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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Quantitative trait locus (QTL) mapping and transcriptome profiling identify QTLs and candidate genes associated with heat stress response during reproductive development in Camelina sativa

Camelina sativa (L.) Crantz is a low-input oilseed crop that has great potential in providing sustainable feedstock for biofuels and bioproducts. Climate change is threatening production of camelina with rising global temperatures. Elucidating the genetic response to high temperatures is essential for successful breeding of heat-tolerant camelina varieties. Here, we report a combinatorial approach to identifying candidate genes associated with heat stress by quantitative trait locus (QTL) mapping and comparative transcriptome profiling. A population of recombinant inbred lines (RILs) was grown in a controlled growth chamber under the high-temperature regimes for 14 days beginning at the onset of the reproductive stage. Several traits related to seed production were evaluated at maturity. The QTL analysis identified several regions with co-located traits on chromosomes 8, 10, and 12. Two RILs with contrasting phenotypic responses to heat stress were chosen for gene expression profiling via RNA sequencing. Multiple pathways and genes were found to be strongly affected by heat stress, and many genes expressed differently between the two RILs. Several genes identified within the QTL regions were considered strong candidates that may control heat tolerance during reproduction in camelina. These studies provide resources for future studies that may assist in improving the heat tolerance of camelina.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Decoding the Mechanisms of Phase Transitions from In Situ Microscopy Observations

Abstract Analysis of the temperature‐ and stimulus‐dependent imaging data toward elucidation of the physical transformations is an ubiquitous problem in multiple fields. Here, temperature‐induced phase transition in BaTiO 3 is explored using the machine learning analysis of domain morphologies visualized via variable‐temperature scanning transmission electron microscopy (STEM) imaging data. This approach is based on the multivariate statistical analysis of the time or temperature dependence of the statistical descriptors of the system, derived in turn from the categorical classification of observed domain structures or projection on the continuous parameter space of the feature extraction‐dimensionality reduction transform. The proposed workflow offers a powerful tool for the exploration of the dynamic data based on the statistics of image representation as a function of the external control variable to visualize the transformation pathways during phase transitions and chemical reactions. This can include the mesoscopic STEM data as demonstrated here, but also optical, chemical imaging, etc., data. It can further be extended to the higher dimensional spaces, for example, analysis of the combinatorial libraries of materials compositions.

Valleti, Sai Mani Prudhvi↗
DOE OSTI2023

High‐Throughput Study of Amorphous Stability and Optical Properties of Superlattice‐Like Ge–Sb–Te Thin Films

A high‐throughput ion beam sputtering system is used to synthesize compositional gradient superlattice‐like (SLL) thin film libraries of Ge–Sb–Te alloys over the entire phase diagram. Here, the optical properties and structural evolution of the Ge–Sb–Te combinatorial SLL thin film are investigated. A systematic screening over the annealing temperature, annealing time, and modulation period has elucidated the critical factors that affect the stability of the metastable phase and optical properties. It is found that amorphous stability and optical constant are highly dependent on the modulation period and chemical composition of the thin film. This data‐driven approach offers new perspectives for accelerating the development of new materials with excellent optical and amorphous stability and for exploring their mechanisms, by greatly expanding the dataset of Ge–Sb–Te alloys with SLL structures through high‐throughput experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

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

Discovery of unknown posttranslational modifications by top-down mass spectrometry

Post-translational modifications can be important biomarkers of function within biological systems. Top-down mass spectrometry is a valuable tool for the characterization of combinatorial modifications on proteins such as histones that have a range of complex modifications. In this chapter, we present a top-down liquid chromatography-mass spectrometry experimental and data analysis workflow for the identification of novel modifications on proteins. The data analysis workflow presented here is reliant on the combination of proteoform searching using TopPIC and data visualization and fragment ion spectral confirmation using LcMsSpectator, part of the Informed-Proteomics package of software.

Wilson, Jesse W.↗
DOE OSTI2020

OpenGraphGym: A Parallel Reinforcement Learning Framework for Graph Optimization Problems

This paper presents an open-source, parallel AI environment (named OpenGraphGym) to facilitate the application of reinforcement learning (RL) algorithms to address combinatorial graph optimization problems. This environment incorporates a basic deep reinforcement learning method, and several graph embeddings to capture graph features, it also allows users to rapidly plug in and test new RL algorithms and graph embeddings for graph optimization problems. This new open-source RL framework is targeted at achieving both high performance and high quality of the computed graph solutions. This RL framework forms the foundation of several ongoing research directions, including 1) benchmark works on different RL algorithms and embedding methods for classic graph problems; 2) advanced parallel strategies for extreme-scale graph computations, as well as 3) performance evaluation on real-world graph solutions.

Zheng, Weijian↗
DOE OSTI2026

Statistics of base polytopes in F-theory

We propose a new statistical ensemble of toric bases for elliptic Calabi-Yaus used in F-theory models, by focusing on only the convex hull of the base, i.e., the base polytope. This physically motivated coarse-graining greatly simplifies the combinatorial complexity of the part of the 4d F-theory landscape with toric bases. We develop a Monte Carlo approach that randomly samples the base polytopes within fixed boxes, with proper statistical weights. We first apply the algorithm to the set of 2d base polytopes, generating an enlarged set of toric 2d bases that include certain types of codimension-two (4,6) points, and we validate our approach against exact numbers. We then explore the set of 3d base polytopes which fit in a set of “maximal” 3d boxes, and estimate the total number of inequivalent 3d base polytopes to be 10 85 –10 90 . We provide statistical data such as the distribution of non-Higgsable gauge groups on these bases. Amusingly, a similar method can also be applied to generate reflexive polytopes in various dimensions. In both the reflexive and base polytope cases, the number of relevant polytopes obeys a Gaussian distribution as a function of the number of vertices, which can be understood in terms of other results on random polytopes in the math literature.

Differential and algebraic geometry↗
DOE OSTI2020

Sign flip triangulations of the amplituhedron

We present new triangulations of the m = 4 amplituhedron relevant for scattering amplitudes in planar N = 4 super-Yang-Mills, obtained directly from the combinatorial definition of the geometry. Using the “sign flip” characterization of the amplituhedron, we reproduce the canonical forms for the all-multiplicity next-tomaximally helicity violating (NMHV) and next-to-next-to-maximally helicity violating (N2MHV) tree-level as well as the NMHV one-loop cases, without using any input from traditional amplitudes methods. Our results provide strong evidence for the equivalence of the original definition of the amplituhedron [1] and the topological one [2], and suggest a new path forward for computing higher loop amplitudes geometrically. In particular, we realize the NMHV one-loop amplituhedron as the intersection of two amplituhedra of lower dimensionality, which is reflected in the novel structure of the corresponding canonical form.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

On the intermediate Jacobian of M5-branes

Abstract We study Euclidean M5-branes wrapping vertical divisors in elliptic Calabi-Yau fourfold compactifications of M/F-theory that admit a Sen limit. We construct these Calabi-Yau fourfolds as elliptic fibrations over coordinate flip O3/O7 orientifolds of toric hypersurface Calabi-Yau threefolds. We devise a method to analyze the Hodge structure (and hence the dimension of the intermediate Jacobian) of vertical divisors in these fourfolds, using only the data available from a type IIB compactification on the O3/O7 Calabi-Yau orientifold. Our method utilizes simple combinatorial formulae (that we prove) for the equivariant Hodge numbers of the Calabi-Yau orientifolds and their prime toric divisors, along with a formula for the Euler characteristic of vertical divisors in the corresponding elliptic Calabi-Yau fourfold. Our formula for the Euler characteristic includes a conjectured correction term that accounts for the contributions of pointlike terminal ℤ 2 singularities corresponding to perturbative O3-planes. We check our conjecture in a number of explicit examples and find perfect agreement with the results of direct computations.

Physics↗
DOE OSTI2025

Measurement of charged hadron multiplicity in Au + Au collisions at $\sqrt{s_{NN}}$ = 200 GeV with the sPHENIX detector

The pseudorapidity distribution of charged hadrons produced in Au + Au collisions at a center-of-mass energy of $\sqrt{s_{NN}}$ = 200 GeV is measured using data collected by the sPHENIX detector. Charged hadron yields are extracted by counting cluster pairs in the inner and outer layers of the Intermediate Silicon Tracker, with corrections applied for detector acceptance, reconstruction efficiency, combinatorial pairs, and contributions from secondary decays. The measured distributions cover |η| < 1.1 across various centralities, and the average pseudorapidity density of charged hadrons at mid-rapidity is compared to predictions from Monte Carlo heavy-ion event generators. This result, featuring full azimuthal coverage at mid-rapidity, is consistent with previous experimental measurements at the Relativistic Heavy Ion Collider, thereby supporting the broader sPHENIX physics program.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

All loop scattering as a counting problem

Abstract This is the first in a series of papers presenting a new understanding of scattering amplitudes based on fundamentally combinatorial ideas in the kinematic space of the scattering data. We study the simplest theory of colored scalar particles with cubic interactions, at all loop orders and to all orders in the topological ’t Hooft expansion. We find novel integral formulas for the amplitudes of this theory, with no trace of the conventional sum over Feynman diagrams, but instead determined by a beautifully simple counting problem attached to any order of the topological expansion. These results represent a significant step forward in the decade-long quest to formulate the fundamental physics of the real world in a radically new language, where the rules of spacetime and quantum mechanics, as reflected in the principles of locality and unitarity, are seen to emerge from deeper mathematical structures.

1/N Expansion↗
DOE OSTI2025

Differential equations for cosmological correlators

Cosmological fluctuations retain a memory of the physics that generated them in their spatial correlations. The strength of correlations varies smoothly as a function of external kinematics, which is encoded in differential equations satisfied by cosmological correlation functions. In this work, we provide a broader perspective on the origin and structure of these differential equations. As a concrete example, we study conformally coupled scalar fields in a power-law cosmology. The wavefunction coefficients in this model have integral representations, with the integrands being the product of the corresponding flat-space results and “twist factors” that depend on the cosmological evolution. Similar twisted integrals arise for loop amplitudes in dimensional regularization, and their recent study has led to the discovery of rich mathematical structures and powerful new tools for computing multi-loop Feynman integrals in quantum field theory. The integrals of interest in cosmology are also part of a finite-dimensional basis of master integrals, which satisfy a system of first-order differential equations. We develop a formalism to derive these differential equations for arbitrary tree graphs. The results can be represented in graphical form by associating the singularities of the differential equations with a set of graph tubings. Upon differentiation, these tubings grow in a local and predictive fashion. In fact, a few remarkably simple rules allow us to predict — by hand — the equations for all tree graphs. While the rules of this “kinematic flow” are defined purely in terms of data on the boundary of the spacetime, they reflect the physics of bulk time evolution. We also study the analogous structures in tr ϕ 3 theory, and see some glimpses of hidden structure in the sum over planar graphs. This suggests that there is an autonomous combinatorial or geometric construction from which cosmological correlations, and the associated spacetime, emerge.

Cosmological models↗
DOE OSTI2021

First measurements of N -subjettiness in central Pb-Pb collisions at $\sqrt{s{NN}}$= 2.76 TeV

The ALICE Collaboration reports the first fully-corrected measurements of the N-subjettiness observable for track-based jets in heavy-ion collisions. This study is performed using data recorded in pp and Pb-Pb collisions at centre-of-mass energies of $\sqrt{s}$= 7 TeV and $\sqrt{s{NN}}$ = 2.76 TeV, respectively. In particular the ratio of 2-subjettiness to 1-subjettiness, τ 2 /τ 1 , which is sensitive to the rate of two-pronged jet substructure, is presented. Energy loss of jets traversing the strongly interacting medium in heavy-ion collisions is expected to change the rate of two-pronged substructure relative to vacuum. The results are presented for jets with a resolution parameter of R = 0.4 and charged jet transverse momentum of 40 ≤ pτ, jet ≤ 60 GeV/c, which constitute a larger jet resolution and lower jet transverse momentum interval than previous measurements in heavy-ion collisions. This has been achieved by utilising a semi-inclusive hadron-jet coincidence technique to suppress the larger jet combinatorial background in this kinematic region. No significant modification of the τ 2 /τ 1 observable for track-based jets in Pb-Pb collisions is observed relative to vacuum PYTHIA6 and PYTHIA8 references at the same collision energy. The measurements of τ 2 /τ 1 , together with the splitting aperture angle ΔR, are also performed in pp collisions at $\sqrt{s}$ = 7 TeV for inclusive jets. These results are compared with PYTHIA calculations at $\sqrt{s}$ = 7 TeV, in order to validate the model as a vacuum reference for the Pb-Pb centre-of-mass energy. The PYTHIA references for τ 2 /τ 1 are shifted to larger values compared to the measurement in pp collisions. This hints at a reduction in the rate of two-pronged jets in Pb-Pb collisions compared to pp collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Hidden zeros for particle/string amplitudes and the unity of colored scalars, pions and gluons

Recent years have seen the emergence of a new understanding of scattering amplitudes in the simplest theory of colored scalar particles — the Tr(Φ 3 ) theory — based on combinatorial and geometric ideas in the kinematic space of scattering data. In this paper we report a surprise: far from the toy model it appears to be, the “stringy” Tr(Φ 3 ) amplitudes secretly contains the scattering amplitudes for pions, as well as non-supersymmetric gluons, in any number of dimensions. The amplitudes for the different theories are given by one and the same function, related by a simple shift of the kinematics. This discovery was spurred by another fundamental observation: the tree-level Tr(Φ 3 ) field theory amplitudes have a hidden pattern of zeros when a special set of non-planar Mandelstam invariants is set to zero. These zeros are not manifest in Feynman diagrams but are made obvious by the connection of these amplitudes to the new understanding of associahedra arising from “causal diamonds” in kinematic space. Furthermore, near these zeros, the amplitudes simplify, by factoring into a non-trivial product of smaller amplitudes. Remarkably the amplitudes for pions and gluons are observed to also vanish in the same kinematical locus. These properties for Tr(Φ 3 ) amplitudes hold and further generalize to the “stringy” Tr(Φ 3 ) amplitudes. The “kinematic causal diamond” picture suggests a unique shift of the kinematic data that preserves the zeros, and this shift is precisely the one that unifies colored scalars, pions, and gluons into a single object. We will focus in this paper on explaining the hidden zeros and factorization properties and the connection between all the colored theories, working for simplicity at tree level. Subsequent works will describe this new formulation for the Non-linear Sigma Model and non-supersymmetric Yang-Mills theory, at all loop orders.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Cosmohedra

It has been a long-standing challenge to find a geometric object underlying the cosmological wavefunction for Tr(ϕ 3 ) theory, generalizing associahedra and surfacehedra for scattering amplitudes. In this note, we describe a new class of polytopes — “cosmohedra” — that provide a natural solution to this problem. The faces of associahedra capture the combinatorics of non-overlapping chords of the momentum polygon, reflecting all partial factorizations of amplitudes. Cosmohedra are far richer — instead of non-overlapping chords, their faces capture the “russian doll” structure of non-overlapping subpolygons that determine the wavefunction. We show that cosmohedra are intimately related to associahedra, obtained by “blowing up” faces of the associahedron in a simple way. We give a full combinatorial description of cosmohedron faces and their factorization properties, and provide an explicit realization in terms of facet inequalities that further “shave” the facet inequalities of the associahedron. We also discuss a novel way for computing the wavefunction from cosmohedron geometry that extends the usual connection with polytope canonical forms. We illustrate cosmohedra with examples at tree-level and one loop; the close connection to surfacehedra suggests the generalization to all loop orders. Moving beyond the wavefunction, we briefly describe “cosmological correlahedra” for full correlators, which are one higher-dimensional polytopes, interpolating between associahedra and cosmohedra on opposite facets in an extra direction associated with the total energy. We speculate on how the existence of cosmohedra might suggest a “stringy” formulation for the cosmological wavefunction/correlators, generalizing the way in which the Minkowski sum decomposition of associahedra naturally extend particle to string amplitudes.

Scattering Amplitudes↗
DOE OSTI2025

Reconstruction of boosted and resolved multi-Higgs-boson events with symmetry-preserving attention networks

The production of multiple Higgs bosons at the CERN LHC provides a direct way to measure the trilinear and quartic Higgs self-interaction strengths as well as potential access to beyond the standard model effects that can enhance production at large transverse momentum p T . The largest event fraction arises from the fully hadronic final state in which every Higgs boson decays to a bottom quark-antiquark pair ($b\bar{b}$). This introduces a combinatorial challenge known as the jet assignment problem: assigning jets to sets representing Higgs boson candidates. Symmetry-preserving attention networks (SPA-Nets) have been developed to address this challenge. However, the complexity of jet assignment increases when simultaneously considering both H → $b\bar{b}$ reconstruction possibilities, i.e., two “resolved” small-radius jets each containing a shower initiated by a b quark or one “boosted” large-radius jet containing a merged shower initiated by a $b\bar{b}$ pair. The latter improves the reconstruction efficiency at high p T . In this work, we introduce a generalization to the SPA-Net approach to simultaneously consider both boosted and resolved reconstruction possibilities and unambiguously interpret an event as “fully resolved”, “fully boosted”, or in between. We report the performance of baseline methods, the original SPA-Net approach, and our generalized version on nonresonant HH and HHH production at the LHC. Considering both boosted and resolved topologies, our SPA-Net approach increases the Higgs boson reconstruction purity by 56–80% and the efficiency by 37–38% compared to the baseline method depending on the final state.

Higgs Production↗
DOE OSTI2023

The endpoint of partial deconfinement

We study the matrix quantum mechanics of two free hermitian N × N matrices subject to a singlet constraint in the microcanonical ensemble. This is the simplest example of a theory that at large N has a confinement/deconfinement transition. In the microcanonical ensemble, it also exhibits partial deconfinement with a Hagedorn density of states. We argue that the entropy of these configurations, based on a combinatorial counting of Young diagrams, are dominated by Young diagrams that have the VKLS shape. When the shape gets to the maximal depth allowed for a Young diagram of SU(N), namely N, we argue that the system stops exhibiting the Hagedorn behavior. The number of boxes (energy) at the transition is N 2 /4, independent of the charge of the state.

1/N Expansion↗