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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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At least 1,441 records · Page 80
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

CRISPR-Cas “Non-Target” Sites Inhibit On-Target Cutting Rates

CRISPR-Cas systems have become ubiquitous for genome editing in eukaryotic as well as bacterial systems. Cas9 forms a complex with a guide RNA (gRNA) and searches DNA for a matching sequence (target site) next to a protospacer adjacent motif (PAM). Once found, Cas9 cuts the DNA. Cas9 is revolutionary for the ability to change the RNA sequence and target a new site easily. However, while algorithms have been developed to predict gRNA-specific Cas9 activity, a fundamental biological understanding of gRNA-specific activity is lacking. Here, the number of PAM sites in the genome is effectively a large pool of inhibitory substrates, competing with the target site for the Cas9/gRNA complex. We demonstrate that increasing the number of non-target sites for a given gRNA reduces on-target activity in a dose-dependent manner. Furthermore, we show that the use of Cas9 mutants with increased PAM specificity toward a smaller subset of PAMs (or smaller pool of competitive substrates) improves cutting rates, while increased PAM promiscuity decreases cutting rates. Decreasing the potential search space by increasing PAM specificity provides a path toward improving on-target activity for slower high-fidelity Cas9 variants. Engineering improved PAM specificity to reduce the competitive search space offers an alternative strategy to engineer Cas9 variants with increased specificity and maintained on-target activity.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Prediction of histone post-translational modifications using deep learning

Abstract Motivation Histone post-translational modifications (PTMs) are involved in a variety of essential regulatory processes in the cell, including transcription control. Recent studies have shown that histone PTMs can be accurately predicted from the knowledge of transcription factor binding or DNase hypersensitivity data. Similarly, it has been shown that one can predict PTMs from the underlying DNA primary sequence. Results In this study, we introduce a deep learning architecture called DeepPTM for predicting histone PTMs from transcription factor binding data and the primary DNA sequence. Extensive experimental results show that our deep learning model outperforms the prediction accuracy of the model proposed in Benveniste et al. (PNAS 2014) and DeepHistone (BMC Genomics 2019). The competitive advantage of our framework lies in the synergistic use of deep learning combined with an effective pre-processing step. Our classification framework has also enabled the discovery that the knowledge of a small subset of transcription factors (which are histone-PTM and cell-type-specific) can provide almost the same prediction accuracy that can be obtained using all the transcription factors data. Availabilityand implementation https://github.com/dDipankar/DeepPTM. Supplementary information Supplementary data are available at Bioinformatics online.

Baisya, Dipankar Ranjan (ORCID:0000000267847359)↗
DOE OSTI2025

Sulfide stress tolerance as a controller of methane production in temperate wetlands

Abstract Wetlands are a major source of methane emissions and contribute to the observed increase in atmospheric methane over the last 20 years. Methane production in wetlands is the final step of carbon decomposition performed by anaerobic archaea. Although hydrogen/carbon dioxide and acetate are the substrates most often attributed to methanogenesis, other substrates—such as methylated compounds—may additionally play important roles in driving methane production in wetland systems. Here we conducted mesocosm experiments combined with genome-resolved metatranscriptomics to investigate the impact of diverse methanogenic substrate amendment on methanogenesis in two high methane-emitting wetlands with distinct geochemistry, termed P7 and P8. Methanol amendment resulted in high methane production at both sites, whereas acetate and formate amendment only stimulated methanogenesis in P7 mesocosms, where aqueous sulfide concentrations were lower. In P7 sediments, formate amendment fueled acetogenic microbes that produced acetate, which was subsequently utilized by acetoclastic methanogens. In contrast to expression profiles in P7 mesocosms, active methylotrophic methanogen genomes from P8 showed increased expression of genes related to membrane remodeling and DNA damage repair, indicative of stress tolerance mechanisms to counter sulfide toxicity. Methylotrophic methanogenesis generates higher free energy yields than acetoclastic methanogenesis, which likely enables allocation of more energy toward stress responses. These findings contribute to the growing body of literature highlighting methylotrophic methanogenesis as an important methane production pathway in wetlands. By using less competitive substrates like methanol that provide greater energy yields, methylotrophic methanogens may invest in physiological strategies that provide competitive advantages across a range of environmental stresses.

Environmental Sciences & Ecology↗
DOE OSTI2018

The effects of magnetic fields and protostellar feedback on low-mass cluster formation

In this paper, we present a large suite of simulations of the formation of low-mass star clusters. Our simulations include an extensive set of physical processes – magnetohydrodynamics, radiative transfer, and protostellar outflows – and span a wide range of virial parameters and magnetic field strengths. Comparing the outcomes of our simulations to observations, we find that simulations remaining close to virial balance throughout their history produce star formation efficiencies and initial mass function (IMF) peaks that are stable in time and in reasonable agreement with observations. Our results indicate that small-scale dissipation effects near the protostellar surface provide a feedback loop for stabilizing the star formation efficiency. This is true regardless of whether the balance is maintained by input of energy from large-scale forcing or by strong magnetic fields that inhibit collapse. In contrast, simulations that leave virial balance and undergo runaway collapse form stars too efficiently and produce an IMF that becomes increasingly top heavy with time. In all cases, we find that the competition between magnetic flux advection towards the protostar and outward advection due to magnetic interchange instabilities, and the competition between turbulent amplification and reconnection close to newly formed protostars renders the local magnetic field structure insensitive to the strength of the large-scale field, ensuring that radiation is always more important than magnetic support in setting the fragmentation scale and thus the IMF peak mass. The statistics of multiple stellar systems are similarly insensitive to variations in the initial conditions and generally agree with observations within the range of statistical uncertainty.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily

Contact-dependent growth inhibition (CDI) is an important mechanism of inter-bacterial competition found in many Gram-negative pathogens. CDI+ cells express cell-surface CdiA proteins that bind neighboring bacteria and deliver C-terminal toxin domains (CdiA-CT) to inhibit target-cell growth. CDI+ bacteria also produce CdiI immunity proteins, which specifically neutralize cognate CdiA-CT toxins to prevent self-inhibition. Here, we present the crystal structure of the CdiA-CT/CdiI(Ykris) complex from Yersinia kris-tensenii ATCC 33638. CdiA-CTYkris adopts the same fold as angiogenin and other RNase A paralogs, but the toxin does not share sequence similarity with these nucleases and lacks the characteristic disulfide bonds of the superfamily. Consistent with the structural homology, CdiA-CTYkris has potent RNase activity in vitro and in vivo. Structure-guided mutagenesis reveals that His175, Arg186, Thr276 and Tyr278 contribute to CdiA-CTYkris activity, suggesting that these residues participate in substrate binding and/or catalysis. CdiI(Ykris) binds directly over the putative active site and likely neutralizes toxicity by blocking access to RNA substrates. Significantly, CdiA-CTYkris is the first non-vertebrate protein found to possess the RNase A superfamily fold, and homologs of this toxin are associated with secretion systems in many Gram-negative and Gram-positive bacteria. These observations suggest that RNase Alike toxins are commonly deployed in inter-bacterial competition.

Batot, Gaëlle↗
DOE OSTI2012

Extinction and ecological retreat in a community of primates

The lemurs of Madagascar represent a prodigious adaptive radiation. At least 17 species ranging from 11 to 160 kg have become extinct during the past 2000 years. The effect of this loss on contemporary lemurs is unknown. The concept of competitive release favours the expansion of living species into vacant niches. Alternatively, factors that triggered the extinction of some species could have also reduced community-wide niche breadth. Here, we use radiocarbon and stable isotope data to examine temporal shifts in the niches of extant lemur species following the extinction of eight large-bodied species. We focus on southwestern Madagascar and report profound isotopic shifts, both from the time when now-extinct lemurs abounded and from the time immediately following their decline to the present. Unexpectedly, the past environments exploited by lemurs were drier than the protected (albeit often degraded) riparian habitats assumed to be ideal for lemurs today. Neither competitive release nor niche contraction can explain these observed trends. We develop an alternative hypothesis: ecological retreat, which suggests that factors surrounding extinction may force surviving species into marginal or previously unfilled niches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Chemical Trend of Transition-Metal Doping in W Se 2

Transition-metal dichalcogenides (TMDs) are promising nanoscale materials with a wide range of applications. Chemical doping is a powerful tool for tailoring the physical and chemical properties of TMDs for targeted functionalities. As one of the most important TMDs, WSe 2 has great potential for applications in field effect transistor and complementary metal oxide semiconductor technologies for its bipolar dopability. Yet, precise control over the type and density of free carriers remains challenging. First-principles calculations are performed to study intrinsic defects and transition-metal (TM) dopants in WSe 2 . Our findings demonstrate that TM doping can effectively control the Fermi level in WSe 2 with no significant compensation by intrinsic defects. Nb and Ta are effective p-type dopants capable of generating a high free hole density in WSe 2 . While n-type doping is possible by Re (under the Se-rich condition) and Cu (under the W-rich condition), the doping efficiency is reduced due to the lower attainable dopant concentration and higher ionization energies. The chemical trend in the attainable concentration of various substitutional TM dopants in WSe 2 is largely determined by the competition between the dopant incorporation in WSe 2 and the formation of the secondary phase TMSe 2 . Such a competition is strongly affected by the different crystal environments of the TM ion in TMSe 2 and WSe 2 , which determine the crystal field splitting and electron filling of TM d levels and consequently the formation energy of the TM dopant.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Notch Fracture Toughness of Glasses: Dependence on Rate, Age, and Geometry

Understanding the fracture toughness (resistance) of glasses is a fundamental problem of prime theoretical and practical importance. Here we theoretically study its dependence on the loading rate, the age (history) of the glass, and the notch radius ρ. Reduced-dimensionality analysis suggests that the notch fracture toughness results from a competition between the initial, age- and history-dependent, plastic relaxation time scale τ$ ^{pl}_0 $ and an effective loading time scale τ ext ($ \dot{K} $ I , ρ ), where KI is the tensile stress-intensity-factor rate. The toughness is predicted to scale with ρ independently of ξ≡τ ext /τ$ ^{pl}_0 $ for ξ «1, to scale as T$ \sqrt{ρ} $log(ξ) for ξ«1 (related to thermal activation, where T is the temperature), and to feature a nonmonotonic behavior in the crossover region ξ~ O (1) (related to plastic yielding dynamics). These predictions are verified using 2D computations, providing a unified picture of the notch fracture toughness of glasses. Here, the theory highlights the importance of time-scale competition and far-from-steady-state elasto-viscoplastic dynamics for understanding the toughness and shows that the latter varies quite significantly with the glass age (history) and applied loading rate. Experimental support for bulk metallic glasses is presented, and possible implications for applications are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Competing orders at higher-order Van Hove points

Van Hove points are special points in the energy dispersion, where the density of states exhibits analytic singularities. When a Van Hove point is close to the Fermi level, tendencies towards density wave orders, Pomeranchuk orders, and superconductivity can all be enhanced, often in more than one channel, leading to a competition between different orders and unconventional ground states. In this study we consider the effects from higher-order Van Hove points, around which the dispersion is flatter than near a conventional Van Hove point, and the density of states has a power-law divergence. We argue that such points are present in intercalated graphene and other materials. We use an effective low-energy model for electrons near higher-order Van Hove points and analyze the competition between different ordering tendencies using an unbiased renormalization-group approach. For purely repulsive interactions, we find that two key competitors are ferromagnetism and chiral superconductivity. For a small attractive interaction, we find an unconventional spin Pomeranchuk order, in wich the spin oder parameter winds around the Fermi surface. The supermetal state, predicted for a single higher-order Van Hove point, is an unstable fixed point in our case.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Twisted bilayer graphene. IV. Exact insulator ground states and phase diagram

Here, we derive the exact insulator ground states of the projected Hamiltonian of magic-angle twisted bilayer graphene (TBG) flat bands with Coulomb interactions in various limits, and study the perturbations away from these limits. We define the (first) chiral limit where the AA stacking hopping is zero, and a flat limit with exactly flat bands. In the chiral-flat limit, the TBG Hamiltonian has a U(4) × U(4) symmetry, and we find that the exact ground states at integer filling – 4 ≤ $\textit{ν}$ ≤ 4 relative to charge neutrality are Chern insulators of Chern numbers $ν_C$ = 4 – |$\textit{ν}$ |, 2 – |$\textit{ν}$ |, $\cdots$, |$\textit{ν}$ | – 4, all of which are degenerate. This confirms recent experiments where Chern insulators are found to be competitive low-energy states of TBG. When the chiral-flat limit is reduced to the nonchiral-flat limit which has a U(4) symmetry, we find $\textit{ν}$ = 0 , ± 2 has exact ground states of Chern number 0, while $\textit{ν}$ = ±1, ± 3 has perturbative ground states of Chern number $ν_C$ = ± 1, which are U(4) ferromagnetic. In the chiral-nonflat limit with a different U(4) symmetry, different Chern number states are degenerate up to second-order perturbations. In the realistic nonchiral-nonflat case, we find that the perturbative insulator states with Chern number $ν_C$ = 0 (0 < |$ν_C$| < 4 – |$\textit{ν}$ |) at integer fillings $\textit{ν}$ are fully (partially) intervalley coherent, while the insulator states with Chern number |$ν_C$| = 4 – |$\textit{ν}$ | are valley polarized. However, for 0 < |$ν_C$| ≤ 4 – |$\textit{ν}$ |, the fully intervalley coherent states are highly competitive (0.005 meV/electron higher). At nonzero magnetic field |$\textit{B}$ | > 0, a first-order phase transition for $\textit{ν}$ = ± 1, ± 2 from Chern number $ν_C$ = sgn ($\textit{νB}$)(2 – |$\textit{ν}$ |) to $ν_C$ = sgn ($\textit{νB}$)(4 – |$\textit{ν}$ |) is expected, which agrees with recent experimental observations. Lastly, the TBG Hamiltonian reduces into an extended Hubbard model in the stabilizer code limit.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Fragility of the nematic spin liquid induced by diagonal couplings in the square-lattice SU(3) model

Here, we present a large-scale density matrix renormalization group (DMRG) study of the spin-1 SU(3) bilinear-biquadratic model on the square lattice, which was suggested to host a nematic spin liquid state in recent DMRG calculations. We report that this spin liquid appears to strongly compete with a three-sublattice magnetic order. To further study the competition between the two states, and the reason of the emergent nematic spin liquid, we included an additional next-nearest-neighbor SU(3) symmetric interactions along one of the two plaquette diagonal directions. This allows to tune the square-lattice model to the triangular-lattice model. By computing spin correlation functions and various order parameters, we find that the three-sublattice order may develop at infinitesimal additional new coupling, at least within the precision of our study. Compared with the previous findings that the nematic spin liquid is stable in extended parameter regions with additional couplings that respect the lattice symmetries of the square lattice, we argue that here the diagonal couplings, which frustrate the bipartite-lattice structure, rapidly suppress the two-sublattice fluctuations and the three-sublattice order thus wins. This numerical result is consistent with the conjecture that the nematic spin liquid emerges from the competition between two- and three-sublattice fluctuations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2011

High-pressure Study of Silane to 150 GPa

We present an extensive study of the optical, electronic, and structural properties of silane (SiH{sub 4}) to 150 GPa through the use of Raman spectroscopy, optical microscopy, synchrotron infrared reflectivity, optical absorption, and synchrotron x-ray diffraction measurements. To mitigate possible contamination from previously reported metal hydride formation, we performed experiments using gold-lined sample gaskets, finding molecular silane remains in the transparent and insulating P2{sub 1}/c structure until {approx}40 GPa. Silane shows a partial loss of crystallinity above {approx}50 GPa and appears to visibly darken. The darkening is plausibly the result of a loss of molecular character with many enthalpically competitive pathways available, including decomposition, combined with the absorptive nature of the sample. Above 100 GPa we observed crystallization into structures partially consistent with the previously reported nonmolecular I4{sup -} 2d and I4{sub 1}/a types. In the absence of decomposition, silane remains partially transparent and nonmetallic to at least 150 GPa with a band gap constrained between 0.6 and 1.8 eV. Under pressure, silane is sensitive to irradiation from x-rays and lasers, and may easily decompose into metallic silicon. We suggest that previous reports of metallization starting from molecular SiH{sub 4} arise from decomposition, and superconductivity may originate from hydrogen-doped silicon. While silane may readily decompose, the inherent metastability provides access to a wide range of path- and sample-history-dependent states and suggests a unique range of physical properties for hydrogen-rich silicon alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Complex state found in the colossal magnetoresistance regime of models for manganites

The colossal magnetoresistance (CMR) effect of manganites is widely believed to be caused by the competition between a ferromagnetic (FM) metallic state induced by the double-exchange mechanism and an insulator with complex spin, charge, and orbital order. Recent computational studies in small clusters have indeed reported a CMR precisely near the frontier between those two states at a realistic hole density x = 1/4. However, the detailed characteristics of the competing insulator were not fully understood in those previous investigations. This insulator is expected to display special properties that lead to the CMR; otherwise any competition between ferromagnetic and antiferromagnetic states would induce such an effect, which is not the case experimentally. In this report, the competing insulator at electronic density x = 1/4 and in the CMR regime is studied in detail using the double-exchange two-orbital model with Jahn-Teller lattice distortions on two-dimensional clusters, employing a careful large-scale cooling down process in the Monte Carlo simulations to avoid being trapped in metastable states. Our investigations show that this competing insulator has an unexpected complex structure, involving diagonal stripes with alternating regions displaying FM and CE-like order. The level of complexity of this new state even surpasses that of the recently unveiled spin-orthogonal-stripe states and their associated high degeneracy. This new state complements the long-standing scenario of phase separation, since the alternating FM-CE pattern appears even in the clean limit. The present and recent investigations are also in agreement with the many glassy characteristics of the CMR state found experimentally, due to the high degeneracy of the insulating states involved in the process. Results for the spin-structure factor of the new states are also here provided to facilitate the analysis of neutron scattering experiments for these materials.

Sen, Cengiz↗
DOE OSTI2015

Strong coupling critique of spin fluctuation driven charge order in underdoped cuprates

Charge order has emerged as a generic feature of doped cuprates, leading to important questions about its origin and its relation to superconductivity. Recent experiments on two classes of hole doped cuprates indicate a novel d -wave symmetry for the order. These were motivated by earlier spin fluctuation theoretical studies based on an expansion about hot spots in the Brillouin zone that indicated such an order would be competitive with d -wave superconductivity. In this work, we reexamine this problem by solving strong coupling equations in the full Brillouin zone for experimentally relevant parameters. We find that bond-oriented order, as seen experimentally, is strongly suppressed. We also include coupling to B 1g phonons and do not see any qualitative change. Our results argue against an itinerant model for the charge order, implying instead that such order is likely due to Coulombic phase separation of the doped holes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Magnetic anisotropy in the frustrated spin-chain compound β - TeVO 4

In this paper, isotropic and anisotropic magnetic behavior of the frustrated spin-chain compound β-TeVO 4 is reported. Three magnetic transitions observed in zero magnetic field are tracked in fields applied along different crystallographic directions using magnetization, heat capacity, and magnetostriction measurements. Qualitatively different temperature-field diagrams are obtained below 10 T for the field applied along a or b and along c , respectively. In contrast, a nearly isotropic high-field phase emerges above 18 T and persists up to the saturation that occurs around 22.5 T. Upon cooling in low fields, the transitions at T N1 and T N2 toward the spin-density-wave and stripe phases are of the second order, whereas the transition at T N3 toward the helical state is of the first order and entails a lattice component. Our microscopic analysis identifies frustrated J 1 -J 2 spin chains with a sizable antiferromagnetic interchain coupling in the bc plane and ferromagnetic couplings along the a direction. The competition between these ferromagnetic interchain couplings and the helical order within the chain underlies the incommensurate order along the a direction, as observed experimentally. While a helical state is triggered by the competition between J 1 and J 2 within the chain, the plane of the helix is not uniquely defined because of competing magnetic anisotropies. Finally, using high-resolution synchrotron diffraction and 125 Te nuclear magnetic resonance, we also demonstrate that the crystal structure of β-TeVO 4 does not change down to 10 K, and the orbital state of V 4+ is preserved.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Rapidly convergent cluster expansion and application to lithium ion battery materials

The convergence of a cluster expansion for lithium transition-metal (TM) oxides is improved by explicit treatment of TM magnetic moments. The approach is applied to layered LiC o y N i 1 - y O 2 (NC). The ground state and low-lying excited state structures are identified, and the distribution of TM ions and magnetic moment in those structures is investigated to explain the origin of Ni-antisite ions and Jahn-Teller distortion. In this work, the developed model also reveals the mechanisms governing the atomic arrangement of NC, including in-plane Co-Co vs Co-Ni competition, magnetic frustration vs disproportionation competition, and cationic interactions spanning adjacent layers.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗