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At least 181 records · Page 10

Utilizing Machine Learning to Improve Neutralization Potency of an HIV-1 Antibody Targeting the gp41 N-Heptad Repeat

The N-heptad repeat (NHR) of the HIV-1 gp41 prehairpin intermediate (PHI) is an attractive potential vaccine target with high sequence conservation across diverse strains. However, despite the potency of NHR-targeting peptides and clinical efficacy of the NHR-targeting entry inhibitor enfuvirtide, no potently neutralizing NHR-directed monoclonal antibodies (mAbs) nor antisera have been identified or elicited to date. The lack of potent NHR-binding mAbs both dampens enthusiasm for vaccine development efforts at this target and presents a barrier to performing passive immunization experiments with NHR-targeting antibodies. To address this challenge, we previously developed an improved variant of the NHR-directed mAb D5, called D5_AR, which is capable of neutralizing diverse tier-2 viruses. Building on that work, here we present the 2.7Å-crystal structure of D5_AR bound to NHR mimetic peptide IQN17. We then utilize protein language models and supervised machine learning to generate small (n < 100) libraries of D5_AR variants that are subsequently screened for improved neutralization potency. We identify a variant with 5-fold improved neutralization potency, D5_FI, which is the most potent NHR-directed monoclonal antibody characterized to date and exhibits broad neutralization of tier-2 and −3 pseudoviruses as well as replicating R5 and X4 challenge strains. Additionally, our work highlights the ability of protein language models to efficiently identify improved mAb variants from relatively small libraries.

Biopolymers

Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder

Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we leverage a Variational Autoencoder to design novel mitochondrial targeting sequences. In silico analysis reveals that a high fraction of the generated peptides (90.14%) are functional and possess features important for mitochondrial targeting. We characterize artificial peptides in four eukaryotic organisms and, as a proof-of-concept, demonstrate their utility in increasing 3-hydroxypropionic acid titers through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Moreover, we employ latent space interpolation to shed light on the evolutionary origins of dual-targeting sequences. Overall, our work demonstrates the potential of generative artificial intelligence for both fundamental research and practical applications in mitochondrial biology.

59 BASIC BIOLOGICAL SCIENCES

Host cell and viral protease targets of human SERPINs identified by in silico docking

Serine protease inhibitors (SERPINs) are involved in various physiological processes and diseases, such as inflammation, cancer metastasis, and neurodegeneration. Their role in viral infections is poorly understood, as their expression patterns during infection and the range of proteases they target have yet to be fully characterized. Here, we show widespread expression of human SERPINs in response to respiratory virus infections, both in bronchioalveolar lavages from COVID-19 patients and in polarized human airway epithelial cultures. Using in silico docking of 10 SERPINs to 48 host proteases, we confirm known targets and predict new interactions. Protease activity assays validated selected interactions, confirming the newly predicted host targets for PAI-1 (SERPINE1) and PAI-2 (SERPINB2). PAI-1 inhibits cathepsin L, essential for SARS-CoV-2 maturation, and suppresses multi-cycle replication of both ancestral SARS-CoV-2 WA-1 and its variant Omicron BA.1. In addition, we identify PAI-2 as an antiviral SERPIN that reduces infectivity of human adenovirus 5 by directly inhibiting the adenoviral protease. Our study leverages in silico docking using full-length 3D protein structures to uncover new SERPIN targets, offering a range of candidate targets for therapeutic interventions.

59 BASIC BIOLOGICAL SCIENCES

Tritium targets for use in solenoidal spectrometers

Nucleon adding and removing reactions are an ideal probe to study the single-particle foundations of nuclear structure. For experiments far away from the valley of stability, one needs to use radioactive beams in inverse kinematics. To maintain excellent resolution, solenoidal spectrometers like HELIOS at Argonne National Laboratory (ANL), ISS at CERN or SOLARIS at the Facility for Rare Isotope Beams (FRIB) are used. Typically, deuterated plastic foils are the targets of choice. Depending on the energy deposited, these targets might degrade quickly in beam. The potential of using tritium-implanted targets in conjunction with the solenoidal spectrometers was realized for access to even more exotic nuclei with outstanding resolving power. While no tritiated polyethylene is commercially available at the moment, tritium-containing titanium targets have been produced in the past. Unfortunately the loading fraction of tritium for the latter was often very low and not reproducible. The progress in the production of tritium-containing targets is presented, including the characterization of the foils.

Müller-Gatermann, Claus

Assessment of dynamic-screw-pinch-driven, current-scaled MagLIF target implosion performance using 3D magnetohydrodynamic simulations

Analytic studies and two-dimensional “clean” radiation-magnetohydrodynamic (rad-MHD) simulations employing dynamical similarity driver-target scaling prescriptions [Ruiz et al., Phys. Plasmas 30, 032708 (2023)] suggest that Magnetized Liner Inertial Fusion (MagLIF) target implosions can scale to > 10 MJ DT fusion yields when peak drive current is increased beyond 60 MA. We present results from three-dimensional (3D) rad-MHD simulations of similarity-scaled MagLIF target implosions at peak drive currents ranging from 15 to 40 MA. Simulations in this study suggest that magneto-Rayleigh–Taylor instability (MRTI) growth and feedthrough to the fuel region are more severe at higher drive current scales, which reduces the fusion yield compared to prior analytic and 2D clean simulation predictions. In contrast to standard MagLIF, simulations of current-scaled MagLIF target implosions driven by a dynamic screw pinch (DSP) demonstrate reduced MRTI feedthrough and greater fuel magnetization, resulting in improved thermonuclear performance and enhanced performance scaling with peak drive current. DSP drive enables additional scaling of the liner mass to increase liner radius but maintain implosion time, resulting in higher implosion velocities at the expense of increased susceptibility to MRTI. We present a current- and mass-scaled simulated DSP-MagLIF target implosion at the ∼ 40 MA peak current level that produces ignition scale performance, demonstrating a burn-averaged Lawson ignition parameter above unity and DT fusion yield above 1 MJ.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Platform for Automated Anomaly Detection in the Mercury Process System at the Target System in the Spallation Neutron Source

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory accelerates proton beams, which are directed toward a mercury target to generate the world’s most intense neutron beams via spallation. The target system consists of several interconnected subsystems and accounts for a major share of the facility’s overall downtime. Early detection of anomalies in the target system response can thus provide the possibility of taking corrective actions to reduce downtime. Accelerator facilities have largely focused on the beam side for data-driven fault prognostics. On the target side, SNS relies on operational shift technicians (OSTs), who respond to alarms and manually flag anomalies onto the System Tracking and Reliability (STAR) platform. This paper presents one of the first studies of using machine learning (ML) to automate anomaly detection in the target system. The study focused on the mercury process system as the first use case and employed reconstruction-based anomaly detection on minutely sampled time series signals. The pipeline was integrated into the STAR platform to autonomously rank and flag anomalies every week. The STAR platform provides a user interface for the OSTs to evaluate the flagged anomalies, thereby incorporating human feedback.

Anomaly detection

Data for "Design of Diverse, Functional Mitochondrial Targeting Sequences Across Eukaryotic Organisms Using Variational Autoencoder"

Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we leverage a Variational Autoencoder to design novel mitochondrial targeting sequences. In silico analysis reveals that a high fraction of the generated peptides (90.14%) are functional and possess features important for mitochondrial targeting. We characterize artificial peptides in four eukaryotic organisms and, as a proof-of-concept, demonstrate their utility in increasing 3-hydroxypropionic acid titers through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Moreover, we employ latent space interpolation to shed light on the evolutionary origins of dual-targeting sequences. Overall, our work demonstrates the potential of generative artificial intelligence for both fundamental research and practical applications in mitochondrial biology.

AI/ML

Multiphysics Simulations of Thermal Shock Testing of Nanofibrous High Power Targets

Increase of primary beam power for neutrino beam-lines leads to a reduced lifespan for production targets. New concepts for robust targets are emerging from the field of High Power Targetry (HPT); one idea being investigated by the HPT R&D Group at Fermilab is an electrospun nanofiber target. As part of their evaluation, samples with different densities were sent to the HiRadMat facility at CERN for thermal shock tests. The samples with the higher density, irradiated under a high intensity beam pulse, exhibit major damage at the impact site whereas those with the lower density show no apparent damage. The exact cause of this failure was unclear at the time. In this paper, we present the results of multiphysics simulations of the thermal shock experienced by the nanofiber targets that suggest the failure originates from the reduced permeability of the high density sample to air flow. The air present in the porous target expands due to heating from the beam, but is unable to flow freely in the high density sample, resulting in a larger back pressure that blows apart the nanofiber mat. We close with a discussion on how to further validate this hypothesis.

43 PARTICLE ACCELERATORS

Bayesian optimization scheme for the design of a nanofibrous high power target

High Power Targetry (HPT) R&D is critical in the context of increasing beam intensity and energy for next generation accelerators. Many target concepts and novel materials are being developed and tested for their ability to withstand extreme beam environments; the HPT R&D Group at Fermilab is developing an electrospun nanofiber material for this purpose. The performance of these nanofiber targets is sensitive to their construction parameters, such as the packing density of the fibers. Lowering the density improves the survival of the target, but reduces the secondary particle yield. Optimizing the lifetime and production efficiency of the target poses an interesting design problem, and in this paper we study the applicability of Bayesian optimization to its solution. We first describe how to encode the nanofiber target design problem as the optimization of an objective function, and how to evaluate that function with computer simulations. We then explain the optimization loop setup. Thereafter, we present the optimal design parameters suggested by the algorithm, and close with discussions of limitations and future refinements.

43 PARTICLE ACCELERATORS

Novel Materials for Next-Generation Accelerator Target Facilities

As beam power continues to increase in next-generation accelerator facilities, high-power target systems face crucial challenges. Components like beam windows and particle-production targets must endure significantly higher levels of particle fluence. The primary beam’s energy deposition causes rapid heating (thermal shock) and induces microstructural changes (radiation damage) within the target material. These effects ultimately deteriorate the components’ properties and lifespan. With conventional materials already stretched to their limits, we are exploring novel materials including High-Entropy Alloys and Electro spun Nanofibers that offer a fresh approach to enhancing tolerance against thermal shock and radiation damage. Following an introduction to the challenges facing high-power target systems, we will give an overview of the promising advancements we have made so far in customizing the compositions and microstructures of these pioneering materials. Our focus is on optimizing their in-beam thermomechanical and physics performance. Additionally, we will outline our ongoing plans for in-beam irradiation experiments and advanced material characterizations. The primary goal of this research is to push the frontiers of target materials, thereby enabling future multi-MW facilities that will benefit various programs in high-energy physics and beyond.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Multiphysics Simulations of Thermal Shock Testing of Nanofibrous High Power Targets

Increase of primary beam power for neutrino beam-lines leads to a reduced lifespan for production targets. The field of High Power Targetry (HPT) is generating new concepts to meet the need for robust targets. One idea being investigated by the HPT Research and Development Group at Fermilab is an electrospun nanofiber target. As part of their evaluation, samples with different densities were sent to the HiRadMat facility at CERN for thermal shock tests. The samples with the higher density, irradiated under a high intensity beam pulse, exhibit major damages at the impact site whereas those with the lower density show no apparent damages. The exact cause of this failure was unclear at the time. In this paper, we present the results of multiphysics simulations of the thermal shock experienced by the nanofiber targets that suggest the failure originates from the reduced permeability of the high density sample to airflow. The air present in the porous target expands due to heating from the beam, but is unable to flow freely in the high density sample, resulting in a larger back pressure that blows apart the mat. We close with a discussion on how to further validate this hypothesis.

43 PARTICLE ACCELERATORS

Bayesian Optimization Scheme for the Design of a Nanofibrous High Power Target

High Power Targetry (HPT) R\&D is critical in the context of increasing beam intensity and energy for next generation accelerators. Many target concepts and novel materials are being developed and tested for their ability to withstand extreme beam environments; the HPT R\&D Group at Fermilab is developing an electrospun nanofiber material for this purpose. The performance of these nanofiber targets is sensitive to their construction parameters, such as the packing density of the fibers. Lowering the density improves the survival of the target, but reduces the secondary particle yield. Optimizing the lifetime and production efficiency of the target poses an interesting design problem, and in this paper we study the applicability of Bayesian optimization to its solution. We first describe how to encode the nanofiber target design problem as the optimization of an objective function, and how to evaluate that function with computer simulations. We then explain the optimization loop setup. Thereafter, we present the optimal design parameters suggested by the algorithm, and close with discussions of limitations and future refinements.

43 PARTICLE ACCELERATORS

Computational study of tungsten and depleted uranium photoneutron targets for a 20 MeV electron linear accelerator

Neutron production can be realized with a high energy electron linear accelerator by using Bremsstrahlung and photoneutron converters. In this study, Monte Carlo N-Particle Code (MCNP) was used to evaluate potential photonuclear target designs for a high energy electron linear accelerator for applications such as neutron radiography and neutron resonance spectroscopy. A computational model was developed to inform a target design that would yield a high number of neutrons. It consists of a 20 MeV electron beam incident on a Bremsstrahlung target and a photonuclear target to generate neutrons. This computational model showed that a thickness of 0.75 inches for both tungsten and depleted uranium yields the most neutrons from photoneutron reactions. Saturation in the total number of generated neutrons was observed at over 0.75-inch thickness for both evaluated materials. Depleted uranium yielded approximately twice the number of neutrons overall compared to tungsten. The highest neutron surface flux for Depleted Uranium was 1.06 × 10-4 neutrons/cm2/source electron, and for Tungsten it was 5.12 × 10-5 neutrons/cm2/source electron. The optimal target design for this study’s application would consist of a 0.75 inch-thick block of depleted uranium with the length, width, and/or diameter varying dependent on application.

43 PARTICLE ACCELERATORS

Focussing Protons from a Kilojoule Laser for Intense Beam Heating Using Proximal Target Structures

Proton beams driven by chirped pulse amplified lasers have multi-picosecond duration and can isochorically and volumetrically heat material samples, potentially providing an approach for creating samples of warm dense matter with conditions not present on Earth. Envisioned on a larger scale, they could heat fusion fuel to achieve ignition. We have shown in an experiment that a kilojoule-class, multi-picosecond short pulse laser is particularly effective for heating materials. The proton beam can be focussed via target design to achieve exceptionally high flux, important for the applications mentioned. The laser irradiated spherically curved diamond-like-carbon targets with intensity 4×10 18 W/cm 2 , producing proton beams with 3MeV slope temperature. A Cu witness foil was positioned behind the curved target, and the gap between was either empty or spanned with a structure. With a structured target, the total emission of Cu Kα fluorescence was increased 18 fold and the emission profile was consistent with a tightly focussed beam. Transverse proton radiography probed the target with ps order temporal and 10 μm spatial resolution, revealing the fast-acting focussing electric field. Complementary particle-in-cell simulations show how the structures funnel protons to the tight focus. The beam of protons and neutralizing electrons induce the bright Kα emission observed and heat the Cu to 100eV.

47 OTHER INSTRUMENTATION

Temperature of a tungsten spallation target

We discuss the heat load inside a neutron spallation target made of tungsten hit by an 800 MeV proton beam. This problem is important for the Neutron Target project, where a spallation target will be surrounded by an extended graphite or beryllium cube to create a neutron target. The idea of a free-neutron target enables the measurement of neutron-induced reactions in inverse kinematics. This idea is part of the LANSCE strategy to stay a worldwide leader for neutron-induced research.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

CRISPR/Cas9-Mediated Multi-Allelic Gene Targeting in Sugarcane Confers Herbicide Tolerance

Sugarcane is the source of 80% of the sugar and 26% of the bioethanol produced globally. However, its complex, highly polyploid genome (2n = 100 – 120) impedes crop improvement. Here, we report efficient and reproducible gene targeting (GT) in sugarcane, enabling precise co-editing of multiple alleles via template-mediated and homology-directed repair (HDR) of DNA double strand breaks induced by the programmable nuclease CRISPR/Cas9. The evaluation of 146 independently transformed plants from five independent experiments revealed a targeted nucleotide replacement that resulted in both targeted amino acid substitutions W574L and S653I in the acetolactate synthase (ALS) in 11 lines in addition to single, targeted amino acid substitutions W574L or S653I in 25 or 18 lines, respectively. Co-editing of up to three ALS copies/alleles that confer herbicide tolerance was confirmed by Sanger sequencing of cloned long polymerase chain reaction (PCR) amplicons. This work will enable crop improvement by conversion of inferior alleles to superior alleles through targeted nucleotide substitutions.

Altpeter, Fredy (ORCID:0000000208944976)

LHCspin: a Polarized Gas Target for LHC

The goal of the LHCspin project is to develop innovative solutions for measuring the 3D structure of nucleons in high-energy polarized fixed-target collisions at LHC, exploring new processes and exploiting new probes in a unique, previously unexplored, kinematic regime. A precise multi-dimensional description of the hadron structure has, in fact, the potential to deepen our understanding of the strong interactions and to provide a much more precise framework for measuring both Standard Model and Beyond Standard Model observables. This ambitious task poses its basis on the recent experience with the successful installation and operation of the SMOG2 unpolarized gas target in front of the LHCb spectrometer. Besides allowing for interesting physics studies ranging from astrophysics to heavy-ion physics, SMOG2 provides an ideal benchmark for studying beam-target dynamics at the LHC and demonstrates the feasibility of simultaneous operation with beam-beam collisions. With the installation of the proposed polarized target system, LHCb will become the first experiment to simultaneously collect data from unpolarized beam-beam collisions at $\sqrt{s}$=14 TeV and polarized and unpolarized beam-target collisions at $\sqrt{s_{NN}}\sim$100 GeV. LHCspin has the potential to open new frontiers in physics by exploiting the capabilities of the world's most powerful collider and one of the most advanced spectrometers. This document also highlights the need to perform an R&D campaign and the commissioning of the apparatus at the LHC Interaction Region 4 during the Run 4, before its final installation in LHCb. This opportunity could also allow to undertake preliminary physics measurements with unprecedented conditions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Penetration of electrons and associated bremsstrahlung through aluminum targets

This paper contains a brief description of Monte Carlo programs designed to calculate the transport of fast electrons and associated bremsstrahlung through extended media. Two applications are discussed: (1) transmission of electrons through plane-parallel targets, and (2) emergence of secondary bremsstrahlung from such targets. It is shown that the predicted results are in reasonably good agreement with recent experiments for electron beams with energies up to 8 MeV incident normally on aluminum targets. Extensive new calculated data for transmission and thick-target bremsstrahlung production are presented for aluminum targets exposed to an isotropic electron flux.

M. J. Berger