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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Energy-conserving contact dynamics of nonspherical rigid-body particles

Understanding the contact dynamics of nonspherical particles is crucial for accurately modeling colloidal and granular systems where shape anisotropy dictates structural organization and transport properties. We here introduce an energy-conserving contact dynamics framework for arbitrary convex rigid-body particles by implementing vertex–boundary interactions in 2D and vertex–surface and edge–edge detection in 3D. The established formulation enables continuous force evaluation and prevents particle overlap while conserving total energy during translational and rotational motion. We demonstrate the framework’s stability and its utility to capture packing behavior, anisotropic diffusion, and equations of state of polygonal and polyhedral particles as examples. The framework establishes a robust and extensible foundation for investigating nonequilibrium dynamics of complex nonspherical particulate systems, enabling enhanced understanding of phenomena across spatiotemporal scales in self- and directed-assembly, granular flows, and hydrodynamics, potentially coupled with interactions that represent underlying physical mechanisms.

Discrete element method↗
DOE OSTI2024

A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex

During development, neural stem cells in the cerebral cortex, also known as radial glial cells (RGCs), generate excitatory neurons, followed by production of cortical macroglia and inhibitory neurons that migrate to the olfactory bulb (OB). Understanding the mechanisms for this lineage switch is fundamental for unraveling how proper numbers of diverse neuronal and glial cell types are controlled. We and others recently showed that Sonic Hedgehog (Shh) signaling promotes the cortical RGC lineage switch to generate cortical oligodendrocytes and OB interneurons. During this process, cortical RGCs generate intermediate progenitor cells that express critical gliogenesis genes Ascl1, Egfr, and Olig2. The increased Ascl1 expression and appearance of Egfr + and Olig2 + cortical progenitors are concurrent with the switch from excitatory neurogenesis to gliogenesis and OB interneuron neurogenesis in the cortex. While Shh signaling promotes Olig2 expression in the developing spinal cord, the exact mechanism for this transcriptional regulation is not known. Furthermore, the transcriptional regulation of Olig2 and Egfr has not been explored. Here, we show that in cortical progenitor cells, multiple regulatory programs, including Pax6 and Gli3, prevent precocious expression of Olig2, a gene essential for production of cortical oligodendrocytes and astrocytes. We identify multiple enhancers that control Olig2 expression in cortical progenitors and show that the mechanisms for regulating Olig2 expression are conserved between the mouse and human. Our study reveals evolutionarily conserved regulatory logic controlling the lineage switch of cortical neural stem cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The GTPase-activating protein p120RasGAP has an evolutionarily conserved “FLVR-unique” SH2 domain

The Src homology 2 (SH2) domain has a highly conserved architecture that recognizes linear phosphotyrosine motifs and is present in a wide range of signaling pathways across different evolutionary taxa. A hallmark of SH2 domains is the arginine residue in the conserved FLVR motif that forms a direct salt bridge with bound phosphotyrosine. In this work, we solve the X-ray crystal structures of the C-terminal SH2 domain of p120RasGAP (RASA1) in its apo and peptide-bound form. We find that the arginine residue in the FLVR motif does not directly contact pTyr1087 of a bound phosphopeptide derived from p190RhoGAP; rather, it makes an intramolecular salt bridge to an aspartic acid. Unexpectedly, coordination of phosphotyrosine is achieved by a modified binding pocket that appears early in evolution. Using isothermal titration calorimetry, we find that substitution of the FLVR arginine R377A does not cause a significant loss of phosphopeptide binding, but rather a tandem substitution of R398A (SH2 position βD4) and K400A (SH2 position βD6) is required to disrupt the binding. These results indicate a hitherto unrecognized diversity in SH2 domain interactions with phosphotyrosine and classify the C-terminal SH2 domain of p120RasGAP as “FLVR-unique.”

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

The effect of curvature induced broken potential vorticity conservation on drift wave turbulences

Abstract The correlation theory of turbulence suppression (Zhang and Mahajan 1993 Phys. Fluids B5 2000) by velocity shear was constructed by invoking the ansatz of potential vorticity conservation (PVC) that holds for relatively simple (slab) models of drift wave turbulence. It is, therefore, surprising that a detailed modern simulation of the H mode pedestal, using the gyrokinetic code GENE (Hatch et al 2018 Plasma Phys. Control. Fusion 60 084003), found ‘striking agreement’ with the predictions of the analytic model. To understand the reasons for this remarkable agreement, an extended theory that contains finite (magnetic) curvature, and which does not conserve potential vorticity, is developed and ‘solved’ by calculating an inhomogeneous Green function reflecting the fact that the new system has a potential vorticity source. It is, then, demonstrated that the effect of the broken PVC is insignificant for the normal operation parameters in tokamaks; the correction due to curvature is at the order of 2 L 0 / R , where L 0 is the scale length of the local gradient and R is the major radius. The excellent agreement between simulation and slab model 1993 theory is therefore not accidental; the latter can be applied with confidence to the tokamak pedestal.

Physics↗
DOE OSTI2023

Identification of conserved skeletal enhancers associated with craniosynostosis risk genes

Abstract Craniosynostosis, defined by premature fusion of one or multiple cranial sutures, is a common congenital defect affecting more than 1/2000 infants and results in restricted brain expansion. Single gene mutations account for 15%–20% of cases, largely as part of a syndrome, but the majority are nonsyndromic with complex underlying genetics. We hypothesized that the two noncoding genomic regions identified by a GWAS for craniosynostosis contain distal regulatory elements for the risk genes BMPER and BMP2. To identify such regulatory elements, we surveyed conserved noncoding sequences from both risk loci for enhancer activity in transgenic Danio rerio. We identified enhancers from both regions that direct expression to skeletal tissues, consistent with the endogenous expression of bmper and bmp2. For each locus, we also found a skeletal enhancer that also contains a sequence variant associated with craniosynostosis risk. We examined the activity of each enhancer during craniofacial development and found that the BMPER-associated enhancer is active in the restricted region of cartilage closely associated with frontal bone initiation. The same enhancer is active in mouse skeletal tissues, demonstrating evolutionarily conserved activity. Using enhanced yeast one-hybrid assays, we identified transcription factors that bind each enhancer and observed differential binding between alleles, implicating multiple signaling pathways. Our findings help unveil the genetic mechanism of the two craniosynostosis risk loci. More broadly, our combined in vivo approach is applicable to many complex genetic diseases to build a link between association studies and specific genetic mechanisms.

He(何璇), Xuan Anita (ORCID:0000000313221972)↗
DOE OSTI2022

Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases

The Plant-Conserved Region (P-CR) and the Class-Specific Region (CSR) are two plant-unique sequences in the catalytic core of cellulose synthases (CESAs) for which specific functions have not been established. Here, we used site-directed mutagenesis to replace amino acids and motifs within these sequences predicted to be essential for assembly and function of CESAs. We developed an in vivo method to determine the ability of mutated CesA1 transgenes to complement an Arabidopsis (Arabidopsis thaliana) temperature-sensitive root-swelling1 (rsw1) mutant. Replacement of a Cys residue in the CSR, which blocks dimerization in vitro, rendered the AtCesA1 transgene unable to complement the rsw1 mutation. Examination of the CSR sequences from 33 diverse angiosperm species showed domains of high-sequence conservation in a class-specific manner but with variation in the degrees of disorder, indicating a nonredundant role of the CSR structures in different CESA isoform classes. The Cys residue essential for dimerization was not always located in domains of intrinsic disorder. Expression of AtCesA1 transgene constructs, in which Pro417 and Arg453 were substituted for Ala or Lys in the coiled-coil of the P-CR, were also unable to complement the rsw1 mutation. Despite an expected role for Arg457 in trimerization of CESA proteins, AtCesA1 transgenes with Arg457Ala mutations were able to fully restore the wild-type phenotype in rsw1. Our data support that Cys662 within the CSR and Pro417 and Arg453 within the P-CR of Arabidopsis CESA1 are essential residues for functional synthase complex formation, but our data do not support a specific role for Arg457 in trimerization in native CESA complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Phylogenetic conservation of soil bacterial responses to simulated global changes.

Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Filling constraints on translation invariant dipole conserving systems

Systems with conserved dipole moment have drawn considerable interest in light of their realization in recent experiments on tilted optical lattices. Here, an important question for such systems is delineating the conditions under which they admit a unique gapped ground state that is consistent with all symmetries. Here, we study one-dimensional translation-invariant lattices that conserve U(1) charge and Z L dipole moment, where discreteness of the dipole symmetry is enforced by periodic boundary conditions, with L the system size. We show that in these systems, a symmetric, gapped, and non-degenerate ground state requires not only integer charge filling, but also a fixed value of the dipole filling, while other fractional dipole fillings enforce either a gapless or symmetry-breaking ground state. In contrast with prior results in the literature, we find that the dipole filling constraint depends both on the charge filling as well as the system size, emphasizing the subtle interplay of dipole symmetry with boundary conditions. We support our results with numerical simulations and exact results.

1-dimensional systems↗
DOE OSTI2023

Pre-equilibrium evolution of conserved charges with initial conditions in the ICCING Monte Carlo event generator

Heavy-ion collisions can be well described through relativistic viscous hydrodynamics, but questions still remain when hydrodynamics is applicable because the initial state may begin very far from equilibrium. Thus, a pre-equilibrium evolution phase is used to bridge the gap between the initial state and hydrodynamics. KøMPøST is one such pre-equilibrium model that propagates the energy-momentum tensor by decomposing it into the background and fluctuations around that background, whose evolution is captured by Green's functions. We extend this formalism to include conserved charges and calculate the corresponding nonequilibrium Green's functions in the relaxation-time approximation. The ICCING algorithm initializes conserved charges in the initial state by sampling $g$ → $q$$\overline{q}$ splitting probabilities and is, thus, perfectly positioned to implement Green's functions for charge propagation. As a result, we show that this method alters the initial-state charge geometries and is applicable in central to mid-central collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Conservative Spin-Magnitude Change in Orbital Evolution in General Relativity

We show that physical scattering observables for compact spinning objects in general relativity can depend on additional degrees of freedom in the spin tensor beyond those described by the spin vector alone. The impulse, spin kick, and leading-order waveforms exhibit such a nontrivial dependence. A signal of this additional structure is the change in the magnitude of the spin vector under conservative Hamiltonian evolution, similar to our previous studies in electrodynamics. These additional degrees of freedom describe dynamical mass multipoles of compact objects and decouple for black holes. We also show that the conservative impulse, spin kick, and change of the additional degrees of freedom are encoded in the eikonal phase.

Classical black holes↗
DOE OSTI2026

Viscous Gubser flow with conserved charges to benchmark fluid simulations

We present semi-analytical solutions for the evolution of both the temperature and chemical potentials for viscous Gubser flow with conserved charges. Such a solution can be especially useful in testing numerical codes intended to simulate relativistic fluids with large chemical potentials. The freeze-out hypersurface profiles for constant energy density are calculated, along with the corresponding normal vectors, and presented as a new unit test for numerical codes. We also compare the influence of the equation of state on the semi-analytical solutions. We benchmark the newly developed smoothed particle hydrodynamics code ccake that includes both shear viscosity and three conserved charges. Here, the numerical solutions are in excellent agreement with the semi-analytical solution and are also able to accurately reproduce the hypersurface at freeze-out.

Hydrodynamic models↗
DOE OSTI2022

A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection

Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a CoV disease 2019 (COVID-19) convalescent donor that exhibits broad reactivity with human β-CoVs. Here, we showed that CC40.8 targets the conserved S2 stem helix region of the CoV spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem peptide at 1.6-Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in β-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted that CC40.8-like bnAbs are relatively rare in human COVID-19 infection, and therefore, their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on β-CoV spike proteins for protective antibodies that may facilitate the development of pan–β-CoV vaccines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A dynamic protein interactome drives energy conservation and electron flux in Thermococcus kodakarensis

ABSTRACT Life is supported by energy gains fueled by catabolism of a wide range of substrates, each reliant on the selective partitioning of electrons through redox ( red uction and ox idation) reactions. Electron flux through tunable and regulated protein interactions provides dynamic routes for energy conservation, but how electron flux is regulated in vivo , particularly for archaeal metabolisms that support rapid growth at the thermodynamic limits of life, is poorly understood. Identification of bona fide in vivo protein assemblies and how such assemblies dictate the totality of electron flux is critical to our understanding of the regulation imposed on metabolism, energy production, and energy conservation. Here, 25 key proteins in central metabolic redox pathways in the model, genetically accessible, hyperthermophilic archaeon Thermococcus kodakarensis , were purified to reveal an extensive, dynamic, and tightly interconnected network of protein interactions that responds to environmental cues (such as the availability of various reductive sinks) to direct electron flux to maximize energetic gains. Interactions connecting disparate functions suggest many catabolic and anabolic activities occur in spatial proximity in vivo , and while protein complexes have been historically defined under optimal conditions, many of these complexes appear to maintain alternative partnerships in changing conditions. The totality of the results obtained redefines our understanding of in vivo assemblies driving ancient metabolic strategies supporting the growth of modern Archaea. IMPORTANCE Given the potential for rational genetic manipulations of biofuel- and biotech-promising archaea to yield transformative results for major markets, it is a priority to define how the metabolisms of such species are controlled, at least in part, by in vivo protein assemblies, and from such, define routes of energy flux that can be most efficiently altered toward biofuel or biotechnological gains. Proteinaceous electron carriers (PECs, such as ferredoxins) offer the potential for specific protein–protein interactions to coordinate selective reductive flow. Employing the model, genetically accessible, hyperthermophilic archaeon, Thermococcus kodakarensis , we establish the metabolic protein interactome of 25 key redox proteins, revealing that each redox active protein has a dynamic partnership profile, suggesting catabolic and anabolic activities may occur in concert and in temporal and spatial proximity in vivo . These results reveal critical importance in evaluating the newly identified partnerships and their role and utility in providing regulated redox flux in T. kodakarensis .

Williams, Sere A. (ORCID:0000000235509590)↗
DOE OSTI2020

Biophysical and Biochemical Characterization of TP0037, a D-Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum

A longstanding conundrum in Treponema pallidum biology concerns how the spirochete generates sufficient energy to fulfill its complex pathogenesis processes during human syphilitic infection. For decades, it has been assumed that the bacterium relies solely on glucose catabolism (via glycolysis) for generation of its ATP. However, the organism’s robust motility, believed to be essential for human tissue invasion and dissemination, would require abundant ATP likely not provided by the parsimony of glycolysis. As such, additional ATP generation, either via a chemiosmotic gradient, substrate-level phosphorylation, or both, likely exists in T. pallidum. Along these lines, we have hypothesized that T. pallidum exploits an acetogenic energy conservation pathway that relies on the redox chemistry of flavins. Central to this hypothesis is the apparent existence in T. pallidum of an acetogenic pathway for the conversion of d-lactate to acetate. Herein we have characterized the structural, biophysical, and biochemical properties of the first enzyme (d-lactate dehydrogenase [d-LDH]; TP0037) predicted in this pathway. Binding and enzymatic studies showed that recombinant TP0037 consumed d-lactate and NAD+ to produce pyruvate and NADH. The crystal structure of TP0037 revealed a fold similar to that of other d-acid dehydrogenases; residues in the cofactor-binding and active sites were homologous to those of other known d-LDHs. The crystal structure and solution biophysical experiments revealed the protein’s propensity to dimerize, akin to other d-LDHs. This study is the first to elucidate the enzymatic properties of T. pallidum’s d-LDH, thereby providing new compelling evidence for a flavin-dependent acetogenic energy conservation (ATP-generating) pathway in T. pallidum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Novel mutation leading to splice donor loss in a conserved site of DMD gene causes Duchenne muscular dystrophy with cryptorchidism

Background As one of the most common congenital abnormalities in male births, cryptorchidism has been found to have a polygenic aetiology according to previous studies of common variants. However, little is known about genetic predisposition of rare variants for cryptorchidism, since rare variants have larger effective size on diseases than common variants. Methods In this study, a cohort of 115 Chinese probands with cryptorchidism was analysed using whole-genome sequencing, alongside 19 parental controls and 2136 unaffected men. Additionally, CRISPR-Cas9 editing of a conserved variant was performed in a mouse model, with MRI screening used to observe the phenotype. Results In 30 of 115 patients (26.1%), we identified four novel genes ( ARSH , DMD , MAGEA4 and SHROOM2 ) affecting at least five unrelated patients and four known genes ( USP9Y , UBA1 , BCORL1 and KDM6A ) with the candidate rare pathogenic variants affecting at least two cases. Burden tests of rare variants revealed the genome-wide significances for newly identified genes (p<2.5×10 −6 ) under the Bonferroni correction. Surprisingly, novel and known genes were mainly found on X chromosome (seven on X and one on Y) and all rare X-chromosomal segregating variants exhibited a maternal inheritance rather than de novo origin. CRISPR-Cas9 mouse modelling of a splice donor loss variant in DMD (NC_000023.11:g.32454661C>G), which resides in a conserved site across vertebrates, replicated bilateral cryptorchidism phenotypes, confirmed by MRI at 4 and 10 weeks. The movement tests further revealed symptoms of Duchenne muscular dystrophy (DMD) in transgenic mice. Conclusion Our results revealed the role of the DMD gene mutation in causing cryptorchidism. The results also suggest that maternal-X inheritance of pathogenic defects could have a predominant role in the development of cryptorchidism.

Chen, Jianhai (ORCID:0000000300932003)↗
DOE OSTI2022

Conservative and Accurate Solution Transfer Between High-Order and Low-Order Refined Finite Element Spaces

Here, in this paper, we introduce general transfer operators between high-order and low-order refined finite element spaces that can be used to couple high-order and low-order simulations. Under natural restrictions on the low-order refined space we prove that both the high-to-low-order and low-to-high-order linear mappings are conservative, constant preserving, and high-order accurate. While the proof holds for affine geometries, numerical experiments indicate that the results hold for more general curved meshes. We present several numerical results confirming our analysis and demonstrate the utility of the new mappings in the context of adaptive mesh refinement and conservative multidiscretization coupling.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

On interpretation of fluctuations of conserved charges at high T

Abstract Fluctuations of conserved charges calculated on the lattice which can be measured experimentally, are well reproduced by a hadron resonanse gas model at temperatures below$$T_{ch} \sim 155$$ T ch ∼ 155 MeV and radically deviate from the hadron resonance gas predictions above the chiral restoration crossover. This behaviour is typically interpreted as an indication of deconfinement in the quark-gluon plasma regime. We present an argument that this interpretation may be too simple. The argument is based on the scaling of quantities with the number of colors: demonstration of deconfinement and QGP requires observable that is sensitive to$$\sim N_c^2$$ ∼ N c 2 gluons while the conserved charges are sensitive only to quarks and above$$T_{ch}$$ T ch scale as$$N_c^1$$ N c 1 . The latter scaling is consistent with the existence of an intermediate regime characterized by restored chiral symmetry and by approximate chiral spin symmetry which is a symmetry of confining interaction. In this regime the energy density, pressure and entropy density scale as$$N_c^1$$ N c 1 . In the large$$N_c$$ N c limit this regime might become a distinct phase separated from the hadron gas and from QGP by phase transitions. A natural observable that associates with deconfinement and is directly sensitive to deconfined$$N_c^2-1$$ N c 2 - 1 gluons is the Polyakov loop; in the$$N_c=3$$ N c = 3 world it remains very close to 0 at temperatures well above chiral crossover, reaches the value$$\sim 0.5$$ ∼ 0.5 around$$\sim 3T_{ch}$$ ∼ 3 T ch and the value close to 1 at temperatures$$\sim 1$$ ∼ 1 GeV.

Physics↗
DOE OSTI2021

Perspective—Mass Conservation in Models for Electrodeposition/Stripping in Lithium Metal Batteries

Electrochemical models at different scales and varying levels of complexity have been used in the literature to study the evolution of the anode surface in lithium metal batteries. This includes continuum, mesoscale (phase-field approaches), and multiscale models. In this paper, using a motivating example of a moving boundary model in one dimension, we show how battery models need proper formulation for mass conservation, especially when simulated over multiple charge and discharge cycles. The article concludes with some thoughts on mass conservation and proper formulation for multiscale models.

25 ENERGY STORAGE↗