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At least 469 records · Page 26

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DOE OSTI2023

Optimization of operational strategies for rich gas enhanced oil recovery based on a pilot test in the Bakken tight oil reservoir

Horizontal well drilling and multistage hydraulic fracturing have been demonstrated as effective approaches for stimulating oil production in the Bakken tight oil reservoir. However, after multiple years of production, primary oil recovery in the Bakken is generally less than 10% of the estimated original oil in place. Gas huff ‘n’ puff (HnP) has been tested in the Bakken Formation as an enhanced oil recovery (EOR) method; however, most field pilot test results showed no significant incremental oil production. One of the factors affecting HnP EOR performance is premature gas breakthrough, which is one of the most critical issues observed in the field because of the presence of interwell fractures. Consequently, injected gas rapidly reaches adjacent production wells without contacting reservoir rock and increasing oil recovery. Proper conformance control is therefore needed to avoid early gas breakthrough and improve EOR performance. In this study, a rich gas EOR pilot in the Bakken was carefully analyzed to collect the essential reservoir and operational data. A simulation model with 16 wells was then developed to reproduce the production history and predict the EOR performance with and without conformance control. EOR operational strategies, including single- and multiple-well HnP, with different gas injection constraints were investigated. The simulation results of single-well HnP without conformance control showed that a rich gas injection rate of at least 10 MMscfd was needed to yield meaningful incremental oil production. The strategy of conformance control via water injection could significantly improve oil production in the HnP well, but injecting an excessive amount of water also leads to water breakthrough and loss of oil production in the offset wells. By analyzing the production performance of the wells individually, the arrangement of wells was optimized for multiple-well HnP EOR. The multiwell results showed that rich gas EOR could improve oil production up to 7.4% by employing conformance control strategies. Furthermore, replacing rich gas with propane as the injection gas could result in 14% of incremental oil production.

02 PETROLEUM↗

DOE OSTI2021

Generalized multifractality at spin quantum Hall transition

Generalized multifractality characterizes scaling of eigenstate observables at Anderson-localization critical points. We explore generalized multifractality in 2D systems, with the main focus on the spin quantum Hall (SQH) transition in superconductors of symmetry class C. Relations and differences with the conventional integer quantum Hall (IQH) transition are also studied. Using the field-theoretical formalism of non-linear sigma-model, we derive the pure-scaling operators representing generalizing multifractality and then “translate” them to the language of eigenstate observables. Performing numerical simulations on network models for SQH and IQH transitions, we confirm the analytical predictions for scaling observables and determine the corresponding exponents. Remarkably, the generalized-multifractality exponents at the SQH critical point strongly violate the generalized parabolicity of the spectrum, which implies violation of the local conformal invariance at this critical point.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch

T-box riboswitches are unique riboregulators where gene regulation is mediated through interactions between two highly structured RNAs. Despite extensive structural insights, how RNA-RNA interactions drive the folding and structural transitions of T-box to achieve functional conformations remains unclear. Here, by combining SAXS, single-molecule FRET and computational modeling, we elaborate the folding energy landscape of a translational T-box aptamer consisting of stems I, II and IIA/B, which Mg 2+ -induced global folding and tRNA binding are cooperatively coupled. smFRET measurements reveal that high Mg 2+ stabilizes IIA/B and its stacking on II, which drives the pre-docking of I and II into a competent conformation, subsequent tRNA binding promotes docking of I and II to form a high-affinity tRNA binding groove, of which the essentiality of IIA/B and S-turn in II is substantiated with mutational analysis. We highlight a delicate balance among Mg 2+ , the intra- and intermolecular RNA-RNA interactions in modulating RNA folding and function.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1986

Multistep modeling of protein structure: application to bungarotoxin

Modelling of bungarotoxin in atomic details is presented in this article. The model-building procedure utilizes the low-resolution crystal coordinates of the c-alpha atoms of bungarotoxin, sequence homology within the neurotoxin family, as well as high-resolution x-ray diffraction data of cobratoxin and erabutoxin. Our model-building procedure involves: (a) principles of comparative modelling, (b) embedding procedures of distance geometry, and (c) use of molecular mechanics for optimizing packing. The model is not only consistent with the c-alpha coordinates of crystal structure, but also agrees with solution conformational features of the triple-stranded beta sheet as observed by NOE measurements.

NASA Discipline Exobiology↗

NASA NTRS1997

Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

Jaffe, Richard↗

DOE OSTI2020

Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane

The small GTPase KRAS is localized at the plasma membrane where it functions as a molecular switch, coupling extracellular growth factor stimulation to intracellular signaling networks. In this process, KRAS recruits effectors, such as RAF kinase, to the plasma membrane where they are activated by a series of complex molecular steps. Defining the membrane-bound state of KRAS is fundamental to understanding the activation of RAF kinase and in evaluating novel therapeutic opportunities for the inhibition of oncogenic KRAS-mediated signaling. We combined multiple biophysical measurements and computational methodologies to generate a consensus model for authentically processed, membrane-anchored KRAS. In contrast to the two membrane-proximal conformations previously reported, we identify a third significantly populated state using a combination of neutron reflectivity, fast photochemical oxidation of proteins (FPOP), and NMR. In this highly populated state, which we refer to as “membrane-distal” and estimate to comprise ~90% of the ensemble, the G-domain does not directly contact the membrane but is tethered via its C-terminal hypervariable region and carboxymethylated farnesyl moiety, as shown by FPOP. Subsequent interaction of the RAF1 RAS binding domain with KRAS does not significantly change G-domain configurations on the membrane but affects their relative populations. Overall, our results are consistent with a directional fly-casting mechanism for KRAS, in which the membrane-distal state of the G-domain can effectively recruit RAF kinase from the cytoplasm for activation at the membrane.

KRAS↗

NASA NTRS2009

Towards Behavioral Reflexion Models

Software architecture has become essential in the struggle to manage today s increasingly large and complex systems. Software architecture views are created to capture important system characteristics on an abstract and, thus, comprehensible level. As the system is implemented and later maintained, it often deviates from the original design specification. Such deviations can have implication for the quality of the system, such as reliability, security, and maintainability. Software architecture compliance checking approaches, such as the reflexion model technique, have been proposed to address this issue by comparing the implementation to a model of the systems architecture design. However, architecture compliance checking approaches focus solely on structural characteristics and ignore behavioral conformance. This is especially an issue in Systems-of- Systems. Systems-of-Systems (SoS) are decompositions of large systems, into smaller systems for the sake of flexibility. Deviations of the implementation to its behavioral design often reduce the reliability of the entire SoS. An approach is needed that supports the reasoning about behavioral conformance on architecture level. In order to address this issue, we have developed an approach for comparing the implementation of a SoS to an architecture model of its behavioral design. The approach follows the idea of reflexion models and adopts it to support the compliance checking of behaviors. In this paper, we focus on sequencing properties as they play an important role in many SoS. Sequencing deviations potentially have a severe impact on the SoS correctness and qualities. The desired behavioral specification is defined in UML sequence diagram notation and behaviors are extracted from the SoS implementation. The behaviors are then mapped to the model of the desired behavior and the two are compared. Finally, a reflexion model is constructed that shows the deviations between behavioral design and implementation. This paper discusses the approach and shows how it can be applied to investigate reliability issues in SoS.

Ackermann, Christopher↗

DOE OSTI2021

Structural Characterization of the Reaction and Substrate Specificity Mechanisms of Pathogenic Fungal Acetyl-CoA Synthetases

Acetyl CoA synthetases (ACSs) are Acyl-CoA/NRPS/Luciferase (ANL) superfamily enzymes that couple acetate with CoA to generate acetyl CoA, a key component of central carbon metabolism in eukaryotes and prokaryotes. Normal mammalian cells are not dependent on ACSs, while tumor cells, fungi, and parasites rely on acetate as a precursor for acetyl CoA. Consequently, ACSs have emerged as a potential drug target. As part of a program to develop antifungal ACS inhibitors, we characterized fungal ACSs from five diverse human fungal pathogens using biochemical and structural studies. ACSs catalyze a two-step reaction involving adenylation of acetate followed by thioesterification with CoA. Our structural studies captured each step of these two half-reactions including the acetyl-adenylate intermediate of the first half-reaction in both the adenylation conformation and the thioesterification conformation and thus provide a detailed picture of the reaction mechanism. We also used a systematic series of increasingly larger alkyl adenosine esters as chemical probes to characterize the structural basis of the exquisite ACS specificity for acetate over larger carboxylic acid substrates. Consistent with previous biochemical and genetic data for other enzymes, structures of fungal ACSs with these probes bound show that a key tryptophan residue limits the size of the alkyl binding site and forces larger alkyl chains to adopt high energy conformers, disfavoring their efficient binding. Together, our analysis provides highly detailed structural models for both the reaction mechanism and substrate specificity that should be useful in designing selective inhibitors of eukaryotic ACSs as potential anticancer, antifungal, and antiparasitic drugs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Improving the five-point bootstrap

We present a new algorithm for the numerical evaluation of five-point conformal blocks in d-dimensions, greatly improving the efficiency of their computation. To do this we use an appropriate ansatz for the blocks as a series expansion in radial coordinates, derive a set of recursion relations for the unknown coefficients in the ansatz, and evaluate the series using a Padé approximant to accelerate its convergence. We then study the 〈σσϵσσ〉 correlator in the 3d critical Ising model by truncating the operator product expansion (OPE) and only including operators with conformal dimension below a cutoff ∆ ⩽ ∆cutoff. We approximate the contributions of the operators above the cutoff by the corresponding contributions in a suitable disconnected five-point correlator. Using this approach, we compute a number of OPE coefficients with greater accuracy than previous methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Simulating Sea-Ice Deformation in Viscous-Plastic Sea-Ice Models With CD-Grids

Linear kinematic features (LKFs) are found everywhere in the Arctic sea-ice cover. They are strongly localized deformations often associated with the formation of leads and pressure ridges. In viscous-plastic (VP) sea-ice models, the simulation of LKFs depends on several factors such as the grid resolution, the numerical solver convergence, and the placement of the variables on the mesh. In this study, we compare two recently proposed discretization with a CD-grid placement with respect to their ability to reproduce LKFs. The first (CD1) is based on a nonconforming finite element discretization, whereas the second (CD2) uses a conforming subgrid discretization. To analyze their resolution properties, we evaluate runs from different models (e.g., FESOM, MPAS) on a benchmark problem using quadrilateral, hexagonal and triangular meshes. Our findings show that the CD1 setup simulates more deformation structure than the CD2 setup. This highlights the importance of the type of spatial discretization for the simulation of LKFs. Due to the higher number of degrees of freedom, both CD-grids resolve more LKFs than traditional A, B, and C-grids at fixed mesh level. This is an advantage of the CD-grid approach, as high spatial mesh resolution is needed in VP sea-ice models to simulate LKFs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Technical and Economic Evaluation of the First Ever Polymer Flood Field Pilot to Enhance the Recovery of Heavy Oils on Alaska's North Slope via Machine Assisted History Matching

Polymer flooding has become globally established as a potential enhanced oil recovery method for heavy oils. To determine whether this technology may be useful in developing the substantial heavy oil resources on the Alaska North Slope, a polymer flood field pilot commenced at the Milne Point Unit in August 2018. This study seeks to evaluate the results of the field pilot on a technical and economic basis. A reservoir simulation model is constructed and calibrated to predict the oil recovery performance of the pilot through machine-assisted reservoir simulation techniques. To replicate the early water breakthrough observed during waterflooding, transmissibility contrasts are introduced into the simulation model, forcing viscous fingering effects. In the ensuing polymer flood, these transmissibility contrasts are reduced to replicate the restoration of injection conformance during polymer flooding. Transmissibility contrasts are later reinstated to replicate fracture overextension interpreted in one of the producing wells. The calibrated simulation models produced at each stage of the history matching process are used to forecast oil recovery. These forecasts are used as input for economic analysis, incremental to waterflooding expectations. The simulation forecasts indicate that polymer flooding significantly increases the heavy oil production for this field pilot compared to waterflooding alone, yielding attractive project economics. However, meaningful variations between simulation scenarios demonstrate that a simulation model is only valid for prediction if flow behavior in the reservoir remains consistent with that observed during the history matched period. Critically, this means that a simulation model calibrated for waterflooding may not fully capture the technical and economic benefits of an enhanced oil recovery process such as polymer flooding. Subsequently, the simulation model and economic model are used in conjunction to conduct a sensitivity analysis for polymer flood design parameters, from which recommendations are provided for both the continued operation of the current field pilot and future polymer flood designs. The results demonstrate that a higher polymer concentration can be injected due to the development of fractures in the reservoir. The throughput rate should remain high without exceeding operating constraints. A calculated point-forward polymer utilization parameter demonstrates the decreasing efficiency of the polymer flood at later times in the pattern life. Future projects will benefit from starting polymer injection earlier in the pattern life. A pattern with tighter horizontal well spacing will observe a greater incremental benefit from polymer flooding.

Keith, Cody↗

DOE OSTI2020

Charge transfer rate constants for the carotenoid-porphyrin-C 60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation

Charge transfer rate constants were calculated for the carotenoid-porphyrin-C 60 (CPC 60 ) molecular triad dissolved in explicit tetrahydrofuran. The calculation was based on mapping the all-atom anharmonic Hamiltonian of this system onto the spin-boson Hamiltonian. The mapping was based on discretizing the spectral density from the time correlation function of the donor–acceptor potential energy gap, as obtained from all-atom molecular dynamics simulations. Different spin-boson Hamiltonians were constructed for each of the possible transitions between the three excited electronic states in two different triad conformations. The rate constants of three possible transitions were calculated via the quantum-mechanically exact Fermi’s golden rule (FGR), as well as a progression of more approximate expressions that lead to the classical Marcus expression. The advantage of the spin-boson approach is that once the mapping is established, the quantum-mechanically exact FGR and the hierarchy of approximations are known in closed form. The classical Marcus charge transfer rate constants obtained with the spin-boson Hamiltonians were found to reproduce those obtained from all-atom simulations with the linearized semiclassical approximation, thereby confirming the equivalence of the two approaches for this system. Furthermore, within the spin-boson Hamiltonian, we also found that the quantum-mechanically exact FGR rate constants were significantly enhanced compared to the classical Marcus theory rate constants for two out of three transitions in one of the two conformations under consideration. The results confirm that mapping to the spin-boson model can yield accurate predictions for charge transfer rate constants in a system as complex as CPC 60 dissolved in tetrahydrofuran.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro )

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M pro , is a promising target for the development of novel antiviral therapeutics. Previous X-ray crystal structures of M pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these data sets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a perturbation-dependent conformational landscape for M pro , including a mobile zinc ion interleaved between the catalytic dyad, mercurial conformational heterogeneity at various sites including a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to aid preparation for future coronavirus pandemics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Highly efficient separation membrane based on cellulose acetate/chitosan fibrous composite substrate with activated carbon functional adsorption layer

Abstract BACKGROUND For improving the permeability and selectivity of adsorption separation membranes, membrane materials, structural morphology and separation technology must continue to be investigated. Development of a membrane that is environmentally friendly, cost‐effective and with high filter precision is an important direction in current research. RESULTS The air pressure spraying method was used to prepare an activated carbon (AC)–cellulose acetate/chitosan (CA/CS) composite membrane. The CA/CS fiber composite membrane was prepared as substrate layer, and AC was loaded on the surface of the CA/CS composite membrane as a functional adsorption layer. When the spraying pressure was 0.01 MPa and the mass ratio of AC/CS was 2:1, a composite membrane with even and compact morphology could be obtained. Both the compact AC functional layer and complete CA/CS substrate layer endowed the AC–CA/CS composite membrane with an excellent water filtration property. At low feeding pressure, the permeate flux and rejection rate of bisphenol A (BPA) could reach 9.27 × 10 3 L m −2 h −1 and 98.31%, respectively. Meanwhile, the adsorption capacities of the membrane were investigated. It tended to equilibrate quickly in 2 min for dyes and BPA. The equilibrium adsorption capacities of the membrane for acid blue, acid yellow and BPA were 175.80, 164.0815 and 79.58 mg g −1 , respectively. The adsorption process conformed to pseudo‐second‐order kinetics and the Langmuir monolayer adsorption model. CONCLUSIONS This work could provide a practical and effective feasibility for membrane separation technology. © 2020 Society of Chemical Industry (SCI)

Zhao, Xiaoyan↗

DOE OSTI2023

The confluence of machine learning and multiscale simulations

Multiscale modeling has a long history of use in structural biology, as computational biologists strive to overcome the time- and length-scale limits of atomistic molecular dynamics. Contemporary machine learning techniques, such as deep learning, have promoted advances in virtually every field of science and engineering and are revitalizing the traditional notions of multiscale modeling. Deep learning has found success in various approaches for distilling information from fine-scale models, such as building surrogate models and guiding the development of coarse-grained potentials. However, perhaps its most powerful use in multiscale modeling is in defining latent spaces that enable efficient exploration of conformational space. In conclusion, this confluence of machine learning and multiscale simulation with modern high-performance computing promises a new era of discovery and innovation in structural biology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. In this work, we demonstrate that cryo-electron microscopy can routinely resolve maps of RNA-only systems and that these maps enable subnanometer-resolution coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. Furthermore ,this hybrid ‘Ribosolve’ pipeline detects and falsifies homologies and conformational rearrangements in 11 previously unknown 119- to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length Vibrio cholerae and Fusobacterium nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and the computer-designed ATP-TTR-3 aptamer with and without AMP. Simulation benchmarks, blind challenges, compensatory mutagenesis, cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA molecules but does not resolve atomic details. These tests offer guidelines for making inferences in future RNA structural studies with similarly accelerated throughput.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Microscopic insights into the solvation of polyethylene glycol chains in water: A machine learning potential approach

Polyethylene glycol (PEG) is a structurally simple, nontoxic, and water-soluble polymer widely utilized in medical and pharmaceutical applications. Notably, when a PEG chain is immersed in water, the surrounding water molecules play a key role in driving conformational changes of this macromolecule. In this study, we explore the solvation behavior of PEG under mechanical strain using molecular dynamics simulations, with an interatomic potential obtained from machine learning. Our focus is on the transition from the favored coil-like conformation to an extended one under external force. Through analyses of radial distribution functions, hydrogen bonding, and solvation dynamics, we uncover how mechanical stretching influences the local hydration environment. Furthermore, we disentangle the enthalpic and entropic contributions to the conformational stability of PEG in water. Surprisingly, our neural network potential model identifies dewetting of PEG C-atoms, and not water H-bonding with PEG O-atoms, as the main enthalpic driving force for the coiling of PEG in water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

The rise of antibiotic resistance calls for new therapeutics targeting resistance factors such as the New Delhi metallo-β-lactamase 1 (NDM-1), a bacterial enzyme that degrades β-lactam antibiotics. We present structure-guided computational methods for designing peptide macrocycles built from mixtures of l - and d -amino acids that are able to bind to and inhibit targets of therapeutic interest. Our methods explicitly consider the propensity of a peptide to favor a binding-competent conformation, which we found to predict rank order of experimentally observed IC 50 values across seven designed NDM-1- inhibiting peptides. We were able to determine X-ray crystal structures of three of the designed inhibitors in complex with NDM-1, and in all three the conformation of the peptide is very close to the computationally designed model. In two of the three structures, the binding mode with NDM-1 is also very similar to the design model, while in the third, we observed an alternative binding mode likely arising from internal symmetry in the shape of the design combined with flexibility of the target. Although challenges remain in robustly predicting target backbone changes, binding mode, and the effects of mutations on binding affinity, our methods for designing ordered, binding-competent macrocycles should have broad applicability to a wide range of therapeutic targets.

42 ENGINEERING↗