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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Models and Algorithms for Equilibrium Analysis of Mixed-Material Nucleic Acid Systems

Dynamic programming algorithms within the NUPACK software suite enable analysis of equilibrium base-pairing properties for complex and test tube ensembles containing arbitrary numbers of interacting nucleic acid strands. Currently, calculations are limited to single-material systems that are either all-RNA or all-DNA. Here, to enable analysis of mixed-material systems that are critical for modern applications in vitro, in situ, and in vivo, we develop physical models and dynamic programming algorithms that allow the material of the system to be specified at nucleotide resolution. Free energy parameter sets are constructed for both RNA/DNA and RNA/2'OMe-RNA mixed-material systems by combining available empirical mixed-material parameters with single-material parameter sets to enable treatment of the full complex and test tube ensembles. New dynamic programming recursions account for the material of each nucleotide throughout the recursive process. For a complex with N nucleotides, the mixed-material dynamic programming algorithms maintain the O(N 3 ) time complexity of the single-material algorithms, enabling efficient calculation of diverse physical quantities over complex and test tube ensembles (e.g., complex partition function, equilibrium complex concentrations, equilibrium base-pairing probabilities, minimum free energy secondary structure(s), and Boltzmann-sampled secondary structures) at a cost increase of roughly 2.0-3.5×. The results of existing single-material algorithms are exactly reproduced when applying the new mixed-material algorithms to single-material systems. Accuracy is significantly enhanced using mixed-material models and algorithms to predict RNA/DNA and RNA/2'OMe-RNA duplex melting temperatures from the experimental literature as well as RNA/DNA melt profiles from new experiments. In conclusion, mixed-material analyses can be performed online using the NUPACK web app (www.nupack.org) or locally using the NUPACK Python module.

2′OMe-RNA↗
DOE OSTI2023

MSTor 2023 : A new version of the computer code for multistructural torsional anharmonicity, now with automatic torsional identification using redundant internal coordinates

The MSTor program is a computer program for calculating partition functions and thermodynamic functions of complex gas-phase molecules with multiple torsions; the multi-structural approximation with torsional anharmonicity (MS-T) can be used based on either a coupled torsional potential or an uncoupled torsional potential. The program can also carry out calculations in the multiple-structure local harmonic (MS-LH) approximation or multi-structural local quasiharmonic (MS-LQ) approximation or by the dual-level MS-T method. Furthermore, the program package includes eight utility codes that can be used as stand-alone programs to help the user to generate the input files for the code or to generate comparison results. The 2023 version of MSTor includes a new capability, namely automatic identification of torsional modes with redundant internal coordinates.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Comments on the quantum field theory of the Coulomb gas formalism

The holomorphic Coulomb gas formalism, as developed by Feigin-Fuchs, Dotsenko-Fateev and Felder, is a set of rules for computing minimal model observables using free field techniques. We attempt to derive and clarify these rules using standard techniques of quantum field theory. We begin with a careful examination of the timelike linear dilaton. Although the background charge of the model breaks the scalar field’s continuous shift symmetry, the exponential of the action remains invariant under a discrete shift because the background charge is imaginary. Gauging this symmetry makes the dilaton compact and introduces winding modes into the spectrum. One of these winding operators corresponds to the anti-holomorphic completion of the BRST current first introduced by Felder, and the full left/right cohomology of this BRST charge isolates the irreducible representations of the Virasoro algebra within the degenerate Fock space of the linear dilaton. The “supertrace” in the BRST complex reproduces the minimal model partition function and exhibits delicate cancellations between states with both momentum and winding. The model at the radius $R=\sqrt{pp^{\prime }}$ has two marginal operators corresponding to the Dotsenko-Fateev “screening charges”. Deforming by them, we obtain a model that might be called a “BRST quotiented compact timelike Liouville theory”. The Hamiltonian of the zero-mode quantum mechanics of this model is not Hermitian, but it is PT -symmetric and exactly solvable. Its eigenfunctions have support on an infinite number of plane waves, suggesting an infinite reduction in the number of independent states in the full quantum field theory. Applying conformal perturbation theory to the exponential interactions reproduces the Coulomb gas calculations of minimal model correlation functions. In contrast to spacelike Liouville, these “resonance correlators” are finite because the zero mode is compact. We comment on subtleties regarding the reflection operator identification, as well as naive violations of truncation in correlators with multiple reflection operators inserted. This work is part of an attempt to understand the relationship between the JT model of two dimen- sional gravity and the worldsheet description of the (2 , p ) minimal string as suggested by Seiberg and Stanford.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Complex eigenvalue instantons and the Fredholm determinant expansion in the Gross-Witten-Wadia model

We study the leading nonperturbative corrections to the strong-coupling (ungapped) phase of the Gross-Witten-Wadia (GWW) integral over unitary matrices, to one-loop order. We compute these corrections directly in terms of eigenvalue tunneling in a holomorphic presentation of the integral over eigenvalues. The leading nonperturbative contribution to the partition function comes from a pair of complex eigenvalue instantons. We show that these are in fact “ghost instantons”, which are extrema of the one-eigenvalue effective potential on the “unphysical sheet” of the spectral curve and have been discussed in detail recently by Mariño, Schiappa, and Schwick. Further, we discuss the relationship of these instantons to the Fredholm determinant expansion of the unitary matrix integral, which has recently become an object of interest in the computations of BPS indices of supersymmetric gauge theories and black holes. We find that, after taking the ’t Hooft limit, the first correction given by the Fredholm determinant expansion of the GWW integral agrees precisely with the leading nonperturbative correction, to one-loop order.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Gauges, loops, and polynomials for partition functions of graphical models

Graphical models represent multivariate and generally not normalized probability distributions. Computing the normalization factor, called the partition function, is the main inference challenge relevant to multiple statistical and optimization applications. The problem is #P-hard that is of an exponential complexity with respect to the number of variables. Here, aimed at approximating the partition function, we consider multi-graph models where binary variables and multivariable factors are associated with edges and nodes, respectively, of an undirected multi-graph. We suggest a new methodology for analysis and computations that combines the Gauge function technique from Chertkov and Chernyak with the technique developed in Anari and Oveis Gharan 2017 arXiv:1702.02937; Gurvits 2011 arXiv:1106.2844; Straszak and Vishnoi 2017 55th Annual Allerton Conf. on Communication, Control, and Computing, based on the recent progress in the field of real stable polynomials. We show that the Gauge function, representing a single-out term in a finite sum expression for the partition function which achieves extremum at the so-called belief-propagation gauge, has a natural polynomial representation in terms of gauges/variables associated with edges of the multi-graph. Moreover, Gauge function can be used to recover the partition function through a sequence of transformations allowing appealing algebraic and graphical interpretations. Algebraically, one step in the sequence consists of the application of a differential operator over gauges associated with an edge. Graphically, the sequence is interpreted as a repetitive elimination/contraction of edges resulting in multi-graph models on decreasing in size (number of edges) graphs with the same partition function as in the original multi-graph model. Even though the complexity of computing factors in the sequence of the derived multi-graph models and respective Gauge functions grow exponentially with the number of eliminated edges, polynomials associated with the new factors remain bi-stable if the original factors have this property. Moreover, we show that BP estimations in the sequence do not decrease, each low-bounding the partition function.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Assessing entropy for catalytic processes at complex reactive interfaces

When chemical reactions are accelerated by a catalyst, entropy differences between reactants and their transient intermediates can be the driving force behind the promotion or inhibition of desired and parasitic chemical pathways. Understanding and controlling catalytic processes therefore requires both a fundamental and practicable understanding of entropy in addition to enthalpy. In unstructured media such as the vapor phase equilibrated with sparsely covered surfaces, entropy can be adequately accounted for by well-established approaches based on translational, rotational, and harmonic vibrational partition functions. However, these approximations become inadequate in more complex condensed phase environments, e.g., solid liquid interfaces of confined reaction spaces. In this chapter, we provide an overview of the state-of-art in the computational quantification of entropy and its known ramifications on catalysis. The fundamental roles of thermodynamics and kinetics in catalysis are covered in enough detail to appreciate and contextualize the computational methods employed to compute chemically accurate estimates of entropy. These methods are discussed in appropriate detail and range from the ubiquitous harmonic oscillator approximation where entropy unrelated to high frequency oscillations is typically underestimated, to enhanced free energy sampling with molecular dynamics where the desired accuracy must be weighed against the associated computational cost of obtaining it. The rising importance of machine learning and artificial intelligence in accelerating methodological progress in this field is touched upon, as well. Finally, applications, successes, and pitfalls of using these methods are provided to showcase past and present accomplishments while clarifying where improvements in both understanding and methodology are still needed.

Kollias, Loukas↗
DOE OSTI2023

Effects of Salt on Phase Behavior and Rheological Properties of Alginate–Chitosan Polyelectrolyte Complexes

Oppositely charged polyelectrolytes often form polyelectrolyte complexes (PECs) due to the association through electrostatic interactions. Obtaining PECs using natural, biocompatible polyelectrolytes is of interest in the food, pharmaceutical, and biomedical industries. In this work, PECs were prepared from two biopolymers, positively charged chitosan and negatively charged alginate. We investigate the changes in the structure and properties of PECs by adding sodium chloride (salt doping) to the system. The shear modulus of PECs can be tuned from ~10 to 10 4 Pa by changing the salt concentration. The addition of salt led to a decrease in the water content of the complex phase with increasing shear modulus. However, at a very high salt concentration, the shear modulus of the complex phase decreased but did not lead to the liquid coacervate formation, typical of synthetic polyelectrolytes. This difference in phase behavior has likely been attributed to the hydrophobicity of chitosan and long semiflexible alginate and chitosan chains that restrict the conformational changes. Large amplitude oscillatory shear experiments captured nonlinear responses of PECs. The compositions of the PECs, determined as a function of salt concentration, signify the preferential partitioning of salt into the complex phase. Small-angle X-ray scattering of the salt-doped PECs indicates that the Kuhn length and radius of the alginate–chitosan associated structure qualitatively agree with the captured phase behavior and rheological data. This study provides insights into the structure–property as a function of salt concentration of natural polymer-based PECs necessary for developing functional materials from natural polyelectrolytes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cation–Ligand Interactions Dictate Salt Partitioning and Diffusivity in Ligand-Functionalized Polymer Membranes

Membranes are an attractive alternative to current thermal separations due to their scalability and energy efficiency in desalinating water. Unfortunately, many of the conventional membrane materials available today are unable to differentiate between ionic solutes, especially alkali cations, compromising their use in ion–ion separations. Inspired by the ion-specific interactions exhibited by biological ion channels, recent research efforts have focused on synthesizing and characterizing new polymeric materials that incorporate ligands into polymer networks to bias solubility and/or diffusivity of one cationic species over another. Despite these efforts, little is known about the influence of incorporating ligands into polymer membranes on solubility and diffusivity of the complexing species. In this study, we first build a qualitative model of salt partitioning, diffusivity, and permeability in generic cation-complexing ligand-functionalized polymer membranes. Next, to validate our model and hypotheses, we perform atomistic molecular dynamics simulations of a 12-crown-4-functionalized membrane in the presence of alkali halide salts at low concentration. Generally, cation complexation enhances cation solubility but decreases diffusivity. Interestingly, the reduction in diffusivity is predicted to be larger than the enhancement in solubility for materials which operate by the mechanisms proposed in our physical picture, ultimately resulting in a reduction in the permeability of the selectively complexing ion.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Computing partition functions in the one-clean-qubit model

We present a method to approximate partition functions of quantum systems using mixed-state quantum computation. For positive-semidefinite Hamiltonians, our method has an expected running-time that is almost linear in [M/( ε rel Z )] 2 , where M is the dimension of the quantum system, Z is the partition function, and ε rel is the relative precision. It is based on approximations of the exponential operator as linear combinations of certain operators related to block-encoding of Hamiltonians or Hamiltonian evolutions. The trace of each operator is estimated using a standard algorithm in the one-clean-qubit model. For large values of Z , our method may run faster than exact classical methods, whose complexities are polynomial in M . We also prove that a version of the partition function estimation problem within additive error is complete for the so-called DQC1 complexity class, suggesting that our method provides a superpolynomial speedup for certain parameter values. Overall, to attain a desired relative precision, we develop a classical procedure based on a sequence of approximations within predetermined additive errors that may be of independent interest.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

Abstract Background Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate how gut microorganisms supplement the energetic and nutritional requirements of animals. Although mammalian gut systems are well-studied in this capacity, the role of microbes in the breakdown and utilization of recalcitrant marine macroalgae in herbivorous fish is relatively understudied and an emerging priority for bioproduct extraction. Here we use a comprehensive survey of the marine herbivorous fish gut microbial ecosystem via parallel 16S rRNA gene amplicon profiling (microbiota) and untargeted tandem mass spectrometry (metabolomes) to demonstrate consistent transitions among 8 gut subsections across five fish of the genus of Kyphosus . Results Integration of microbial phylogenetic and chemical diversity data reveals that microbial communities and metabolomes covaried and differentiated continuously from stomach to hindgut, with the midgut containing multiple distinct and previously uncharacterized microenvironments and a distinct hindgut community dominated by obligate anaerobes. This differentiation was driven primarily by anaerobic gut endosymbionts of the classes Bacteroidia and Clostridia changing in concert with bile acids, small peptides, and phospholipids: bile acid deconjugation associated with early midgut microbiota, small peptide production associated with midgut microbiota, and phospholipid production associated with hindgut microbiota. Conclusions The combination of microbial and untargeted metabolomic data at high spatial resolution provides a new view of the diverse fish gut microenvironment and serves as a foundation to understand functional partitioning of microbial activities that contribute to the digestion of complex macroalgae in herbivorous marine fish.

Sparagon, Wesley J. (ORCID:0000000296274174)↗
DOE OSTI2021

Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair

Transcription-coupled repair is essential for the removal of DNA lesions from the transcribed genome. The pathway is initiated by CSB protein binding to stalled RNA polymerase II. Mutations impairing CSB function cause severe genetic disease. Yet, the ATP-dependent mechanism by which CSB powers RNA polymerase to bypass certain lesions while triggering excision of others is incompletely understood. Here we build structural models of RNA polymerase II bound to the yeast CSB ortholog Rad26 in nucleotide-free and bound states. This enables simulations and graph-theoretical analyses to define partitioning of this complex into dynamic communities and delineate how its structural elements function together to remodel DNA. We identify an allosteric pathway coupling motions of the Rad26 ATPase modules to changes in RNA polymerase and DNA to unveil a structural mechanism for CSB-assisted progression past less bulky lesions. Our models allow functional interpretation of the effects of Cockayne syndrome disease mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Zentropy Theory for Transformative Functionalities of Magnetic and Superconducting Materials

The proposed research developed the zentropy theory through applications to complex magnetic materials and superconductors under the hypothesis that the emergent properties of complex magnetic materials and superconductors can be predicted by statistical mechanics of ergodic microstates with their partition functions computed from DFT-predicted free energies. The key objective is to develop approaches to systematically determine the types and number of microstates and the supercell size in DFT-based calculations through convergency of macroscopic functionalities, with the incorporation of our mixed-space approach accounting for the interactions between periodic supercells. In addition to use scientific intuitions to guide the design of important microstates, the key innovation of the proposed research is to integrate the domain knowledge and the material-property-descriptor database (MPDD) with 4 million microstates, which is supported by our deep neural network machine learning models (SIPFENN: structure-informed prediction of formation energy using neural networks) and integrated with our high throughput DFT Tool Kit (DFTTK). For complex magnetic materials, one of the objectives is to develop approaches to calculate short-range ordering from the statistical distribution of each microstate. For superconductors, the divergency of quasiparticle effective mass at a quantum critical point will be investigated, and the superconducting and non-superconducting microstates will be delineated through analysis of electronic band structure, density of states, charge density, and Fermi surface.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Universality driven analytic structure of QCD crossover: radius of convergence and QCD critical point

Recent lattice QCD calculations show strong indications that the crossover of QCD at zero baryon chemical potential (µB) is a remnant of the second order chiral phase transition. The non-universal parameters needed to map temperature T and µ B to the universal properties of the second order chiral phase transition were determined by lattice QCD calculations. Motivated by these advances, first, we discuss the analytic structure of the partition function - the so-called Yang-Lee edge singularity - in the QCD crossover regime, solely based on universal properties. Then, utilizing the lattice calculated non-universal parameters, we map this singularity to the real T and complex µ B plane, in order to find the radius of convergence for a Taylor series expansion of QCD partition function around µ B = 0 in the QCD crossover regime. Our most important findings are: (i) An universality-based estimate of the radius of convergence around µ B = 0; (ii) Universality and lattice QCD based constraints on the location of the QCD critical point in the T - µ B plane.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

SNPeffect: identifying functional roles of SNPs using metabolic networks

Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2021

An Information Theory Approach to Physical Domain Discovery

The project of physics discovery is often equivalent to finding the most concise description of a physical system. The description with optimum predictive capability for a dataset generated by a physical system is one that minimizes both predictive error on the dataset and the complexity of the description. The discovery of the governing physics of a system can therefore be viewed as a mathematical optimization problem. We outline here a method to optimize the description of arbitrarily complex physical systems by minimizing the entropy of the description of the system. The Recursive Domain Partitioning (RDP) procedure finds the optimum partitioning of each physical domain into subdomains, and the optimum predictive function within each subdomain. Penalty functions are introduced to limit the complexity of the predictive function within each domain. Examples are shown in 1D and 2D. In 1D, the technique effectively discovers the elastic and plastic regions within a stress-strain curve generated by simulations of amorphous carbon material, while in 2D the technique discovers the free-flow region and the inertially-obstructed flow region in the simulation of fluid flow across a plate.

Daniel Shea↗