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Results for “Expression systems”

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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Space flight associated changes in astronauts’ plasma-derived small extracellular vesicle microRNA: Biomarker identification

This pilot study suggests relatively short (median 12 days long) low-Earth orbit (LEO) spaceflight induces changes in circulating plasma small extracellular vesicle (sEV) microRNA expression. Normalization of small RNA sequencing (sRNAseq) data and quantitative polymerase chain reaction (qPCR) validation confirmed miR-4732-3p is significantly upregulated up to 3 days post-landing, and enrichment analysis suggests this miRNA is expressed in various central nervous system tissues and hematopoietic cells and may be linked to different organ disorders.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

The Rankine-Kirchhoff approximations for moist thermodynamics

The Rankine-Kirchhoff equation for the saturation vapor pressure has been derived independently many times, sometimes with the presumption of novelty. As a result, the equation is referred to in the literature by a bewildering number of different names and, often, by no name at all. In this work, the history of the Rankine-Kirchhoff equation is reviewed. The three approximations used to derive it (ideal gas, constant heat capacities, and zero-volume condensates) can be used to derive a whole system of accurate and analytic expressions of relevance to the atmosphere. Consequently, it is proposed that this set of approximations be elevated to a named entity, e.g., the Rankine-Kirchhoff approximations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Phonon Screening of Excitons in Semiconductors: Halide Perovskites and Beyond

The ab initio Bethe-Salpeter equation (BSE) approach, an established method for the study of excitons in materials, is typically solved in a limit where only static screening from electrons is captured. Here, we generalize this framework to include dynamical screening from phonons at lowest order in the electron-phonon interaction. We apply this generalized BSE approach to a series of inorganic lead halide perovskites, CsPbX 3 , with X=Cl, Br, and I. We find that inclusion of screening from phonons significantly reduces the computed exciton binding energies of these systems. By deriving a simple expression for phonon screening effects, we reveal general trends for their importance in semiconductors and insulators, based on a hydrogenic exciton model. We demonstrate that the magnitude of the phonon screening correction in isotropic materials can be reliably predicted using four material specific parameters: the reduced effective mass, static and optical dielectric constants, and frequency of the most strongly coupled longitudinal-optical phonon mode. Finally, this framework helps to elucidate the importance of phonon screening and its relation to excitonic properties in a broad class of semiconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Hydrodynamic electron transport in graphene Hall-bar devices

Here we consider hydrodynamic electron transport in the Hall-bar geometry. The theory is developed for systems with non-Galilean-invariant electron liquids. We show that inhomogeneity of the electron density induced by long-range disorder and gating leads to mixing between the hydrodynamic transport mode and transport relative to the electron liquid. For graphene systems near charge neutrality, these effects lead to strong coupling of the hydrodynamic flow to charge transport. As a result, the effective electrical conductivity of the system may significantly exceed the intrinsic conductivity of the electron liquid. We obtain analytic expressions for the thermoelectric transport coefficients of the system as a function of density in the full crossover region between clean and disorder-dominated regimes.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A two-and-a-half dimensional symplectic space-charge solver

The nonlinear space-charge effect plays a significant role in high-intensity accelerators and has been extensively studied using multi-particle tracking methods. In this paper, we present a novel 2.5- dimensional symplectic space-charge solver specifically designed for long beam bunches. We begin by detailing its application to a transverse Gaussian density distribution under open boundary conditions in a straight system, where a semi-analytical expression is derived. We then demonstrate the solver’s adaptation to arbitrary distributions in open space, as well as within rectangular and round conducting pipes. Finally, we discuss the extension of this solver to circular accelerator systems. This study shows that the fast 2.5-dimensional solver can be a good approximation to the fully three-dimensional solver for long bunches in large circular accelerators.

Beam code development & simulation techniques↗
DOE OSTI2022

Leading-color two-loop amplitudes for four partons and a $\textit{W}$ boson in QCD

We present the leading-color two-loop QCD corrections for the scattering of four partons and a W boson, including its leptonic decay. The amplitudes are assembled from the planar two-loop helicity amplitudes for four partons and a vector boson decaying to a lepton pair, which are also used to determine the planar two-loop amplitudes for four partons and a $Z/γ^\ast$ boson with a leptonic decay. The analytic expressions are obtained by setting up a dedicated Ansatz and constraining the free parameters from numerical samples obtained within the framework of numerical unitarity. The large linear systems that must be solved to determine the analytic expressions are constructed to be in Vandermonde form. Such systems can be very efficiently solved, bypassing the bottleneck of Gaussian elimination. Our results are expressed in a basis of one-mass pentagon functions, which opens the possibility of their efficient numerical evaluation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

A Corrected Score Function Framework for Modelling Circadian Gene Expression

Many biological processes display oscillatory behaviour based on an approximately 24 h internal timing system specific to each individual. One process of particular interest is gene expression, for which several circadian transcriptomic studies have identified associations between gene expression during a 24 h period and an individual's health. A challenge with analysing data from these studies is that each individual's internal timing system is offset relative to the 24 h day-night cycle, where day–night cycle time is recorded for each collected sample. Laboratory procedures can accurately determine each individual's offset and determine the internal time of sample collection. However, these laboratory procedures are labour-intensive and expensive. Here, in this paper, we propose a corrected score function framework to obtain a regression model of gene expression given internal time when the offset of each individual is too burdensome to determine. A feature of this framework is that it does not require the probability distribution generating offsets to be symmetric with a mean of zero. Simulation studies validate the use of this corrected score function framework for cosinor regression, which is prevalent in circadian transcriptomic studies. Illustrations with data from three circadian transcriptomic studies further demonstrate that the proposed framework consistently mitigates bias relative to using a score function that does not account for this offset.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Statistical learning for predicting density–matrix-based electron dynamics

In this study, we consider the problem of learning density-dependent molecular Hamiltonian matrices from time series of electron density matrices, all in the context of Hartree–Fock theory. Prior work developed a solution to this problem for small molecular systems with density and Hamiltonian matrices of size at most 6 × 6. Here, using a battery of techniques, we scale prior methods to larger molecular systems with, for example, 29 × 29 matrices. This includes systems that either have more electrons or are expressed in large basis sets such as 6-311++G**. Scaling the method to larger systems enhances its relevance for realistic applications in chemistry and physics. To achieve this scaling, we apply dimensionality reduction, ridge regression and analytic computation of Hessians. Through the combination of these techniques, we are able to learn Hamiltonians by minimizing an objective function that encodes local propagation error. Importantly, these learned Hamiltonians can then be used to predict electron dynamics for thousands of steps: When we use our learned Hamiltonians to numerically solve the time-dependent Hartree–Fock equation, we obtain predicted dynamics that are in close quantitative agreement with ground truth dynamics. This includes field-off trajectories similar to the training data and field-on trajectories outside of the training data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP

Abstract Bacterial DNA methylation is involved in diverse cellular functions, including modulation of gene expression, DNA repair, and restriction–modification systems for defense against viruses and other foreign DNA. Restriction systems hinder efforts to engineer organisms to produce fuels and chemicals from waste and renewable feedstocks by degrading DNA during transformation. Methylome analysis allows identification of motifs within a bacterial chromosome that may be targeted by native restriction enzymes. Further expression of the corresponding methyltransferases in Escherichia coli allows plasmid DNA to be protected from restriction in the target organism, thereby drastically enhancing transformation efficiency. Nanopore sequencing can detect methylated bases, but software is needed to transform modified base coordinates into methylated motifs. Here, we develop MIJAMP (MIJAMP Is Just A MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONT’s Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating incorrect motifs. MIJAMP also reports methylation data on specific, user-defined motifs. Using MIJAMP, we determined the methylated motifs both in a control strain (wild-type E. coli) and in Synecococcus sp. strain PCC7002, laying the foundation for improved transformation in this organism. MIJAMP is available at https://code.ornl.gov/alexander-public/mijamp/. One Sentence Summary: Here we describe software written to discover DNA methylation motifs from nanopore sequencing data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Heat Transport Hysteresis Generated Through Frequency Switching of a Time-Dependent Temperature Gradient

A stochastic energetics framework is applied to examine how periodically shifting the frequency of a time-dependent oscillating temperature gradient affects heat transport in a nanoscale molecular model. We specifically examine the effects that frequency switching, i.e., instantaneously changing the oscillation frequency of the temperature gradient, has on the shape of the heat transport hysteresis curves generated by a particle connected to two thermal baths, each with a temperature that is oscillating in time. Analytical expressions are derived for the energy fluxes in/out of the system and the baths, with excellent agreement observed between the analytical expressions and the results from nonequilibrium molecular dynamics simulations. We find that the shape of the heat transport hysteresis curves can be significantly altered by shifting the frequency between fast and slow oscillation regimes. We also observe the emergence of features in the hysteresis curves such as pinched loops and complex multi-loop patterns due to the frequency shifting. The presented results have implications in the design of thermal neuromorphic devices such as thermal memristors and thermal memcapacitors.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Modeling Cyber Supply Chain Incidents with Multilayered Graph Motifs

As noted within the literature, supply chain includes people and organizations---manufacturers, integrators, and third-party vendors---that are involved in one or more stages of a product lifecycle. Since supply chains, by definition, include organizations and people, supply chain risk management activities must consider dependencies between an organization's business processes and third-party resources. Just as adversarial tactics can be implemented via techniques implemented via networked computer systems, so can such tactics be expressed via legal business relationships. A cyber incident may have an exponential impact downstream, for example, by leveraging a product's distribution channel (e.g. malicious updates in SolarWinds, buggy updates in CrowdStrike). Similarly, legitimate and legal business relationships also affect the attack surface exposure of systems, enabling long-term persistence and/or unknown impacts to product quality that are hard to detect. This paper catalogs several recent digital supply chain incidents and applies a multilayered network formalism to develop structural indicators (graph motifs) that reflect potentially-adversarial behavior. Finally, we compare and contrast the characteristics of adversarial tactics (e.g. Loss of Availability, Data Collection) that leverage cyber-physical dependencies to those that leverage legal organizational relationships.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Identifying stochastic dynamics via finite expression methods

Modeling stochastic differential equations (SDEs) is crucial for understanding complex dynamical systems in various scientific fields. Recent methods often employ neural network-based models, which typically represent SDEs through a combination of deterministic and stochastic terms. However, these models usually lack interpretability and have difficulty in generalizing beyond their training domain. Here, this paper introduces the Finite Expression Method (FEX), a symbolic learning approach designed to derive interpretable mathematical representations of the deterministic component of SDEs. For the stochastic component, we integrate FEX with advanced generative modeling techniques to provide a comprehensive representation of SDEs. The numerical experiments on linear, nonlinear, and multidimensional SDEs demonstrate that FEX generalizes well beyond the training domain and delivers more accurate long-term predictions compared to neural network-based methods. The symbolic expressions identified by FEX not only improve prediction accuracy but also offer valuable scientific insights into the underlying dynamics of the systems.

Complex dynamical systems↗
DOE OSTI2024

Recombineering machinery to increase homology directed genome editing in thermophilic microbes

A native Type I-B and heterologous Type II Clustered Regularly-Interspaced Short Palindromic Repeat/cas systems were developed and characterize to improve the ability to engineer C. thermocellum and other thermophilic microbes. The native Type I-B system was engineered for genome editing. For the Type I-B system, an engineered strain, termed LL1586, yielded 40% genome editing efficiency at the pyrF locus. When recombineering machinery was expressed the efficiency was increased to 71%. For the Type II GeoCas9 system, 12.5% genome editing efficiency was observed. When recombineering machinery was expressed, this increased to 94%. By combining the thermophilic CRISPR system (either Type I-B or Type II) with the recombinases, a new tool was developed that allows for efficient CRISPR editing. The tools provided herein enable CRISPR technologies to better engineer C. thermocellum, including engineering C. thermocellum for both increased lignocellulose degradation and biofuel production.

Eckert, Carrie↗
DOE OSTI2023

Small-Signal Angle Stability-Oriented False Data Injection Cyber-Attacks on Power Systems

The small-signal angle stability (SSAS) of a power system is determined by the property of operation points. The widely applied false data injection (FDI) cyber-attack, however, is able to stealthily mislead the optimal power flow (OPF) and thus compromise operation points, leading to damages to the SSAS margin. Here, to provide insights for cyber defenders, this paper proposes and investigates a stealthy SSAS-oriented FDI cyber-attack focusing on two attacking purposes, i.e., the SSAS margin and operation cost, with higher priority on the former one. First, this paper establishes a novel bi-level model with an implicit SSAS constraint based on a structure preserving model to compromise operation points. Then, for the SSAS interarea mode in a typical two-area system, this paper formulates closed-form expressions of how the SSAS margin and operation cost behave with respect to stealthy injections. By comparison, for the SSAS local mode in general power systems, this paper proposes a moving target cyber-attack-based hierarchical solution algorithm. Simulation results on a two-area system, a Kundur 11 bus system, and a modified IEEE 14 bus system demonstrate the significant damaging effects of the proposed SSAS-oriented FDI cyber-attack and the conflict between the two attacking purposes.

Benders decomposition↗
DOE OSTI2026

Generating entangled steady states in multistable open quantum systems via initial state control

Entanglement underpins the power of quantum technologies, yet it is fragile and typically destroyed by dissipation. Paradoxically, the same dissipation, when carefully engineered, can drive a system toward robust entangled steady states. However, this engineering task is nontrivial, as dissipative many-body systems are complex, particularly when they support multiple steady states. Here, we derive analytic expressions that predict how the steady state of a system evolving under a Lindblad equation depends on the initial state, without requiring integration of the dynamics. These results extend Refs. [V. V. Albert and L. Jiang, Phys. Rev. A 89, 022118 (2014); V. V. Albert et al., Phys. Rev. X 6, 041031 (2016)], showing that while the steady-state manifold is determined by the Liouvillian kernel, the weights within it depend on both the Liouvillian and the initial state. We identify a special class of Liouvillians for which the steady state depends only on the initial overlap with the kernel. Our framework provides analytical insight and a computationally efficient tool for predicting steady states in open quantum systems. As an application, we propose schemes to generate metrologically useful entangled steady states in spin ensembles via balanced collective decay.

Dissipative dynamics↗
DOE OSTI2020

Thermodynamics of optical Bloch equations

Abstract Optical Bloch equations (OBE) describe the coherent exchange of energy between a quantum bit (qubit) and a quasi-resonant driving field in the presence of a thermal bath. Despite it being an ubiquitous process in quantum technologies, a sound thermodynamic analysis is still missing. We hereby provide such an analysis, by deriving the relevant framework from first principles. We start from a complete microscopic description of the qubit-bath system where definitions of heat, work and entropy production are unambiguous. We trace out the bath and coarse-grain the resulting expressions in time, using a methodology similar to the derivation of the dynamical master equation, to derive closed expressions for the first and second law in terms of system properties. Long coarse graining times yield the Floquet Master equation and its already known thermodynamic description. Short coarse-graining times yield instead the OBE and a novel thermodynamic framework which explicitly depends on quantum coherences in the qubit’s energy basis which produce quantum signatures in the heat and entropy production flows. This allows us to characterize a genuinely quantum non-equilibrium situation, where the coherences created by the driving field are continuously erased by the bath. Our findings can be readily extended to larger open quantum systems. They carry the seeds for future thermodynamic analyses of quantum gates and the design of quantum engines in the strong coherent driving regime.

Elouard, Cyril↗
DOE OSTI2022

Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences

Abstract RNA-guided nucleases from CRISPR-Cas systems expand opportunities for precise, targeted genome modification. Endogenous CRISPR-Cas systems in many prokaryotes are attractive to circumvent expression, functionality, and unintended activity hurdles posed by heterologous CRISPR-Cas effectors. However, each CRISPR-Cas system recognizes a unique set of protospacer adjacent motifs (PAMs), which requires identification by extensive screening of randomized DNA libraries. This challenge hinders development of endogenous CRISPR-Cas systems, especially those based on multi-protein effectors and in organisms that are slow-growing or have transformation idiosyncrasies. To address this challenge, we present Spacer2PAM, an easy-to-use, easy-to-interpret R package built to predict and guide experimental determination of functional PAM sequences for any CRISPR-Cas system given its corresponding CRISPR array as input. Spacer2PAM can be used in a ‘Quick’ method to generate a single PAM prediction or in a ‘Comprehensive’ method to inform targeted PAM libraries small enough to screen in difficult to transform organisms. We demonstrate Spacer2PAM by predicting PAM sequences for industrially relevant organisms and experimentally identifying seven PAM sequences that mediate interference from the Spacer2PAM-informed PAM library for the type I-B CRISPR-Cas system from Clostridium autoethanogenum. We anticipate that Spacer2PAM will facilitate the use of endogenous CRISPR-Cas systems for industrial biotechnology and synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Planar, longitudinal, compressive waves in solids: Thermodynamics and uniaxial strain restrictions

A new tri-axial pressure-based constitutive expression has been found using Cauchy's stress tensor. This stress state emphasizes pressure and shear stress. The description is a pressure plus an effective shear stress allowing for a constitutive law based on atomic solid-state phase changes in crystalline cells due to pressure plus shear-based dislocation motion commonly associated with plasticity. Pressure has a new role in the material's constitutive response as it is separated from plasticity. The thermo-mechanical system describes third-order Gibbs’ expressions without specific volume restrictions placed upon the material. Isothermally, the ratio of heat to shear work in elastic copper is shown to approach zero at a very low temperature and become larger than one as temperature approaches melting. Wave compression models investigated are elastic and plastic: in fully elastic materials, the planar wave is restricted by Poisson's effect although plastic shear changes this constraint. Plastic deformation, dominated by dissipative shear stresses in uniaxial strain, heats the material while excluding phase changes from hydrostatic pressures. The material properties per se across Hugoniot shocks are described with entropy concepts. Shock waves are exceedingly complex since the constitutive laws are linked at extreme temperatures, pressures, and shear stresses. Isothermal, isentropic, isochoric, and iso-shear conditions are used throughout with Jacobian algebra.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗