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At least 919 records · Page 51

Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design

Enzyme substrate promiscuity has significant implications for metabolic engineering. The ability to predict the space of possible enzymatic side reactions is crucial for elucidating underground metabolic networks in microorganisms, as well as harnessing novel biosynthetic capabilities of enzymes to produce desired chemicals. Reaction rule-based cheminformatics platforms have been implemented to computationally enumerate possible promiscuous reactions, relying on existing knowledge of enzymatic transformations to inform novel reactions. However, past versions of curated reaction rules have been limited by a lack of comprehensiveness in representing all possible transformations, as well as the need to prune rules to enhance computational efficiency in pathway expansion. To this end, we curated a set of 1224 most generalized reaction rules, automatically abstracted from atom-mapped MetaCyc reactions and verified to uniquely cover all common enzymatic transformations. Additionally, we developed a framework to systematically identify and correct redundancies and errors in the curation process, resulting in a minimal, yet comprehensive, rule set. These reaction rules were capable of reproducing more than 85% of all reactions in the KEGG and BRENDA databases, for which a large fraction of reactions is not present in MetaCyc. Our rules exceed all previously published rule sets for which reproduction was possible in this coverage analysis, which allows for the exploration of a larger space of known enzymatic transformations. By leveraging the entire knowledge of possible metabolic reactions through generalized enzymatic reaction rules, we are able to better utilize underground metabolic pathways and accelerate novel biosynthetic pathway design to enable bioproduction towards a wider range of new molecules.

59 BASIC BIOLOGICAL SCIENCES↗

Involving the new generations in Fermilab endeavors

Since 1984 the Italian groups of the Istituto Nazionale di Fisica Nucleare (INFN) and Italian Universities, collaborating with the DOE laboratory of Fermilab (US) have been running a two-month summer training program for Italian university students. While in the first year the program involved only four physics students of the University of Pisa, in the following years it was extended to engineering students. This extension was very successful and the engineering students have been since then extremely well accepted by the Fermilab Technical, Accelerator, and Scientific Computing Division groups. Over the many years of its existence, this program has proven to be the most effective way to engage new students in Fermilab endeavors. Many students have extended their collaboration with Fermilab with their Master’s Thesis and PhD. Since 2004 the program has been supported in part by DOE in the frame of an exchange agreement with INFN. Over its almost 40 years of history, the program has grown in scope and size and has involved more than 550 Italian students from more than 20 Italian Universities, Several Institutes of Research, including ASI and INAF in Italy, and the ISSNAF Foundation in the US, have provided additional financial support. Since the program does not exclude appropriately selected non-Italian students, a handful of students from European and non-European Universities were also accepted over the years. Each intern is supervised by a Fermilab Mentor responsible for performing the training program. Training programs spanned from Tevatron, CMS, Muon (g-2), Mu2e, and Short Baseline Neutrino Experiments and DUNE design and experimental data analysis, development of particle detectors (silicon trackers, calorimeters, drift chambers, neutrino and dark matter detectors), design of electronic and accelerator components, development of infrastructures and software for exascale data handling, research on superconductive elements and on accelerating cavities, and theory of particle accelerators. Since 2010, within an extended program supported by the Italian Space Agency and the Italian National Institute of Astrophysics, a total of 30 students in physics, astrophysics, and engineering have been hosted for two months in the summer at US space science Research Institutes and laboratories. In 2015 the University of Pisa included these programs within its educational programs. Accordingly, Summer School students are enrolled at the University of Pisa for the duration of the internship and are identified and ensured as such. At the end of the internship, the students are required to write summary reports on their achievements. After positive evaluation by a University Examining Board, interns are acknowledged credits for their Diploma Supplement. The program was canceled in 2020 and 2021 due to the pandemic but restarted successfully in 2022. We believe this program can be taken as a model and easily adopted by interested institutions.

99 GENERAL AND MISCELLANEOUS↗

Reliability Assessment of Cooling Fans for PV Inverters: Testing, Modeling, and Case Studies

The reliability of photovoltaic (PV) inverters is critical for long-term solar system performance, with cooling fan failures frequently leading to costly downtime. While much research exists on general cooling fan reliability, little attention has been given to fans operating within PV inverters and their unique environmental challenges. Here, this article proposes a comprehensive methodology to address this gap. First, a failure mode and effects analysis is performed on fans to identify the key failure mechanisms in PV applications, their corresponding stressors, and the models necessary for lifetime prediction. Second, an accelerated life test is designed and conducted to collect valuable experimental data for PV inverter fans in a reasonable amount of time. Third, a mathematical conversion of dynamic mission profiles into effective constant stress levels is derived. Fourth, case studies are given, showcasing lifetime estimates that account for geographic variations in mission profile data. The results demonstrate that this integrated approach leads to an accurate reliability assessment for PV inverter cooling fans.

accelerated life testing (ALT)↗

High-Throughput Microfluidic Electroporation (HTME): A Scalable, 384-Well Platform for Multiplexed Cell Engineering

Electroporation-mediated gene delivery is a cornerstone of synthetic biology, offering several advantages over other methods: higher efficiencies, broader applicability, and simpler sample preparation. Yet, electroporation protocols are often challenging to integrate into highly multiplexed workflows, owing to limitations in their scalability and tunability. These challenges ultimately increase the time and cost per transformation. As a result, rapidly screening genetic libraries, exploring combinatorial designs, or optimizing electroporation parameters requires extensive iterations, consuming large quantities of expensive custom-made DNA and cell lines or primary cells. To address these limitations, we have developed a High-Throughput Microfluidic Electroporation (HTME) platform that includes a 384-well electroporation plate (E-Plate) and control electronics capable of rapidly electroporating all wells in under a minute with individual control of each well. Fabricated using scalable and cost-effective printed-circuit-board (PCB) technology, the E-Plate significantly reduces consumable costs and reagent consumption by operating on nano to microliter volumes. Furthermore, individually addressable wells facilitate rapid exploration of large sets of experimental conditions to optimize electroporation for different cell types and plasmid concentrations/types. Use of the standard 384-well footprint makes the platform easily integrable into automated workflows, thereby enabling end-to-end automation. We demonstrate transformation of E. coli with pUC19 to validate the HTME's core functionality, achieving at least a single colony forming unit in more than 99% of wells and confirming the platform's ability to rapidly perform hundreds of electroporations with customizable conditions. This work highlights the HTME's potential to significantly accelerate synthetic biology Design-Build-Test-Learn (DBTL) cycles by mitigating the transformation/transfection bottleneck.

Gaillard, William R↗

Mechanical Design of the PIP-II ORBUMP Pulsed Dipole Magnet

The Proton Improvement Plan-II (PIP-II) is a vital upgrade to Fermilab's accelerator complex. The upgrade is designed to power the world s most intense high-energy neutrino beam in future experiments. The magnet pulse repetition rate of the PIP-II injection system is being upgraded from 15 Hz to 20 Hz and requires a roughly 30% increase in the magnetic field of the new Orbital Bump (ORBUMP) magnets in the Booster. The magnet is secured in a vacuum box and the core is made up of 0.127 mm thick, low carbon steel laminations with a C-5 inorganic coating. The core is clamped using external tie bars welded to the core end plates. ANSYS Finite Element Analysis (FEA) was used to evaluate the clamping design to minimize the deflection of the core post welding of the tie bars. The water-cooled single turn coil is electrically isolated from the core using virgin PEEK insulating material in the gap. An investigation into the high voltage performance of the virgin PEEK insulator was conducted. The design of the coil which shapes the magnetic field by acting as the pole tips is critical for the integrated field homogeneity. The coil manufacturing tolerances and fabrication techniques were evaluated to ensure the magnetic properties of the magnet could be obtained. The ORBUMP magnet mechanical design is presented in this paper.

Karas, Dino [Fermilab] (ORCID:0000000304340670)↗

A robust controller for second-order systems using acceleration measurements

This paper presents a robust control design using strictly positive realness for second-order dynamic systems. The robust strictly positive real controller allows the system to be stabilized with only acceleration measurements. An important property of this design is that stabilization of the system is independent of the system parameters. The control design connects a virtual system to the given plant. The combined system is positive real regardless of system parameter uncertainty. Then any strictly positive real controllers can be used to achieve robust stability. A spring-mass system example and its computer simulations are presented to demonstrate this controller design. Robust performance property of this design is also demonstrated in a simple example.

Chuang, C.-H.↗

Physics Opportunities for the Fermilab Booster Replacement

This white paper presents opportunities afforded by the Fermilab Booster Replacement and its various options. Its goal is to inform the design process of the Booster Replacement about the accelerator needs of the various options, allowing the design to be versatile and enable, or leave the door open to, as many options as possible. The physics themes covered by the paper include searches for dark sectors and new opportunities with muons.

43 PARTICLE ACCELERATORS↗

Active and Transfer Learning of High-Dimensional Neural Network Potentials for Transition Metals

Classical molecular dynamics (MD) simulations represent a very popular and powerful tool for materials modeling and design. The predictive power of MD hinges on the ability of the interatomic potential to capture the underlying physics and chemistry. There have been decades of seminal work on developing interatomic potentials, albeit with a focus predominantly on capturing the properties of bulk materials. Such physics-based models, while extensively deployed for predicting the dynamics and properties of nanoscale systems over the past two decades, tend to perform poorly in predicting nanoscale potential energy surfaces (PESs) when compared to high-fidelity first-principles calculations. These limitations stem from the lack of flexibility in such models, which rely on a predefined functional form. Machine learning (ML) models and approaches have emerged as a viable alternative to capture the diverse size-dependent cluster geometries, nanoscale dynamics, and the complex nanoscale PESs, without sacrificing the bulk properties. Here, in this study, we introduce an ML workflow that combines transfer and active learning strategies to develop high-dimensional neural networks (NNs) for capturing the cluster and bulk properties for several different transition metals with applications in catalysis, microelectronics, and energy storage, to name a few. Our NN first learns the bulk PES from the high-quality physics-based models in literature and subsequently augments this learning via retraining with a higher-fidelity first-principles training data set to concurrently capture both the nanoscale and bulk PES. Our workflow departs from status-quo in its ability to learn from a sparsely sampled data set that nonetheless covers a diverse range of cluster configurations from near-equilibrium to highly nonequilibrium as well as learning strategies that iteratively improve the fingerprinting depending on model fidelity. All the developed models are rigorously tested against an extensive first-principles data set of energies and forces of cluster configurations as well as several properties of bulk configurations for 10 different transition metals. Our approach is material agnostic and provides a methodology to transfer and build upon the learnings from decades of seminal work in molecular simulations on to a new generation of ML-trained potentials to accelerate materials discovery and design.

36 MATERIALS SCIENCE↗

Electromagnetic propulsion test facility

A test facility for the exploration of electromagnetic propulsion concept is described. The facility is designed to accommodate electromagnetic rail accelerators of various lengths (1 to 10 meters) and to provide accelerating energies of up to 240 kiloJoules. This accelerating energy is supplied as a current pulse of hundreds of kiloAmps lasting as long as 1 millisecond. The design, installation, and operating characteristics of the pulsed energy system are discussed. The test chamber and its operation at pressures down to 1300 Pascals (10 mm of mercury) are described. Some aspects of safety (interlocking, personnel protection, and operating procedures) are included.

Gooder, S. T.↗

Bubble Chamber Detectors with Light Nuclear Targets: A Snowmass 2021 White Paper

Neutrino cross sections are a critical ingredient in experiments that depend on neutrino scattering to reconstruct event kinematics and infer neutrino characteristics, like NOvA and T2K. An opportunity exists to reduce the 5-10% broad uncertainty on neutrino cross sections by producing more measurements of neutrino scattering from light nuclear targets at the relevant energies. Bubble chambers with light nuclear targets would be ideal for these measurements but the most recent device designed for use with an accelerator neutrino source is at least fifty years old. A new bubble chamber with light nuclear targets could be designed by observing how the technology has progressed for use in dark matter experiments and producing smaller modular devices that use more efficient cooling systems. A smaller modular device could also be designed for deployment to all functioning neutrino beams, but an investigation of the proper operating characteristics is necessary to adapt newer detectors to the structure of contemporary neutrino beams.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Conceptual Design of a 20 T Hybrid Cos-Theta Di- pole Superconducting Magnet for Future High-Energy Particle Accelerators

High energy physics research will need more and more powerful circular accelerators in the next decades. It is therefore desirable to have dipole magnets able to produce the largest possible magnetic field, in order to keep the machine diameter within a reasonable size. A 20 T dipole is considered a desired achievement since it would allow the construction of an 80 km machine, able to circulate 100 TeV proton beams. In order to reach 20 T, a hybrid Low-Temperature Superconductor (LTS) - High-Temperature Superconductor (HTS) magnet is needed, since LTS technology is presently limited to ~16 T for accelerator magnet applications. In this paper, we present the design of a 6 layers 20 T hybrid dipole magnet using Nb3Sn (LTS) and Bi2212 (HTS). We show that it is possible to achieve this magnetic field with accelerator field quality, with sufficient margin on a realistic conductor, keeping the stresses within safe limit, avoiding conductor degradation

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Overview of the LHeC and FCC-he accelerator concepts

The Large Hadron–Electron Collider is designed to move the field of deep inelastic scattering to the energy and intensity frontier of particle physics. Exploiting energy-recovery technology, it collides a novel, intense electron beam with a proton or ion beam from the High-Luminosity Large Hadron Collider. The accelerator and interaction regions are designed for concurrent electron–proton and proton–proton operations. This paper represents the concepts of an updated design study and discusses the design challenges of the project.

Holzer, B. J.↗

Controlled Growth and Chemical Engineering of FeSe‐Based Superconducting Films

Abstract Chemical engineering tailors functional materials to meet the demands of physical and chemical properties, accelerating materials discovery and design in a multidisciplinary field. However, stereotyped synthetic paradigms in physical and chemical approaches obstruct the effective integration of multiple advantages of respective materials exploration methods. Solid state reaction is often considered separately with wet chemistry synthesis route, such as film growth using physical vapor deposition and hydrothermal methods. Here, the controlled growth of FeSe thin films by physical deposition techniques followed by the chemical engineering to create heterogenous interface in FeSe films via a solution‐based environment is demonstrated. The two‐step route allows an expanded crystal structure and enhanced superconducting transition temperature from 3.6 to 38 K, providing a new strategy to design functional hybrid materials.

Huang, Yulong↗

Proton-regulated alcohol oxidation for high-capacity ketone-based flow battery anolyte

Redox flow batteries have a unique architecture that potentially enables cost-effective long-duration energy storage to address the intermittency introduced by increased renewable integration for the decarbonization of the electric power sector. Targeted molecular engineering has demonstrated electrochemical reversibility in natively redox-inactive ketone molecules in aqueous electrolytes. Yet, the kinetics of fluorenone-based flow batteries continue to be limited by slow alcohol oxidation. We show how strategically designed proton regulators can accelerate alcohol oxidation and thus enhance battery kinetics. Fluorenone-based flow batteries with the organic additive ß-cyclodextrin demonstrate enhanced rate capability, high capacity, and long cycling. This study opens a new avenue to improve the kinetics of aqueous organic flow batteries by modulating the reaction pathway with a homogeneous catalyst.

25 ENERGY STORAGE↗

A survey of techniques for optimizing transformer inference

Recent years have seen a phenomenal rise in the performance and applications of transformer neural networks. The family of transformer networks, including Bidirectional Encoder Representations from Transformer (BERT), Generative Pretrained Transformer (GPT) and Vision Transformer (ViT), have shown their effectiveness across Natural Language Processing (NLP) and Computer Vision (CV) domains. Transformer-based networks such as ChatGPT have impacted the lives of common men. However, the quest for high predictive performance has led to an exponential increase in transformers' memory and compute footprint. Researchers have proposed techniques to optimize transformer inference at all levels of abstraction. Further, this paper presents a comprehensive survey of techniques for optimizing the inference phase of transformer networks. We survey techniques such as knowledge distillation, pruning, quantization, neural architecture search and lightweight network design at the algorithmic level. We further review hardware-level optimization techniques and the design of novel hardware accelerators for transformers. We summarize the quantitative results on the number of parameters/FLOPs and the accuracy of several models/techniques to showcase the tradeoff exercised by them. We also outline future directions in this rapidly evolving field of research. We believe that this survey will educate both novice and seasoned researchers and also spark a plethora of research efforts in this field.

97 MATHEMATICS AND COMPUTING↗

Two-Dimensional Energy Histograms as Features for Machine Learning to Predict Adsorption in Diverse Nanoporous Materials

A major obstacle for machine learning (ML) in chemical science is the lack of physically informed feature representations that provide both accurate prediction and easy interpretability of the ML model. In this work, we describe adsorption systems using novel two-dimensional energy histogram (2D-EH) features, which are obtained from the probe-adsorbent energies and energy gradients at grid points located throughout the adsorbent. The 2D-EH features encode both energetic and structural information of the material and lead to highly accurate ML models (coefficient of determination R2 ~ 0.94–0.99) for predicting single-component adsorption capacity in metal–organic frameworks (MOFs). Here, we consider the adsorption of spherical molecules (Kr and Xe), linear alkanes with a wide range of aspect ratios (ethane, propane, n-butane, and n-hexane), and a branched alkane (2,2-dimethylbutane) over a wide range of temperatures and pressures. The interpretable 2D-EH features enable the ML model to learn the basic physics of adsorption in pores from the training data. We show that these MOF-data-trained ML models are transferrable to different families of amorphous nanoporous materials. We also identify several adsorption systems where capillary condensation occurs, and ML predictions are more challenging. Nevertheless, our 2D-EH features still outperform structural features including those derived from persistent homology. The novel 2D-EH features may help accelerate the discovery and design of advanced nanoporous materials using ML for gas storage and separation in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Oxidation, Oligomerization, Isomerization of Hydrocarbons Using Metal–Organic Frameworks

The selective conversion of hydrocarbons into higher-value fuels and feedstocks is essential to the global energy and chemistry landscape. While porous inorganic materials have enabled significant progress in these transformations, achieving high activity, selectivity, and stability under industrially relevant conditions remains challenging. Metal–organic frameworks (MOFs) are a promising platform to precisely control active-site environments and interrogate structure–function relationships due to their crystallinity, tunability, and porosity. This review highlights relevant hydrocarbon transformations and outlines the general mechanisms for oxidation, oligomerization, and isomerization. Metal node acidity, confinement effects, and active site dispersion are analyzed for their impact on reactivity and selectivity across the three reactions. Lastly, we discuss current limitations in catalyst stability and offer a perspective on integrating reticular chemistry with high-throughput experimentation and machine learning to accelerate the discovery and design of robust, next-generation MOF catalysts.

Catalysts↗

A charge-density-based general cation insertion algorithm for generating new Li-ion cathode materials

Future lithium (Li) energy storage technologies, in particular solid-state configurations with a Li metal anode, opens up the possibility of using cathode materials that do not necessarily contain Li in its as-made state. To accelerate the discovery and design of such materials, we develop a general, chemically, and structurally agnostic methodology for identifying the optimal Li sites in any crystalline material. For a given crystal structure, we attempt multiple Li insertions at symmetrically in-equivalent positions by analyzing the electronic charge density obtained from first-principles density functional theory. In this report, we demonstrate the effectiveness of this procedure in successfully identifying the positions of the Li ion in well-known cathode materials using only the empty host (charged) material as guidance. Furthermore, applying the algorithm to over 2000 candidate cathode empty host materials we obtain statistics of Li site preferences to guide future developments of novel Li-ion cathode materials, particularly for solid-state applications.

25 ENERGY STORAGE↗