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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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Multistate, multichannel coupled diabatic state representations of adiabatic states coupled by conical intersections. CH 2 OH photodissociation

In this work, a coupled diabatic state representation, H d , of the 1, 2, 3 2 A states of CH 2 OH suitable for the description of the three channel, three state photodissociation process CH 2 OH(1 2 A) + hv → CH 2 OH(2, 3 2 A) → CH 2 O(X, A) + H, cis-CHOH + H, trans-CHOH + H, is reported. The representation is based on electronic structure data (energies, energy gradients, and derivative couplings) obtained exclusively from multireference configuration interaction single and double excitation wave functions. Diabat shifting is employed to improve the representation’s agreement with accurate experimental energetics. A careful analysis of the numerous minima, saddle points, and conical intersection seams is reported. The computed T 0 (3 2 A) ~ 35 220 cm -1 is in excellent agreement with the experimental estimate of 35 053 cm -1 , and the computed channel dissociation energies, D 0 , for CH 2 O 9453 (10 160), cis-HCOH 30 310.2 (29 923), and trans-HCOH 28 799 (28 391) cm -1 are in good accord with the measured values given parenthetically. Lastly, these accurate energetics over a wide range of nuclear configurations strongly support the ability of this H d to enable quality simulations of nonadiabatic dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers

Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode structure and functionality by having various side chains. Through molecular dynamics (MD) simulations, the triazine polymers have been shown to form particular sequential stacks, have stable backbone-backbone interactions through hydrogen bonding and π–π interactions, and conserve their cis/trans conformations throughout the simulation. However, we do not know the effects of having different side chains and backbone structures on the entire conformation and whether the cis or trans conformation is more stable for the triazine polymers. For this reason, we investigate the role of non-covalent interactions for different side chains and backbone structures on the conformation and assembly of triazine polymers in MD simulations. Since there is a high energy barrier associated with the cis-trans isomerization, we use replica exchange molecular dynamics (REMD) to sample various conformations of triazine hexamers. To obtain rates and intermediate conformations, we use the recently developed concurrent adaptive sampling (CAS) algorithm for dimers of triazine trimers. Here, we found that the hydrogen bonding ability of the backbone structure is critical for the triazine polymers to self-assemble into nanorod-like structures, rather than that of the side chains, which can help researchers design more robust materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Laser calibration of the DIII-D coherence imaging system

Here, we describe an in situ calibration technique for Coherence Imaging Spectroscopy (CIS) that measures 2-D images of ion flows on DIII-D. A low power CW diode laser that is tuneable in the range 464-468 nm along with a precision wavemeter (10 –5 nm resolution) is used to characterize the interferometer phase as a function of wavelength in the region of C iii (465 nm) and He ii (468 nm). The interferometer is stabilized both mechanically and thermally to minimize drift during the calibration. Optical stirring and an integration sphere are utilized to obtain spatially uniform calibration images. The quality of the calibration data enables a measurement of phase versus wavelength over approximately 10 fringes of the interferometer. These coefficients can also be related to the geometry of the optics and the birefringent crystal of the interferometer. On DIII-D, the integration sphere with the laser light is inserted into the CIS optical system between shots and the laser image and wavelength are automatically recorded, providing a zero velocity reference

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein

Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Geometric phase in coupled cluster theory

It has been well-established that the topography around conical intersections between excited electronic states is incorrectly described by coupled cluster and many other single reference theories (the intersections are “defective”). Despite this, we show both analytically and numerically that the geometric phase effect (GPE) is correctly reproduced upon traversing a path around a defective excited-state conical intersection (CI) in coupled cluster theory. The theoretical analysis is carried out by using a non-Hermitian generalization of the linear vibronic coupling approach. Interestingly, the approach qualitatively explains the characteristic (incorrect) shape of the defective CIs and CI seams. Moreover, the validity of the approach and the presence of the GPE indicate that defective CIs are local (and not global) artifacts. This implies that a sufficiently accurate coupled cluster method could predict nuclear dynamics, including geometric phase effects, as long as the nuclear wavepacket never gets too close to the conical intersections.

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

Alternative CNDOL Fockians for fast and accurate description of molecular exciton properties

CNDOL is an a priori, approximate Fockian for molecular wave functions. In this study, we employ several modes of singly excited configuration interaction (CIS) to model molecular excitation properties by using four combinations of the one electron operator terms. Those options are compared to the experimental and theoretical data for a carefully selected set of molecules. The resulting excitons are represented by CIS wave functions that encompass all valence electrons in the system for each excited state energy. The Coulomb–exchange term associated to the calculated excitation energies is rationalized to evaluate theoretical exciton binding energies. This property is shown to be useful for discriminating the charge donation ability of molecular and supermolecular systems. Multielectronic 3D maps of exciton formal charges are showcased, demonstrating the applicability of these approximate wave functions for modeling properties of large molecules and clusters at nanoscales. This modeling proves useful in designing molecular photovoltaic devices. Our methodology holds potential applications in systematic evaluations of such systems and the development of fundamental artificial intelligence databases for predicting related properties.

Chemistry↗
DOE OSTI2012

Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography

To understand how signaling proteins function, it is necessary to know the time-ordered sequence of events that lead to the signaling state. We recently developed on the BioCARS 14-IDB beamline at the Advanced Photon Source the infrastructure required to characterize structural changes in protein crystals with near-atomic spatial resolution and 150-ps time resolution, and have used this capability to track the reversible photocycle of photoactive yellow protein (PYP) following trans-to-cis photoisomerization of its p-coumaric acid (pCA) chromophore over 10 decades of time. The first of four major intermediates characterized in this study is highly contorted, with the pCA carbonyl rotated nearly 90° out of the plane of the phenolate. A hydrogen bond between the pCA carbonyl and the Cys69 backbone constrains the chromophore in this unusual twisted conformation. Density functional theory calculations confirm that this structure is chemically plausible and corresponds to a strained cis intermediate. This unique structure is short-lived (~600 ps), has not been observed in prior cryocrystallography experiments, and is the progenitor of intermediates characterized in previous nanosecond time-resolved Laue crystallography studies. The structural transitions unveiled during the PYP photocycle include trans/cis isomerization, the breaking and making of hydrogen bonds, formation/relaxation of strain, and gated water penetration into the interior of the protein. This mechanistically detailed, near-atomic resolution description of the complete PYP photocycle provides a framework for understanding signal transduction in proteins, and for assessing and validating theoretical/computational approaches in protein biophysics.

Schotte, Friedrich↗
DOE OSTI2015

Engineering Escherichia coli coculture systems for the production of biochemical products

Significance Production of industrial compounds by using engineered microorganisms is a robust method to reduce our reliance on nonrenewable petroleum resources and increase the utility of renewable resources, such as lignocellulose. Because there are major limitations for engineering a single microbial cell to achieve high-yield production, we developed microbial coculture systems consisting of two different microbial cell types to use sugar mixtures that can be derived from lignocellulose efficiently. We demonstrate that this approach is successful for achieving high-level production of two important value-added molecules, cis , cis -muconic acid and 4-hydroxybenzoic acid. This accomplishment establishes a previously unidentified technology for advancing future research in metabolic engineering and synthetic biology.

4-hydroxybenzoic acid↗
DOE OSTI2019

Regulation of photoprotection gene expression in Chlamydomonas by a putative E3 ubiquitin ligase complex and a homolog of CONSTANS

Photosynthetic organisms use nonphotochemical quenching (NPQ) mechanisms to dissipate excess absorbed light energy and protect themselves from photooxidation. In the model green alga Chlamydomonas reinhardtii , the capacity for rapidly reversible NPQ (qE) is induced by high light, blue light, and UV light via increased expression of LHCSR and PSBS genes that are necessary for qE. Here, we used a forward genetics approach to identify SPA1 and CUL4, components of a putative green algal E3 ubiquitin ligase complex, as critical factors in a signaling pathway that controls light-regulated expression of the LHCSR and PSBS genes in C. reinhardtii . The spa1 and cul4 mutants accumulate increased levels of LHCSR1 and PSBS proteins in high light, and unlike the wild type, they express LHCSR1 and exhibit qE capacity even when grown in low light. The spa1-1 mutation resulted in constitutively high expression of LHCSR and PSBS RNAs in both low light and high light. The qE and gene expression phenotypes of spa1-1 are blocked by mutation of CrCO, a B-box Zn-finger transcription factor that is a homolog of CONSTANS, which controls flowering time in plants. CONSTANS-like cis -regulatory sequences were identified proximal to the qE genes, consistent with CrCO acting as a direct activator of qE gene expression. We conclude that SPA1 and CUL4 are components of a conserved E3 ubiquitin ligase that acts upstream of CrCO, whose regulatory function is wired differently in C. reinhardtii to control qE capacity via cis -regulatory CrCO-binding sites at key photoprotection genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Evidence that Criegee intermediates drive autoxidation in unsaturated lipids

Significance Autoxidation leads to the slow persistent destruction of organic molecules causing oxidative stress and associated disease. The prevailing autoxidation mechanism of unsaturated lipids involves chain reactions initiated and propagated by H-atom abstraction, mediated by peroxy radicals and other reactive oxygen species. Here we report experimental evidence for an autoxidation mechanism initiated by OH, which is unanticipated and proceeds by OH addition followed by pathways involving Criegee intermediates (CIs). Although CIs are routinely encountered in atmospheric and synthetic organic chemistry, their role in autoxidation is unexpected. Our results suggest that in all likelihood these exotic species play a much more prominent and general role in the chemistry of cells, food, petrochemicals, and the environment beyond what is currently believed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

The first astrophysical detection, terahertz spectrum, and database for the monodeuterated species of methyl formate HCOOCH{sub 2}D

Based on new measurements carried out in the laboratory from 0.77 to 1.2 THz and on a line-frequency analysis of these new data, along with previously published data, we build a line list for HCOOCH{sub 2}D that leads to its first detection in the Orion KL nebula. The observed lines, both in space and in the laboratory, involve the cis D-in-plane and trans D-out-of-plane conformations of HCOOCH{sub 2}D and the two tunneling states arising from the large-amplitude motion connecting the two trans configurations. The model used in the line position calculation accounts for both cis and trans conformations, as well as the large-amplitude motion.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

DMINDA: an integrated web server for DNA motif identification and analyses

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http: //csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Evolution-guided engineering of small-molecule biosensors

Allosteric transcription factors (aTFs) have proven widely applicable for biotechnology and synthetic biology as ligand-specific biosensors enabling real-time monitoring, selection and regulation of cellular metabolism. However, both the biosensor specificity and the correlation between ligand concentration and biosensor output signal, also known as the transfer function, often needs to be optimized before meeting application needs. Here, we present a versatile and high-throughput method to evolve prokaryotic aTF specificity and transfer functions in a eukaryote chassis, namely baker's yeast Saccharomyces cerevisiae. From a single round of mutagenesis of the effector-binding domain (EBD) coupled with various toggled selection regimes, we robustly select aTF variants of the cis,cis-muconic acid-inducible transcription factor BenM evolved for change in ligand specificity, increased dynamic output range, shifts in operational range, and a complete inversion-of-function from activation to repression. Importantly, by targeting only the EBD, the evolved biosensors display DNA-binding affinities similar to BenM, and are functional when ported back into a prokaryotic chassis. The developed platform technology thus leverages aTF evolvability for the development of new host-agnostic biosensors with user-defined small-molecule specificities and transfer functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

ABSTRACT The Shox2 homeodomain transcriptional regulator is known for its critical functions during mouse embryogenesis, enabling accurate development of limbs, craniofacial structures, neural populations and the cardiac conduction system. At the genomic level, the Shox2 gene is flanked by an extensive gene desert, a continuous non-coding genomic region spanning over 500 kilobases that contains a multitude of evolutionarily conserved elements with predicted cis -regulatory activities. However, the transcriptional enhancer potential of the vast majority of these elements in combination with the biological necessity of the gene desert have not yet been explored. Using transgenic reporter assays in mouse embryos to validate an extensive set of stringent epigenomic enhancer predictions, we identify several novel gene desert enhancers with distinct tissue-specific activities in Shox2 expressing tissues. 4C-seq chromatin conformation capture further uncovers a repertoire of gene desert enhancers with overlapping activities in the proximal limb, in a compartment essential for Shox2 -mediated stylopod formation. Leveraging CRISPR/Cas9 to delete the gene desert region contained in the Shox2 topologically associated domain (TAD), we demonstrate that this complex cis -regulatory platform is essential for embryonic survival and required for control of region-specific Shox2 expression in multiple developing tissues. While transcription of Shox2 in the embryonic limb is only moderately affected by gene desert loss, Shox2 expression in craniofacial and cardiac domains is nearly abolished. In particular, Shox2 transcripts in the sinus venosus (SV) encompassing the sinoatrial node (SAN) were depleted in embryos lacking the gene desert, likely accounting for the embryonic lethality due to Shox2 -dependency of the SAN pacemaker. Finally, we discover a 1.5kb SV enhancer within the deleted gene desert region, which may act as a genomic module controlling the development of the cardiac conduction system. In summary, our results identify a gene desert indispensable for pleiotropic patterning and highlight the importance of these extensive regulatory landscapes for embryonic development and viability.

Abassah-Oppong, Samuel↗
DOE OSTI2016

Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C 4 grass

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C 4 grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. While less well-represented, we observe 1294 genes (7.8%) with trans effects. Trans-by-environment interactions are weaker and much less common than cis G×E, occurring in only 0.7% of trans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant G×E. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among G×E genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting G×E and trans regulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites. P. hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

High-harmonic spectroscopy of molecular isomers

We demonstrate that high-order-harmonic generation (HHG) spectroscopy can be used to probe stereoisomers of randomly oriented 1,2-dichloroethylene (C{sub 2}H{sub 2}Cl{sub 2}) and 2-butene (C{sub 4}H{sub 8}). The high-harmonic spectra of these isomers are distinguishable over a range of laser intensities and wavelengths. Time-dependent numerical calculations of angle-dependent ionization yields for 1,2-dichloroethylene suggest that the harmonic spectra of molecular isomers reflect differences in their strong-field ionization. The subcycle ionization yields for the cis isomer are an order of magnitude higher than those for the trans isomer. The sensitivity in discrimination of the harmonic spectra of cis- and trans- isomers is greater than 8 and 5 for 1,2-dichloroethylene and 2-butene, respectively. We show that HHG spectroscopy cannot differentiate the harmonic spectra of the two enantiomers of the chiral molecule propylene oxide (C{sub 3}H{sub 6}O).

2-METHYLPROPENE↗
DOE OSTI2017

Hydrogen bonds are a primary driving force for de novo protein folding

The protein-folding mechanism remains a major puzzle in life science. Purified soluble activation-induced cytidine deaminase (AID) is one of the most difficult proteins to obtain. Starting from inclusion bodies containing a C-terminally truncated version of AID (residues 1–153; AID 153 ), an optimized in vitro folding procedure was derived to obtain large amounts of AID 153 , which led to crystals with good quality and to final structural determination. Interestingly, it was found that the final refolding yield of the protein is proline residue-dependent. The difference in the distribution of cis and trans configurations of proline residues in the protein after complete denaturation is a major determining factor of the final yield. A point mutation of one of four proline residues to an asparagine led to a near-doubling of the yield of refolded protein after complete denaturation. It was concluded that the driving force behind protein folding could not overcome the cis -to- trans proline isomerization, or vice versa , during the protein-folding process. Furthermore, it was found that successful refolding of proteins optimally occurs at high pH values, which may mimic protein folding in vivo . It was found that high pH values could induce the polarization of peptide bonds, which may trigger the formation of protein secondary structures through hydrogen bonds. It is proposed that a hydrophobic environment coupled with negative charges is essential for protein folding. Combined with our earlier discoveries on protein-unfolding mechanisms, it is proposed that hydrogen bonds are a primary driving force for de novo protein folding.

59 BASIC BIOLOGICAL SCIENCES↗