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At least 235 records · Page 13

Learning to simulate high energy particle collisions from unlabeled data

In many scientific fields which rely on statistical inference, simulations are often used to map from theoretical models to experimental data, allowing scientists to test model predictions against experimental results. Experimental data is often reconstructed from indirect measurements causing the aggregate transformation from theoretical models to experimental data to be poorly-described analytically. Instead, numerical simulations are used at great computational cost. We introduce Optimal-Transport-based Unfolding and Simulation (OTUS), a fast simulator based on unsupervised machine-learning that is capable of predicting experimental data from theoretical models. Without the aid of current simulation information, OTUS trains a probabilistic autoencoder to transform directly between theoretical models and experimental data. Identifying the probabilistic autoencoder’s latent space with the space of theoretical models causes the decoder network to become a fast, predictive simulator with the potential to replace current, computationally-costly simulators. Here, we provide proof-of-principle results on two particle physics examples, Z-boson and top-quark decays, but stress that OTUS can be widely applied to other fields.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Advanced genomics identifies growth effectors for proteotoxic ER stress recovery in Arabidopsis thaliana

Abstract Adverse environmental and pathophysiological situations can overwhelm the biosynthetic capacity of the endoplasmic reticulum (ER), igniting a potentially lethal condition known as ER stress. ER stress hampers growth and triggers a conserved cytoprotective signaling cascade, the unfolded protein response (UPR) for ER homeostasis. As ER stress subsides, growth is resumed. Despite the pivotal role of the UPR in growth restoration, the underlying mechanisms for growth resumption are yet unknown. To discover these, we undertook a genomics approach in the model plant species Arabidopsis thaliana and mined the gene reprogramming roles of the UPR modulators, basic leucine zipper28 (bZIP28) and bZIP60, in ER stress resolution. Through a network modeling and experimental validation, we identified key genes downstream of the UPR bZIP-transcription factors (bZIP-TFs), and demonstrated their functional roles. Our analyses have set up a critical pipeline for functional gene discovery in ER stress resolution with broad applicability across multicellular eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of an unusual SARS-CoV-2 main protease natural variant exhibiting resistance to nirmatrelvir and ensitrelvir

We investigate the effects of two naturally selected substitution and deletion (Δ) mutations, constituting part of the substrate binding subsites S2 and S4, on the structure, function, and inhibition of SARS CoV-2 main protease. Comparable to wild-type, MPro D48Y/ΔP168 undergoes N-terminal autoprocessing essential for stable dimer formation and mature-like catalytic activity. The structures are similar, but for an open active site conformation in MPro D48Y/ΔP168 and increased dynamics of the S2 helix, S5 loop, and the helical domain. Some dimer interface contacts exhibit shorter H bond distances corroborating the ~40-fold enhanced dimerization of the mutant although its thermal sensitivity to unfolding is 8 °C lower, relative to wild-type. ITC reveals a 3- and 5-fold decrease in binding affinity for nirmatrelvir and ensitrelvir, respectively, and similar GC373 affinity, to MPro D48Y/ΔP168 relative to wild-type. Structural differences in four inhibitor complexes of MPro D48Y/ΔP168 compared to wild-type are described. Consistent with enhanced dynamics, the S2 helix and S5 loop adopting a more open conformation appears to be a unique feature of MPro D48Y/ΔP168 both in the inhibitor-free and bound states. Our results suggest that mutational effects are compensated by changes in the conformational dynamics and thereby modulate N-terminal autoprocessing, K dimer , catalytic efficiency, and inhibitor binding.

60 APPLIED LIFE SCIENCES↗

Selective bond formation triggered by short optical pulses: quantum dynamics of a four-center ring closure

Here we report bond formation induced by an ultrashort UV pulse. The photochemical process is described by quantum dynamics as coherent electronic and nuclear motions during the ultrashort pulse induced ring closure of norbornadiene to quadricyclane. Norbornadiene consists of two ethylene moieties connected by a rigid (CH 2 ) 3 bridge. Upon photoexcitation, two new sigma bonds are formed, resulting in the closure of a four-atom ring. As a medium-sized polyatomic molecule, norbornadiene exhibits a high density of strongly coupled electronic states from about 6 eV above the ground state. We report on inducing the formation of the new bonds using a short femtosecond UV pulse to pump a non-equilibrium electronic density in the open form that evolves towards the closed ring form. As the coherent electronic-nuclear coupled dynamics unfold, the excited states change character through non-adiabatic interactions and become valence states for the two new C–C bonds of quadricyclane. Our three-dimensional fully quantum dynamical grid simulations during the first 200 fs show that short UV pulses of different polarization initiate markedly different initial non-equilibrium electronic densities that follow different dynamical paths to the S 0 /S 1 conical intersection. They lead to different initial relative yields of quadricyclane, thereby opening the way to controlling bond-making with attopulses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The rupture mechanism of rubredoxin is more complex than previously thought

The surprisingly low rupture force and remarkable mechanical anisotropy of rubredoxin have been known for several years. Exploiting the first combination of steered molecular dynamics and the quantum chemical Judgement of Energy DIstribution (JEDI) analysis, the common belief that hydrogen bonds between neighboring amino acid backbones and the sulfur atoms of the central FeS 4 unit in rubredoxin determine the low mechanical resistance of the protein is invalidated. The distribution of strain energy in the central part of rubredoxin is elucidated in real-time with unprecedented detail, giving important insights into the mechanical unfolding pathway of rubredoxin. While structural anisotropy as well as the contribution of angle bendings in the FeS 4 unit have a significant influence on the mechanical properties of rubredoxin, these factors are insufficient to explain the experimentally observed low rupture force. Instead, the rupture mechanism of rubredoxin is far more complex than previously thought and requires more than just a hydrogen bond network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Harnessing biomimetic cryptic bonds to form self-reinforcing gels

Cryptic sites, which lay hidden in folded biomolecules, become exposed by applied force and form new bonds that reinforce the biomaterial. While these binding interactions effectively inhibit mechanical deformation, there are few synthetic materials that harness mechano-responsive cryptic sites to forestall damage. Here, we develop a computational model to design polymer gels encompassing cryptic sites and a lower critical solution temperature (LCST). LCST gels swell with a decrease in temperature, thereby generating internal stresses within the sample. The gels also encompass loops held together by the cryptic sites, as well as dangling chains with chemically reactive ends. A decrease in temperature or an applied force causes the loops to unfold and expose the cryptic sites, which then bind to the dangling chains. We show that these binding interactions act as “struts” that reinforce the network, as indicated by a significant decrease in the volume of the gel (from 44% to 80%) and shifts in the volume phase transition temperature. Once the temperature is increased or the deformation is removed, the latter “cryptic bonds” are broken, allowing the loops to refold and the gel to return to its original state. These findings provide guidelines for designing polymer networks with reversible, mechano-responsive bonds, which allow gels to undergo a self-stiffening behavior in response to a temperature-induced internal stress or external force. When applied as a coating, these gels can prevent the underlying materials from undergoing damage and thus, extend the lifetime of the system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational design of thermoelectric alloys through optimization of transport and dopability

Alloying is a common technique to optimize the functional properties of materials for thermoelectrics, photovoltaics, energy storage etc. Designing thermoelectric (TE) alloys is especially challenging because it is a multi-property optimization problem, where the properties that contribute to high TE performance are interdependent. In this work, we develop a computational framework that combines first-principles calculations with alloy and point defect modeling to identify alloy compositions that optimize the electronic, thermal, and defect properties. We apply this framework to design n-type Ba 2(1–x) Sr 2x CdP 2 Zintl thermoelectric alloys. Our predictions of the crystallographic properties such as lattice parameters and site disorder are validated with experiments. To optimize the conduction band electronic structure, we perform band unfolding to sketch the effective band structures of alloys and find a range of compositions that facilitate band convergence and minimize alloy scattering of electrons. Here, we assess the n-type dopability of the alloys by extending the standard approach for computing point defect energetics in ordered structures. Through the application of this framework, we identify an optimal alloy composition range with the desired electronic and thermal transport properties, and n-type dopability. Such a computational framework can also be used to design alloys for other functional applications beyond TE.

36 MATERIALS SCIENCE↗

Revealing the effect of LiOH on forming a SEI using a Co magnetic “probe”

The solid-electrolyte-interphase (SEI) plays a critical role in lithium-ion batteries (LIBs) because of its important influence on electrochemical performance, such as cycle stability, coulombic efficiency, etc. Although LiOH has been recognized as a key component of the SEI, its influence on the SEI and electrochemical performance has not been well clarified due to the difficulty in precisely controlling the LiOH content and characterize the detailed interface reactions. Here, a gradual change of LiOH content is realized by different reduction schemes among Co(OH) 2 , CoOOH and CoO. With reduced Co nanoparticles as magnetic “probes”, SEI characterization is achieved by operando magnetometry. By combining comprehensive characterization and theoretical calculations, it is verified that LiOH leads to a composition transformation from lithium ethylene di-carbonate (LEDC) to lithium ethylene mono-carbonate (LEMC) in the SEI and ultimately results in capacity decay. This work unfolds the detailed SEI reaction scenario involving LiOH, provides new insights into the influence of SEI composition, and has value for the co-development between the electrode materials and electrolyte.

25 ENERGY STORAGE↗

Reconstruction framework advancements to support streaming for the ePIC detector at the EIC

The ePIC collaboration adopted the JANA2 framework to manage its reconstruction algorithms. This framework has since evolved substantially in response to ePIC’s needs. There have been three main design drivers: integrating cleanly with the Podio-based data models and other layers of the key4hep stack, enabling external configuration of existing components, and supporting timeframe splitting for streaming readout. The result is a unified component model featuring a new declarative interface for specifying inputs, outputs, parameters, services, and resources. This interface enables the user to instantiate, configure, and wire components via an external file. One critical new addition to the component model is a hierarchical decomposition of data boundaries into levels such as Run, Timeframe, PhysicsEvent, and Subevent. Two new component abstractions, Folder and Unfolder, are introduced in order to traverse this hierarchy, e.g. by splitting or merging. The pre-existing components can now operate at different event levels, and JANA2 will automatically construct the corresponding parallel processing topology. This means that a user may write an algorithm once, and configure it at runtime to operate on timeframes or on physics events. Overall, these changes mean that the user requires less knowledge about the framework internals, obtains greater flexibility with configuration, and gains the ability to reuse the existing abstractions in new streaming contexts.

Brei, Nathan [Thomas Jefferson National Accelerato↗

The MCNP ® 6 code: A decade of progress

After several years of effort involved in merging the Los Alamos National Laboratory MCNP5 and MCNPX codes, in 2013 the first production release of version 6 of the Monte Carlo N-Particle ® , or MCNP ® , code MCNP6.1 was distributed publicly. Since then, three significant releases have been issued: MCNP6.1.1beta in 2014, MCNP6.2 in 2018, and MCNP6.3 in 2023. While each release always contains new features, code enhancements, and bug fixes, each version has had a different primary focus, ranging from improved calculational efficiency to new powerful utilities and tools, to software modernization of the code base. With all that has been learned over the first decade of the MCNP6 code, continuous progress is being made toward a modernized, general-purpose Monte Carlo radiation transport code that remains a trusted resource for the global community of practitioners. This paper describes these first 10+ years of the MCNP6 code and its continually improving data libraries, and gives some insight into how the next decade is expected to unfold.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Solution characterization of the dynamic conjugative entry exclusion protein TraG

The R100 plasmid and the secretion system it encodes are representative of F-like conjugative type IV secretion systems for the transmission of mobile DNA elements in gram-negative bacteria, serving as a major contributor to the spread of antibiotic resistance in bacterial pathogens. The TraG protein of F-like systems consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain, denoted TraG*. TraG* is essential in preventing redundant DNA transfer through a process termed entry exclusion. In the donor cell, it interacts with TraN to facilitate mating pair stabilization; however, if a mating pore forms between bacteria with identical plasmids, TraG* interacts with its cognate TraS in the inner membrane of the recipient bacterium to prevent redundant donor–donor conjugation. Structural studies of TraG* from the R100 plasmid have revealed the presence of a dynamic region between the N- and C-terminal domains of TraG. Thermofluor, circular dichroism, collision-induced unfolding–mass spectrometry, and size exclusion chromatography linked to multiangle light scattering and small angle x-ray scattering experiments indicated an N-terminal truncation mutant displayed higher stability and less disordered content relative to full-length TraG*. The 45 N-terminal residues of TraG* are hypothesized to serve as part of a flexible linker between the two independently functioning domains.

59 BASIC BIOLOGICAL SCIENCES↗

Spectral sensor error analysis for measuring x-ray radiation drive using the DANTE diagnostic toward inertial confinement fusion experiments

DANTE is a diagnostic used to measure the x-radiation drive produced by heating a high-Z cavity (“hohlraum”) with high-powered laser beams. It records the spectrally and temporally resolved radiation flux at x-ray energies between 50 eV and 20 keV. Each sensor configuration on DANTE is composed of filters, mirrors, and x-ray diodes to define 18 different x-ray channels whose output is voltage as a function of time. The absolute flux is then determined from the photometric calibration of the sensor configuration and a spectral reconstructing algorithm. The reconstruction of the spectra vs time from the measured voltages and known response of each channel has presented challenges. Here we demonstrate a novel approach here for quantifying the error on the determined flux based on the channel sensor configuration and most commonly used reconstruction algorithm. In general, we find that the integrated spectral flux from a hohlraum can robustly be reconstructed (within ~14%) using a traditional unfold approach with as few as ten channels due to the underlying assumption of a largely Planckian spectral intensity distribution.

47 OTHER INSTRUMENTATION↗

Measurement of L-shell emission from mid-Z targets under non-LTE conditions using Transmission Grating Spectrometer and DANTE power diagnostics

In this work, we present the measurement of L-band emission from buried Sc/V targets in experiments performed at the OMEGA laser facility. The goal of these experiments was to study non-local thermodynamic equilibrium plasmas and benchmark atomic physics codes. The L-band emission was measured simultaneously by the time resolved DANTE power diagnostic and the recently fielded time integrated Soreq-Transmission Grating Spectrometer (TGS) diagnostic. The TGS measurement was used to support the spectral reconstruction process needed for the unfolding of the DANTE data. The Soreq-TGS diagnostic allows for broadband spectral measurement in the 120 eV–2000 eV spectral band, covering L- and M-shell emission of mid- and high-Z elements, with spectral resolution λ/Δλ = 8–30 and accuracy better than 25%. The Soreq-TGS diagnostic is compatible with ten-inch-manipulator platforms and can be used for a wide variety of high energy density physics, laboratory astrophysics, and inertial confinement fusion experiments.

Fraenkel, M. (ORCID:0000000291939544)↗

An accurate and efficient Ehrenfest dynamics approach for calculating linear and nonlinear electronic spectra

Linear and nonlinear electronic spectra provide an important tool to probe the absorption and transfer of electronic energy. Here, we introduce a pure state Ehrenfest approach to obtain accurate linear and nonlinear spectra that is applicable to systems with large numbers of excited states and complex chemical environments. We achieve this by representing the initial conditions as sums of pure states and unfolding multi-time correlation functions into the Schrödinger picture. By doing this, we show that one can obtain significant improvements in accuracy over the previously used projected Ehrenfest approach and that these benefits are particularly pronounced in cases where the initial condition is a coherence between excited states. While such initial conditions do not arise when calculating linear electronic spectra, they play a vital role in capturing multidimensional spectroscopies. We demonstrate the performance of our method by showing that it is able to quantitatively capture the exact linear, 2D electronic spectroscopy, and pump–probe spectra for a Frenkel exciton model in slow bath regimes and is even able to reproduce the main spectral features in fast bath regimes.

Chemistry↗

Ice phonon spectra and Bayes inference: A gateway to a new understanding of terahertz sound propagation in water

Understanding how molecules engage in collective motions in a liquid where a network of bonds exists has both fundamental and applied relevance. On the one hand, it can elucidate the “ordering” role of long-range correlations and inspire new avenues to control such order to implement sound manipulation. Water represents an ideal investigation case to unfold these general aspects, and, across the decades, it has been the focus of thorough scrutiny. Further, despite this investigative effort, the spectrum of terahertz density fluctuations of water largely remains a puzzle for condensed matter physicists. To unravel it, we compare previous scattering measurements of water spectra with new ones on ice. Owing to the unique asset of Bayesian inference, we draw a more detailed portrayal of the phonon response of ice. The comparison with the one of liquid water challenges the current understanding of density fluctuations in water, or more in general, of any networked liquid.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Graphic contrastive learning analyses of discontinuous molecular dynamics simulations: Study of protein folding upon adsorption

A comprehensive understanding of the interfacial behaviors of biomolecules holds great significance in the development of biomaterials and biosensing technologies. In this work, we used discontinuous molecular dynamics (DMD) simulations and graphic contrastive learning analysis to study the adsorption of ubiquitin protein on a graphene surface. Our high-throughput DMD simulations can explore the whole protein adsorption process including the protein structural evolution with sufficient accuracy. Contrastive learning was employed to train a protein contact map feature extractor aiming at generating contact map feature vectors. Subsequently, these features were grouped using the k-means clustering algorithm to identify the protein structural transition stages throughout the adsorption process. The machine learning analysis can illustrate the dynamics of protein structural changes, including the pathway and the rate-limiting step. Our study indicated that the protein–graphene surface hydrophobic interactions and the π–π stacking were crucial to the seven-stage adsorption process. Upon adsorption, the secondary structure and tertiary structure of ubiquitin disintegrated. The unfolding stages obtained by contrastive learning-based algorithm were not only consistent with the detailed analyses of protein structures but also provided more hidden information about the transition states and pathway of protein adsorption process and structural dynamics. Our combination of efficient DMD simulations and machine learning analysis could be a valuable approach to studying the interfacial behaviors of biomolecules.

97 MATHEMATICS AND COMPUTING↗