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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Fission Fragment Intrinsic Spins and Their Correlations

The intrinsic spins and their correlations are the least understood characteristics of fission fragments from both theoretical and experimental points of view. In many nuclear reactions, the emerging fragments are typically excited and acquire an intrinsic excitation energy and an intrinsic spin depending on the type of the reactions and interaction mechanism. Both the intrinsic excitation energies and the fragments’ intrinsic spins and parities are controlled by the interaction mechanism and conservations laws, which lead to their correlations and determines the character of their deexcitation mechanism. We outline here a framework for the theoretical extraction of the intrinsic spin distributions of the fragments and their correlations within the fully microscopic real-time density-functional theory formalism and illustrate it on the example of induced fission of 236 U and 240 Pu, using two nuclear energy density functionals. Here, these fission fragment intrinsic spin distributions display new qualitative features previously not discussed in literature. Within this fully microscopic framework, we extract for the first time the intrinsic spin distributions of fission fragments of 236 U and 240 Pu as well as the correlations of their intrinsic spins, which have been debated in literature for more than six decades with no definite conclusions so far.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Fragmentation of faceted crystalline wires

The reduction of surface energy is a well-known driving force for the fragmentation of nanowires. Fragmentation can limit the service life of those small low-dimensional building blocks or can be controlled to induce beneficial shape changes. For isotropic surface energy, fragmentation is analogous to the classic Rayleigh-Plateau instability of liquid jets. However, commonly synthesized crystalline nanowires have strongly anisotropic surface energies and exhibit facets coinciding with cusps in the Wulff plot. Depending on growth orientation, different fragmentation behaviors have been seen in nanowires. Using phase-field simulations, we show that fragmentation of faceted nanowires with cubic crystal symmetry may occur by a finite-amplitude nonlinear instability, as opposed to a Rayleigh-Plateau-like linear instability, depending on nanowire growth orientation. Here, we carry out a weakly nonlinear analysis based on sharp interface theory to characterize the faceted nanowire shape corresponding to a surface-energy saddle point. The analysis predicts that the minimum amplitude of a periodic shape perturbation to trigger fragmentation increases with cusp strength but decreases inversely proportionally to the perturbation wavelength for long wavelengths, in good quantitative agreement with phase-field predictions. The results provide the theoretical foundation to predict nanowire stability as a function of length and surface energy in diverse applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Crystallographic Fragment Screening of a Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates for Proline Dehydrogenase and L-Glutamate-γ-semialdehyde Dehydrogenase

The proline catabolic pathway consisting of proline dehydrogenase (PRODH) and L-glutamate-γ-semialdehyde (GSAL) dehydrogenase (GSALDH) catalyzes the four-electron oxidation of L-proline to L-glutamate. Chemical probes to these enzymes are of interest for their role in cancer and inherited metabolic disease. Here, we report the results of a crystallographic fragment-screening campaign targeting both enzymes. A unique aspect of our approach is the screening of both enzymes simultaneously using crystals of the bifunctional PRODH-GSALDH enzyme, proline utilization A (PutA). A 288-fragment library from Zenobia was screened in crystallo in cocktails of six fragments. Validation X-ray crystallography with individual fragments identified seven crystal hits distributed in the PRODH active site, GSALDH aldehyde substrate-binding site, and GSALDH NAD+ adenine-binding site. The fragment bound in the PRODH active site, 4-methoxybenzyl alcohol, is structurally distinct from all known PRODH inhibitors as it lacks an anionic anchor and stabilizes open conformations of the active site, motivating the study of eighteen analogs. In total, thirteen crystal structures with resolutions ranging from 1.32 Å to 1.80 Å were determined, resolving the poses and interactions of seven fragments from the Zenobia library and five analogs of 4-methoxybenzyl alcohol. These results expand the chemical space of probes targeting proline catabolic enzymes and provide new structural information for further inhibitor development.

Biochemistry & Molecular Biology↗
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 OSTI2023

Atomistic simulations for investigation of substrate effects on lipid in-source fragmentation in secondary ion mass spectrometry

In beam-based ionization methods, the substrate plays an important role on the desorption mechanism of molecules from surfaces. Both the specific orientation that a molecule adopts at a surface and the strength of the molecule-surface interaction can greatly influence desorption processes, which in turn will affect the ion yield and the degree of in-source fragmentation of a molecule. In the beam-based method of secondary ion mass spectrometry (SIMS), in-source fragmentation can be significant and molecule specific due to the hard ionization method of using a primary ion beam for molecule desorption. To investigate the role of the substrate on orientation and in-source fragmentation, we have used atomistic simulations—molecular dynamics in combination with density functional theory calculations—to explore the desorption of a sphingolipid (palmitoylsphingomyelin) from a model surface (gold). We then compare SIMS data from this model system to our modeling findings. Using this approach, we found that the combined adsorption and binding energy of certain bonds associated with the headgroup fragments (C3H8N+, C5H12N+, C5H14NO+, and C5H15PNO4+) was a good predictor for fragment intensities (as indicated by relative ion yields). This is the first example where atomistic simulations have been applied in beam-based ionization of lipids, and it presents a new approach to study biointerfacial lipid ordering effects on SIMS imaging.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Collins-type fragmentation energy correlator in semi-inclusive deep inelastic lepton-hadron scattering

We initiate a systematic study of fragmentation energy correlators (FECs), which generalize traditional fragmentation functions and encode non-perturbative information about transverse dynamics in parton fragmentation processes. We define boost-invariant, non-perturbative FECs and derive a corresponding collinear factorization formula. A spin decomposition of the FECs is carried out, analogous to that of transverse-momentum-dependent fragmentation functions. In this work we focus particularly on the Collins-type quark FEC, which is sensitive to chiral symmetry breaking and characterizes the azimuthal asymmetry in the fragmentation of a transversely polarized quark. We perform a next-to-leading-order calculation of the corresponding hard coefficient in semi-inclusive deep-inelastic scattering for the quark non-singlet component, thereby validating the consistency of our theoretical framework.

Deep Inelastic Scattering or Small-x Physics↗
DOE OSTI2026

Effect of spacer grids on high-burnup fuel fragmentation, relocation, and dispersal

Increasing the fuel burnup limit in light-water reactors to improve fuel cycle economics requires a strong technical foundation. Experimental observations from the Halden and Studsvik programs have revealed severe fuel fragmentation during loss-of-coolant accident (LOCA) conditions, highlighting the need for additional technical evaluation. Consequently, further LOCA test data are needed to complement existing findings and improve the understanding of fuel fragmentation, relocation, and dispersal (FFRD) behavior. Oak Ridge National Laboratory’s Severe Accident Test Station has played a significant role in advancing the understanding of high-burnup fuel fragmentation, relocation, and dispersal phenomena. One remaining gap in the available experimental database is the effect of fuel assembly structural features on cladding deformation behavior during a LOCA, and more specifically, their impact on the fuel’s ability to fragment, relocate, and disperse. Recent analyses using the BISON fuel performance code suggest that cladding deformation near grid spacers will remain below the 3% threshold that has been reported in the NRC Research Information Letter, indicating that the cladding could remain mechanically constrained during the LOCA event. This paper builds upon the BISON analyses to design and conduct a series of out-of-cell tests aimed at further evaluating cladding deformation in and around grid spacers. In addition, these tests were used to assess local cladding temperature conditions and compare them against analytical predictions in order to better replicate expected in-reactor behavior. Finally, an in-cell high-burnup LOCA test was designed and performed to evaluate the effects of a grid spacer, or cladding restraint, on fuel fragmentation, relocation, and dispersal susceptibility. The high-burnup test results differed from those of historical LOCA experiments, with a recorded rupture temperature of 861°C. Two ballooned regions and corresponding rupture openings were observed, with rupture widths of approximately 0.64 mm for both ruptures and rupture lengths of 4.8 mm and 5.6 mm, respectively.

Capps, Nathan [ORNL]↗
DOE OSTI2024

State Preparation in Quantum Algorithms for Fragment-Based Quantum Chemistry

State preparation for quantum algorithms is crucial for achieving high accuracy in quantum chemistry and competing with classical algorithms. The localized active space–unitary coupled cluster (LAS–UCC) algorithm iteratively loads a fragment-based multireference wave function onto a quantum computer. Here, in this study, we compare two state preparation methods, quantum phase estimation (QPE) and direct initialization (DI), for each fragment. We test the two state preparation methods on three systems, ranging from a model system, a set of interacting hydrogen molecules, to more realistic chemical problems, like the C–C double bond breaking in transbutadiene and the spin ladder in a bimetallic system. We analyze the impact of QPE parameters, such as the number of ancilla qubits and Trotter steps, on the prepared state. We find a trade-off between the methods, where DI requires fewer resources for smaller fragments, while QPE is more efficient for larger fragments. Our resource estimates highlight the benefits of system fragmentation in state preparation for subsequent quantum chemical calculations. These findings have broad applications for preparing multireference quantum chemical wave functions on quantum circuits that can be used for realistic chemical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R cut . R cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

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

Convergent Protocols for Computing Protein–Ligand Interaction Energies Using Fragment-Based Quantum Chemistry

Fragment-based quantum chemistry methods offer a way to sidestep the steep nonlinear scaling of electronic structure calculations so that large molecular systems can be investigated using high-level methods. Here, we use fragmentation to compute protein–ligand interaction energies in systems with several thousand atoms, using a new software platform for managing fragment-based calculations that implements a screened many-body expansion. Convergence tests using a minimal-basis semiempirical method (HF-3c) indicate that two-body calculations, with single-residue fragments and simple hydrogen caps, are sufficient to reproduce interaction energies obtained using conventional supramolecular electronic structure calculations, to within 1 kcal/mol at about 1% of the computational cost. We also demonstrate that the HF-3c results are illustrative of trends obtained with density functional theory in basis sets up to augmented quadruple-ζ quality. Strategic deployment of fragmentation facilitates the use of converged biomolecular model systems alongside high-quality electronic structure methods and basis sets, bringing ab initio quantum chemistry to systems of hitherto unimaginable size. This will be useful for generation of high-quality training data for machine learning applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Identification of Unique Fragmentation Patterns of Fentanyl Analog Protomers Using Structures for Lossless Ion Manipulations Ion Mobility-Orbitrap Mass Spectrometry

The opioid crisis in the United States is being fueled by the rapid emergence of new fentanyl analogs and precursors that can elude traditional library-based screening methods, which require data from known reference compounds. Since reference compounds are unavailable for new fentanyl analogs, we examined if fentanyls (fentanyl + fentanyl analogs) could be identified in a reference-free manner using a combination of electrospray ionization (ESI), high-resolution ion mobility (IM) spectrometry, high-resolution mass spectrometry (MS), and higher-energy collision-induced dissociation (MS/MS). We analyzed a mixture containing nine fentanyls and W-15 (a structurally similar molecule) and found that the protonated forms of all fentanyls uniquely exhibited two baseline separated IM distributions that produced different MS/MS patterns. Upon fragmentation, both IM distributions of all fentanyls produced two high intensity fragments resulting from amine site cleavages. The higher mobility distributions of all fentanyls also produced several low intensity fragments, but surprisingly, these same fragments exhibited much greater intensities in the lower mobility distributions. This observation demonstrates that many fragments of fentanyls predominantly originate from one of two different gas-phase structures (suggestive of protomers). Furthermore, increasing the water concentration in the ESI solution increased the intensity of the lower mobility distribution relative to the higher mobility distribution, which further supports that fentanyls exist as two gas-phase protomers. In conclusion, our new observations on the IM and MS/MS properties of fentanyls can be exploited to positively identify them as fentanyls without requiring reference libraries and will hopefully assist first responders and law enforcement in combating new and emerging fentanyls.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Anisotropy in fission fragment and prompt neutron angular distributions

Several physics mechanisms can lead to the deviation from an isotropic angular distribution for both fission fragments and the neutrons that are emitted during the fission event. Two of these effects have recently been implemented into CGMF, the Monte Carlo fission event generator developed at Los Alamos National Laboratory: angular distribution sampling for fission fragments and pre-equilibrium neutrons (those emitted before the compound nucleus forms). Using these new developments, we show that the anisotropy of the neutrons reflects the anisotropy of the fission fragments, in particular as the outgoing energy of neutrons increases. Correlations between the fission fragment and neutron anisotropies could be used to extract the fission fragment anisotropy from the neutron angular distributions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Native frames: An approach for separating sequential and concerted three-body fragmentation

Disentangling sequential and concerted three-body fragmentation has been a longstanding endeavor in studies of molecular dynamics. To accomplish this goal, we recently introduced a novel method to separate sequential from concerted breakup, where the sequential events are analyzed in their native frames [J. Rajput et al., Phys. Rev. Lett. 120, 103001 (2018)]. The essence of this method is the use of the Jacobi coordinates' conjugate momenta to reduce the dimensionality of the multibody fragmentation in combination with a clear signature for sequential breakup. To demonstrate this method, we employ coincidence momentum imaging to study the strong-field dissociative ionization of OCS into O + +C + + S + , which typically undergoes concerted fragmentation or sequential breakup involving either a metastable CO 2+ or CS 2+ molecule. We identify sequential breakup using a uniform distribution as a function of the angle between the conjugate momenta, associated with the first and second fragmentation steps, which is due to the rotation of the intermediate molecule in the fragmentation plane. Furthermore, by exploiting this uniform distribution, we separate the sequential and concerted distributions in any plot created from the measured momenta.

Atomic & molecular processes in external fields↗
DOE OSTI2023

Effect of the Coulomb force on fission fragment angular momenta

Nuclear fission produces fragments endowed with typically half a dozen units of angular momentum. After scission has occurred, the fragments are still interacting via the Coulomb force which exerts a torque on deformed fragments, thereby accelerating their rotations. Here, the essential features of this effect can be understood by simple perturbative considerations from which the effect on the fragment spin distributions can be obtained. Complete dynamical calculations of the coupled evolution of the spins validate the perturbative treatment, which ignores the second-order terms, showing that the fragment spins evolve essentially independently in the presence of the Coulomb torques.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Generation of Fragment Angular Momentum in Fission

A recent analysis of experimental data [J. Wilson et al., Nature (London) 590, 566 (2021)] found that the angular momenta of nuclear fission fragments are uncorrelated. Based on this finding, the authors concluded that the spins are therefore determined only after scission has occurred. We show here that the nucleon-exchange mechanism, as implemented in the well-established event-by-event fission model freya, while agitating collective rotational modes in which the two spins are highly correlated, nevertheless leads to fragment spins that are largely uncorrelated. We find that this counterexample invalidates the conclusion in [J. Wilson et al.] that uncorrelated spins must necessarily have been generated after scission (a potentious conclusion that would rule out all models that generate the fragment spins prior to scission). Furthermore, it was reported [J. Wilson et al.] that the mass dependence of the average fragment spin has a sawtooth structure. We demonstrate that such a behavior naturally emerges when shell and deformation effects are included in the moments of inertia of the fragments at scission.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Fragmentation in Collisions of Snow with Graupel/Hail: New Formulation from Field Observations

Abstract Secondary ice production (SIP) has been attributed to the generation of most ice particles observed in precipitating clouds with cloud tops warmer than −36°C, from various aircraft- and ground-based field observations across the globe. One of the known SIP mechanisms is fragmentation during collisions among ice particles. It has been studied with our theoretical formulation, which has been applied in microphysical schemes of atmospheric models in a few studies. These have predicted an extensive impact on cloud glaciation and radiative properties. However, there has been a lack of experimental field studies, especially involving naturally falling snowflakes, to better understand this particular mechanism of SIP. This study reports the first field measurements with modern technology for fragmentation during collisions between naturally falling snowflakes and graupel/hail particles. This was observed with an innovatively designed portable chamber that was deployed outdoors in northern Sweden. Applying the observations from this field-based study, we optimized the existing formulation for predicting numbers of fragments from collisions of snow with graupel/hail. The observations show the average numbers of fragments per collision for dendritic (3–12 mm) and nondendritic (1–3 mm) snow were about 12 and 1, respectively. This represents a boost of predicted fragment numbers relative to our original formulation published in 2017. The updated formulation for breakup in ice–ice collisions can be implemented in the microphysical schemes of atmospheric models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Boson Fermion Nucleus Explanation for Fission Fragment Anisotropy: Monograph #13

Since 1952, anisotropy has been observed in the paths of fission fragments following the assimilation of an incident neutron or photon in the nucleus. Fission fragment flux favors certain angles relative to the path of the incident particle, constituting anisotropy. The amount of anisotropy is dependent on the energy of the incident particle. Fission fragment anisotropy can be explained by the disruption of nuclear structure combined with the requirement of a specific rotational orientation in theta and phi of that structure relative to the incident neutron or photon flux. A specific and limited area in the nucleus can assimilate the incident particle and induce upset within the structure, followed by scission and fission of the nucleus. The orientation and nature of the structure upset dictates fission fragment trajectory and is responsible for fission fragment anisotropy. This concept can be explained and supported by the theory of boson fermion nucleus (BFN) structure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗