A spatially explicit evolutionary algorithm for the spatial partitioning problem
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Liu, Yan Y. (ORCID:0000000322984728)↗
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Ultra high energy cosmic rays The intersection of the Cosmic and Energy Frontiers
The present white paper is submitted as part of the "Snowmass" process to help inform the long-term plans of the United States Department of Energy and the National Science Foundation for high-energy physics. Further, it summarizes the science questions driving the Ultra-High-Energy Cosmic-Ray (UHECR) community and provides recommendations on the strategy to answer them in the next two decades.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Ultra high energy cosmic rays The intersection of the Cosmic and Energy Frontiers
The present white paper is submitted as part of the “Snowmass” process to help inform the long-term plans of the United States Department of Energy and the National Science Foundation for high-energy physics. It summarizes the science questions driving the Ultra-High-Energy Cosmic-Ray (UHECR) community and provides recommendations on the strategy to answer them in the next two decades.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Can we mitigate tropical cyclone formation using aerosols? A review of cyclogenesis and aerosol effects as a theoretical basis
Tropical cyclogenesis is a complex phenomenon, involving processes across multiple scales, with various theories proposed to explain its mechanisms. This paper provides an up-to-date summary of the established physical mechanisms and controlling factors of cyclogenesis. Understanding the nature of tropical cyclone formation is necessary to improve tropical cyclone forecasts and inform tropical cyclone mitigation strategies targeting early-stage intervention. Despite the disparities among theories, the critical role of persistent, intensified convection in tropical cyclone initiation is universally acknowledged. Therefore, our hypothesis is that interrupting convective development using aerosol injection is a potential strategy for mitigating tropical cyclone formation. Targetted injection of coarse and fine aerosols at the formation stage are two proposed potential approaches for mitigating tropical cyclones. These methods have completely different microphysical effects but each may ultimately interfere with the formation of the nascent cyclone. In conclusion, these potential interventions open new areas of further research, which are important and necessary to establish a solid scientific foundation for cyclogenesis mitigation.
Tropical cyclone formation↗
Competitive effects of glucan’s main hydrolysates on biochar formation: A combined experiment and density functional theory analysis
We report the complexity of polysaccharide hydrothermal products increases the difficulty of exploring the formation of biochar, limiting the development of biochar. This work clarifies the completive effects of glucan’s main hydrolysates on biochar formation from three aspects: experimental, thermodynamic, and kinetic. The products distribution illustrates that 5-HMF, FA, and LA are mainly involved in the formation of biochar. Biochar mainly includes furan ring, ether group, and ester group by the analysis of magic-angle-spinning nuclear magnetic resonance, X-ray photoelectron spectroscopy, and elemental analysis. Combined experiments and density functional theory analysis, the etherification reaction of 5-HMF itself is most likely to occur and is key to form biochar, followed by the esterification of FA with 5-HMF, and then the etherification of 5-HMF and LA. The further verified experiments also manifest these results. This work will develop a foundation for exploring the complex formation mechanism of cellulose-based biochar.
59 BASIC BIOLOGICAL SCIENCES↗
Building an expanded bio-based economy through synthetic biology
The field of synthetic biology is essential to the continued development of a bio-based economy, creating mechanisms to supply carbon needed in the economy by both converting existing end-of-life wastes as well as by creating novel, purpose-grown and sustainable feedstocks. Here, we first discuss the near- and long-term resources available for use as feedstocks for bioconversion as well as the output molecules needed for building the foundation of an expanded bio-based economy. We then outline the organisms and phenotypic traits that are needed for the performance-advantaged chassis organisms of the future. Furthermore, we detail the advances, challenges, and opportunities in both microbial and plant synthetic biology relevant to expanding the bio-based economy. Finally, we explore technologies that have and will further enable advances in synthetic biology and the greater bio-based economy.
09 BIOMASS FUELS↗
Generative $β$-hairpin design using a residue-based physicochemical property landscape
De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the -hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial -hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Not so HOT Triangulations
Here, we propose primal–dual mesh optimization algorithms that overcome shortcomings of the standard algorithm while retaining some of its desirable features. “Hodge-Optimized Triangulations” defines the “HOT energy” as a bound on the discretization error of the diagonalized Delaunay Hodge star operator. HOT energy is a natural choice for an objective function, but unstable for both mathematical and algorithmic reasons: it has minima for collapsed edges, and its extrapolation to non-regular triangulations is inaccurate and has unbounded minima. We propose a different extrapolation with a stronger theoretical foundation, and avoid extrapolation by recalculating the objective just beyond the flip threshold. We propose new objectives, based on normalizations of the HOT energy, with barriers to edge collapses and other undesirable configurations. We propose mesh improvement algorithms coupling these. When HOT optimization nearly collapses an edge, we actually collapse the edge. Otherwise, we use the barrier objective to update positions and weights and remove vertices. By combining discrete connectivity changes with continuous optimization, we more fully explore the space of possible meshes and obtain higher quality solutions.
97 MATHEMATICS AND COMPUTING↗
Generation of random geological models using multi-randomization for machine learning
Generating high-fidelity geological models is essential for advancing machine learning (ML) methods in automated seismic interpretation. For instance, seismic images paired with corresponding fault labels are foundational for ML-based fault detection from seismic migration sections. While several open-access datasets of random geological models exist, open-source tools specifically designed to produce large volumes of such models for ML applications remain scarce. To address this gap, we present RGM (Random Geological Model), an open-source software package for efficiently generating 2D and 3D synthetic geological models tailored for ML workflows. RGM supports the creation of diverse model components, including medium property distributions (P-/S-wave velocities and density), seismic reflectivity images (i.e., synthetic migration sections), relative geological time, and discrete fault attributes such as probability, dip, strike, rake, and displacement. It also accommodates the creation of complex geological features such as salt bodies and unconformities. The model generation algorithm employs a multi-randomization strategy, yielding an effectively infinite-dimensional model space that encompasses a wide range of geological scenarios and associated seismic features. Furthermore, RGM incorporates a method to generate synthetic elastic migration images using analytical elastic reflection coefficients combined with frequency-dependent scaling. This functionality enables the creation of training datasets for ML models that leverage elastic seismic images. RGM is implemented in modern object-oriented Fortran, allowing users to flexibly control statistical parameters governing model variability. We demonstrate the capability, performance, and geological realism of the package through comprehensive 2D and 3D examples.
58 GEOSCIENCES↗
Thermodynamics and its prediction and CALPHAD modeling: Review, state of the art, and perspectives
Thermodynamics is a science concerning the state of a system, whether it is stable, metastable, or unstable, when interacting with its surroundings. The combined law of thermodynamics derived by Gibbs about 150 years ago laid the foundation of thermodynamics. In Gibbs combined law, the entropy production due to internal processes was not included, and the 2nd law was thus practically removed from the Gibbs combined law, so it is only applicable to systems under equilibrium, thus commonly termed as equilibrium or Gibbs thermodynamics. Gibbs further derived the classical statistical thermodynamics in terms of the probability of configurations in a system in the later 1800's and early 1900's. With the quantum mechanics (QM) developed in 1920's, the QM-based statistical thermodynamics was established and connected to classical statistical thermodynamics at the classical limit as shown by Landau in the 1940's. In 1960's the development of density functional theory (DFT) by Kohn and co-workers enabled the QM prediction of properties of the ground state of a system. On the other hand, the entropy production due to internal processes in non-equilibrium systems was studied separately by Onsager in 1930's and Prigogine and co-workers in the 1950's. In 1960's to 1970's the digitization of thermodynamics was developed by Kaufman in the framework of the CALculation of PHAse Diagrams (CALPHAD) modeling of individual phases with internal degrees of freedom. CALPHAD modeling of thermodynamics and atomic transport properties has enabled computational design of complex materials in the last 50 years. Our recently termed zentropy theory integrates DFT and statistical mechanics through the replacement of the internal energy of each individual configuration by its DFT-predicted free energy. The zentropy theory is capable of accurately predicting the free energy of individual phases, transition temperatures and properties of magnetic and ferroelectric materials with free energies of individual configurations solely from DFT-based calculations and without fitting parameters, and is being tested for other phenomena including superconductivity, quantum criticality, and black holes. Those predictions include the singularity at critical points with divergence of physical properties, negative thermal expansion, and the strongly correlated physics. Furthermore, those individual configurations may thus be considered as the genomic building blocks of individual phases in the spirit of the materials genome®. This has the potential to shift the paradigm of CALPHAD modeling from being heavily dependent on experimental inputs to becoming fully predictive with inputs solely from DFT-based calculations and machine learning models built on those calculations and existing experimental data through newly developed and future open-source tools. Furthermore, through the combined law of thermodynamics including the internal entropy production, it is shown that the kinetic coefficient matrix of independent internal processes is diagonal with respect to the conjugate potentials in the combined law, and the cross phenomena that the phenomenological Onsager flux and reciprocal relationships are due to the dependence of the conjugate potential of a molar quantity on nonconjugate molar quantities and other potentials, which can be predicted by the zentropy theory and CALPHAD modeling.
42 ENGINEERING↗
Band structure dependent electronic localization in macroscopic films of single-chirality single-wall carbon nanotubes
Significant understanding has been achieved over the last few decades regarding chirality-dependent properties of single-wall carbon nanotubes (SWCNTs), primarily through single-tube studies. However, macroscopic manifestations of chirality dependence have been limited, especially in electronic transport, despite the fact that such distinct behaviors are needed for many applications of SWCNT-based devices. In addition, developing reliable transport theory is challenging since a description of localization phenomena in an assembly of nanoobjects requires precise knowledge of disorder on multiple spatial scales, particularly if the ensemble is heterogeneous. Here, we report an observation of pronounced chirality-dependent electronic localization in temperature and magnetic field dependent conductivity measurements on macroscopic films of single-chirality SWCNTs. The samples included large-gap semiconducting (6,5) and (10,3) films, narrow-gap semiconducting (7,4) and (8,5) films, and armchair metallic (6,6) films. Experimental data and theoretical calculations revealed Mott variable-range-hopping dominated transport in all samples, while localization lengths fall into three distinct categories depending on their band gaps. Armchair films have the largest localization length. Here our detailed analyses on electronic transport properties of single-chirality SWCNT films provide significant new insight into electronic transport in ensembles of nanoobjects, offering foundations for designing and deploying macroscopic SWCNT solid-state devices.
36 MATERIALS SCIENCE↗
Engineering phonon transport through cation disorder in dimensionally constricted high entropy MXene
Designing materials with low thermal conductivity is a crucial objective for applications in thermal insulation and thermoelectrics. Traditional methods such as doping, mechanical strain and introducing defects in perfect crystals have been widely explored to impede the flow of heat. Here, this work introduces dimensional constriction and cationic disorder as novel avenues to manipulate lattice thermal conductivity (LTC). High entropy materials characterized by random distribution of multiple elements, creates a suitable environment for thermal insulation due to its configurational disorder and local lattice distortions. On the other hand, MXenes, derived from MAX-phase, have garnered considerable attention due to their unique structural attributes, leading to potential applications in catalysis and energy storage. Ti 2 AlC MAX-phase is examined to understand the impact of dimensional constriction on phonon transport of Ti 2 C with cationic disorder, i.e., (Ti 0.25 Nb 0.25 Cr 0.25 Ta 0.25 ) 2 C. The exponential reduction in LTC of HE-MXene is attributed to disorder scattering that significantly limits phonon mean free path (MFP) and relaxation time. The spread of mode-resolved LTC with MFP highlights the influence of disorder on phonon scattering. This work provides a systematic approach to engineer LTC through dimensional constriction and cationic disorder, laying the foundation for tailored materials with desired thermal properties.
2D materials↗
Machine learning assisted phase and size-controlled synthesis of iron oxide particles
Synthesis of iron oxides with specific phases and particle sizes is a crucial challenge in various fields, including materials science, energy storage, biomedical applications, environmental science, and earth science. However, despite significant advances in this area, much of the current palette of particle outcomes has been based on time-consuming trial-and-error exploration of synthesis conditions. The present study was designed to explore a very different approach to 1) predict the outcome of synthesis from specified reaction parameters based on using machine learning (ML) techniques, and 2) correlate sets of parameters to obtain products with desired outcomes by a newly designed recommendation algorithm. To achieve this, four ML algorithms were tested, namely random forest, logistic regression, support vector machine, and k-nearest neighbor. Among the models, random forest outperformed the others, attaining 96% and 81% accuracy when predicting the phase and size of iron oxide particles in the test dataset. Surprisingly, the permutation feature importance analysis revealed that volume, which may strongly relate to pressure, was one of the important features, along with precursor concentration, pH, temperature, and time, influencing the phase and size of iron oxide particles during synthesis. To verify the robustness of the random forest models, prediction and experimental results were compared based on 24 randomly generated methods in additive and non-additive systems not included in the datasets. The predictions of product phase and particle size from the models agreed well with the experimental results. Furthermore, a searching and ranking algorithm was developed to recommend potential synthesis parameters for obtaining iron oxide products with the desired phase and particle size from previous studies in the dataset. Furthermore, this study lays the foundation for a closed-loop approach in materials synthesis and preparation, beginning with suggesting potential reaction parameters from the dataset and predicting potential outcomes, followed by conducting experiments and analyses, and ultimately enriching the dataset.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Selectively extracting lithium from single and mixed cathode materials
With the burgeoning reliance on lithium-ion batteries for sustainable energy solutions and electric transportation, the environmental and resource management associated with battery disposal are increasingly critical. Addressing these challenges necessitates innovative recycling techniques that recover valuable battery components, particularly lithium. This research introduces a universal, eco-friendly approach tailored for the efficient selective extraction of lithium from both single and mixed cathode materials, achieving impressive selective leaching efficiencies of lithium (99.51 % for LFP, 90 % for NMC, and 97.24 % for mixed cathode). Surprisingly, leaching efficiency of lithium from NMC can be significantly improved by introducing LFP since LFP can remove the dense transition-metal salts on the surface of NMC. The extracted lithium is recovered as lithium carbonate with battery-grade purity. This study also highlights the reuse of formic acid and the adoption of oxygen as an oxidizing agent to prevent wastewater production. Therefore, this method provides a robust foundation for sustainable lithium battery recycling.
economically and environmentally feasible↗
Transient kinetic insights into selective propene oxidation over industrial bismuth molybdate catalysts
Selective oxidation of propene to acrolein over industrial multicomponent bismuth molybdate (BMO) catalysts significantly depends on reaction conditions that include operating parameters and catalyst state. Here, this work investigates selective propene oxidation in the intrinsic kinetic paradigm of Temporal Analysis of Products (TAP) reactor by systematically varying catalyst redox state, temperature, and oxygen-to-propene feed ratio. A 93 % propene conversion with an acrolein yield of 80 % is achieved at elevated temperatures (450 °C) on oxidized catalysts under oxygen-rich conditions (O 2 :C 3 H 6 = 10). However, these conditions diminish acrolein-to-CO 2 selectivity due to enhanced total oxidation to CO 2 . In contrast, a reduced catalyst state, moderate temperature (350 °C), and lower oxygen feed (O 2 :C 3 H 6 = 1) nearly doubles the acrolein to-CO 2 selectivity, albeit at a lower acrolein yield (33 %). Transient kinetic studies together with a kinetic model that simplify the major product formation pathways in lumped non-elementary forms reveal that the availability of surface oxygen species plays a pivotal role in governing reaction pathways. Additionally, density functional theory (DFT) calculations on pure BMO catalysts inform the role of surface redox states on propene and oxygen activation barriers. Lattice oxygen at acrolein-selective sites drives both acrolein and CO 2 formation, while adsorbed oxygen at activation sites favors unselective CO 2 generation. This work establishes a critical relationship between transient product selectivity and surface oxygen availability, which is strongly influenced by catalyst redox state, feed ratio, and reaction temperature. These insights underscore the importance of dynamic reactor operation strategies and offer a foundation for designing next-generation propene oxidation processes with tunable acrolein selectivity.
42 - ENGINEERING↗
Multiscale modeling of packed-bed microwave reactors and estimation of intrinsic materials' permittivity
Modeling of packed-bed microwave reactors relies on an accurate representation of particle size, shape, and distribution within the bed, as well as the particles' dielectric properties. The measured permittivity of microwave susceptors (powders or structured materials) depends on the geometric features of the particles and the porosity of the bed, as well as the specific form factor of a structured material. These are effective properties and cannot be used to analyze other reactor configurations unless the geometric effects are removed. Therefore, we introduce a methodology for extracting the intrinsic particle permittivity from experimentally measured effective permittivity by combining cavity-based measurements with multiscale simulations and machine learning. Further, we develop the first multiscale model of packed-bed microwave reactors that incorporate particle effects (geometric features, random packing, and particle contact). This approach bridges macroscopic observables with mesoscopic physics, enabling analysis of local hotspots, arcing, and contact effects that control reactor performance. Using polymer-based spherical activated carbon (PBSAC) and silicon carbide (SiC) as examples, we demonstrate that the inferred particle permittivity is consistent with independent experimental heating profiles we collect from microwave reactors without adjustable parameters. Finally, this methodology establishes a foundation for predictive, multiscale design of microwave packed-bed reactors that explicitly accounts for particle-scale effects, enabling the estimation of intrinsic permittivity for the first time.
97 MATHEMATICS AND COMPUTING↗
Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies
Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.
59 BASIC BIOLOGICAL SCIENCES↗
Mucus-derived glycans are inhibitory signals for Salmonella Typhimurium SPI-1-mediated invasion
Mucus forms a critical barrier against enteric pathogens like Salmonella enterica serovar Typhimurium. While in vivo studies indicate that secreted, gel-forming mucins and specifically core 3 glycosylation are protective against S. Typhimurium, the molecular mechanisms involved remain unclear. Here, we demonstrate that native intestinal mucins inhibit Salmonella invasion of colonic epithelial cells by downregulating the type 3 secretion system through suppression of the key virulence regulator, HilD. Our study identifies mucin glycans and specific mucin sugars, namely N-acetyl galactosamine and N-acetyl glucosamine, as the components responsible for mucin’s anti-virulence effect, likely via functional or direct interaction with HilD’s putative carbohydrate-binding domain. Notably, we find that the native presentation of these sugars is important for activity. These insights provide a mechanistic foundation for mucin-based strategies to combat enteric infections and, given the prevalence of homologous AraC-type regulators in other pathogens, suggest mucins’ potential as broad-spectrum anti-virulence agents.
60 APPLIED LIFE SCIENCES↗