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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Reaction Chemistry at Discrete Organometallic Fragments on Black Phosphorus

Abstract Black phosphorus (bP) is a two‐dimensional van der Waals material unique in its potential to serve as a support for single‐site catalysts due to its similarity to molecular phosphines, ligands quintessential in homogeneous catalysis. However, there is a scarcity of synthetic methods to install single metal centers on the bP lattice. Here, we demonstrate the functionalization of bP nanosheets with molecular Re and Mo complexes. A suite of characterization techniques, including infrared, X‐ray photoelectron and X‐ray absorption spectroscopy as well as scanning transmission electron microscopy corroborate that the functionalized nanosheets contain a high density of discrete metal centers directly bound to the bP surface. Moreover, the supported metal centers are chemically accessible and can undergo ligand exchange transformations without detaching from the surface. The steric and electronic properties of bP as a ligand are estimated with respect to molecular phosphines. Sterically, bP resembles tri(tolyl)phosphine when monodentate to a metal center, and bis(diphenylphosphino)propane when bidentate, whereas electronically bP is a σ‐donor as strong as a trialkyl phosphine. This work is foundational in elucidating the nature of black phosphorus as a ligand and underscores the viability of using bP as a basis for single‐site catalysts.

Chemistry↗
DOE OSTI2021

Prospects for Surrogate Neutron Capture Measurements with Radioactive Ion Beams and GODDESS

Neutron capture reactions are responsible for the synthesis of almost all of the elements heavier than iron through the slow s-process, that proceeds close to the line of stability, and the rapid r-process, with very neutron-rich waiting points. Uncertainties in (n,γ) rates in neutron rich nuclei, especially near closed neu- tron shells, can have significant impact [1] on the predictions of final abundances for different astrophysical scenarios for the r process. Understanding (n,γ) rates on neutron-rich fission fragments is also important for nuclear forensics and stockpile stewardship science. Ratkiewicz et al. [2 and references therein] has recently demonstrated that the (d,pγ) reaction is a valid surrogate for (n,γ), where the formation of the compound nucleus from the breakup of the deuteron has been calculated in a reaction model and the subsequent measured gamma-decay probabilities are reproduced with standard level density and strength functions in a Bayesian approach. In parallel to the surrogate validation efforts, we have demonstrated that the (d,pγ) reaction can be measured in inverse kinematics with Gammasphere ORRUBA: Dual Detectors for Experimental Structure Studies (GODDESS) [3] where the Gammasphere array of Compton-suppressed HPGe detectors is coupled to the Oak Ridge Rutgers University Barrel Array of position-sensitive silicon strip detectors. During the commissioning campaign we measured the (d,pγ) reaction with 134 Xe and 95 Mo beams, the latter to demonstrate the surrogate method in inverse kinematics. The present talk will present preliminary results from this campaign including γ-decay probabilities and prospects for surrogate (n,γ) measurements with 143 Ba fission-fragment beams.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Bottom-Up Simulation, Reconstruction, and Quantification of Macromolecule Sequences from Experimental Polymerizations

Motivated by the canonical sequence–structure–function paradigm, tools to characterize chemical patterning in natural biomacromolecules, from proteins to nucleic acids, have grown exponentially in recent years. However, analogous strategies for synthetic macromolecules remain in nascent stages, complicated by sequence polydispersity and analytical limitations. To address this, we have developed a comprehensive and open-source Python package, PRISM (polymer rate insights and sequence modeling), an end-to-end workflow that provides a path from experimental kinetics measurements to quantitative and qualitative metrics for describing chemical patterning in stochastic polymers. First, a numerical integration strategy was constructed to simulate and fit experimental data from reversible addition–fragmentation chain transfer (RAFT) polymerization kinetics, enabling the facile estimation of relevant reactivity ratios. These ratios were then used in a mechanism-specific stochastic kinetic simulation strategy to simulate sequence ensembles corresponding to model systems spanning experimental copolymers, classes of statistical polymers (e.g., alternating, block, and gradient), and multiblock copolymers. Lastly, inspired by sequence homology metrics from bioinformatics, we introduce visualization strategies and quantitative metrics to facilitate comparisons of different sequence ensembles. As the sequence–structure–function paradigm becomes increasingly central in de novo design of synthetic macromolecules, this toolkit provides a first step toward accurate and representative sequence description and featurization.

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

Engineering a tumor-selective prodrug T-cell engager bispecific antibody for safer immunotherapy

T-cell engaging (TCE) bispecific antibodies are potent drugs that trigger the immune system to eliminate cancer cells, but administration can be accompanied by toxic side effects that limit dosing. TCEs function by binding to cell surface receptors on T cells, frequently CD3, with one arm of the bispecific antibody while the other arm binds to cell surface antigens on cancer cells. On-target, off-tumor toxicity can arise when the target antigen is also present on healthy cells. The toxicity of TCEs may be ameliorated through the use of pro-drug forms of the TCE, which are not fully functional until recruited to the tumor microenvironment. This can be accomplished by masking the anti-CD3 arm of the TCE with an autoinhibitory motif that is released by tumor-enriched proteases. Here, we solve the crystal structure of the antigen-binding fragment of a novel anti-CD3 antibody, E10, in complex with its epitope from CD3 and use this information to engineer a masked form of the antibody that can activate by the tumor-enriched protease matrix metalloproteinase 2 (MMP-2). We demonstrate with binding experiments and in vitro T-cell activation and killing assays that our designed prodrug TCE is capable of tumor-selective T-cell activity that is dependent upon MMP-2. Furthermore, we demonstrate that a similar masking strategy can be used to create a pro-drug form of the frequently used anti-CD3 antibody SP34. This study showcases an approach to developing immune-modulating therapeutics that prioritizes safety and has the potential to advance cancer immunotherapy treatment strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Shape evolution in neutron-rich odd-even 105–109 Nb isotopes

Background: Neutron-rich nuclei around 𝑍 ≈ 40 are well known for exhibiting multiple shape transitions. Here, this region shows one of the sharpest shape transitions in the nuclear chart, evolving from a spherical vibrator at 𝑁 = 58 to a strongly deformed prolate shape at 𝑁 = 60. The largest deformations are observed for 38 Sr and 40 Zr . This abrupt shape transition disappears at 𝑍 = 36 and below, where a shape transition from spherical to oblate nuclei is predicted. On the other hand, for 𝑍 ≥ 42 and 𝑁 ≥ 60, the shape is known to evolve from axial to triaxial. While the even-𝑍 nuclei in this region have already been extensively studied, new insights can be gained from the studies of odd-𝑍 isotopes for a better understanding of the underlying mechanisms driving these phenomena. Purpose: The 41 Nb nuclei lie at the boundary between axially deformed Zr and triaxially deformed Mo nuclei. This work investigates the nuclear structure of very neutron-rich Nb nuclei up to 𝑁 = 68. The goal is to understand how the nuclear shape evolves as a function of isospin in this isotopic chain and provide new insights into the emergence of triaxial deformation. Methods: The structure of the neutron-rich Nb isotopes was investigated using state-of-the-art high-resolution 𝛾-ray spectroscopy of fission fragments produced via two different fission reactions. The use of 9 Be ⁢( 238 U, 𝑓) inverse kinematics, with a detection system comprising AGATA, EXOGAM, and VAMOS++, enabled the measurement of prompt and delayed 𝛾 rays from isotopically identified fission fragments, and 𝛾−𝛾−𝛾−𝛾 highfold data were obtained from a spontaneous fission source of 252 Cf using the Gammasphere array. Results: The level scheme of 105 Nb has been significantly extended, with the addition of two negative-parity bands observed for the first time. A new level scheme is proposed for 107 Nb, which is not in agreement with an earlier measurement, and new levels and transitions have been added to the very neutron-rich 109 Nb. The degree of triaxiality of the new bands is discussed on the basis of signature splitting analysis. The recently reported level scheme of 99 Nb has been revised. Conclusions: This systematic study on the Nb isotopic chain, compared to Zr and Mo, indicates that while the ground-state band exhibits a triaxial deformation, attributed to a proton hole coupled to a triaxially deformed Mo core, the negative-parity bands, based on isomeric bandheads, display an axially symmetric deformed structure, similar to that observed in the Zr isotopes, revealing the existence of a shape coexistence in the neutron-rich Nb nuclei.

Abushawish, M. [Université Claude-Bernard Lyon 1 (↗
DOE OSTI2025

THE STRUCTURE FUNCTION OF THE FREE NEUTRON AT HIGH X-BJORKEN

Understanding the internal structure of nucleons is one of the primary goal of nuclear physicists. As protons and neutrons are only the bound state solution of the QCD lagrangian (at least inside atomic nuclei), studying protons and neutrons helps uncover nuclear struc ture. Due to its easy availability, many studies on protons have been done on a wide range of kinematics. However, free neutron targets are not readily achievable. So, any information on neutrons has to be extracted from neutron-rich nuclei, and some nuclear models have to be used to subtract the contributions from other nucleons to extract the information on neutrons. So, the Barely Off-shell Nucleon Structure (BONuS12) experiment at Jefferson Lab was conducted to overcome these challenges by using spectator tagging. The experiment effectively created a quasi-free neutron target by scattering electrons off a deuterium target and detecting low-momentum, backward-moving protons using a custom-built Radial Time Projection Chamber (RTPC). Selecting the low momentum and backward-moving spectators would enable us to minimize the model-dependent effects due to final state interactions and target fragmentation. The RTPC was a 40 cm-long cylindrical detector that works on the principle of gaseous ionization. It had three layers of Gas Electron Multipliers (GEMs) for charge amplification and a surrounding readout pad. The scattered electrons were measured using the CLAS12 detector, and data were collected using a 10.4 GeV electron beam dur ing Spring and Summer 2020. Using spectator tagging, we extracted the structure function ratio Fn 2 of the quasi-free neutron in the deep inelastic scattering at high x, upto x ~ 0.8. The result was extracted in the region with the invariant mass W > 1.8 GeV/c2, and Q2 in the range 1.3 to 11 GeV2. This dissertation presents the methodology, event selection criteria and refinements, estimation and subtraction of backgrounds, and complete analysis of extraction of Fn 2/Fp 2 in a model-independent way. Also, systematic uncertainties in our final analysis will be discussed in detail.

Pokhrel, Madhusudhan [Old Dominion Univ., Norfolk,↗
DOE OSTI2022

Forces from Stochastic Density Functional Theory under Nonorthogonal Atom-Centered Basis Sets

We develop a formalism for calculating forces on the nuclei within the linear-scaling stochastic density functional theory (sDFT) in a nonorthogonal atom-centered basis set representation (Fabian et al. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2019, 9, e1412, 10.1002/wcms.1412) and apply it to the Tryptophan Zipper 2 (Trp-zip2) peptide solvated in water. We use an embedded-fragment approach to reduce the statistical errors (fluctuation and systematic bias), where the entire peptide is the main fragment and the remaining 425 water molecules are grouped into small fragments. We analyze the magnitude of the statistical errors in the forces and find that the systematic bias is of the order of 0.065 eV/Å (~1.2 × 10 -3 E h / a 0 ) when 120 stochastic orbitals are used, independently of system size. This magnitude of bias is sufficiently small to ensure that the bond lengths estimated by stochastic DFT (within a Langevin molecular dynamics simulation) will deviate by less than 1% from those predicted by a deterministic calculation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3

Abstract Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic and diseases caused by other coronaviruses.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Longitudinal double helicity asymmetry $A_{LL}$ from direct photon, jet and charged pion production in polarized $\vec{p}+\vec{p}$ collisions

Understanding the proton spin composition from the quarks and gluons spin polarization and their motion is important to test various kinds of sum rules and nonperturbative properties of hadrons. At the Relativistic Heavy Ion Collider (RHIC), we collide longitudinally polarized proton beams and measure the double helicity asymmetry A_{LL} A L L , which is an important physical quantity for extracting the polarized parton distribution functions (PDFs) of the proton. Direct photon, jet and charged pion production are good channels to probe the gluon spin polarization inside the proton, with the ability to probe also the sign of the gluon spin. Direct photon production is the theoretically ``cleanest’’ channel, with little fragmentation contribution, but limited by statistics. On the other hand, jet and charged pion production have more statistics, but include more hard processes and hadronization effects. I will present the recent measurements of direct photon, jet and charged pion A_{LL} A L L s at PHENIX and show their complementary roles in extracting the gluon spin.

Ji, Zhongling↗
DOE OSTI2020

Analysis and visualization of energy densities. I. Insights from real-time time-dependent density functional theory simulations

In this article, we report a scheme to analyze and visualize the energy density fluctuations during the real-time time-dependent density functional theory (RT-TDDFT) simulations. Using Ag 4 –N 2 complexes as examples, here we show that the grid-based Kohn–Sham energy density can be computed at each time step using a procedure from Nakai and coworkers. Then the instantaneous energy of each molecular fragment (such as Ag 4 and N 2 ) can be obtained by partitioning the Kohn–Sham energy densities using Becke or fragment-based Hirshfeld (FBH) scheme. A strong orientation-dependence is observed for the energy flow between the Ag 4 cluster and a nearby N 2 molecule in the RT-TDDFT simulations. Future applications of such an energy density analysis in electron dynamics simulations are discussed.

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

Topological alloy engineering and locally linearized gap dependence on concentration

Alloy engineering is a well-established approach to tune various materials’ properties, but its application to topological alloys remains rudimentary. Of special interest is the band gap, the most defining property of topological materials; however, the concentration dependence of energy gaps in topological alloys remains unknown. Here we systematically investigate the band gap evolution of a topological alloy as a function of alloy concentration, using KZnSb 1-x Bi x as a prototype, based on first-principles calculations. In contrast to the well-established smooth bowing curve for a trivial gap in semiconductor alloys, we found that the topological gap evolves generally with a complex fragmented pattern due to topological phase transitions, and most strikingly a linear dependence on concentration locally in each distinct phase. Such gap linearization is fundamentally rooted in the linear dependence on alloy concentration of spin-orbit coupling (SOC) that predominantly determines a topological gap. Furthermore, we demonstrate topological alloy engineering as a general approach to tune the topological order by modulating the band edge composition and degeneracy through the alloying-induced interplay of SOC and atomic orbital on-site energy, while the linear gap dependence on alloy concentration remains independent of the degree of topological order.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions

While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present a robust Goldilocks (GL) computational discovery protocol to efficiently innovate inhibitor tools and preclinical drug candidates for cellular and structural biologists without requiring extensive virtual screen (VS) and chemical synthesis expertise. By computationally targeting DDR replication and repair proteins, we exemplify the identification of DDR target sites and compounds to probe cancer biology. Our GL pipeline integrates experimental and predicted structures to efficiently discover leads, allowing early-structure and early-testing (ESET) experiments by many laboratories. By employing an efficient VS protocol to examine protein-protein interfaces (PPIs) and allosteric interactions, we identify ligand binding sites beyond active sites, leveraging in silico advances for molecular docking and modeling to screen PPIs and multiple targets. A diverse 3,174 compound ESET library combines Diamond Light Source DSI-poised, Protein Data Bank fragments, and FDA-approved drugs to span relevant chemotypes and facilitate downstream hit evaluation efficiency for academic laboratories. Two VS per library and multiple ranked ligand binding poses enable target testing for several DDR targets. This GL library and protocol can thus strategically probe multiple DDR network targets and identify readily available compounds for early structural and activity testing to overcome bottlenecks that can limit timely breakthrough drug discoveries. By testing accessible compounds to dissect multi-functional DDRs and suggesting inhibitor mechanisms from initial docking, the GL approach may enable more groups to help accelerate discovery, suggest new sites and compounds for challenging targets including emerging biothreats and advance cancer biology for future precision medicine clinical trials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Jet modification via 𝜋 0 -hadron correlations in Au + Au collisions at $\sqrt{s_{NN}}$ = 200 GeV

High-momentum two-particle correlations are a useful tool for studying jet-quenching effects in the quark-gluon plasma. Angular correlations between neutral-pion triggers and charged hadrons with transverse momenta in the range 4–12 GeV/𝑐 and 0.5–7 GeV/𝑐, respectively, have been measured by the PHENIX experiment in 2014 for Au + Au collisions at $\sqrt{s_{NN}}$ = 200 GeV. Suppression is observed in the yield of high-momentum jet fragments opposite the trigger particle, which indicates jet suppression stemming from in-medium partonic energy loss, while enhancement is observed for low-momentum particles. The ratio and differences between the yield in Au + Au collisions and 𝑝 + 𝑝 collisions, 𝐼 𝐴⁢𝐴 and Δ 𝐴⁢𝐴 , as a function of the trigger-hadron azimuthal separation, Δ⁢𝜙, are measured for the first time at the BNL Relativistic Heavy Ion Collider. Finally, these results better quantify how the yield of low-𝑝 𝑇 associated hadrons is enhanced at wide angle, which is crucial for studying energy loss as well as medium-response effects.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

A deformation-dependent coupled Lagrangian/semi-Lagrangian meshfree hydromechanical formulation for landslide modeling

Abstract The numerical modelling of natural disasters such as landslides presents several challenges for conventional mesh-based methods such as the finite element method (FEM) due to the presence of numerically challenging phenomena such as severe material deformation and fragmentation. In contrast, meshfree methods such as the reproducing kernel particle method (RKPM) possess unique features conducive to modelling extreme events such as the absence of a structured mesh and the ease of adaptive refinement, among others. While the semi-Lagrangian reproducing kernel (SL-RK) shape functions of RKPM defined in the current configuration have proven to be effective in extreme event modelling, the computational cost for the re-evaluation of the shape functions at every time step is costly. In this work, a deformation-dependent coupling of the Lagrangian reproducing kernel (L-RK) and SL-RK approximations is proposed for the solution of a hydro-mechanical formulation for effective simulations of landslides. The ramp function is constructed based on an equivalent plastic strain as a deformation-dependent transition from L-RK shape functions to SL-RK ones as the deformation progresses. The particular focus of the paper will be on modelling seepage-induced landslides with a mixed $$u$$ u – $$p$$ p formulation to couple the solid and fluid phases. Examples are presented to examine the effectiveness of this coupled Lagrangian/semi-Lagrangian reproducing kernel (L–SL RK) formulation and to highlight its performance in landslide modelling.

Baek, Jonghyuk↗
DOE OSTI2022

Constructing a multi-functional polymer network for ultra-stable and safe Li-metal batteries

We report the practical application of lithium (Li) metal electrodes is impeded by Li dendrite growth and unstable solid electrolyte interphase (SEI). Herein, a multi-grafting polymer network, poly(dimethyl siloxane)-g-[poly(poly(ethylene glycol) methyl ether methacrylate)-r-sodium poly(p-styrene sulfonate)] (PPS), is chemically synthesized from reversible addition-fragmentation chain transfer (RAFT) polymerization. With integrated stretchability, ionic conductivity, and mechanical robustness, it serves a dual role to stabilize the Li electrode. As artificial SEI layer, the PPS enables superior electrochemical performance in half cells, symmetric cells, and full cells (PPS@Li/LiFePO 4 , capacity retention of >70% after 600 cycles). Utilized as solid polymer electrolyte (SPE), the all-solid-state Li/SPE/LiFePO 4 full cell delivers excellent cycling performance with an unprecedented capacity retention of 90% over 1,700 cycles at 0.5 C and 81% over 1,000 cycles at 1.0 C. With high-voltage LiNi 0.8 Mn 0.1 Co 0.1 O 2 (NMC811) as cathode, the Li/SPE/NMC811 cell exhibits an initial discharge capacity of 162.2 mAh g -1 with a capacity retention of 72% after 200 cycles. The assembled solid-state Li/SPE/LiFePO4 pouch cell with SPE exhibits stable cycling performance over 200 cycles with a capacity retention of 75% and still operates well even after curling, folding, and cutting, demonstrating great potential for achieving ultra-safe and high energy density batteries.

25 ENERGY STORAGE↗
DOE OSTI2026

Resolving Competing Ultraviolet Photoinduced Ring-Opening and Dissociation Pathways in Iodothiophenes by Ultrafast Electron Diffraction

The ultraviolet photochemistry of halothiophenes is thought to proceed via competing pathways, prompt C–X (X = halogen) bond fission, and parent ring opening followed by fragmentation, yet direct structural evidence distinguishing these mechanisms is limited. Here, time-resolved gas-phase ultrafast electron diffraction (UED) has been used to directly follow the structural dynamics of 2- and 3-iodothiophene following photoexcitation at 247 nm. For both isomers, the time-resolved pair distribution functions reveal the appearance of new interatomic distances that cannot be explained by simple C–I bond cleavage and formation of C 4 SH 3 radical cofragments. The signatures, particularly those for 2-iodothiophene, are consistent with a rival ring-opening channel of the intact parent, which evolve on time scales distinct from those associated with the direct C–I bond cleavage. In addition, the extracted kinetics indicate that the ring-opening channel occurs faster in 2-iodothiophene than in the 3-isomer at this excitation wavelength. Furthermore, these measurements provide direct geometric evidence for competing pathways leading to different structures following photodissociation in a model heteroaromatic and further establish UED as a sensitive probe of complex excited-state chemistry.

Bond cleavage↗
DOE OSTI2023

LISE$^{++}_{cute}$, the latest generation of the LISE ++ package, to simulate rare isotope production with fragment-separators

The LISE ++ software for fragment separator simulations has undergone a major update. The package, widely used at rare isotope beam facilities, can be used to predict intensities and purities of rare isotope beams and for planning and running of experiments using in-flight separators. It is especially useful for radioactive beam production as its results can be quickly compared to on-line data. The LISE ++ package has been ported to the Qt-framework in order to support modern compilers and computing methods. The benefits include 64-bit operation and LISE ++ availability on three different platforms: Windows, MacOS and Linux. In addition, the porting provides the ability to take advantage of future computational improvements. The updated package is named LISE$^{++}_{cute}$ to indicate a major step forward from the previous Borland-based versions. In addition to porting to the new platform, new main features and modifications have been added, mostly devoted to improving models and implementing other codes involved in rare isotope production at FRIB. Finally, a summary of modifications completed to improve the functionality of the code are discussed in this work, as well as future plans.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

ChemEcho v1.0

ChemEcho is a tool that converts tandem mass spectra into embeddings used to build machine learning (ML) models with fully explainable predictions. It provides an API for transforming raw tandem mass spectral data into embeddings, along with functions for training and validating ML models. Additionally, it includes utilities for retrieving and cleaning training data. ChemEcho is broadly applicable in ML pipelines that use tandem mass spectra for a variety of tasks, such as chemical classification or bioactivity mining. While there are existing methods to generate embeddings from fragmentation data, ChemEcho's approach ensures that predictions remain interpretable, enabling experts to evaluate results and generate hypotheses about the underlying data.

Harwood, Thomas [Lawrence Berkeley National Labora↗