136 research outputs found

    SE(3)-Invariant Multiparameter Persistent Homology for Chiral-Sensitive Molecular Property Prediction

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    In this study, we present a novel computational method for generating molecular fingerprints using multiparameter persistent homology (MPPH). This technique holds considerable significance for drug discovery and materials science, where precise molecular property prediction is vital. By integrating SE(3)-invariance with Vietoris-Rips persistent homology, we effectively capture the three-dimensional representations of molecular chirality. This non-superimposable mirror image property directly influences the molecular interactions, serving as an essential factor in molecular property prediction. We explore the underlying topologies and patterns in molecular structures by applying Vietoris-Rips persistent homology across varying scales and parameters such as atomic weight, partial charge, bond type, and chirality. Our method's efficacy can be improved by incorporating additional parameters such as aromaticity, orbital hybridization, bond polarity, conjugated systems, as well as bond and torsion angles. Additionally, we leverage Stochastic Gradient Langevin Boosting in a Bayesian ensemble of GBDTs to obtain aleatoric and epistemic uncertainty estimates for gradient boosting models. With these uncertainty estimates, we prioritize high-uncertainty samples for active learning and model fine-tuning, benefiting scenarios where data labeling is costly or time consuming. Compared to conventional GNNs which usually suffer from oversmoothing and oversquashing, MPPH provides a more comprehensive and interpretable characterization of molecular data topology. We substantiate our approach with theoretical stability guarantees and demonstrate its superior performance over existing state-of-the-art methods in predicting molecular properties through extensive evaluations on the MoleculeNet benchmark datasets.Comment: NeurIPS 2023 AI for Science Worksho

    Current status of MCNP6 as a simulation tool useful for space and accelerator applications

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    For the past several years, a major effort has been undertaken at Los Alamos National Laboratory (LANL) to develop the transport code MCNP6, the latest LANL Monte-Carlo transport code representing a merger and improvement of MCNP5 and MCNPX. We emphasize a description of the latest developments of MCNP6 at higher energies to improve its reliability in calculating rare-isotope production, high-energy cumulative particle production, and a gamut of reactions important for space-radiation shielding, cosmic-ray propagation, and accelerator applications. We present several examples of validation and verification of MCNP6 compared to a wide variety of intermediate- and high-energy experimental data on reactions induced by photons, mesons, nucleons, and nuclei at energies from tens of MeV to about 1 TeV/nucleon, and compare to results from other modern simulation tools.Comment: 4 pages, 3 figures, Proc. 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP 2012), St. Petersburg, FL, May 28 - June 3, 201

    Getting to Know FRED: Introducing Workflows for Born-Digital Content

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    Presentation from the MARAC conference in Roanoke, VA on October 7–10, 2015. S6 - Digital Archives: New Colleagues, New Solutions

    Merging the CEM2k and LAQGSM Codes with GEMINI

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    An improved version of the Cascade-Exciton Model (CEM) of nuclear reactions contained in the code CEM2k and the Los Alamos version of the Quark-Gluon String Model (LAQGSM) are merged with the well-known sequential-binary-decay model GEMINI by Charity. We present some results on proton-induced fragmentation, fission-product yields and on particle spectra predicted by these extended versions of CEM2k and LAQGSM. We show that merging CEM2k and LAQGSM with GEMINI allows us to describe many fission and fragmentation reactions in addition to the spallation and evaporation reactions which are already described well by these codes. Nevertheless, the current version of GEMINI we use does not provide a completely satisfactory description of some complex-particle spectra, fragment emission, and spallation yields for some reactions, and is not yet a universal tool for applications. Our results show that GEMINI contains a powerful model to describe evaporation/fission/fragmentation reactions and often provides better results when compared to other models, especially for emission of heavy fragments from reactions on medium-heavy nuclei (where most other models simply fail), but it must be further extended and improved in order to properly describe arbitrary reactions.Comment: Revised version of an ND2004 contribution (2004, Santa Fe, USA): minor revision of the text, Fig. 5 revised, references updated. We thank Dr. Claude Volant for noticing that the stated values of the fission delay time used in GEMINI were in error for several reactions in the earlier version of this pape

    Improved Intranuclear Cascade Models for the Codes CEM2k and LAQGSM

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    An improved version of the Cascade-Exciton Model (CEM) of nuclear reactions implemented in the codes CEM2k and the Los Alamos version of the Quark-Gluon String Model (LAQGSM) has been developed recently at LANL to describe reactions induced by particles and nuclei at energies up to hundreds of GeV/nucleon for a number of applications. We present several improvements to the intranuclear cascade models used in CEM2k and LAQGSM developed recently to better describe the physics of nuclear reactions. First, we incorporate the photonuclear mode from CEM2k into LAQGSM to allow it to describe photonuclear reactions, not previously modeled there. Then, we develop new approximations to describe more accurately experimental elementary energy and angular distributions of secondary particles from hadron-hadron and photon-hadron interactions using available data and approximations published by other authors. Finally, to consider reactions involving very highly excited nuclei (E* > 2-3 MeV/A), we have incorporated into CEM2k and LAQGSM the Statistical Multifragmentation Model (SMM), as a possible reaction mechanism occurring after the preequilibrium stage. A number of other refinements to our codes developed recently are also listed.Comment: 5 pages, pdf, 6 figures, to be published in Proc. Int. Conf. on Nuclear Data for Science & Technology (ND2004), Santa Fe, USA, Sept. 26 - Oct. 1, 200
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