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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Initial Fermi orbital descriptors for FLOSIC calculations: The quick-FOD method

Fermi orbital descriptors (FODs) play a key role in Fermi-Löwdin orbital self-interaction correction (FLOSIC) calculations used to remove self-interaction from approximate density functionals. Optimal FODs are obtained by minimizing the self-interaction-corrected total energy, and, in this process, identifying initial sets of FODs becomes crucial. Here we propose, implement and test a novel method for automatically initializing FODs, quick-FOD, based on the minimization of an empirical energy expression that involves a Coulomb-like FOD-electron density attraction, an FOD-FOD short-range repulsion, and an exchange-like FOD-density repulsion. Quick-FOD successfully reproduces FOD arrangements in qualitatively good agreement with Lewis theory and with full-fledged FLOSIC calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

FAST irradiations and initial post irradiation examinations – Part I

The Advanced Fuels Campaign Fission Accelerated Steady-state Test (FAST) at Idaho National Laboratory (INL) completed its first irradiation cycle within the Advanced Test Reactor (ATR). The test focused on the irradiation of alloy fuel forms for use in sodium fast reactors. Tests included the use of fuel additives (Sn, Sb, and Pd) for reducing the gettering of lanthanide fission products, zirconium liners to mitigate fuel-cladding chemical interaction, and annular fuel geometry for sodium-free fuel designs. The first cycle of FAST testing was completed and a series of rodlets were removed for the initial post irradiation examination (PIE) of FAST rodlets. The rodlet irradiation conditions was evaluated using Monte Carlo N-Particle (MCNP) for as-run power history and COMSOL for temperature analysis. These rodlets include a set of low burnups (~2.5 % heavy metal [%FIMA]) control rodlets and a helium bonded annular rodlet (4.7 %FIMA). Initial non-destructive PIE has been completed and includes, visual inspection, neutron radiography and gamma scanning of the FAST rodlets. Radiography confirmed the integrity of the experiments as well as showing the complete filling of the annulus in the annular fuel at a modest burnup (4.7 %FIMA) and potential slumping of the cooler rodlets at lower burnup. Precision gamma scanning indicated mostly usual fission product behavior with the exception of the ceasium in the He-bonded annular fuel. Future destructive PIE will be necessary in order to fully understand the effects of accelerated irradiation on U-Zr metallic fuel behavior.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Initial demonstration of automated fuel performance modeling with 1977 EBR-II metallic fuel pins using BISON code with FIPD and IMIS databases

Using the BISON fuel performance code, simulations were conducted using an automated process to read initial and operating conditions from the Fuels Irradiation and Physics Database (FIPD) and Integral Fast Reactor materials information system (IMIS) database, which contains metallic fuel data from the Experimental Breeder Reactor-II (EBR-II). This work demonstrates use of an integrated framework to access the vast majority of EBR-II experimental fuel pin data to support rapid development of fuel performance models for next-generation metallic fuel systems. With this capability, validation for fuel qualification can be performed rapidly. Between IMIS and FIPD, there is enough information to conduct 1977 unique EBR-II metallic fuel pin histories from 24 different experiments, at varying levels of detail between the two databases. Each of these histories includes a high-resolution power history, flux history, coolant channel flow rates, and coolant channel temperatures. Fission gas release (FGR), cumulative damage fraction (CDF), fuel axial swelling, cladding profilometry, and burnup were all simulated in BISON. The results were compared to post-irradiation examination (PIE) results for the initial demonstration of automated BISON modeling. BISON simulations conducted with IMIS and FIPD were in rough agreement with PIE measurements and calculations. Cladding profilometry, FGR, and fuel axial swelling were found to be in rough agreement with PIE measurements, depending on the physics used within the BISON input files. Here, the mechanical contact solver chosen was found to significantly impact axial fuel swelling and cladding strain predictions. CDF values were assessed to see whether pin failure may have been predicted (CDF ≥ 1). This work suggests that continued development of an automated tool for BISON should focus on inclusion of the Fast Flux Test Facility (FFTF) experimental data for a larger database for metallic fuel, improved physical models to better capture fuel performance, such as fuel-cladding interactions, and a more detailed comparison with available PIE data to further the BISON model development.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Robust scalable initialization for Bayesian variational inference with multi-modal Laplace approximations

Predictive modeling typically relies on Bayesian model calibration to provide uncertainty quantification. Variational inference utilizing fully independent (“mean-field”) Gaussian distributions are often used as approximate probability density functions. This simplification is attractive since the number of variational parameters grows only linearly with the number of unknown model parameters. However, the resulting diagonal covariance structure and unimodal behavior can be too restrictive to provide useful approximations of intractable Bayesian posteriors that exhibit highly non-Gaussian behavior, including multimodality. High-fidelity surrogate posteriors for these problems can be obtained by considering the family of Gaussian mixtures. Gaussian mixtures are capable of capturing multiple modes and approximating any distribution to an arbitrary degree of accuracy, while maintaining some analytical tractability. Unfortunately, variational inference using Gaussian mixtures with full-covariance structures suffers from a quadratic growth in variational parameters with the number of model parameters. The existence of multiple local minima due to strong nonconvex trends in the loss functions often associated with variational inference present additional complications, These challenges motivate the need for robust initialization procedures to improve the performance and computational scalability of variational inference with mixture models. In this work, we propose a method for constructing an initial Gaussian mixture model approximation that can be used to warm-start the iterative solvers for variational inference. The procedure begins with a global optimization stage in model parameter space. In this step, local gradient-based optimization, globalized through multistart, is used to determine a set of local maxima, which we take to approximate the mixture component centers. Around each mode, a local Gaussian approximation is constructed via the Laplace approximation. Finally, the mixture weights are determined through constrained least squares regression. The robustness and scalability of the proposed methodology is demonstrated through application to an ensemble of synthetic tests using high-dimensional, multimodal probability density functions. Here, the practical aspects of the approach are demonstrated with inversion problems in structural dynamics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Directionally supervised cellular automaton for the initial peopling of Sahul

Reconstructing the patterns of Homo sapiens expansion out of Africa and across the globe has been advanced using demographic and travel-cost models. However, modelled routes are ipso facto influenced by migration rates, and vice versa. We combined movement ‘superhighways’ with a demographic cellular automaton to predict one of the world's earliest peopling events — Sahul between 75000 and 50000 years ago. Novel outcomes from the superhighways-weighted model include (i) an approximate doubling of the predicted time to continental saturation (~10,000 years) compared to that based on the directionally unsupervised model (~5000 years), suggesting that rates of migration need to account for topographical constraints in addition to rate of saturation; (ii) a previously undetected movement corridor south through the centre of Sahul early in the expansion wave based on the scenarios assuming two dominant entry points into Sahul; and (iii) a better fit to the spatially de-biased, Signor-Lipps-corrected layer of initial arrival inferred from dated archaeological material. Our combined model infrastructure provides a data-driven means to examine how people initially moved through, settled, and abandoned different regions of the globe.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

Impacts of Initial Ca/P on Amorphous Calcium Phosphate

Amorphous calcium phosphate (ACP) is a metastable phase in the crystallization pathway of calcium phosphates. Understanding its chemical and structural properties could provide critical insights into biomineralization mechanisms. Of particular interest is the impact of the initial Ca/P on the structure of ACP. Further, the influence of Ca/P on the size, precipitate chemistry, and transformation of ACP is crucial to understanding the metastability of amorphous phosphates. In situ pair distribution function (PDF) analysis results 5 min after mixing show that the Ca-P bonding geometry varies from predominantly monodentate, to mixed monodentate and bidentate, to predominantly bidentate as Ca/P increases from 0.2 to 5.0. This relationship is consistent across a pH range of 6-11. Samples with only monodentate Ca-P geometries transform directly to hydroxylapatite, while samples some or all bidentate geometries form brushite. Regardless of the initial ratio, the Ca/P of precipitates is close to 1.0. In situ small-angle X-ray scattering shows particle size increases with increasing Ca/P. This is the first evidence of structural variations in ACP and is directly linked to system chemistry. Finally, synthesis of ACP with monodentate Ca-P geometries is a promising method to control the crystallization pathway to form hydroxylapatite at circumneutral pH without stabilizing ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

First-Principles Elucidation of Initial Dehydrogenation Pathways in Mg(BH 4 ) 2

Complex borohydrides such as Mg(BH 4 ) 2 offer one of highest capacities to chemically store hydrogen for onboard applications; however, it suffers greatly from kinetic constraints that prevent realization of full capacity and reversibility. Understanding these kinetic limitations solely from experiments is extremely challenging due to the unusual complexity of various competing elemental reaction steps involved during the de/rehydrogenation reaction. This work aims to map out the energetics associated with initial dehydrogenation of Mg(BH 4 ) 2 from first-principles simulations and to identify the preferred reaction pathways. Our calculations suggest the rate-limiting step during BH 4 – –B 3 H 8 – conversion is the formation of the B 2 H 7 – intermediate. We further emphasize and clarify that the B 3 H 8 – and H – intermediates, formed during initial Mg(BH 4 ) 2 decomposition, appear as molecular species that are embedded in the Mg–BH 4 –Mg matrix as evidenced in the nuclear magnetic resonance measurements and not as bulk MgH 2 and Mg(B 3 H 8 ) 2 as previously assumed in theoretical predictions of the thermodynamics.

08 HYDROGEN↗
DOE OSTI2026

Surface-Initiated Atom Transfer Radical Polymerization Using Hydrogel Reactors

Atom transfer radical polymerization (ATRP) is a controlled radical polymerization method that enables the synthesis of tailored polymeric materials with low dispersity, highlighting its immense potential for green fabrication of advanced materials. However, its broader implementation is limited by challenges in product isolation, maintaining catalyst activity, and mitigating atmospheric sensitivity arising from oxygen-sensitive metal catalysts. Here, gelatin hydrogels (GHs) are introduced as a soft “reactor” matrix for interfacial ATRP, operating with minimal metal-catalyst loading while exhibiting possibly an organoreductive behavior. This strategy leverages activator regeneration via electron transfer through a ligand–metal charge-transfer (LMCT) mechanism to reduce oxidized metal catalysts within the GH network. Polymerization is evaluated by growing polymer brushes at an active interface formed between GHs swollen in monomer solution and an initiating surface, and sequential growth experiments confirmed that GH-mediated ATRP preserves living character. Under UV illumination, LMCT is activated, producing polymers both at the desired interface and within the GH bulk. UV–Vis spectroscopy revealed active reduction of Cu(II) to Cu(I) along with concentration-dependent complex formation, indicating dynamic coordination chemistry within the hydrogel. The redox-active arginine- and glutamic acid-rich gelatin backbone coordinates and reduces the metal center, enabling ATRP at ppm-level catalyst concentrations. While polymerization proceeds in GH-Cu(II) reactors, adding external mobile ligands to the GH results in longer polymer brushes. Here, the results reported here are exploratory. More experiments are needed to characterize polymer brush growth in GHs and compare it to conventional surface-initiated polymerization in solution.

Absorption↗
DOE OSTI2021

Effect of Fluoroethylene Carbonate Additives on the Initial Formation of the Solid Electrolyte Interphase on an Oxygen-Functionalized Graphitic Anode in Lithium-Ion Batteries

The formation of a solid electrolyte interphase (SEI) at the electrode/electrolyte interface substantially affects the stability and lifetime of lithium-ion batteries (LIBs). One of the methods to improve the lifetime of LIBs is by the inclusion of additive molecules to stabilize the SEI. To understand the effect of additive molecules on the initial stage of SEI formation, in this work we compare the decomposition and oligomerization reactions of a fluoroethylene carbonate (FEC) additive on a range of oxygen-functionalized graphitic anodes to those of an ethylene carbonate (EC) organic electrolyte. A series of density functional theory (DFT) calculations augmented by ab initio molecular dynamics (AIMD) simulations reveal that EC decomposition on an oxygen-functionalized graphitic ($11\bar{2}0$) edge facet through a nucleophilic attack on an ethylene carbon site (C E ) of an EC molecule (S2 mechanism) is spontaneous during the initial charging process of LIBs. However, decomposition of EC through a nucleophilic attack on a carbonyl carbon (C C ) site (S1 mechanism) results in alkoxide species regeneration that is responsible for continual oligomerization along the graphitic surface. In contrast, FEC prefers to decompose through an S1 pathway, which does not promote alkoxide regeneration. Including FEC as an additive is thus able to suppress alkoxide regeneration and results in a smaller and thinner SEI layer that is more flexible toward lithium intercalation during the charging/discharging process. In addition, we find that the presence of different oxygen functional groups at the surface of graphite dictates the oligomerization products and the LiF formation mechanism in the SEI.

25 ENERGY STORAGE↗
DOE OSTI2023

Role of Surface Features on the Initial Dissolution of CH 3 NH 3 PbI 3 Perovskite in Liquid Water: An Ab Initio Molecular Dynamics Study

In this study, the degradation of CH 3 NH 3 PbI 3 (MAPbI 3 ) hybrid organic inorganic perovskite (HOIP) by water has been the major issue hampering its use in commercial perovskites solar cells (PSCs) as MAPbI 3 HOIP have been known to easily degrade in the presence of water molecules. However, even though there have been numerous studies investigating this phenomenon, there is still no consensus on the mechanisms of initial stages of dissolution. Here, we attempt to consolidate differing mechanistic interpretations previously reported in the literature through the use of the first-principles constrained ab-initio molecular dynamics (AIMD) to study the mechanisms, kinetics, and thermodynamics that accompany the degradation of MAPbI 3 HOIP in liquid water. We consider not only the dissolution of the species found on the pristine MAPbI 3 HOIP surfaces, but also the dissolution from defect sites to imitate the successive degradation steps, and propose a sequence of events in the initial phase of MAPbI 3 HOIP dissolution. By comparing the dissolution free energy barrier between surface species of different surficial types, we find that the dominant dissolution mechanisms of surface species varies widely based on the specific surface features adjacent to the dissolving ion. The high sensitivity of dissolution mechanism to surface features has contributed to the many dissolution mechanisms proposed in the literature. In contrast, the dissolution free energy barriers are mainly determined by the dissolving species rather than the type of surfaces, and the type of surfaces the ions are dissolving from are inconsequential toward the dissolution free energy barrier. However, the presence of surface defects such as vacancy sites are found to significantly lower the dissolution free energy barriers. Based on the estimated dissolution free energy barriers from different types of surfaces that we investigated in this study, we proposed that the dissolution of MAPbI 3 HOIP in liquid water originates from surface defect sites that propagate laterally along the surface layer of the MAPbI 3 HOIP crystal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The Role of Catholyte Modulation in Suppressing the Initial Capacity Fade of Zinc Electrolytic Manganese Dioxide Coin Cells

Despite its potential for zinc–manganese oxide batteries, electrolytic manganese dioxide (EMD) can experience capacity fade due to a deficiency in the Mn 2+ supply at the cathode electrolyte interphase (CEI) from side reactions, even in the presence of an electrolyte additive. In this work, electrolyte loading modulation at the cathode electrolyte interface (CEI) was correlated with Zn∥EMD cell capacity retention and cycling performance, as a proposed measure to curb the initial capacity fade observed in EMD. Initial galvanostatic charge/discharge cycling, with varied electrolyte loading, revealed severe capacity fade (from ~188 to 10 mAh g –1 for the highest loading of 200 μL) within the first 15 cycles. Such a decrease in cell capacity is correlated with the formation of a Mn 4+ deposit on the current collector and consequently, the Mn 2+ depletion at CEI, as was supported by elemental and Raman analyses. Interestingly, confinement of the electrolyte to the CEI at a lower (≤15 μL) electrolyte loading mitigated Mn 4+ side-deposition, maintaining the cell capacity at >80% over the first 15 cycles. Interfacial Mn supply/depletion could be monitored via voltammetric analysis based on changes of the Zn 2+ insertionreduction peak. Additional galvanostatic experiments corroborated the voltammetric interpretation and the proposed degradation pathway in the studied cell conditions. The outcomes of this work provide practical insight into coin-cell design and configuration strategies for developing Zn∥EMD batteries.

25 ENERGY STORAGE↗
DOE OSTI2021

Coupling of Flavonoid Initiation Sites with Monolignols Studied by Density Functional Theory

Lignin recalcitrance presents a challenge for the development of a bioeconomy that employs lignocellulosic feedstocks. The efficiency of lignin deconstruction is improved by a reduction of molecular weight, and given the discovery that flavones serve as initiation sites in lignin biosynthesis, these molecular weight reductions could potentially be achieved with plant metabolic engineering to over-express flavonoids. Upon increasing the flavonoid content in lignin, the bond strengths and properties of flavonoid-monolignol linkages become increasingly important. To that end, the current work applies density functional theory calculations to elucidate the bond dissociation enthalpies (BDEs) of flavonoid-monolignol linkages, including dimers with oxidized monolignols. Specifically, the dimer bond strengths and monomer hydrogen abstraction energies for the flavonoids tricin, chrysoeriol, luteolin, apigenin, catechin, epicatechin, epigallocatechin, and epigallocatechin gallate are calculated, when coupled to seven natural and engineered monolignols. Results indicate that 4'-O-ß linkage strengths between flavonoids and monolignols are of comparable strength to inter-monolignol ß-O-4 linkages, with average flavonoid-monolignol BDEs of 70.7 kcal/mol relative to ~69.3 kcal/mol in analogous canonical monolignols. Epigallocatechin yielded the lowest 4'-O-ß bond strength of 52.3 kcal/mol when coupled to an oxidized monolignol, while the flavones overall produced lower average BDEs, relative to the flavanols. Substituents at the 3'-C and 5'-C positions on flavonoids affected the dimer linkage strengths to a greater extent than glycosylation or substituents further from the linkage. Erythro and threo stereochemistry across the flavonoid-monolignol linkage library exhibited only small energetic differences and no pronounced correlations. Taken together, the predictions from this work support the concept that higher concentrations of flavonoid initiation sites in lignin may afford linkage properties conducive to more facile lignin depolymerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Calibration and Initial Results of Space Radiation Dosimetry Using the iMESA-R

The integrated Miniaturized Electrostatic Analyzer-Reflight (iMESA-R) is a space weather instrument designed to measure plasma density, temperature, and spacecraft charging, along with total ionizing dose and dose rate. A constellation consisting of five nearly identical instruments has been designed and developed to act as science payloads hosted on-board Department of Defense satellites operating in low-Earth orbit. To validate the dosimetry component of the iMESA-R, a radiation test study was performed to calibrate the dosimeter and ascertain the attenuation due to the instrument aluminum housing. An 80 curie Cobalt-60 radioisotope source emitting beta, X-ray, and gamma ray radiation decay products was used to calibrate the dosimeter response as a function of distance and instrument shielding. We present results of the calibration study along with initial on-orbit data presented from the first operational iMESA-R hosted on-board Space Test Program Satellite 5 in a polar Earth orbit. The initial on-orbit data demonstrate the ability to map the radiation environment, particularly the South Atlantic Anomaly and the auroral regions using total ionizing dose rate due to electrons of E > 1.5 MeV and protons of E > 25 MeV.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Accelerating Multiphase Simulations With Denoising Diffusion Model Driven Initializations

This study introduces a hybrid fluid simulation approach that integrates generative diffusion models with physics‐based simulations, aiming at reducing the computational costs of flow simulations while still honoring all the physical properties of interest. Pore‐scale simulations enhance our understanding of applications such as assessing hydrogen and storage efficiency in underground reservoirs. Nevertheless, they are computationally expensive and the presence of non‐unique solutions can require multiple simulations within a single geometry. To overcome the computational cost hurdle, we propose a method that couples generative diffusion models and physics‐based simulations. While training the data‐driven model, we simultaneously generate initial conditions and perform physics‐based simulations using these. This integrated approach enables us to receive real‐time feedback on a single compute node equipped with both CPUs and GPUs. By efficiently managing these processes within a single compute node, we can continuously monitor performance and halt training once the model meets the specified criteria. To test our model, we generate realizations in a real Berea sandstone fracture which shows that our technique is up to 4.4 times faster than commonly used flow simulation initializations.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structural basis of BAK activation in mitochondrial apoptosis initiation

BCL-2 proteins regulate mitochondrial poration in apoptosis initiation. How the pore-forming BCL-2 Effector BAK is activated remains incompletely understood mechanistically. Here we investigate autoactivation and direct activation by BH3-only proteins, which cooperate to lower BAK threshold in membrane poration and apoptosis initiation. We define in trans BAK autoactivation as the asymmetric “BH3-in-groove” triggering of dormant BAK by active BAK. BAK autoactivation is mechanistically similar to direct activation. The structure of autoactivated BAK BH3-BAK complex reveals the conformational changes leading to helix α1 destabilization, which is a hallmark of BAK activation. Helix α1 is destabilized and restabilized in structures of BAK engaged by rationally designed, high-affinity activating and inactivating BID-like BH3 ligands, respectively. Altogether our data support the long-standing hit-and-run mechanism of BAK activation by transient binding of BH3-only proteins, demonstrating that BH3-induced structural changes are more important in BAK activation than BH3 ligand affinity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Initial-site characterization of hydrogen migration following strong-field double-ionization of ethanol

Abstract An essential problem in photochemistry is understanding the coupling of electronic and nuclear dynamics in molecules, which manifests in processes such as hydrogen migration. Measurements of hydrogen migration in molecules that have more than two equivalent hydrogen sites, however, produce data that is difficult to compare with calculations because the initial hydrogen site is unknown. We demonstrate that coincidence ion-imaging measurements of a few deuterium-tagged isotopologues of ethanol can determine the contribution of each initial-site composition to hydrogen-rich fragments following strong-field double ionization. These site-specific probabilities produce benchmarks for calculations and answer outstanding questions about photofragmentation of ethanol dications; e.g., establishing that the central two hydrogen atoms are 15 times more likely to abstract the hydroxyl proton than a methyl-group proton to form H $${}_{3}^{+}$$ 3 + and that hydrogen scrambling, involving the exchange of hydrogen between different sites, is important in H 2 O + formation. The technique extends to dynamic variables and could, in principle, be applied to larger non-cyclic hydrocarbons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Can a simple topological-constraints-based model predict the initial dissolution rate of borosilicate and aluminosilicate glasses?

Tuning glass composition to obtain targeted properties generally relies on empirical approaches. However, a deep understanding of the physical and chemical mechanisms linking glass composition to its structure and properties would enable developing reliable predictive models. Indeed, although empirical models are usually able to interpolate composition–property relationships within a given compositional envelope, they often fail at extrapolating predictions far from their training domain. Here, as an alternative route to empirical models, we show that a structural descriptor based on the number of topological constraints per atom can be used to predict the initial dissolution rate of aluminosilicate and borosilicate glasses after being parameterized on different families of glasses (specific series of borosilicate glasses). Sixteen glasses belonging to these families were studied and their initial dissolution rates were determined at 90 °C and pH 90 °C = 9, covering rates spanning over 5 orders of magnitude. The model based on topological constraints was trained based on seven select borosilicate glasses (R 2 = 0.997) and used to predict the dissolution rate of nine additional borosilicate and aluminosilicate glasses. We show that, provided that corrections are made for high alkali content glasses that dissolve incongruently (preferential release of Na), the model gives reasonable predictions, even far from its training domain.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Redefining fundamental concepts of transcription initiation in bacteria

Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Furthermore, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.

59 BASIC BIOLOGICAL SCIENCES↗