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These data are pure standard mass spectral libraries were collected on Orbitrap (Thermo QE-HF) and Q-TOF (SCIEX 5600) mass spectrometers for 192 compounds using 6 different collision energies, respectively. Libraries were acquired while using different solvent additives, precursor adducts, and ion polarities.
Users of digital image libraries are often not interested in image data per se but in derived products such as catalogs of objects of interest. Converting an image database into a usable catalog is typically carried out manually at present. For many larger image databases the purely manual approach is completely impractical. In this paper we describe the development of a trainable cataloging system: the user indicates the location of the objects of interest for a number of training images and the system learns to detect and catalog these objects in the rest of the database. In particular we describe the application of this system to the cataloging of small volcanoes in radar images of Venus. The volcano problem is of interest because of the scale (30,000 images, order of 1 million detectable volcanoes), technical difficulty (the variability of the volcanoes in appearance) and the scientific importance of the problem. The problem of uncertain or subjective ground truth is of fundamental importance in cataloging problems of this nature and is discussed in some detail. Experimental results are presented which quantify and compare the detection performance of the system relative to human detection performance. The paper concludes by discussing the limitations of the proposed system and the lessons learned of general relevance to the development of digital image libraries.
Shared Mobility Inc. (SMI) has used their mission of community-controlled transportation to partner with community based organizations on the launch and operations of E-Bike Libraries (EBLs) in Western New York (WNY) and beyond since 2021. For almost four years, the WNY EBLs have provided e-bikes at no cost to underserved communities in Buffalo and Niagara Falls. Participants used the e-bikes for commuting, recreational rides, community bike rides, running errands, and accessing essential services. This program significantly increased e-bike accessibility, with 71% of participants being first-time riders and 78% identifying as Black/African American. Challenges such as bike maintenance, battery charging logistics, and the need for suitable storage were addressed through partnerships with community-based organizations and adjustments to program logistics. Those lessons have been applied to additional EBLs in Pacoima, California and Carlisle, Pennsylvania, which have also been launched by SMI with a continued emphasis on the importance of community based approaches to sustainable transportation. All of these programs demonstrate the potential of e-bikes to provide an affordable, efficient, and fun transportation option, particularly for underserved communities. By leveraging community partnerships and focusing on accessibility and inclusivity, E-Bike Libraries can significantly contribute to sustainable transportation solutions and promote broader participation in the transportation electrification revolution.
In vitro directed evolution techniques, such as mRNA display, enable peptide ligand discovery and optimization. However, physical libraries that rely on a genetic code can only search a small fraction of sequence space due to inherent biases in the genetic code and experimental limitations. To address this challenge, denoising diffusion implicit models (DDIMs) are applied to generate novel peptide ligands against B‐cell lymphoma extra‐large (Bcl‐x L ), a key cancer target. Starting with high‐throughput sequencing data from previous selections, a DDIM is trained to produce novel sequences with high affinity binding. Experimental validation confirms that most generated sequences are functionally equivalent to the original library members for Bcl‐x L binding and demonstrated comparable binding kinetics and affinity relative to the wildtype and nearest original neighbors. Importantly, this approach generated rare sequences not easily accessible via mutation and directed evolution. These results indicate that DDIMs can complement and expand directed evolution data, efficiently exploring underrepresented regions of sequence space. This approach provides a broadly applicable framework for accelerating ligand discovery and optimizing molecular properties across diverse targets.
Abstract Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H‐dependent reduction of Δ 1 ‐pyrroline‐5‐carboxylate toL‐proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of thePYCR1gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X‐ray crystallography and kinetic assays to determine affinity parameters. The library was counter‐screened against human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (S)‐tetrahydro‐2H‐pyran‐2‐carboxylic acid (70 μM) has higher affinity than the current best tool compoundN‐formyl‐l‐proline, is 30 times more specific for PYCR1 over human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure‐affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1‐hydroxyethane‐1‐sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed withl‐pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.
Accurate modeling of running-in and equilibrium conditions in pebble-bed reactors (PBRs) requires precise microscopic multigroup neutron cross sections. In Griffin, deterministic neutronics calculations rely on multivariate interpolation over large cross section libraries, resulting in significant memory usage and performance bottlenecks. This work, together with a companion paper on Griffin integration, explores reduced-order models (ROMs) to replace interpolation with lightweight surrogates. Several ROM techniques are benchmarked, with deep neural networks (DNNs) demonstrating superior memory efficiency, scalability, and predictive accuracy. A total of 295 DNNs were trained to build a comprehensive isotope library, integrated into Griffin through a custom LibTorch interface for depletion analysis. Initial results demonstrate that DNN-based ROMs drastically reduce memory demands while preserving accuracy, enabling finer tabulations and additional state variables without overhead. In conclusion, the framework also supports online cross section generation and real-time DNN updates through transfer learning, improving fidelity by capturing self-shielding and evolving nuclide compositions during burnup.
In this paper, we introduce PYSIMFRAC, an open-source python library for generating 3-D synthetic fracture realizations, integrating with fluid simulators, and performing analysis. PYSIMFRAC allows the user to specify one of three fracture generation techniques (Box, Gaussian, or Spectral) and perform statistical analysis including the autocorrelation, moments, and probability density functions of the fracture surfaces and aperture. This analysis and accessibility of a python library allows the user to create realistic fracture realizations and vary properties of interest. In addition, PYSIMFRAC includes integration examples to two different pore-scale simulators and the discrete fracture network simulator, dfnWorks. The capabilities developed in this work provides opportunity for quick and smooth adoption and implementation by the wider scientific community for accurate characterization of fluid transport in geologic media. We present PYSIMFRAC along with integration examples and discuss the ability to extend PYSIMFRAC from a single complex fracture to complex fracture networks.
The Scintillator Library (scintillator.lbl.gov) is a database of scintillator properties hosted by Lawrence Berkeley National Laboratory in a web-accessible format. It contains a variety of measured inorganic and organic scintillator properties extracted from peer-reviewed literature and manufacturer specifications. Data housed within the Scintillator Library supply an important resource for developers of scintillator-based detection systems and an aid for scientists seeking to establish connections between fundamental material and chemical properties and the associated scintillation performance.
Derivative enhanced Gaussian Processes (DEGPs) can significantly improve surrogate model accuracy over standard Gaussian Process (GP) formulations by incorporating derivative information. However, standard implementations scale poorly with dimension, limiting their use in high dimensional engineering problems. JetGP is a Python framework that unifies existing derivative enhanced GP methodologies into a single library and extends them to support arbitrary order derivative information. The library implements four complementary formulations: standard derivative enhanced Gaussian Processes (DEGP), directional DEGP (DDEGP), generalized directional DEGP (GDDEGP), and weighted DEGP (WDEGP). By unifying these approaches in a consistent interface with robust numerical implementations, JetGP enables practitioners to balance predictive accuracy and computational efficiency for high dimensional optimization, uncertainty quantification, and sensitivity analysis in engineering design.
There is a growing need in the simulation community for software that provides a transparent, reproducible, usable, and extensible (TRUE) Monte Carlo (MC) simulation framework employing energies from ab initio methods and machine-learning interatomic potentials (MLIPs). We introduce a Python library (ASE-MC) that adds Monte Carlo functionality to the Atomic Simulation Environment (ASE) package. Now, we can combine the powerful tools used to build systems and perform ab initio and MLIP in ASE with MC simulation algorithms to sample the configurational space with a concise Python script. After presenting the design philosophy, we demonstrate the flexibility of our approach using selected examples. These example simulations include liquid water described with a message-passing MLIP in the canonical and isothermal–isobaric ensembles, sampling the characteristic dihedral angle of biphenyl and comparing an MLIP to first-principles calculations, and a grand canonical Monte Carlo simulation of ammonia adsorption on Pt(111). These examples showcase the main features of the software, which include flexibility in the choice of ab initio or MLIP engine, ab initio or MLIP grand canonical MC with cavity bias insertions and deletions, the ability to add custom MC moves to the move set, and how users can condense complex MC workflows into a single Python script. Finally, this library serves as a framework for reproducible Monte Carlo simulations, facilitating easy reproduction of the work and application to new systems.
Nanoparticle-mediated mRNA delivery has emerged as a promising therapeutic modality, but its growth is still limited by the discovery and optimization of effective and well-tolerated delivery strategies. Lipid nanoparticles containing charged or ionizable lipids are an emerging standard for in vivo mRNA delivery, so creating facile, tunable strategies to synthesize these key lipid-like molecules is essential to advance the field. Here, we generate a library of N-substituted glycine oligomers, peptoids, and undertake a multistage down-selection process to identify lead candidate peptoids as the ionizable component in our Nutshell nanoparticle platform. First, we identify a promising peptoid structural motif by clustering a library of >200 molecules based on predicted physical properties and evaluate members of each cluster for reporter gene expression in vivo. Then, the lead peptoid motif is optimized using design of experiments methodology to explore variations on the charged and lipophilic portions of the peptoid, facilitating the discovery of trends between structural elements and nanoparticle properties. We further demonstrate that peptoid-based Nutshells leads to expression of therapeutically relevant levels of an anti-respiratory syncytial virus antibody in mice with minimal tolerability concerns or induced immune responses compared to benchmark ionizable lipid, DLin-MC3-DMA. Through this work, we present peptoid-based nanoparticles as a tunable delivery platform that can be optimized toward a range of therapeutic programs.
Engineering colloidally stable multimetallic nanocrystals offers many benefits in a wide range of applications and allows manipulation of physical, chemical, and electronic properties of materials at the nanoscale. Synthesis routes are challenged by the chemical complexity required to temporally and spatially coordinate the reduction and alloying of multiple metal species, which has hampered the development of tunable libraries of colloidal materials to date. Here, in this work, we demonstrate a seed-mediated synthesis method to incorporate five or more metal elements into uniform, colloidally stable nanocrystals. By integrating machine learning-accelerated simulations, the synthesis of shortlisted high-entropy alloy nanocrystals was demonstrated. Multiple seed materials can be used, leading to a library of multimetallic nanocrystals with tunable electronic, physical, and alloy structures. The advantage of this synthetic protocol is highlighted in the preparation of catalytic materials that showed 2 orders of magnitude higher reaction rates than monometallic catalysts and outstanding thermal stability, thus highlighting the promise of this approach for high-performance materials in many areas.
The rapid growth of automated and autonomous instrumentation brings forth opportunities for the co-orchestration of multimodal tools that are equipped with multiple sequential detection methods or several characterization techniques to explore identical samples. This is exemplified by combinatorial libraries that can be explored in multiple locations via multiple tools simultaneously or downstream characterization in automated synthesis systems. In co-orchestration approaches, information gained in one modality should accelerate the discovery of other modalities. Correspondingly, an orchestrating agent should select the measurement modality based on the anticipated knowledge gain and measurement cost. Herein, we propose and implement a co-orchestration approach for conducting measurements with complex observables, such as spectra or images. The method relies on combining dimensionality reduction by variational autoencoders with representation learning for control over the latent space structure and integration into an iterative workflow via multi-task Gaussian Processes (GPs). This approach further allows for the native incorporation of the system's physics via a probabilistic model as a mean function of the GPs. We illustrate this method for different modes of piezoresponse force microscopy and micro-Raman spectroscopy on a combinatorial Sm-BiFeO3 library. However, the proposed framework is general and can be extended to multiple measurement modalities and arbitrary dimensionality of the measured signals.
High-throughput polymer synthesis enables rapid exploration of chemical space but remains limited by batch-to-batch inconsistencies that can obscure structure–property relationship trends. To address this challenge, we developed a synthetic approach to produce multifunctional copolymers using post-polymerization modification of activated ester modular polymers with commercially available amines. Easily derivitized parent polymers—poly(tetrafluorophenyl acrylate) and poly(tetrafluorophenyl styrene sulfonate)—were synthesized by RAFT polymerization to yield single polymer batches containing highly reactive tetrafluorophenyl esters or sulfonate esters on each repeat unit. Tuning post-polymerization modification reaction conditions enabled the addition of sub-stoichiometric amounts of amines (relative to the repeat unit) to yield partially functionalized intermediates that could then be further derivatized. Reaction monitoring by 19 F NMR spectroscopy confirmed good control over these sequential post-polymerization modifications. This synthetic route produced a variety of copolymers with defined comonomer ratios while preserving the underlying polymer structure (degree of polymerization, dispersity, tacticity) for both the acrylate and styrene sulfonate backbones. We further applied this approach in a divergent manner to create a small library of structurally distinct copolymers from a single parent batch in three synthetic steps. This modular, divergent synthesis demonstrates a general route to structurally consistent copolymer libraries that enable systematic studies of structure–property relationships and can accelerate functional materials discovery.
ion Library for Parallel Kernel Acceleration) is a header-only C++ library that provides performance portability across different back-ends, abstracting the underlying levels of parallelism. It supports serial and parallel execution on CPUs, and extremely parallel execution on NVIDIA, AMD and Intel GPUs.This contribution will show how alpaka is used in the CMS software to develop and maintain a single code base; to use different toolchains to build the code for each supported back-end, and link them into a single application; to seamlessly select the best backend at runtime, and implement portable reconstruction algorithms that run efficiently on CPUs and GPUs from different vendors. It will describe the validation and deployment of the alpaka-based implementation in the CMS High Level Trigger, and highlight how it achieves near-native performance.
The conversion efficiency of CdTe solar cells may be improved by bandgap engineering, i.e., changing the bandgap value through the addition of Se in the absorber. The Se alloying enables a short-circuit current density improvement, as it leads to a bandgap energy value decrease. Furthermore, it has been associated with increased minority carrier lifetimes, assuring high open-circuit voltage values. An Se gradient profile control can further optimize the solar cell performance. Thus, an optical model baseline of the CdSe x Te 1–x (CST) compound was developed. Spectroscopic ellipsometry measurements were conducted to accurately extract the optical constants of ten CST layers deposited through coevaporation with x varying from 0 to 1. Using the measured dielectric function spectra from the discrete CST layers with varying x, and considering the composition-induced shift in the critical point energies, an energy-shift model was employed to develop the accurate optical library for the CST compound for any x value to provide data for future modeling and optimization. Furthermore, the library accuracy was validated through optical simulations of the quantum efficiency of a graded CST solar cell using the finite-difference time-domain method by replicating the Se profile in the absorber layer measured through secondary ion mass spectrometry.
This software library serves as a Python wrapper for Geotab's Altitude API. It streamlines querying of the API, converts loosely structured API outputs into a standardized tabular data format, and enables analysis of the resulting data tables. It also includes example notebooks showing how to use the library.
FuelLib is a library that utilizes the group contribution method (GCM) for calculating thermodynamic properties of hydro-carbon jet fuels. FuelLib utilizes the tables and functions of the GCM as proposed by Constantinou and Gani (1994) and Constantinou, Gani and O'Connel (1995), with additional physical properties discussed in Govindaraju & Ihme (2016). The code is based on Pavan B. Govindaraju's Matlab implementation of the GCM, and has been expanded to include additional thermodynamic properties and mixture properties. The fuel library contains gas chromatography (GC x GC) data for a variety of fuels ranging from simple single component fuels to complex jet fuels. The GC x GC data for POSF jet fuels comes from Edwards (2020).