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DOE OSTI2020

Probing Nuclear Gluons with Heavy Flavor Production at EIC

The nuclear modifications of the parton densities in different regions of x (EMC effect, antishadowing, shadowing) reveal aspects of the fundamental QCD substructure of nucleon interactions in the nucleus. Here, we study the feasibility of measuring nuclear gluon densities at large x using open heavy flavor production (charm, beauty) in DIS at EIC. This in- cludes (a) charm production rates and kinematic dependences; (b) charm reconstruction at large x B using exclusive and inclusive modes, enabled by particle identification and vertex detection; (c) impact of inclusive charm data on nuclear gluon density.

EMC effect↗

DOE OSTI2020

Polarization and Vorticity in the Quark–Gluon Plasma

The quark–gluon plasma (QGP) produced by collisions between ultrarelativistic heavy nuclei is well described in the language of hydrodynamics. Noncentral collisions are characterized by very large angular momentum, which in a fluid system manifests as flow vorticity. This rotational structure can lead to a spin polarization of the hadrons that eventually emerge from the plasma, and thus these collisions provide experimental access to flow substructure at unprecedented detail. Recently, the first observations of Λ hyperon polarization along the direction of collisional angular momentum were reported. These measurements are in broad agreement with hydrodynamic and transport-based calculations and reveal that the QGP is the most vortical fluid ever observed. However, there remain important tensions between theory and observation that might be fundamental in nature. In the relatively mature field of heavy-ion physics, the discovery of global hyperon polarization and 3D simulations of the collision have opened an entirely new direction of research. We discuss the current status of this rapidly developing area and directions for future research.

heavy-ion collisions↗

DOE OSTI2012

Analysis of Casein Biopolymers Adsorption to Lignocellulosic Biomass as a Potential Cellulase Stabilizer

Although lignocellulosic materials have a good potential to substitute current feedstocks used for ethanol production, conversion of these materials to fermentable sugars is still not economical through enzymatic hydrolysis. High cost of cellulase has prompted research to explore techniques that can prevent from enzyme deactivation. Colloidal proteins of casein can form monolayers on hydrophobic surfaces that alleviate the de-activation of protein of interest. Scanning electron microscope (SEM), fourier transform infrared spectroscopy (FT-IR), capillary electrophoresis (CE), and Kjeldahl and BSA protein assays were used to investigate the unknown mechanism of action of induced cellulase activity during hydrolysis of casein-treated biomass. Adsorption of casein to biomass was observed with all of the analytical techniques used and varied depending on the pretreatment techniques of biomass. FT-IR analysis of amides I and II suggested that the substructure of protein from casein or skim milk were deformed at the time of contact with biomass. With no additive, the majority of one of the cellulase mono-component, 97.1 ± 1.1, was adsorbed to CS within 24 h, this adsorption was irreversible and increased by 2% after 72 h. However, biomass treatment with skim-milk and casein reduced the adsorption to 32.9% ± 6.0 and 82.8% ± 6.0, respectively.

Eckard, Anahita Dehkhoda↗

DOE OSTI2026

EvoDiffMol: evolutionary diffusion framework for 3D molecular design with optimized properties

Designing molecules with specific target properties remains a fundamental challenge in computational chemistry. While existing approaches show promise, most rely on simplified representations like SMILES strings or 2D graphs that lack essential three-dimensional geometric information. We present EvoDiffMol, a computational framework that integrates evolutionary algorithms with three-dimensional diffusion models for property-driven molecular generation. The method operates through adaptive evolutionary optimization, where population-based selection guides the generation process toward desired property landscapes. EvoDiffMol supports both unconstrained molecular design and scaffold-constrained generation that preserves fixed substructures while optimizing complementary regions. Comprehensive evaluation demonstrates exceptional performance, achieving the highest drug-likeness score (0.94) among all compared state-of-the-art methods while maintaining excellent validity, uniqueness, and novelty. Beyond single property optimization, the framework demonstrates flexible multi-property optimization capabilities, simultaneously controlling multiple molecular descriptors including synthetic accessibility, lipophilicity, topological polar surface area, and clinically relevant ADMET properties such as cardiotoxicity (hERG) and intestinal permeability (Caco-2). This adaptability spans from simple descriptors to practical pharmaceutical endpoints without requiring complete model retraining. The framework achieves precise control over target property values, generating molecules with properties closely matching specified targets for both single and multiple descriptors. Scaffold-constrained experiments preserve fixed molecular cores while maintaining effective property optimization. The three-dimensional representation offers advantages in maintaining structural validity during iterative optimization, with potential for geometry-aware applications in materials science and drug discovery.

3D molecular generation↗

DOE OSTI2020

Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET

To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor–acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. In this work, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Advances in MINLP to Identify Energy-Efficient Distillation Configurations

Separation of mixtures of chemicals, ubiquitous in chemical and petrochemical industries, by distillation is energy intensive. Nearly 3% of the overall energy is used for distillation in the United States. Improving the distillation process is crucial for making chemical industries more sustainable. However, designing distillation sequences is challenging because the choice set is vast, and the equations governing the physical process are highly nonconvex. Traditional design practices rely on heuristics and often result in suboptimal solutions. Tumbalam Gooty et al. present the first approach that reliably identifies the distillation sequence that requires the least energy for a given separation. By embedding convex hulls of substructures and adapting the reformulation-linearization technique to fractions of polynomials, they demonstrated that their approach outperforms the state-of-the-art. Their work will help the chemical industry reduce greenhouse gas emissions associated with distillation.

Business & Economics↗

DOE OSTI2014

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks

Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation. However, this view has changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases (IDH), succinate dehydrogenase (SDH), and fumarate hydratase (FH) that produce oncometabolites that competitively inhibit epigenetic regulation. In this study, we demonstrate in silico predictions of oncometabolites that have the potential to dysregulate epigenetic controls in nine types of cancer by incorporating massive scale genetic mutation information (collected from more than 1,700 cancer genomes), expression profiling data, and deploying Recon 2 to reconstruct context-specific genome-scale metabolic models. Our analysis predicted 15 compounds and 24 substructures of potential oncometabolites that could result from the loss-of-function and gain-of-function mutations of metabolic enzymes, respectively. These results suggest a substantial potential for discovering unidentified oncometabolites in various forms of cancers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Genome-wide association study identifies four pan-ancestry loci for suicidal ideation in the Million Veteran Program

Suicidal ideation (SI) often precedes and predicts suicide attempt and death, is the most common suicidal phenotype and is over-represented in veterans. The genetic architecture of SI in the absence of suicide attempt (SA) is unknown, yet believed to have distinct and overlapping risk with other suicidal behaviors. We performed the first GWAS of SI without SA in the Million Veteran Program (MVP), identifying 99,814 SI cases from electronic health records without a history of SA or suicide death (SD) and 512,567 controls without SI, SA or SD. GWAS was performed separately in the four largest ancestry groups, controlling for sex, age and genetic substructure. Ancestry-specific results were combined via meta-analysis to identify pan-ancestry loci. Four genome-wide significant (GWS) loci were identified in the pan-ancestry meta-analysis with loci on chromosomes 6 and 9 associated with suicide attempt in an independent sample. Pan-ancestry gene-based analysis identified GWS associations with DRD2, DCC, FBXL19, BCL7C, CTF1, ANNK1, and EXD3. Gene-set analysis implicated synaptic and startle response pathways (q’s<0.05). European ancestry (EA) analysis identified GWS loci on chromosomes 6 and 9, as well as GWS gene associations in EXD3, DRD2, and DCC. No other ancestry-specific GWS results were identified, underscoring the need to increase representation of diverse individuals. The genetic correlation of SI and SA within MVP was high (r G = 0.87; p = 1.09e-50), as well as with post-traumatic stress disorder (PTSD; r G = 0.78; p = 1.98e-95) and major depressive disorder (MDD; r G = 0.78; p = 8.33e-83). Conditional analysis on PTSD and MDD attenuated most pan-ancestry and EA GWS signals for SI without SA to nominal significance, with the exception of EXD3 which remained GWS. Our novel findings support a polygenic and complex architecture for SI without SA which is largely shared with SA and overlaps with psychiatric conditions frequently comorbid with suicidal behaviors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Intraspecific evolutionary relationships among peregrine falcons in western North American high latitudes

Subspecies relationships within the peregrine falcon (Falco peregrinus) have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons–F. p. tundrius, anatum, and pealei–for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, pealei, was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between anatum and tundrius were generally higher than between pealei and either anatum or tundrius. Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings–a coastal grouping (pealei) and a boreal/Arctic grouping (currently anatum and tundrius)– each comprised of discrete populations that are variously intra-regionally connected.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Theoretically and practically efficient parallel nucleus decomposition

This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves a work complexity matching the best sequential algorithm while also having low depth (parallel running time), which significantly improves upon the only existing parallel nucleus decomposition algorithm (Sariyüce et al. , PVLDB 2018). The key to the theoretical efficiency of our algorithm is a new lemma that bounds the amount of work done when peeling cliques from the graph, combined with the use of a theoretically-efficient parallel algorithms for clique listing and bucketing. We introduce several new practical optimizations, including a new multi-level hash table structure to store information on cliques space-efficiently and a technique for traversing this structure cache-efficiently. On a 30-core machine with two-way hyper-threading on real-world graphs, we achieve up to a 55x speedup over the state-of-the-art parallel nucleus decomposition algorithm by Sariyüce et al. , and up to a 40x self-relative parallel speedup. We are able to efficiently compute larger nucleus decompositions than prior work on several million-scale graphs for the first time.

Computer Science↗

DOE OSTI2011

Zn13(CrxAl1-x)27 (x = 0.34-0.37): a new intermetallic phase containing icosahedra as building units

The title compounds Zn{sub 13}(Cr{sub x}Al{sub 1-x}){sub 27} (x = 0.34-0.37) were obtained by melting the pure elements at 923 K, and followed by a heat treatment at 723 K in a tantalum container. According to single crystal structural analysis, the title compounds crystallize in the rhombohedral system, adopting a new structure type (R-3m, a = 7.5971(8), c = 36.816(6), for crystal I). Single crystal X-ray structural analysis reveals a statistical mixing of Cr/Al in their crystallographic positions. Single crystal and powder X-ray diffraction as well as energy dispersive X-ray analyses suggested the title phase to have a narrow homogeneity range. The substructure of Zn{sub 13}(Cr{sub x}Al{sub 1-x}){sub 27} shows close resemblance with the Mn{sub 3}Al{sub 10} structure type. A bonding analysis, through crystal orbital Hamiltonian populations (COHPs), of 'Cr{sub 9}Al{sub 18}Zn{sub 13}' as a representative composition indicated that both homo- and heteronuclear interactions are important for the stability of this new phase.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Physico-chemical properties of lignin fractions from acid pretreated corn stover and their effects on enzymatic hydrolysis of microcrystalline cellulose

Lignin has been shown to be a recalcitrance factor in many biomass conversion studies. To better understand the effects of lignin on cellulose conversion, different lignin fractions were extracted from the same dilute acid pretreated corn stover by three sequential isolation methods, namely ethanol extraction, dioxane extraction, and enzyme purification. The physicochemical properties of each lignin fraction including molecular weight distribution, surface area, surface charge, and other structural features varied, depending on the isolation methods. All three lignin fractions had negative surface charges, and ethanol-extracted lignin carried the highest surface charges, followed by dioxane-extracted lignin and cellulase-purified residual lignin. These physicochemical properties of lignin fractions also resulted in different extent of inhibitory effects on enzymatic hydrolysis of microcrystalline cellulose (MCC). Dioxane-extracted lignin exhibited the highest inhibitory effect on glucose release from MCC, followed by the cellulase-purified residual lignin fraction and ethanol-extracted lignin. Furthermore, lignin fractions with higher contents of syringyl (S) substructure and β-O-4 aryl ether interunit linkages showed a stronger negative effect on cellulase hydrolysis of MCC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Search for W ′ → t b → q q b b decays in p p collisions at s = 8 TeV with the ATLAS detector

A search for a massive WPRIME gauge boson is performed with the ATLAS detector at the LHC in P P collisions at a centre-of-mass energy of sqrt(s) = 8 TeV, corresponding to 20.3 fb-1 of integrated luminosity. This analysis is done in the WPRIME --> TOP BOTTOM --> QUARK QUARK BOTTOM BOTTOM mode for WPRIME masses above 1.5 TeV, where the WPRIME decay products are highly boosted. Novel jet substructure techniques are used to identify jets from high-momentum top quarks to ensure high sensitivity, independent of WPRIME mass, up to 3 TeV; b-tagging is also used to identify jets originating from b-quarks. The data are consistent with Standard Model background-only expectations, and upper limits at 95% confidence level are set on the WPRIME --> TOP BOTTOM cross section times branching ratio ranging from 0.16 pb to 0.33 pb for left-handed WPRIME bosons, and ranging from 0.10 pb to 0.21 pb for WPRIME bosons with purely right-handed couplings. Upper limits at 95% confidence level are set on the WPRIME-boson coupling to TOP BOTTOM as a function of the WPRIME mass using an effective field theory approach, which is independent of details of particular models predicting a WPRIME boson.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

Search for W ′ → t b decays in the hadronic final state using pp collisions at s = 13 TeV with the ATLAS detector

CERN-LHC. A search for W'-boson production in the W'->tb -> qq'bb decay channel is presented using 36.1 fb^{-1} of 13 TeV proton–proton collision data collected by the ATLAS detector at the Large Hadron Collider in 2015 and 2016. The search is interpreted in terms of both a left-handed and right-handed chiral W' boson within the mass range 1–5 TeV. Identification of the hadronically decaying top quark is performed using jet substructure tagging techniques base on a shower deconstruction algorithm. No significant deviation from the Standard Model prediction is observed and the results are expressed as upper limits on the W'-> tb production cross-section times branching ratio as a function of the W'-boson mass. These limits exclude W' bosons with right-handed couplings with masses below 3.0 TeV and W' bosons with left-handed couplngs with masses below 2.9 TeV, at the 95% confidence level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

The Effect of Splashback on Weak Lensing Mass Estimates of Galaxy Clusters and Groups

The splashback radius of a dark matter halo, which corresponds to the first apocenter radius reached by infalling matter and substructures, has been detected around galaxy clusters using a multitude of observational methods, including weak lensing measurements. In this manuscript, we present how the splashback feature in the halo density profile affects galaxy cluster masses derived through weak lensing measurements if it is not accounted for. We find that the splashback radius has an increasingly large effect on group-sized halos towards $M_{200m} \sim 10^{13.5} \mathrm{M_\odot}$. Depending on the model and the radial scale used, the cluster/group masses can be biased low by more than 0.1 dex. This bias, in turn, would result in a slightly lower $\Omega_m$ value if propagated into a cluster cosmology analysis. The splashback effect with group-sized dark matter halos may become important to consider, given the increasingly stringent cosmological constraints coming from optical wide-field surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Generative unfolding with distribution mapping

Machine learning enables unbinned, highly-differential cross section measurements. A recent idea uses generative models to morph a starting simulation into the unfolded data. We show how to extend two morphing techniques, Schrödinger Bridges and Direct Diffusion, in order to ensure that the models learn the correct conditional probabilities. This brings distribution mapping (DM) to a similar level of accuracy as the state-of-the-art conditional generative unfolding methods. Numerical results are presented with a standard benchmark dataset of single jet substructure as well as for a new dataset describing a 22-dimensional phase space of Z+2 -jets.

Butter, Anja↗

DOE OSTI2026

Les Houches study on inclusive jet production at NNLO+NNLL

Jet production at the LHC is a powerful probe of QCD, making it ideal for precision tests and determinations of QCD parameters such as parton distribution functions and the strong coupling constant. To make the most of the abundant jet production data collected at the LHC, precise calculations are required. While state-of-the-art calculations reach next-to-next-to-leading order (NNLO) QCD accuracy, a critical assessment of the remaining uncertainties arising from non-perturbative effects and missing higher orders remains crucial for correctly interpreting comparisons between theory and data. Scale variation is nearly always used to determine effects from missing higher orders. In this article, we reassess this method in the context of inclusive jet production by performing NNLO QCD calculations supplemented by small-jet-radius resummation through next-to-next-to-leading-logarithmic accuracy (NNLL). We find that NNLL resummation can have an appreciable impact on the scale uncertainty for inclusive jet cross sections, and, for some scale choices, can lead to sizeable shifts of the central cross section. We conclude that scale variations in fixed-order and resummed calculations can drastically underestimate the impact of higher orders for commonly used jet radius parameters, and that missing higher-order estimates obtained via scale variations should be considered unreliable. Our findings add further evidence to the importance of going beyond scale variations in jet and jet substructure calculations.

Lee, Kyle↗

DOE OSTI2011

Enhancing the CDF's B physics program with a faster data acquisition system.

The physics program of Run II at the Tevatron includes precision electroweak measurements such as the determination of the top quark and W boson masses; bottom and charm physics including the determination of the B{sub s} and D{sup 0} mixing parameters; studies of the strong interaction; and searches for the Higgs particle, supersymmetric particles, hidden space-time dimensions and quark substructure. All of these measurements benefit from a high-resolution tracking detector. Most of them rely heavily on the efficient identification of heavy flavored B hadrons by detection of displaced secondary vertices, and are enhanced by the capability to trigger on tracks not coming from the primary vertex. This is uniquely provided by CDF's finely-segmented silicon detectors surrounding the interaction region. Thus CDF experiment's physics potential critically depends on the performance of its silicon detectors. The CDF silicon detectors were designed to operate up to 2-3 fb{sup -1} of accumulated pji collisions, with an upgrade planned thereafter. However, the upgrade project was canceled in 2003 and Run II has been extended through 2011, with an expected total delivered integrated luminosity of 12 fb{sup -1} or more. Several preventive measures were taken to keep the original detector operational and maintain its performance. The most important of these are the decrease in the operating temperature of the detector, which reduces the impact of radiation exposure, and measures to minimize damage due to integrated radiation dose, thermal cycles, and wire bond resonance conditions. Despite these measures the detectors operating conditions continue to change with issues arising from radiation damage to the sensors, aging infrastructure and electronics. These, together with the basic challenges posed by the inaccessibility of the detector volume and large number (about 750 thousand) of readout channels, make the silicon detector operations the single most complex and high priority job in the CDF experiment.

43 PARTICLE ACCELERATORS↗