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At least 1,801 records · Page 100

Python Library for Monte Carlo Simulations with Ab Initio and Machine-Learned Interatomic Potentials

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.

97 MATHEMATICS AND COMPUTING↗

Field Programmable Gate Arrays for Enhancing the Speed and Energy Efficiency of Quantum Dynamics Simulations

We present the first application of field programmable gate arrays (FPGAs) as new, customizable hardware architectures for carrying out fast and energy-efficient quantum dynamics simulations of large chemical/material systems. Instead of tailoring the software to fixed hardware, which is the typical case for writing quantum chemistry code for central processing units (CPUs) and graphics processing units (GPUs), FPGAs allow us to directly customize the underlying hardware (even at the level of specific electrical signals in the circuit) to give a truly optimized computational performance for quantum dynamics calculations. By offloading the most intensive and repetitive calculations onto an FPGA, we show that the computational performance of our real-time electron dynamics calculations can even exceed that of optimized commercial mathematical libraries running on high-performance GPUs. In addition to this impressive computational speedup, we show that FPGAs are immensely energy-efficient and consume 4 times less energy than modern GPU or CPU architectures. These energy savings are a practical and important metric for supercomputing centers (many of which exceed over $1 million in power costs alone), as exascale computing capabilities become more widespread and commonplace. Taken together, the implementation techniques and performance metrics of our study demonstrate that FPGAs could play a promising role in upcoming quantum chemistry and materials science applications, particularly for the acceleration and energy-efficient execution of quantum dynamics calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-Temperature Reaction Kinetics of the e aq – and HO 2 • Radicals with Iron(II) Ions in Aqueous Solutions

Pulsed electron radiolysis was used to determine the chemical reaction kinetics and Arrhenius parameters for iron(II) reactions in aqueous solutions under irradiation. The second-order Fe 2+ reactions with the hydrated electron (e aq – ) and the perhydroxyl radical (HO 2 • ), arising from water radiolysis, were measured to high temperatures using custom-built flow-through cells with a multichannel optical detection system. The reaction with the HO 2 • radical was found to proceed via the formation of a metal-ion adduct species, Fe 2+ –HO 2 • . Additionally, the adduct’s molar extinction coefficient and its first-order decay rate coefficients are reported.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Excited-State Charge Distribution of a Donor–π–Acceptor Zn Porphyrin Probed by N K-Edge Transient Absorption Spectroscopy

Zinc porphyrin solar cell dyes with donor-π–acceptor architectures combine light absorber (π), electron-donor, and electron-acceptor moieties inside a single molecule with atomic precision. The donor-π–acceptor design promotes the separation of charge carriers following optical excitation. Here, we probe the excited-state electronic structure within such molecules by combining time-resolved X-ray absorption spectroscopy at the N K-edge with first-principles time-dependent density functional theory (TD-DFT) calculations. Furthermore, customized Zn porphyrins with strong-donor triphenylamine groups or weak-donor tri-tert-butylbenzene groups were synthesized. Energetically well-separated N K-edge absorption features simultaneously probe the excited-state electronic structure from the perspectives of the macrocycle and triphenylamine N atoms. New absorption transitions between the macrocycle N atoms and the excited-state HOMO vacancy are observed, and the triphenylamine associated absorption feature blue-shifts, consistent with partial oxidation of the donor groups in the excited state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data

Proteoforms, the different forms of a protein with sequence variations including post-translational modifications (PTMs), execute vital functions in biological systems such as cell signaling and epigenetic regulation. Precisely defining the stoichiometry of PTMs has been challenging because, in the widely used bottom-up proteomics methods, the detection occurs at the peptide level and thus the link between peptides and their specific modification site is lost, resulting in proteoform ambiguity. Advances in top-down mass spectrometry (MS) technology have permitted the direct characterization of intact proteoforms and their exact number of modification sites, allowing for the relative quantification of positional isomers (PI). Proteins with positional isomers refers to proteoforms with identical total mass and set of modifications but varying PTM site combinations. The relative abundance of PI can be estimated by matching proteoform-specific fragment ions to top-down tandem MS (MS2) data to localize and quantify modifications. However, current approaches heavily rely on manual annotation. Here, we present IsoForma, an open-source R package for relative quantification of PI within a single tool. We benchmarked IsoForma’s performance against two existing workflows and highlight the similarity of the results and improvements in speed. Overall, IsoForma provides a streamlined process, reduces the time of conducting isoform-based analyses, and offers an essential framework for developing customized proteoform analysis workflows. Finally, the software is open source and available at https://github.com/EMSL-Computing/isoforma-lib.

59 BASIC BIOLOGICAL SCIENCES↗

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format

Advances in mass spectrometry (MS) instrumentation, such as higher resolution, faster scan speeds, and improved sensitivity, have significantly increased the volume and complexity of data. The growing adoption of imaging and ion mobility further amplifies these challenges across MS-based omics fields, including proteomics, metabolomics, and lipidomics. While these technologies unlock new possibilities, they also present significant challenges in data management, storage, and accessibility. Existing open formats, such as the XML-based community standards mzML and imzML, struggle to meet the demands of modern MS workflows due to their large file sizes, slow data access, and limited metadata support. Vendor-specific formats, while optimized for proprietary instruments, lack interoperability, comprehensive metadata support and long-term archival reliability. This white paper lays the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multi-dimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will enable enhanced interoperability across platforms, seamless support for complex workflows including ion mobility and MS imaging, and faster data access compared to existing community formats such as mzML. Its design will ensure data is managed in compliance with regulatory standards, essential for applications such as precision medicine and chemical safety, where long-term data integrity and accessibility are critical. For vendors, mzPeak provides a streamlined, open alternative to proprietary formats, reducing the burden of regulatory compliance while aligning with the industry's push for transparency and standardization. By offering a high-performance, interoperable solution, mzPeak positions vendors to meet customer demands for sustainable data management tools which will be able to handle emerging and future data types and workflows. mzPeak aspires to become the cornerstone of MS data management, empowering researchers, vendors, and developers to innovate and collaborate more effectively.

data formats↗

Imaging Supramolecular Morphogenesis with Confocal Laser Scanning Microscopy at Elevated Temperatures

The morphogenesis of supramolecular assemblies is a highly dynamic process that has only recently been recognized, and our understanding of this phenomenon will require imaging techniques capable of crossing scales. Shape transformations depend both on the complex energy landscapes of supramolecular systems and the kinetically controlled pathways that define their structures and functions. We report here the use of confocal laser scanning microscopy coupled with a custom-designed variable-temperature sample stage that enables in situ observation of such shape changes. The submicrometer resolution of this technique allows for real-time observation of the nanostructures in the native liquid environments in which they transform with thermal energy. We use this technique to study the temperature-dependent morphogenic behavior of peptide amphiphile nanofibers and photocatalytic chromophore amphiphile nanoribbons. Furthermore, the variable-temperature confocal microscopy technique demonstrated in this work can sample a large volume and provides real-time information on thermally induced morphological changes in the solution.

36 MATERIALS SCIENCE↗

Bifunctional Janus Particles as Multivalent Synthetic Nanoparticle Antibodies (SNAbs) for Selective Depletion of Target Cells

Monoclonal antibodies (mAb) have had a transformative impact on treating cancers and immune disorders. SNAbs However, their use is limited by high development time and monetary cost, manufacturing complexities, suboptimal pharmacokinetics, and availability of disease-specific targets. To address some of these challenges, we developed an entirely synthetic, multivalent, Janus nanotherapeutic platform, called Synthetic Nanoparticle Antibodies (SNAbs). SNAbs, with phage-display-identified cell-targeting ligands on one "face" and Fc-mimicking ligands on the opposite "face", were synthesized using a custom, multistep, solid-phase chemistry method. SNAbs efficiently targeted and depleted myeloid-derived immune-suppressor cells (MDSCs) from mouse-tumor and rat-trauma models, ex vivo. Systemic injection of MDSC-targeting SNAbs efficiently depleted circulating MDSCs in a mouse triple-negative breast cancer model, enabling enhanced T cell and Natural Killer cell infiltration into tumors. Finally, our results demonstrate that SNAbs are a versatile and effective functional alternative to mAbs, with advantages of a plug- and-play, cell-free manufacturing process, and high-throughput screening (HTS)-enabled library of potential targeting ligands.

60 APPLIED LIFE SCIENCES↗

Resolving Current-Dependent Regimes of Electroplating Mechanisms for Fast Charging Lithium Metal Anodes

Poor fast-charge capabilities limit the usage of rechargeable Li metal anodes. Understanding the connection between charging rate, electroplating mechanism, and Li morphology could enable fast-charging solutions. In this report we develop a combined electroanalytical and nanoscale characterization approach to resolve the current-dependent regimes of Li plating mechanisms and morphology. Measurement of Li + transport through the solid electrolyte interphase (SEI) shows that low currents induce plating at buried Li||SEI interfaces, but high currents initiate SEI-breakdown and plating at fresh Li||electrolyte interfaces. The latter pathway can induce uniform growth of {110}-faceted Li at extremely high currents, suggesting ion-transport limitations alone are insufficient to predict Li morphology. At battery relevant fast-charging rates, SEI-breakdown above a critical current density produces detrimental morphology and poor cyclability. Thus, prevention of both SEI-breakdown and slow ion-transport in the electrolyte is essential. This mechanistic insight can inform further electrolyte engineering and customization of fast-charging protocols for Li metal batteries.

25 ENERGY STORAGE↗

Signature of Correlated Insulator in Electric Field Controlled Superlattice

On a two-dimensional crystal, a “superlattice” with nanometer-scale periodicity can be imposed to tune the Bloch electron spectrum, enabling novel physical properties inaccessible in the original crystal. While creating 2D superlattices by means of nanopatterned electric gates has been studied for band structure engineering in recent years, evidence of electron correlations-which drive many problems at the forefront of physics research-remains to be uncovered. Here, in this work, we demonstrate signatures of a correlated insulator phase in Bernal-stacked bilayer graphene modulated by a gate-defined superlattice potential, manifested as resistance peaks centered at integer multiples of single electron per superlattice unit cell carrier densities. The observation is consistent with the formation of a stack of flat low-energy bands due to the superlattice potential combined with inversion symmetry breaking. Our work paves the way to custom-designed superlattices for studying band structure engineering and strongly correlated electrons in 2D materials.

36 MATERIALS SCIENCE↗

Volumetric Shaping of Nanoparticle-DNA Crystals by Light-Induced Milling

DNA-programmable self-assembly enables the formation of nanoparticle crystals with controlled lattice symmetry. While this approach offers the formation of complexly ordered nanostructures for optical, mechanical, and biological applications, a mesoscale control over such nanomaterials is limited. Directing the material formation process through the assembly pathway or external fields allows for modulating crystal morphology, but achieving arbitrary morphology remains challenging. Here, we present a photothermal method for shaping 3D DNA-programmable crystals of gold nanoparticles. Through local heating of nanoparticles due to plasmonic light absorption, we induce targeted volumetric dissolution of specifically defined crystal areas with micron-scale accuracy. This technique effectively prescribes crystal shaping and creates arbitrarily shaped voids within crystals. We further investigate both computationally and experimentally the key factors governing volumetric material subtraction. The developed automated light-milling platform enables the fabrication of nanomaterials exhibiting both DNA-programmable nanoscale order and custom-designed mesoscale architecture.

36 MATERIALS SCIENCE↗

Compressive Creep of Polymer Electrolyte Membranes: A Case Study for Electrolyzers

For proton-exchange membrane (PEM) water electrolyzers to be commercially feasible, PEMs must perform over long lifetimes in liquid environments under compression while maintaining mechanical stability. A hydrated environment, while inherent for operation and conductivity, undermines PEM stability. Mechanical stability of PEMs is commonly characterized in tension, which is not applicable to electrolyzers, wherein PEMs could undergo high pressures. In this study, a compression creep procedure is developed using a custom-designed setup to monitor creep response of hydrated PEMs. Furthermore, our results show that PEMs exhibit continuous creep response under compression over 24 h, with a dependence on the applied pressure and hydration state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polymer Hole Transport Material Functional Group Tuning for Improved Perovskite Solar Cell Performance

As lead halide perovskites (LHPs) continue to achieve success as a light-harvesting material in perovskite solar cells (PSCs), exploring and understanding other materials in the device stack become increasingly important. Particularly, selection of suitable hole transport materials (HTMs) that demonstrate high performance and stability is imperative in the design of P-I-N PSCs. Presented here are a family of 12 structurally related polymers based on either fluorene or carbazole main chains with select aromatic side groups that introduce tunable properties for use in PSCs. How properties such as the highest occupied molecular orbital energy level, conductivity, glass-transition temperature, and wettability of the HTM affect the PSC performance is explored. Devices that incorporate the polymer HTMs perform well relative to PTAA in benchmark P-I-N PSC architectures while exhibiting similar or superior stability under accelerated aging studies. The relative synthetic simplicity and resultant performance of the HTMs in PSCs coupled with the ability to customize properties with different functional groups demonstrates the potential of this family of HTMs for a variety of LHP materials.

14 SOLAR ENERGY↗

Room-Temperature Pseudo-Solid-State Iron Fluoride Conversion Battery with High Ionic Conductivity

Li-metal batteries (LMBs) employing conversion cathode materials (e.g., FeF 3 ) are a promising way to prepare inexpensive, environmentally friendly batteries with high energy density. Pseudo-solid-state ionogel separators harness the energy density and safety advantages of solid-state LMBs, while alleviating key drawbacks (e.g., poor ionic conductivity and high interfacial resistance). In this work, a pseudo-solid-state conversion battery (Li-FeF 3 ) is presented that achieves stable, high rate (1.0 mA cm –2 ) cycling at room temperature. The batteries described herein contain gel-infiltrated FeF 3 cathodes prepared by exchanging the ionic liquid in a polymer ionogel with a localized high-concentration electrolyte (LHCE). The LHCE gel merges the benefits of a flexible separator (e.g., adaptation to conversion-related volume changes) with the excellent chemical stability and high ionic conductivity (~2 mS cm –1 at 25 °C) of an LHCE. The latter property is in contrast to previous solid-state iron fluoride batteries, where poor ionic conductivities necessitated elevated temperatures to realize practical power levels. Importantly, the stable, room-temperature Li-FeF 3 cycling performance obtained with the LHCE gel at high current densities paves the way for exploring a range of architectures including flexible, three-dimensional, and custom shape batteries.

25 ENERGY STORAGE↗

Nanoscale Imaging and Measurements of Grain Boundary Thermal Resistance in Ceramics with Scanning Thermal Wave Microscopy

Material thermal conductivity is a key factor in various applications, from thermal management to energy harvesting. With microstructure engineering being a widely used method for customizing material properties, including thermal properties, understanding and controlling the role of extended phonon-scattering defects, like grain boundaries, is crucial for efficient material design. However, systematic studies are still lacking primarily due to limited tools. In this study, we demonstrate an approach for measuring grain boundary thermal resistance by probing the propagation of thermal waves across grain boundaries with a temperature-sensitive scanning probe. The method, implemented with a spatial resolution of about 100 nm on finely grained Nb-substituted SrTiO 3 ceramics, achieves a detectability of about 2 × 10 –8 K m 2 W –1 , suitable for chalcogenide-based thermoelectrics. The measurements indicated that the thermal resistance of the majority of grain boundaries in the STiO 3 ceramics is below this value. While there are challenges in improving sensitivity, considering spatial resolution and the amount of material involved in the detection, the sensitivity of the scanning probe method is comparable to that of optical thermoreflectance techniques, and the method opens up an avenue to characterize thermal resistance at the level of single grain boundaries and domain walls in a spectrum of microstructured materials.

36 MATERIALS SCIENCE↗

Phosphonium-Based Metal Halide Semiconductors: When a Single Atom Dictates Water and Thermal Stability

Phosphonium-based (R-P(R’) 3 + ) metal halide semiconductors (MHS) emerged recently as a promising family of materials offering enhanced water and thermal stability over conventional ammonium-based (R-NH 3 + ) MHS. Despite this performance, there is a lack of systematic studies that elucidate the origin of these features as well as the underlying optoelectronic properties. Here, we report here the synthesis of nine new 1D materials (L)PbX 3 (L= C4-P, C6-P, C6-N, P3-P, P4-P, X= I, Br), using custom made organic ligands, namely butyl(triethyl)phosphonium bromide (C4-P), hexyl(triethyl)phosphonium bromide (C6-P), benzyl(triethyl)phosphonium bromide (P3-P), benzyl(trimethyl)phosphonium bromide (P4-P), and hexyl(triethyl)ammonium bromide (C6-N). Most of the materials are water stable for over 21 months, while the assembly of the isostructural (C6-N)PbBr 3 and (C6-P)PbBr 3 allowed us to directly identify the impact of a single atom (phosphorus versus nitrogen), on water stability. Notably, the C6-P analog remains water stable for 21 months, whereas the C6-N analog dissolves in water. It was found that neither crystal packing nor the lack of hydrogen bond interactions with water is responsible for this record stability performance, challenging currently established claims on the 1 origin of water stability in MHS. All materials feature broad light emission at RT, with (P3-P)PbBr 3 exhibiting a PLQY of 22.0% ascribed to permanent traps, while electrochemical studies uncovered for the first time the redox properties and their strong potential for the sensing of per- and polyfluoroalkyl substances (PFAS) in water samples. Our work showcases the potential of these compounds for applications where thermal and water stability are interwoven, potentially rendering their (R-NH 3 + ) based counterparts obsolete.

PFAS sensing↗

Mechanical Properties of 2D LiInP 2 Se 6 : Implication for Semiconductor Applications

Metal phosphorus trichalcogenides (MPTCs) are emerging 2D semiconductor materials with unique functional properties that set them apart from other 2D systems. Despite the importance of their mechanical properties for improving the semiconductor device’s durability and performance, as well as for utilizing strain effects to customize material properties and create new functionality, our current understanding of MPTCs’ mechanical behavior is lacking and lags behind our knowledge of their other properties. Here, we use LiInP 2 Se 6 as a model example of MPTCs and report the first experimental measurements of the elastic and plastic (fracture) properties along both in-plane and out-of-plane directions by atomic force microscopy and nanoindentation. Being a 2D material that is entirely inorganic, LiInP 2 Se 6 surprisingly exhibits mechanical properties that resemble those of hybrid organic–inorganic materials rather than pure inorganic 2D materials. It has a soft crystal structure with low elastic moduli, a low difference in in-plane vs out-of-plane mechanical properties, and a combination of elastic and plastic characteristics of hybrid organic–inorganic materials. Furthermore, our work provides the mechanical information critically needed to mitigate and/or harness the strain effects in LiInP 2 Se 6 -based semiconductor devices and sheds light on the mechanical behaviors of MPTCs with indispensable insights.

2D semiconductor↗

Mechanically and Thermally Enhanced 3D-Printed Photocurable Polymer Nanocomposites Containing Functionalized Chitin Nanowhiskers by Stereolithography

Additive manufacturing, or simply 3D printing (3DP), where objects are built through layer-wise material deposition, has gained significant academic and industrial attention as a result of the development of advanced and functional materials requiring rapid, customized, and flexible solutions. In the context of green manufacturing, diversifying environmentally and economically sustainable material portfolios is an essential endeavor for the success of 3DP technology that uses widely available, highly valuable, and renewable materials. Here, we used stereolithography (SLA) for processing methacrylate-based photocurable resins containing crab shell-derived chitin nanowhiskers (CNWs), which are surface-functionalized by reactive acrylate groups. Results from full spectral, thermal, structural, and topological analyses corroborate not only the surface functionalization of CNWs but also indicate the presence of these photocurable CNW (pCNW) fillers in the 3D-printed nanocomposites. Owing to the strong interfacial bond induced by the physical and chemical crosslinking between the pCNW and methacrylate (MA) polymer matrix, the internally formulated nanocomposites displayed enhanced thermomechanical properties (e.g., storage modulus and glass transition temperature) compared to those of commercially available pure SLA resins. For instance, the inclusion of 0.5 wt % pCNW improved the tensile strength and stiffness to up to 78 and 71%, respectively, without compromising the toughness and ductility of the printed material. Accordingly, this result also evidences the compatibility between the filler and resin materials. Consequently, the formation of a crosslinked network in the nanocomposite structure results in a higher thermal stability and activation energy (i.e., up to ~79%) for all the hybrid materials than the pristine MA. Finally, the high-resolution SLA print features, dimensional accuracy, and enhanced mechanical performance of our microstructure-forming functionalized chitin-based nanocomposites make them promising materials for a wide range of robust and high-performance industrial applications.

36 MATERIALS SCIENCE↗

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