible/near–infrared photoresponsive perovskite oxides for solar energy conversion, near–infrared detection, and other multifunctional applications.
36 MATERIALS SCIENCE↗
Advances and Challenges in Low‐Temperature Upcycling of Waste Polyolefins via Tandem Catalysis
Abstract Polyolefin waste is the largest polymer waste stream that could potentially serve as an advantageous hydrocarbon feedstock. Upcycling polyolefins poses significant challenges due to their inherent kinetic and thermodynamic stability. Traditional methods, such as thermal and catalytic cracking, are straightforward but require temperatures exceeding 400 °C for complete conversion because of thermodynamic constraints. We summarize and critically compare recent advances in upgrading spent polyolefins and model reactants via kinetic (and thermodynamic) coupling of the endothermic C─C bond cleavage of polyolefins with exothermic reactions including hydrogenation, hydrogenolysis, metathesis, cyclization, oxidation, and alkylation. These approaches enable complete conversion to desired products at low temperatures (<300 °C). The goal is to identify challenges and possible pathways for catalytic conversions that minimize energy and carbon footprints.
Zhang, Wei [State Key Laboratory of Petroleum Mole↗
Advances and Challenges in Low‐Temperature Upcycling of Waste Polyolefins via Tandem Catalysis
Abstract Polyolefin waste is the largest polymer waste stream that could potentially serve as an advantageous hydrocarbon feedstock. Upcycling polyolefins poses significant challenges due to their inherent kinetic and thermodynamic stability. Traditional methods, such as thermal and catalytic cracking, are straightforward but require temperatures exceeding 400 °C for complete conversion because of thermodynamic constraints. We summarize and critically compare recent advances in upgrading spent polyolefins and model reactants via kinetic (and thermodynamic) coupling of the endothermic C─C bond cleavage of polyolefins with exothermic reactions including hydrogenation, hydrogenolysis, metathesis, cyclization, oxidation, and alkylation. These approaches enable complete conversion to desired products at low temperatures (<300 °C). The goal is to identify challenges and possible pathways for catalytic conversions that minimize energy and carbon footprints.
C-C cleavage↗