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Results for “Thermophoresis”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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17 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Microscale thermophoresis as a powerful tool for screening glycosyltransferases involved in cell wall biosynthesis

Background: Identification and characterization of key enzymes associated with cell wall biosynthesis and modification is fundamental to gain insights into cell wall dynamics. However, it is a challenge that activity assays of glycosyltransferases are very low throughput and acceptor substrates are generally not available. Results: We optimized and validated microscale thermophoresis (MST) to achieve high throughput screening for glycosyltransferase substrates. MST is a powerful method for the quantitative analysis of protein-ligand interactions with low sample consumption. The technique is based on the motion of molecules along local temperature gradients, measured by fluorescence changes. We expressed glycosyltransferases as YFP-fusion proteins in tobacco and optimized the MST method to allow the determination of substrate binding affinity without purification of the target protein from the cell lysate. The application of this MST method to the β-1,4-galactosyltransferase AtGALS1 validated the capability to screen both nucleotide-sugar donor substrates and acceptor substrates. We also expanded the application to members of glycosyltransferase family GT61 in sorghum for substrate screening and function prediction. Conclusions: This method is rapid and sensitive to allow determination of both donor and acceptor substrates of glycosyltransferases. MST enables high throughput screening of glycosyltransferases for likely substrates, which will narrow down their in vivo function and help to select candidates for further studies. Additionally, this method gives insight into biochemical mechanism of glycosyltransferase function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microscale Thermophoresis (MST) as a Tool to Study Binding Interactions of Oxygen-Sensitive Biohybrids

Microscale thermophoresis (MST) is a technique used to measure the strength of molecular interactions. MST is a thermophoretic-based technique that monitors the change in fluorescence associated with the movement of fluorescent-labeled molecules in response to a temperature gradient triggered by an IR LASER. MST has advantages over other approaches for examining molecular interactions, such as isothermal titration calorimetry, nuclear magnetic resonance, biolayer interferometry, and surface plasmon resonance, requiring a small sample size that does not need to be immobilized and a high-sensitivity fluorescence detection. In addition, since the approach involves the loading of samples into capillaries that can be easily sealed, it can be adapted to analyze oxygen-sensitive samples. In this Bio-protocol, we describe the troubleshooting and optimization we have done to enable the use of MST to examine protein–protein interactions, protein–ligand interactions, and protein–nanocrystal interactions. The salient elements in the developed procedures include 1) loading and sealing capabilities in an anaerobic chamber for analysis using a NanoTemper MST located on the benchtop in air, 2) identification of the optimal reducing agents compatible with data acquisition with effective protection against trace oxygen, and 3) the optimization of data acquisition and analysis procedures. The procedures lay the groundwork to define the determinants of molecular interactions in these technically demanding systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Forced Crowding of Colloids by Thermophoresis and Convection in a Custom Liquid Clusius–Dickel Microdevice

Here, we report a study demonstrating that simultaneous induction of a steady-state convection current and temperature gradient in a confined geometry can be an effective way to force crowding of dissolved particulates. To investigate this thermogravitationally driven concentration of particles in-situ, we developed a micro-device capable of sustaining controlled transverse temperature gradients within a 5 cm long, 0.1 mm inner diameter capillary that allowed visualization of particle movement with standard optical microscopy. Experiments were conducted on two material systems representative of nano-scale small molecules and micro-scale particles. With the small molecules (aromatic dyes, 530-790 g/mol, 1-1.5 nm) thermophoretic and gravitational effects in the micro-device resulted in an asymmetrical 2x concentration change along the capillary height over 3 days. In contrast, the concentration change under similar conditions for 40-micron diameter latex colloids is 50-fold in 30 minutes. This dramatic difference in separation times is consistent with simulations and models of thermophoresis where the thermophoretic effect scales with particle size. Induced crowding of particulates leads to formation of accumulation and depletion zones in at the bottom and top of the capillary respectively. Both the concentration of dye molecules over time in the depletion zone and spatial distribution of colloids over the entire capillary length were found to be good fits to simple first-order exponential decay functions. Furthermore, these results suggest potential applications of thermogravitational separation in developing new functional materials via thermophoretic and convective effects.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Effects of thermophoresis on high-pressure binary-species boundary layers with uniform and non-uniform compositions

Direct numerical simulations of high-pressure binary-species temporal boundary layers are performed to investigate the flow physics for three situations: (1) uniform and equal composition, (2) uniform but unequal compositions and (3) non-uniform composition. Both colder- and hotter-wall situations compared with the free stream are simulated. The working fluid is a nitrogen/methane mixture. The analysis is performed at a case-specific self-similar state. Even when the initial composition is uniform, the methane mean mass fraction decreases near the colder wall, whereas it increases near the hotter wall and the mass fraction fluctuates in the entire boundary layer. Analysis of the species-mass diffusion balance and flow structures reveal that both mass-fraction variation and fluctuations are induced by the Soret effect. When the initial composition is non-uniform and the wall is colder, the methane mean mass fraction monotonically increases from the wall akin to its initial profile. However, when the wall is hotter the mean mass fraction decreases near the wall in contrast to its initial profile, a fact traced through the species-mass diffusion balance to the Soret effect being large and enriching methane near the wall. In contrast, the direction of the Soret flux is opposite for the colder wall, thus keeping the methane concentration small. Although the initial magnitude of the difference between the wall and free-stream temperature is the same in all cases, the situation is not symmetric between colder- and hotter-wall cases; the flow structure exhibits much smaller scales when the wall is hotter than when the wall is colder.

Mechanics↗
DOE OSTI2022

An expanded role for the transcription factor WRINKLED1 in the biosynthesis of triacylglycerols during seed development

The transcription factor WRINKLED1 ( WRI1 ) is known as a master regulator of fatty acid synthesis in developing oilseeds of Arabidopsis thaliana and other species. WRI1 is known to directly stimulate the expression of many fatty acid biosynthetic enzymes and a few targets in the lower part of the glycolytic pathway. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors is controlled by WRI 1. To shortlist possible gene targets for future in-planta experimental validation, here we present a strategy that combines phylogenetic foot printing of cis-regulatory elements with additional layers of evidence. Upstream regions of protein-encoding genes in A. thaliana were searched for the previously described DNA-binding consensus for WRI1, the ASML1/WRI1 (AW)-box. For about 900 genes, AW-box sites were found to be conserved across orthologous upstream regions in 11 related species of the crucifer family. For 145 select potential target genes identified this way, affinity of upstream AW-box sequences to WRI1 was assayed by Microscale Thermophoresis. This allowed definition of a refined WRI1 DNA-binding consensus. We find that known WRI1 gene targets are predictable with good confidence when upstream AW-sites are phylogenetically conserved, specifically binding WRI1 in the in vitro assay, positioned in proximity to the transcriptional start site, and if the gene is co-expressed with WRI1 during seed development. When targets predicted in this way are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in glycolysis and fatty acid biosynthesis by WRI1. Several of the newly predicted targets are in the upper glycolysis pathway and the pentose phosphate pathway. Of these, plastidic isoforms of fructokinase ( FRK 3) and of phosphoglucose isomerase ( PGI 1) are particularly corroborated by previously reported seed phenotypes of respective null mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

High Affinity Electrostatic Interactions Support the Formation of CdS Quantum Dot:Nitrogenase MoFe Protein Complexes

Nitrogenase MoFe protein can be coupled with CdS nanocrystals (NCs) to enable photocatalytic N 2 reduction. The nature of interactions that support complex formation is of paramount importance in intermolecular electron transfer that supports catalysis. In this work we have employed microscale thermophoresis to examine binding interactions between 3-mercaptopropionate capped CdS quantum dots (QDs) and MoFe protein over a range of QD diameters (3.4-4.3 nm). The results indicate that the interactions are largely electrostatic, with the strength of interactions similar to that observed for the physiological electron donor. In addition, the strength of interactions is sensitive to the QD diameter, and the binding interactions are significantly stronger for QDs with smaller diameters. Furthermore, the ability to quantitatively assess NC protein interactions in biohybrid systems supports strategies for understanding properties and reaction parameters that are important for obtaining optimal rates of catalysis in biohybrid systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Expression, purification and characterization of human proton-coupled oligopeptide transporter 1 hPEPT1

The human peptide transporter hPEPT1 (SLC15A1) is responsible for uptake of dietary di- and tripeptides and a number of drugs from the small intestine by utilizing the proton electrochemical gradient, and hence an important target for peptide-like drug design and drug delivery. hPEPT1 belongs to the ubiquitous major facilitator superfamily that all contain a 12TM core structure, with global conformational changes occurring during the transport cycle. Several bacterial homologues of these transporters have been characterized, providing valuable insight into the transport mechanism of this family. Here we report the overexpression and purification of recombinant hPEPT1 in a detergent-solubilized state. Thermostability profiling of hPEPT1 at different pH values revealed that hPEPT1 is more stable at pH 6 as compared to pH 7 and 8. Micro-scale thermophoresis (MST) confirmed that the purified hPEPT1 was able to bind di- and tripeptides respectively. To assess the in-solution oligomeric state of hPEPT1, negative stain electron microscopy was performed, demonstrating a predominantly monomeric state.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A general metriplectic framework with application to dissipative extended magnetohydrodynamics

General equations for conservative yet dissipative (entropy producing) extended magnetohydrodynamics are derived from two-fluid theory. Keeping all terms generates unusual cross-effects, such as thermophoresis and a current viscosity that mixes with the usual velocity viscosity. While the Poisson bracket of the ideal version of this model has already been discovered, we determine its metriplectic counterpart that describes the dissipation. This is done using a new and general thermodynamic point of view to derive dissipative brackets, a means of derivation that is natural for understanding and creating dissipative dynamics without appealing to underlying kinetic theory orderings. Finally, the formalism is used to study dissipation in the Lagrangian variable picture where, in the context of extended magnetohydrodynamics, non-local dissipative brackets naturally emerge.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Depletion of the Protein Hydration Shell with Increasing Temperature Observed by Small-Angle X-ray Scattering and Molecular Simulations

The hydration shell is an integral part of proteins since it plays key roles in conformational transitions, molecular recognition, and enzymatic activity. While the dynamics of the hydration shell have been described by spectroscopic techniques, the structure of the hydration shell remains less understood due to the lack of hydration shell-sensitive structural probes with high spatial resolution. We combined temperature-ramp small-angle X-ray scattering (T-ramp SAXS) from 255 to 335 K with molecular simulations to demonstrate that the hydration shells of the IgG-binding domain of Protein G (GB3) and the villin headpiece are remarkably temperature-sensitive. For proteins in the folded state, T-ramp SAXS data and explicit-solvent SAXS predictions consistently demonstrate decays of protein contrasts and radii of gyration with increasing temperature, which are shown to reflect predominantly temperature-sensitive, depleting hydration shells. The depletion is caused not merely by enhanced disorder within the hydration shells but also by partial displacements of surface-coordinated water molecules. Together, T-ramp SAXS and explicit-solvent SAXS calculations provide a novel structural view of the protein hydration shell, which underlies temperature-dependent processes such as cold denaturation, thermophoresis, or biomolecular phase separation.

electron density↗
DOE OSTI2024

Deficiency in PHD2-mediated hydroxylation of HIF2α underlies Pacak-Zhuang syndrome

Pacak-Zhuang syndrome is caused by mutations in the EPAS1 gene, which encodes for one of the three hypoxia-inducible factor alpha (HIFα) paralogs HIF2α and is associated with defined but varied phenotypic presentations including neuroendocrine tumors and polycythemia. However, the mechanisms underlying the complex genotype-phenotype correlations remain incompletely understood. Here, we devised a quantitative method for determining the dissociation constant (K d ) of the HIF2α peptides containing disease-associated mutations and the catalytic domain of prolyl-hydroxylase (PHD2) using microscale thermophoresis (MST) and showed that neuroendocrine-associated Class 1 HIF2α mutants have distinctly higher K d than the exclusively polycythemia-associated Class 2 HIF2α mutants. Based on the co-crystal structure of PHD2/HIF2α peptide complex at 1.8 Å resolution, we showed that the Class 1 mutated residues are localized to the critical interface between HIF2α and PHD2, adjacent to the PHD2 active catalytic site, while Class 2 mutated residues are localized to the more flexible region of HIF2α that makes less contact with PHD2. Concordantly, Class 1 mutations were found to significantly increase HIF2α-mediated transcriptional activation in cellulo compared to Class 2 counterparts. These results reveal a structural mechanism in which the strength of the interaction between HIF2α and PHD2 is at the root of the general genotype-phenotype correlations observed in Pacak-Zhuang syndrome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A glycan receptor kinase facilitates intracellular accommodation of arbuscular mycorrhiza and symbiotic rhizobia in the legume Lotus japonicus

Receptors that distinguish the multitude of microbes surrounding plants in the environment enable dynamic responses to the biotic and abiotic conditions encountered. In this study, we identify and characterise a glycan receptor kinase, EPR3a, closely related to the exopolysaccharide receptor EPR3. Epr3a is up-regulated in roots colonised by arbuscular mycorrhizal (AM) fungi and is able to bind glucans with a branching pattern characteristic of surface-exposed fungal glucans. Expression studies with cellular resolution show localised activation of the Epr3a promoter in cortical root cells containing arbuscules. Fungal infection and intracellular arbuscule formation are reduced in epr3a mutants. In vitro , the EPR3a ectodomain binds cell wall glucans in affinity gel electrophoresis assays. In microscale thermophoresis (MST) assays, rhizobial exopolysaccharide binding is detected with affinities comparable to those observed for EPR3, and both EPR3a and EPR3 bind a well-defined β-1,3/β-1,6 decasaccharide derived from exopolysaccharides of endophytic and pathogenic fungi. Both EPR3a and EPR3 function in the intracellular accommodation of microbes. However, contrasting expression patterns and divergent ligand affinities result in distinct functions in AM colonisation and rhizobial infection in Lotus japonicus . The presence of Epr3a and Epr3 genes in both eudicot and monocot plant genomes suggest a conserved function of these receptor kinases in glycan perception.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Comparing the MELCOR Aerosol Deposition Model with Exact Analytical Solutions

Exact analytical solutions are presented for the evolution of the aerosol particle mass density function in a control volume for particle deposition due to gravitational settling, thermophoresis, and diffusion. The solutions are for arbitrary initial mass density functions and are applied for an initial lognormal density function. Integration of these solutions provides the suspended mass in the control volume as a function of time. These solutions serve as an exact benchmark to assess the accuracy of numerical methods. For the numerical algorithm used in MELCOR, excellent agreement is obtained for gravitational settling, diffusive deposition, and thermophoretic deposition for the suspended aerosol mass. In all cases, the default number of discrete particle size bins of 10 is shown to converge, with hardly any advantage to using 20 size bins.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Energy coupling and stoichiometry of Zn 2+ /H + antiport by the prokaryotic cation diffusion facilitator YiiP

YiiP from Shewanella oneidensis is a prokaryotic Zn 2+ /H + antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn 2+ binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn 2+ binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn 2+ binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn 2+ to 2–3 H + depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn 2+ .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Implementing a Stochastic Soot Model in a 3D Domain

In this document a highly detailed stochastic soot model limited to 0D simulations is coupled to 3D domains through the use of a Lagrangian parcel-Eulerian fluid method. Although both the stochastic soot model used and the Lagrangian parcel-Eulerian fluid method have long histories of development, their use, as described in this document, is novel and useful. Previous works significant to the model's development include documents from both the stochastic and simpler soot model genre and the fuel, aerosol, and other particle tracking and Lagrangian parcel-Eulerian fluid genres. Developing the theory behind the model is crucial to its implementation because of the unconventional Lagrangian parcel-Eulerian fluid representation. In fact, the Lagrangian parcel-Eulerian fluid coupling is only a means of simplifying the much more difficult theoretical model. Despite the accompanying assumptions, the complete model is validated from the bottom up and then again in a holistic fashion with promising results. Then the model is used in multiple case studies, showcasing capabilities not had by other models. The optical properties of soot generated in a Spray A simulation are calculated to find measured results are likely overpredicting the mass of soot along the central axis via KL extinction measurements. A thermophoresis submodel that calculates force based on the soot particles' shape is installed to find it has a high influence on the path of the heaviest soot particles. Investigations into the HACA mechanism for soot growth and the effect of syngas on soot in 3D domains are performed with much more detail than has been available before.

Strickland, Tyler↗
DOE OSTI2021

Thermal gradient effect on helium and self-interstitial transport in tungsten

First-wall materials in a fusion reactor are expected to withstand harsh conditions, with high heat and particle fluxes that modify the materials microstructure. These fluxes will create strong gradients of temperature and concentration of diverse species. Besides the He ash and the hydrogenic species, neutron particles generated in the fusion reaction will collide with the material creating intrinsic defects, such as vacancies, self-interstitials atoms (SIAs), and clusters of such point defects. These defects and the He atoms will then migrate in the presence of the aforementioned gradients. In this study, we use nonequilibrium molecular dynamics to analyze the transport of He and SIAs in the presence of a thermal gradient in tungsten. We observe that, in all cases, the defects and impurity atoms tend to migrate toward the hot regions of the tungsten sample. The resulting species concentration profiles are exponential distributions, rising toward the hot regions of the sample, in agreement with irreversible thermodynamics analysis. For both He atoms and SIAs, we find that the resulting species flux is directed opposite to the heat flux, indicating that species transport is governed by a Soret effect (thermal-gradient-driven diffusion) characterized by a negative heat of transport that drives species diffusion uphill (from the cooler to the hot regions of the sample). Here, we demonstrate that the steady-state species profiles obtained accounting for the Soret effect vary significantly from those where temperature-gradient-driven transport is not considered and discuss the implications of such a Soret effect on the response to plasma exposure of plasma-facing tungsten.

36 MATERIALS SCIENCE↗