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Molecular crystals are difficult to model with accurate first-principles methods due to large unit cells. On the other hand, accurate modeling is required as polymorphs often differ by only 1 kJ/mol. Machine learning interatomic potentials promise to provide accuracy of the baseline first-principles methods with a cost lower by orders of magnitude. Using the existing databases of the density functional theory calculations for molecular crystals and molecules, we train global machine learning interatomic potentials, usable for any molecular crystal. We test the performance of the potentials on experimental benchmarks and show that they perform better than classical force fields and, in some cases, are comparable to the density functional theory calculations. [ABSTRACT FROM AUTHOR]

Detecting and analyzing the local environment is crucial for investigating the dynamical processes of crystal nucleation and shape colloidal particle self-assembly. Recent developments in machine learning provide a promising avenue for better order parameters in complex systems that are challenging to study using traditional approaches. However, the application of machine learning to self-assembly on systems of particle shapes is still underexplored. To address this gap, we propose a simple, physics-agnostic, yet powerful approach that involves training a multilayer perceptron (MLP) as a local environment classifier for systems of particle shapes, using input features such as particle distances and orientations. Our MLP classifier is trained in a supervised manner with a shape symmetry-encoded data augmentation technique without the need for any conventional roto-translations invariant symmetry functions. We evaluate the performance of our classifiers on four different scenarios involving self-assembly of cubic structures, two-dimensional and three-dimensional patchy particle shape systems, hexagonal bipyramids with varying aspect ratios, and truncated shapes with different degrees of truncation. The proposed training process and data augmentation technique are both straightforward and flexible, enabling easy application of the classifier to other processes involving particle orientations. Our work thus presents a valuable tool for investigating self-assembly processes on systems of particle shapes, with potential applications in structure identification of any particle-based or molecular system where orientations can be defined. [ABSTRACT FROM AUTHOR]

This document is an erratum for an article titled "The quaternary question: Determining allostery in spastin through dynamics classification learning and bioinformatics." The authors found errors in the network and community analysis section of the methods, specifically in the calculation of DCCM maps. As a result, figures 3-5, which report results from the network analysis, have been updated. The correction also led to changes in the analysis of network centrality and optimal and sub-optimal paths between allosterically important positions in the results and discussion section. The updated tables and figures can be found in the supplementary material. [Extracted from the article]

We present a detailed assessment of deep neural network potentials developed within the Deep Potential Molecular Dynamics (DeePMD) framework and trained on the MB-pol data-driven many-body potential energy function. Specific focus is directed at the ability of DeePMD-based potentials to correctly reproduce the accuracy of MB-pol across various water systems. Analyses of bulk and interfacial properties as well as many-body interactions characteristic of water elucidate inherent limitations in the transferability and predictive accuracy of DeePMD-based potentials. These limitations can be traced back to an incomplete implementation of the "nearsightedness of electronic matter" principle, which may be common throughout machine learning potentials that do not include a proper representation of self-consistently determined long-range electric fields. These findings provide further support for the "short-blanket dilemma" faced by DeePMD-based potentials, highlighting the challenges in achieving a balance between computational efficiency and a rigorous, physics-based representation of the properties of water. Finally, we believe that our study contributes to the ongoing discourse on the development and application of machine learning models in simulating water systems, offering insights that could guide future improvements in the field. [ABSTRACT FROM AUTHOR]

Finite-temperature calculations are relevant for rationalizing material properties, yet they are computationally expensive because large system sizes or long simulation times are typically required. Circumventing the need for performing many explicit first-principles calculations, tight-binding and machine-learning models for the electronic structure emerged as promising alternatives, but transferability of such methods to elevated temperatures in a data-efficient way remains a great challenge. In this work, we suggest a tight-binding model for efficient and accurate calculations of temperature-dependent properties of semiconductors. Our approach utilizes physics-informed modeling of the electronic structure in the form of hybrid-orbital basis functions and numerically integrating atomic orbitals for the distance dependence of matrix elements. We show that these design choices lead to a tight-binding model with a minimal amount of parameters that are straightforwardly optimized using density functional theory or alternative electronic-structure methods. The temperature transferability of our model is tested by applying it to existing molecular-dynamics trajectories without explicitly fitting temperature-dependent data and comparison with density functional theory. We utilize it together with machine-learning molecular dynamics and hybrid density functional theory for the prototypical semiconductor gallium arsenide. We find that including the effects of thermal expansion on the onsite terms of the tight-binding model is important in order to accurately describe electronic properties at elevated temperatures in comparison with experiment. [ABSTRACT FROM AUTHOR]

Solar interfacial evaporation, as a novel practical freshwater production method, requires continuous research on how to improve the evaporation rates to increase water production. In this study, sets of data were obtained from molecule dynamics simulation and literature, in which the parameters included height, diameter, height–radius ratio, evaporation efficiency, and evaporation rate. Initially, the correlation between the four input parameters and the output of the evaporation rate was examined through traditional pairwise plots and Pearson correlation analysis, revealing weak correlations. Subsequently, the accuracy and generalization performance of the evaporation rate prediction models established by neural network and random forest were compared, with the latter demonstrating superior performance and reliability confirmed via random data extraction. Furthermore, the impact of different percentages (10%, 20%, and 30%) of the data on the model performance was explored, and the result indicated that the model performance is better when the test set is 20% and all the constructed model converge. Moreover, the mean absolute error and mean squared error of the evaporation rate prediction model for the three ratios were calculated to evaluate their performance. However, the relationship between the height- radius ratio and optimal evaporation rate was investigated using the enumeration method, and it was determined that the evaporation efficiency was optimal when the height–radius ratio was 6. Finally, the importance of height, diameter, height– radius ratio, and evaporation efficiency were calculated to optimize evaporator structure, increase evaporation rate, and facilitate the application of interfacial evaporation in solar desalination. [ABSTRACT FROM AUTHOR]

The lattice thermal conductivity stands as a pivotal thermos-physical parameter of high-entropy alloys; nonetheless, achieving precise predictions of the lattice thermal conductivity for high-entropy alloys poses a formidable challenge due to their complex composition and structure. In this study, machine learning models were built to predict the lattice thermal conductivity of AlCoCrNiFe high-entropy alloy based on molecular dynamic simulations. Our model shows high accuracy with R2, mean absolute percentage error, and root mean square error of the test set is 0.91, 0.031, and 1.128 W m−1 k−1, respectively. In addition, a high-entropy alloy with low a lattice thermal conductivity of 2.06 W m−1 k−1 (Al8Cr30Co19Ni20Fe23) and with a high lattice thermal conductivity of 5.29 W m−1 k−1 (Al0.5Cr28.5Co25Ni25.5Fe20.5) was successfully predicted, which shows good agreement with the results from molecular dynamics simulations. The mechanisms of the thermal conductivity divergence are further explained through their phonon density of states and elastic modulus. The established model provides a powerful tool for developing high-entropy alloys with the desired properties. [ABSTRACT FROM AUTHOR]

With the increasing integration of AI tools like Yewno Discover, Scholarcy, and Grammarly in academic libraries, undergraduate research has witnessed transformative changes. These tools, while elevating the research process, also bring forth challenges rooted in ethics and application. This paper explores the synergy between modern technology and academic exploration, highlighting the benefits and potential pitfalls of using AI in the research workflow. It emphasizes that while Yewno Discover and similar tools offer streamlined navigation of vast information databases, it is imperative for undergraduates to remain cognizant of potential biases and other ethical considerations. This paper underscores the need for proactive measures in academic settings, including specialized training and policy development, to ensure that undergraduate researchers harness the power of AI responsibly and efficiently. [ABSTRACT FROM AUTHOR]

The giant impact between proto-Earth and a Mars-sized planet called Theia resulted in the formation of the Earth–Moon system, and the silicate mantles of the initial bodies may have partly been vaporized. Here, we develop a machine learning potential for MgSiO3 based on the data from first-principles calculations to estimate its critical point. The variations in pressure along different isotherms yield the position of the critical point of MgSiO3 at 0.54 g cm−3 and 6750 ± 250 K, which agrees with the previous theoretical estimation. We also simulate the MgSiO3 melt under a spectrum of critical conditions to understand the changes in coordination environment with density and temperature. The fourfold Si–O coordination hardly changes with increasing density at 3000 K. However, with increasing temperature, the dominance of four-coordinated Si–O diminishes rapidly as density decreases. Regarding Mg–O coordination, the overall trend, which varies with temperature and density, remains largely consistent with Si–O but with a greater diversity in the types of coordination due to more bond breaking events. Our work opens a new avenue by employing machine learning methods to estimate the critical point of silicates. [ABSTRACT FROM AUTHOR]

Generative models in the field of artificial intelligence and their applications and deployment have demonstrated their great strength in the past few years. Of the vast spectrum of generative models, diffusion probabilistic models have proven to be particularly powerful and productive, transforming notions such as text-to-image and text-to-video generation from ideas into practical applications. In our previous works, we proposed a thermal metamaterial-based periodic interparticle interaction mechanism for heat management, with a specific application in thermal transparency. To address the challenging problems associated with the inverse design of thermal metamaterial structures, we employed an autoencoder-based machine learning approach and a reinforcement learning-based approach successfully. In this work, we demonstrate that our particular problems with the inverse design of thermal metamaterial-based periodic lattices for the realization of thermal transparency can also be reframed and efficiently solved by training a generative diffusion probabilistic model that can generate the design parameters corresponding to the desired response. Furthermore, we show that for a specific response, multiple sets of design parameters can be obtained by simply performing multiple inferences with the generative diffusion probabilistic model, enabling us to select the ones that can be more economical to fabricate and implement. Our work is among the first to use a diffusion model for the inverse design of thermal metamaterial-based structures and demonstrates the effectiveness of generating low-dimensional design parameters through a diffusion model. [ABSTRACT FROM AUTHOR]

Heterogeneous ice nucleation (HIN) has applications in climate science, nanotechnology, and cryopreservation. Ice nucleation on the earth's surface or in the atmosphere usually occurs heterogeneously involving foreign substrates, known as ice nucleating particles (INPs). Experiments identify good INPs but lack sufficient microscopic resolution to answer the basic question: What makes a good INP? We employ molecular dynamics (MD) simulations in combination with machine learning (ML) to address this question. Often, the large amount of computational cost required to cross the nucleation barrier and observe HIN in MD simulations is a practical limitation. We use information obtained from short MD simulations of atomistic surface and water models to predict the likelihood of HIN. We consider 153 atomistic substrates with some surfaces differing in elemental composition and others only in terms of lattice parameters, surface morphology, or surface charges. A range of water features near the surface (local) are extracted from short MD simulations over a time interval (≤ 300 ns) where ice nucleation has not initiated. Three ML classification models, Random Forest (RF), support vector machine, and Gaussian process classification are considered, and the accuracies achieved by all three approaches lie within their statistical uncertainties. Including local water features is essential for accurate prediction. The accuracy of our best RF classification model obtained including both surface and local water features is 0.89 ± 0.05. A similar accuracy can be achieved including only local water features, suggesting that the important surface properties are largely captured by the local water features. Some important features identified by ML analysis are local icelike structures, water density and polarization profiles perpendicular to the surface, and the two-dimensional lattice match to ice. We expect that this work, with its strong focus on realistic surface models, will serve as a guide to the identification or design of substrates that can promote or discourage ice nucleation. [ABSTRACT FROM AUTHOR]

Anharmonic effects play a crucial role in determining thermochemical properties of liquids and gases. For such extended phases, the inclusion of anharmonicity in reliable electronic structure methods is computationally extremely demanding, and hence, anharmonic effects are often lacking in thermochemical calculations. In this study, we apply the quantum cluster equilibrium method to transfer density functional theory calculations at the cluster level to the macroscopic, liquid, and gaseous phase of hydrogen fluoride. This allows us to include anharmonicity, either via vibrational self-consistent field calculations for smaller clusters or using a regression model for larger clusters. We obtain the structural composition of the fluid phases in terms of the population of different clusters as well as isobaric heat capacities as an example for thermodynamic properties. We study the role of anharmonicities for these analyses and observe that, in particular, the dominating structural motifs are rather sensitive to the anharmonicity in vibrational frequencies. The regression model proves to be a promising way to get access to anharmonic features, and the extension to more sophisticated machine-learning models is promising. [ABSTRACT FROM AUTHOR]

Finding low-energy structures of ligand-protected clusters is challenging due to the enormous conformational space and the high computational cost of accurate quantum chemical methods for determining the structures and energies of conformers. Here, we adopted and utilized a kernel rigid regression based machine learning method to accelerate the search for low-energy structures of ligand-protected clusters. We chose the Au25(Cys)18 (Cys: cysteine) cluster as a model system to test and demonstrate our method. We found that the low-energy structures of the cluster are characterized by a specific hydrogen bond type in the cysteine. The different configurations of the ligand layer influence the structural and electronic properties of clusters. [ABSTRACT FROM AUTHOR]

Although professional women's football has benefitted from recent surges in popularity, challenges to progress and distinguish the sport persist. The gender-schema theory explains the tendency for individuals to hold female sports to male standards, a phenomenon that leads to negative outcomes in areas such as media representation and consumer perception. One area in which schemas have a more discreet effect is player and team performance, where the assumption that technical metrics developed in men's football are transferable to women's football remains unfounded. Using expected goals, a metric synonymous with the probability of a shot being scored, we highlight how variables important to shot quality and shot execution differ across gender, and how attempts to evaluate female footballers with models built on men's data increase estimation errors. These results have theoretical and practical implications for the role they play in reframing schemas and improving the methods used to evaluate performance in women's sports. [ABSTRACT FROM AUTHOR]

Fractures in body-centered-cubic metals and alloys below the ductile-to-brittle transition temperature are brittle. This is theoretically explained by the notion that the critical stress intensity factor of a given crack front for brittle fracture is smaller than that for plastic deformation; hence, brittle fracture is selected over plastic deformation. Although this view is true from a macroscopic perspective, such a fracture is always accompanied by small-scale plastic deformation near the crack tip, that is, crack tip plasticity. This paper investigates the origin of this plasticity using atomistic modeling with the machine learning interatomic potential of α -Fe. Some plastic modes are activated by rapid crack propagation, whereas no plasticity is activated when the crack tips are gradually fractured. The group of activated atoms dynamically caused by brittle crack propagation was identified as the precursor of plasticity. [ABSTRACT FROM AUTHOR]

The evaluation of thermoelectric materials relies significantly on the thermoelectric figure of merit, ZT, which serves as a crucial parameter in assessing their properties. The accurate prediction of ZT values can be accomplished by utilizing machine learning models to learn material characteristics. However, factors such as the size of the dataset, model hyperparameters, and data quality can all impact the accuracy of machine learning. In contrast to previous research where high-dimensional features were simply discarded to transform them into low-dimensional ones, deep learning models such as autoencoder can extract more effective information. Therefore, in this article, the combination of autoencoders and the Light Gradient Boosting Machine (LightGBM) is employed to learn the chemical characteristics and ZT values of various materials. The reliability of the model was confirmed by achieving an R2 score of 0.94 during tenfold cross-validation. 130 000 materials were predicted and screened, the temperature dependence of the screened materials was studied in depth, and 13 materials with high ZT values were identified. Four of the 13 most promising candidates identified are existing thermoelectric materials, while nine are ideal candidates for future experimental studies and validation. This work utilizes autoencoders for extensive prediction and screening of promising materials, providing an effective approach for handling high-dimensional material data. [ABSTRACT FROM AUTHOR]

Machine learning potentials (MLPs) have attracted significant attention in computational chemistry and materials science due to their high accuracy and computational efficiency. The proper selection of atomic structures is crucial for developing reliable MLPs. Insufficient or redundant atomic structures can impede the training process and potentially result in a poor quality MLP. Here, we propose a local-environment-guided screening algorithm for efficient dataset selection in MLP development. The algorithm utilizes a local environment bank to store unique local environments of atoms. The dissimilarity between a particular local environment and those stored in the bank is evaluated using the Euclidean distance. A new structure is selected only if its local environment is significantly different from those already present in the bank. Consequently, the bank is then updated with all the new local environments found in the selected structure. To demonstrate the effectiveness of our algorithm, we applied it to select structures for a Ge system and a Pd13H2 particle system. The algorithm reduced the training data size by around 80% for both without compromising the performance of the MLP models. We verified that the results were independent of the selection and ordering of the initial structures. We also compared the performance of our method with the farthest point sampling algorithm, and the results show that our algorithm is superior in both robustness and computational efficiency. Furthermore, the generated local environment bank can be continuously updated and can potentially serve as a growing database of feature local environments, aiding in efficient dataset maintenance for constructing accurate MLPs. [ABSTRACT FROM AUTHOR]

Clathrate hydrates continue to be the focus of active research efforts due to their use in energy resources, transportation, and storage-related applications. Therefore, it is crucial to define their essential characteristics from a molecular standpoint. Understanding molecular structure in particular is crucial because it aids in understanding the mechanisms that lead to the formation or dissociation of clathrate hydrates. In the past, a wide variety of order parameters have been employed to classify and evaluate hydrate structures. An alternative approach to inventing bespoke order parameters is to apply machine learning techniques to automatically generate effective order parameters. In earlier work, we suggested a method for automatically designing novel parameters for ice and liquid water structures with Graph Neural Networks (GNNs). In this work, we use a GNN to implement our method, which can independently produce feature representations of the molecular structures. By using the TeaNet-type model in our method, it is possible to directly learn the molecular geometry and topology. This enables us to build novel parameters without prior knowledge of suitable order parameters for the structure type, discover structural differences, and classify molecular structures with high accuracy. We use this approach to classify the structures of clathrate hydrate structures: sI, sII, and sH. This innovative approach provides an appealing and highly accurate replacement for the traditional order parameters. Furthermore, our method makes clear the process of automatically designing a universal parameter for liquid water, ice, and clathrate hydrate to analyze their structures and phases. [ABSTRACT FROM AUTHOR]

Expanding the pool of stable halide perovskites with attractive optoelectronic properties is crucial to addressing current limitations in their performance as photovoltaic (PV) absorbers. In this article, we demonstrate how a high-throughput density functional theory (DFT) dataset of halide perovskite alloys can be used to train accurate surrogate models for property prediction and subsequently perform inverse design using genetic algorithm (GA). Our dataset consists of decomposition energies, bandgaps, and photovoltaic efficiencies of nearly 800 pure and mixed composition ABX3 compounds from both the GGA-PBE and HSE06 functionals, and are combined with ∼100 experimental data points collected from the literature. Multi-fidelity random forest regression models are trained on the DFT + experimental dataset for each property using descriptors that one-hot encode composition, phase, and fidelity, and additionally include well-known elemental or molecular properties of species at the A, B, and X sites. Rigorously optimized models are deployed for experiment-level prediction over >150 000 hypothetical compounds, leading to thousands of promising materials with low decomposition energy, band gap between 1 and 2 eV, and efficiency of >15%. Surrogate models are further combined with GA using an objective function to maintain chemical feasibility, minimize decomposition energy, maximize PV efficiency, and keep bandgap between 1 and 2 eV; thus, hundreds more optimal compositions and phases are discovered. We present an analysis of the screened and inverse-designed materials, visualize ternary phase diagrams generated for many systems of interest using machine learning predictions, and suggest strategies for further improvement and expansion in the future. [ABSTRACT FROM AUTHOR]

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT: an endeavor with many open questions and technical challenges. In this work, we present GradDFT a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange–correlation energy functionals. GradDFT employs a pioneering parametrization of exchange–correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, GradDFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy. [ABSTRACT FROM AUTHOR]

In this work, we propose a linear machine learning force matching approach that can directly extract pair atomic interactions from ab initio calculations in amorphous structures. The local feature representation is specifically chosen to make the linear weights a force field as a force/potential function of the atom pair distance. Consequently, this set of functions is the closest representation of the ab initio forces, given the two-body approximation and finite scanning in the configurational space. We validate this approach in amorphous silica. Potentials in the new force field (consisting of tabulated Si–Si, Si–O, and O–O potentials) are significantly different than existing potentials that are commonly used for silica, even though all of them produce the tetrahedral network structure and roughly similar glass properties. This suggests that the commonly used classical force fields do not offer fundamentally accurate representations of the atomic interaction in silica. The new force field furthermore produces a lower glass transition temperature (Tg ∼ 1800 K) and a positive liquid thermal expansion coefficient, suggesting the extraordinarily high Tg and negative liquid thermal expansion of simulated silica could be artifacts of previously developed classical potentials. Overall, the proposed approach provides a fundamental yet intuitive way to evaluate two-body potentials against ab initio calculations, thereby offering an efficient way to guide the development of classical force fields. [ABSTRACT FROM AUTHOR]

Computational exploration of the compositional spaces of materials can provide guidance for synthetic research and thus accelerate the discovery of novel materials. Most approaches employ high-throughput sampling and focus on reducing the time for energy evaluation for individual compositions, often at the cost of accuracy. Here, we present an alternative approach focusing on effective sampling of the compositional space. The learning algorithm PhaseBO optimizes the stoichiometry of the potential target material while improving the probability of and accelerating its discovery without compromising the accuracy of energy evaluation. [ABSTRACT FROM AUTHOR]

Global change is currently impacting ecosystems and their contributions to people (i.e. ecosystem services). These impacts have consequences for societies and human well-being, especially in Africa. Historically, efforts have focused on assessing global change from a social or biophysical perspective, treating them as separate entities. Yet, our understanding of impacts to social-ecological systems remains limited, particularly in the Global South, due to a lack of data, tools, and approaches accounting for social and ecological aspects of ecosystem services. This is especially relevant for cultural ecosystem services as they are less tangible. We use a simple indicator and important provider of a multitude of cultural ecosystem services, birding, to understand how climate, biodiversity, and land use change will impact cultural ecosystem services across Africa. We explore how emerging tools and data can overcome limitations in mapping and modeling cultural ecosystem services, particularly in analyzing human preferences and behavior at large spatiotemporal scales and in data-poor regions. Leveraging crowdsourced data from eBird and using machine learning techniques we map and model recreational birding to assess the underlying social-ecological relationships and the impact of future climate and environmental change. We show that bird species richness, protected areas, accessibility, and max temperature contribute most to birding suitability across the continent. Further, we show spatial shifts in the suitability of birding under three future climate scenarios (SSP126, 370, and 585). Models suggest climate and biodiversity change will increasingly constrain the flow of birding related cultural ecosystem services across Africa. This has implications for human-nature interactions, development of countries, management of protected areas, and overall human well-being in the future. More generally, we highlight opportunities for crowdsourced datasets and machine learning to integrate non-material ecosystem services in models and thus, enhance the understanding of future impacts to ecosystem services and human well-being.

UNLABELLED: There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (functional modules), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida. Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE: This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

UNLABELLED: Limosilactobacillus reuteri, a probiotic microbe instrumental to human health and sustainable food production, adapts to diverse environmental shifts via dynamic gene expression. We applied the independent component analysis (ICA) to 117 RNA-seq data sets to decode its transcriptional regulatory network (TRN), identifying 35 distinct signals that modulate specific gene sets. Our findings indicate that the ICA provides a qualitative advancement and captures nuanced relationships within gene clusters that other methods may miss. This study uncovers the fundamental properties of L. reuteris TRN and deepens our understanding of its arginine metabolism and the co-regulation of riboflavin metabolism and fatty acid conversion. It also sheds light on conditions that regulate genes within a specific biosynthetic gene cluster and allows for the speculation of the potential role of isoprenoid biosynthesis in L. reuteris adaptive response to environmental changes. By integrating transcriptomics and machine learning, we provide a system-level understanding of L. reuteris response mechanism to environmental fluctuations, thus setting the stage for modeling the probiotic transcriptome for applications in microbial food production. IMPORTANCE: We have studied Limosilactobacillus reuteri, a beneficial probiotic microbe that plays a significant role in our health and production of sustainable foods, a type of foods that are nutritionally dense and healthier and have low-carbon emissions compared to traditional foods. Similar to how humans adapt their lifestyles to different environments, this microbe adjusts its behavior by modulating the expression of genes. We applied machine learning to analyze large-scale data sets on how these genes behave across diverse conditions. From this, we identified 35 unique patterns demonstrating how L. reuteri adjusts its genes based on 50 unique environmental conditions (such as various sugars, salts, microbial cocultures, human milk, and fruit juice). This research helps us understand better how L. reuteri functions, especially in processes like breaking down certain nutrients and adapting to stressful changes. More importantly, with our findings, we become closer to using this knowledge to improve how we produce more sustainable and healthier foods with the help of microbes.

During learning, synaptic connections between excitatory neurons in the brain display considerable dynamism, with new connections being added and old connections eliminated. Synapse elimination offers an opportunity to understand the features of synapses that the brain deems dispensable. However, with limited observations of synaptic activity and plasticity in vivo, the features of synapses subjected to elimination remain poorly understood. Here, we examined the functional basis of synapse elimination in the apical dendrites of L2/3 neurons in the primary motor cortex throughout motor learning. We found no evidence that synapse elimination is facilitated by a lack of activity or other local forms of plasticity. Instead, eliminated synapses display asynchronous activity with nearby synapses, suggesting that functional synaptic clustering is a critical component of synapse survival. In addition, eliminated synapses show delayed activity timing with respect to postsynaptic output. Thus, synaptic inputs that fail to be co-active with their neighboring synapses or are mistimed with neuronal output are targeted for elimination.

First-order thalamic nuclei receive feedforward signals from peripheral receptors and relay these signals to primary sensory cortex. Primary sensory cortex, in turn, provides reciprocal feedback to first-order thalamus. Because the vast majority of sensory thalamocortical inputs target primary sensory cortex, their complementary corticothalamic neurons are assumed to be similarly restricted to primary sensory cortex. We upend this assumption by characterizing morphologically diverse neurons in multiple mid-level visual cortical areas of the primate (Macaca mulatta) brain that provide direct feedback to the primary visual thalamus, the dorsal lateral geniculate nucleus (LGN). Although the majority of geniculocortical neurons project to primary visual cortex (V1), a minority, located mainly in the koniocellular LGN layers, provide direct input to extrastriate visual cortex. These "V1-bypassing" projections may be implicated in blindsight. We hypothesized that geniculocortical inputs directly targeting extrastriate cortex should be complemented by reciprocal corticogeniculate circuits. Using virus-mediated circuit tracing, we discovered corticogeniculate neurons throughout three mid-level extrastriate areas: MT, MST, and V4. Quantitative morphological analyses revealed nonuniform distributions of unique cell types across areas. Many extrastriate corticogeniculate neurons had spiny stellate morphology, suggesting possible targeting of koniocellular LGN layers. Importantly though, multiple morphological types were observed across areas. Such morphological diversity could suggest parallel streams of V1-bypassing corticogeniculate feedback at multiple stages of the visual processing hierarchy. Furthermore, the presence of corticogeniculate neurons across visual cortex necessitates a reevaluation of the LGN as a hub for visual information rather than a simple relay.

PURPOSE: The Medical Imaging and Data Resource Center (MIDRC) was created to facilitate medical imaging machine learning (ML) research for tasks including early detection, diagnosis, prognosis, and assessment of treatment response related to the coronavirus disease 2019 pandemic and beyond. The purpose of this work was to create a publicly available metrology resource to assist researchers in evaluating the performance of their medical image analysis ML algorithms. APPROACH: An interactive decision tree, called MIDRC-MetricTree, has been developed, organized by the type of task that the ML algorithm was trained to perform. The criteria for this decision tree were that (1) users can select information such as the type of task, the nature of the reference standard, and the type of the algorithm output and (2) based on the user input, recommendations are provided regarding appropriate performance evaluation approaches and metrics, including literature references and, when possible, links to publicly available software/code as well as short tutorial videos. RESULTS: Five types of tasks were identified for the decision tree: (a) classification, (b) detection/localization, (c) segmentation, (d) time-to-event (TTE) analysis, and (e) estimation. As an example, the classification branch of the decision tree includes two-class (binary) and multiclass classification tasks and provides suggestions for methods, metrics, software/code recommendations, and literature references for situations where the algorithm produces either binary or non-binary (e.g., continuous) output and for reference standards with negligible or non-negligible variability and unreliability. CONCLUSIONS: The publicly available decision tree is a resource to assist researchers in conducting task-specific performance evaluations, including classification, detection/localization, segmentation, TTE, and estimation tasks.

UNLABELLED: Rapid proliferation is a hallmark of cancer associated with sensitivity to therapeutics that cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via molecular pathways that are incompletely understood. Here, we develop an ensemble of predictive models that elucidate how cancer mutations impact the response to common RS-inducing (RSi) agents. The models implement recent advances in deep learning to facilitate multidrug prediction and mechanistic interpretation. Initial studies in tumor cells identify 41 molecular assemblies that integrate alterations in hundreds of genes for accurate drug response prediction. These cover roles in transcription, repair, cell-cycle checkpoints, and growth signaling, of which 30 are shown by loss-of-function genetic screens to regulate drug sensitivity or replication restart. The model translates to cisplatin-treated cervical cancer patients, highlighting an RTK-JAK-STAT assembly governing resistance. This study defines a compendium of mechanisms by which mutations affect therapeutic responses, with implications for precision medicine. SIGNIFICANCE: Zhao and colleagues use recent advances in machine learning to study the effects of tumor mutations on the response to common therapeutics that cause RS. The resulting predictive models integrate numerous genetic alterations distributed across a constellation of molecular assemblies, facilitating a quantitative and interpretable assessment of drug response. This article is featured in Selected Articles from This Issue, p. 384.

The recognition and delineation of cryptic species remains a perplexing problem in systematics, evolution, and species delimitation. Once recognized as such, cryptic species complexes provide fertile ground for studying genetic divergence within the context of phenotypic and ecological divergence (or lack thereof). Herein we document the discovery of a new cryptic species of trapdoor spider, Promyrmekiaphila korematsui sp. nov. Using subgenomic data obtained via target enrichment, we document the phylogeography of the California endemic genus Promyrmekiaphila and its constituent species, which also includes P. clathrata and P. winnemem. Based on these data we show a pattern of strong geographic structuring among populations but cannot entirely discount recent gene flow among populations that are parapatric, particularly for deeply diverged lineages within P. clathrata. The genetic data, in addition to revealing a new undescribed species, also allude to a pattern of potential phenotypic differentiation where species likely come into close contact. Alternatively, phenotypic cohesion among genetically divergent P. clathrata lineages suggests that some level of gene flow is ongoing or occurred in the recent past. Despite considerable field collection efforts over many years, additional sampling in potential zones of contact for both species and lineages is needed to completely resolve the dynamics of divergence in Promyrmekiaphila at the population-species interface.

Many machine learning applications in bioinformatics currently rely on matching gene identities when analyzing input gene signatures and fail to take advantage of preexisting knowledge about gene functions. To further enable comparative analysis of OMICS datasets, including target deconvolution and mechanism of action studies, we develop an approach that represents gene signatures projected onto their biological functions, instead of their identities, similar to how the word2vec technique works in natural language processing. We develop the Functional Representation of Gene Signatures (FRoGS) approach by training a deep learning model and demonstrate that its application to the Broad Institutes L1000 datasets results in more effective compound-target predictions than models based on gene identities alone. By integrating additional pharmacological activity data sources, FRoGS significantly increases the number of high-quality compound-target predictions relative to existing approaches, many of which are supported by in silico and/or experimental evidence. These results underscore the general utility of FRoGS in machine learning-based bioinformatics applications. Prediction networks pre-equipped with the knowledge of gene functions may help uncover new relationships among gene signatures acquired by large-scale OMICs studies on compounds, cell types, disease models, and patient cohorts.

PurposeIntegrating machine learning models into electronic medical record systems can greatly enhance decision-making, patient outcomes, and value-based care in healthcare systems. Challenges related to data accessibility, privacy, and sharing can impede the development and deployment of effective predictive models in spine surgery. Federated learning (FL) offers a decentralized approach to machine learning that allows local model training while preserving data privacy, making it well-suited for healthcare settings. Our objective was to describe federated learning solutions for enhanced predictive modeling in spine surgery.MethodsThe authors reviewed the literature.ResultsFL has promising applications in spine surgery, including telesurgery, AI-based prediction models, and medical image segmentation. Implementing FL requires careful consideration of infrastructure, data quality, and standardization, but it holds the potential to revolutionize orthopedic surgery while ensuring patient privacy and data control.ConclusionsFederated learning shows great promise in revolutionizing predictive modeling in spine surgery by addressing the challenges of data privacy, accessibility, and sharing. The applications of FL in telesurgery, AI-based predictive models, and medical image segmentation have demonstrated their potential to enhance patient outcomes and value-based care.

Estimation of temporospatial clinical features of gait (CFs), such as step count and length, step duration, step frequency, gait speed, and distance traveled, is an important component of community-based mobility evaluation using wearable accelerometers. However, accurate unsupervised computerized measurement of CFs of individuals with Duchenne muscular dystrophy (DMD) who have progressive loss of ambulatory mobility is difficult due to differences in patterns and magnitudes of acceleration across their range of attainable gait velocities. This paper proposes a novel calibration method. It aims to detect steps, estimate stride lengths, and determine travel distance. The approach involves a combination of clinical observation, machine-learning-based step detection, and regression-based stride length prediction. The method demonstrates high accuracy in children with DMD and typically developing controls (TDs) regardless of the participants level of ability. Fifteen children with DMD and fifteen TDs underwent supervised clinical testing across a range of gait speeds using 10 m or 25 m run/walk (10 MRW, 25 MRW), 100 m run/walk (100 MRW), 6-min walk (6 MWT), and free-walk (FW) evaluations while wearing a mobile-phone-based accelerometer at the waist near the bodys center of mass. Following calibration by a trained clinical evaluator, CFs were extracted from the accelerometer data using a multi-step machine-learning-based process and the results were compared to ground-truth observation data. Model predictions vs. observed values for step counts, distance traveled, and step length showed a strong correlation (Pearsons r = -0.9929 to 0.9986, p < 0.0001). The estimates demonstrated a mean (SD) percentage error of 1.49% (7.04%) for step counts, 1.18% (9.91%) for distance traveled, and 0.37% (7.52%) for step length compared to ground-truth observations for the combined 6 MWT, 100 MRW, and FW tasks. Our study findings indicate that a single waist-worn accelerometer calibrated to an individuals stride characteristics using our methods accurately measures CFs and estimates travel distances across a common range of gait speeds in both DMD and TD peers.

The nervous system reorganizes memories from an early site to a late site, a commonly observed feature of learning and memory systems known as systems consolidation. Previous work has suggested learning rules by which consolidation may occur. Here, we provide conditions under which such rules are guaranteed to lead to stable convergence of learning and consolidation. We use the theory of Lyapunov functions, which enforces stability by requiring learning rules to decrease an energy-like (Lyapunov) function. We present the theory in the context of a simple circuit architecture motivated by classic models of learning in systems consolidation mediated by the cerebellum. Stability is only guaranteed if the learning rate in the late stage is not faster than the learning rate in the early stage. Further, the slower the learning rate at the late stage, the larger the perturbation the system can tolerate with a guarantee of stability. We provide intuition for this result by mapping the consolidation model to a damped driven oscillator system, and showing that the ratio of early-to late-stage learning rates in the consolidation model can be directly identified with the (square of the) oscillator's damping ratio. This work suggests the power of the Lyapunov approach to provide constraints on nervous system function.

SignificanceOver the past decade, machine learning (ML) algorithms have rapidly become much more widespread for numerous biomedical applications, including the diagnosis and categorization of disease and injury.AimHere, we seek to characterize the recent growth of ML techniques that use imaging data to classify burn wound severity and report on the accuracies of different approaches.ApproachTo this end, we present a comprehensive literature review of preclinical and clinical studies using ML techniques to classify the severity of burn wounds.ResultsThe majority of these reports used digital color photographs as input data to the classification algorithms, but recently there has been an increasing prevalence of the use of ML approaches using input data from more advanced optical imaging modalities (e.g., multispectral and hyperspectral imaging, optical coherence tomography), in addition to multimodal techniques. The classification accuracy of the different methods is reported; it typically ranges from ∼70% to 90% relative to the current gold standard of clinical judgment.ConclusionsThe field would benefit from systematic analysis of the effects of different input data modalities, training/testing sets, and ML classifiers on the reported accuracy. Despite this current limitation, ML-based algorithms show significant promise for assisting in objectively classifying burn wound severity.

Abstract: Toxic cyanobacterial blooms (CBs) are becoming more frequent globally, posing a threat to freshwater ecosystems. While making long‐range forecasts is overly challenging, predicting imminent CBs is possible from precise monitoring data of the underlying covariates. It is, however, infeasibly costly to conduct precise monitoring on a large scale, leaving most lakes unmonitored or only partially monitored. The challenge is hence to build a predictive model that can use the incomplete, partially‐monitored data to make near‐future CB predictions. By using 30 years of monitoring data for 78 water bodies in Alberta, Canada, combined with data of watershed characteristics (including natural land cover and anthropogenic land use) and meteorological conditions, we train a Bayesian network that predicts future 2‐week CB with an area under the curve (AUC) of 0.83. The only monitoring data that the model needs to reach this level of accuracy are whether the cell count and Secchi depth are low, medium, or high, which can be estimated by advanced high‐resolution imaging technology or trained local citizens. The model is robust against missing values as in the absence of any single covariate, it performs with an AUC of at least 0.78. While taking a major step toward reduced‐cost, less data‐intensive CB forecasting, our results identify those key covariates that are worth the monitoring investment for highly accurate predictions.

Radiation damage in semiconductor materials is a crucial concern for electronic applications, especially in the fields of space, military, nuclear, and medical electronics. With the advancements in semiconductor fabrication techniques and the trend of miniaturization, the quality of semiconductor materials and their susceptibility to radiation-induced defects have become more important than ever. In this context, machine learning (ML) algorithms have emerged as a promising tool to study minor radiation-induced defects in semiconductor materials. In this study, we propose a sensitive non-destructive technique for investigating radiation-induced defects using multivariate statistical analyses combined with Raman spectroscopy. Raman spectroscopy is a contactless and non-destructive method widely used to characterize semiconductor materials and their defects. The multivariate statistical methods applied in analyzing the Raman spectra provide high sensitivity in detecting minor radiation-induced defects. The proposed technique was demonstrated by categorizing 100–500 kGy irradiated GaAs wafers into samples with low and high irradiation levels using linear discrimination analysis ML algorithms. Despite the high similarity in the obtained Raman spectra, the ML algorithms correctly predicted the blind testing samples, highlighting the effectiveness of ML in defect study. This study provides a promising approach for detecting minor radiation-induced defects in semiconductor materials and can be extended to other semiconductor materials and devices. [ABSTRACT FROM AUTHOR]

The design of metallic glasses (MGs) with good properties is one of the long-standing bottlenecks in materials science and engineering, which has been relying mostly on far less efficient traditional trial-and-error methods. Even the currently popular machine learning-based forward designs, which use manual input to navigate high dimensional compositional space, often become inefficient with the increasing compositional complexity in MGs. Here, we developed an inverse design machine learning model, leveraging the variational autoencoder (VAE), to directly generate the MGs with good glass-forming ability (GFA). We demonstrate that our VAE with the property prediction model is not only an expressive generative model but also able to do accurate property prediction. Our model allows us to automatically generate novel MG compositions by performing simple operations in the latent space. After randomly generating 3000MG compositions using the model, a detailed analysis of four typical metallic alloys shows that unreported MG compositions with better glass-forming ability can be predicted. Moreover, our model facilitates the use of powerful optimization algorithms to efficiently guide the search for MGs with good GFA in the latent space. We believe that this is an efficient way to discover MGs with excellent properties. [ABSTRACT FROM AUTHOR]

The Random-Phase approximation (RPA) provides an appealing framework for semi-local density functional theory. In its Resolution-of-the-Identity (RI) approach, it is a very accurate and more cost-effective method than most other wavefunction-based correlation methods. For widespread applications, efficient implementations of nuclear gradients for structure optimizations and data sampling of machine learning approaches are required. We report a well scaling implementation of RI-RPA nuclear gradients on massively parallel computers. The approach is applied to two polymorphs of the benzene crystal obtaining very good cohesive and relative energies. Different correction and extrapolation schemes are investigated for further improvement of the results and estimations of error bars. [ABSTRACT FROM AUTHOR]

Kohn–Sham density functional theory has been the most popular method in electronic structure calculations. To fulfill the increasing accuracy requirements, new approximate functionals are needed to address key issues in existing approximations. It is well known that nonlocal components are crucial. Current nonlocal functionals mostly require orbital dependence such as in Hartree–Fock exchange and many-body perturbation correlation energy, which, however, leads to higher computational costs. Deviating from this pathway, we describe functional nonlocality in a new approach. By partitioning the total density to atom-centered local densities, a many-body expansion is proposed. This many-body expansion can be truncated at one-body contributions, if a base functional is used and an energy correction is approximated. The contribution from each atom-centered local density is a single finite-range nonlocal functional that is universal for all atoms. We then use machine learning to develop this universal atom-centered functional. Parameters in this functional are determined by fitting to data that are produced by high-level theories. Extensive tests on several different test sets, which include reaction energies, reaction barrier heights, and non-covalent interaction energies, show that the new functional, with only the density as the basic variable, can produce results comparable to the best-performing double-hybrid functionals, (for example, for the thermochemistry test set selected from the GMTKN55 database, BLYP based machine learning functional gives a weighted total mean absolute deviations of 3.33 kcal/mol, while DSD-BLYP-D3(BJ) gives 3.28 kcal/mol) with a lower computational cost. This opens a new pathway to nonlocal functional development and applications. [ABSTRACT FROM AUTHOR]

The carbon nano-peapod is a representative structure with interlayer van der Waals (vdW) interactions, in which encapsulated fullerene molecules play a critical role in modulating the transport properties of the carbon nanotubes (CNTs). In particular, their influence on the thermal transport characteristics has been the focal point of considerable attention. In this study, we trained an accurate machine learning potential for fullerene-encapsulated CNTs based on the efficient NEP model to investigate their thermal properties. Using equilibrium molecular dynamics simulation along with the spectral decomposition method for thermal conductivity, we find that the thermal conductivity of fullerene-encapsulated CNTs is roughly 55 % lower than that of empty CNTs, aligning with experimental observations for CNT bundles with fullerene encapsulation [Kodama et al., Nat. Mater. 16, 892 (2017)]. The research suggests that weak vdW interactions between both the fullerene and CNTs, as well as between fullerene molecules themselves, hinder phonon propagation. The encapsulated fullerene contributes to an increase in phonon scattering within the CNTs, ultimately leading to a reduction in thermal conductivity. We utilized machine learning potential to investigate the structure of fullerene-encapsulated CNTs and their heat transport property. This approach provides valuable insights for performance research of complex systems featuring interlayer vdW interactions. [ABSTRACT FROM AUTHOR]

Understanding interparticle interactions has been one of the most important topics of research in the field of micro/nanoscale materials. Many significant characteristics of such materials directly stem from the way their building blocks interact with each other. In this work, we investigate the efficacy of a specific category of Machine Learning (ML) methods known as interaction networks in predicting interparticle interactions within colloidal systems. We introduce and study Local Neighborhood Graph Neural Networks (LN-GNNs), defined according to the local environment of colloidal particles derived from particle trajectory data. The LN-GNN framework is trained for unique categories of particle neighborhood environments in order to predict interparticle interactions. We compare the performance of the LN-GNN to a baseline interaction network with a simpler architecture and to an Instance-Based ML algorithm, which is computationally more expensive. We find that the prediction performance of LN-GNN measured as an average normalized mean absolute error outperforms the baseline interaction network by a factor of 2–10 for different local neighborhood configurations. Furthermore, LN-GNN's performance turns out to be very comparable to the instance-based ML framework while being an order of magnitude less expensive in terms of the required computation time. The results of this work can provide the foundations for establishing accurate models of colloidal particle interactions that are derived from real particle trajectory data. [ABSTRACT FROM AUTHOR]

Machine learning (ML) of kinetic energy functionals (KEFs), in particular kinetic energy density (KED) functionals, is a promising way to construct KEFs for orbital-free density functional theory (DFT). Neural networks and kernel methods including Gaussian process regression (GPR) have been used to learn Kohn–Sham (KS) KED from density-based descriptors derived from KS DFT calculations. The descriptors are typically expressed as functions of different powers and derivatives of the electron density. This can generate large and extremely unevenly distributed datasets, which complicates effective application of ML techniques. Very uneven data distributions require many training datapoints, can cause overfitting, and can ultimately lower the quality of an ML KED model. We show that one can produce more accurate ML models from fewer data by working with smoothed density-dependent variables and KED. Smoothing palliates the issue of very uneven data distributions and associated difficulties of sampling while retaining enough spatial structure necessary for working within the paradigm of KEDF. We use GPR as a function of smoothed terms of the fourth order gradient expansion and KS effective potential and obtain accurate and stable (with respect to different random choices of training points) kinetic energy models for Al, Mg, and Si simultaneously from as few as 2000 samples (about 0.3% of the total KS DFT data). In particular, accuracies on the order of 1% in a measure of the quality of energy–volume dependence B ′ = E V 0 − Δ V − 2 E V 0 + E ( V 0 + Δ V) Δ V / V 0 2 (where V0 is the equilibrium volume and ΔV is a deviation from it) are obtained simultaneously for all three materials. [ABSTRACT FROM AUTHOR]

We investigated the accelerated prediction of the thermal conductivity of materials through end-to-end structure-based approaches employing machine learning methods. Due to the non-availability of high-quality thermal conductivity data, we first performed high-throughput calculations based on first principles and the Boltzmann transport equation for 225 materials, effectively more than doubling the size of the existing dataset. We assessed the performance of state-of-the-art machine learning models for thermal conductivity prediction on this expanded dataset and observed that all these models suffered from overfitting. To address this issue, we introduced a different graph-based neural network model, which demonstrated more consistent and regularized performance across all evaluated datasets. Nevertheless, the best mean absolute percentage error achieved on the test dataset remained in the range of 50–60%. This suggests that while these models are valuable for expediting material screening, their current accuracy is still limited. [ABSTRACT FROM AUTHOR]

Coarse-grained (CG) molecular dynamics can be a powerful method for probing complex processes. However, most CG force fields use pairwise nonbonded interaction potentials sets, which can limit their ability to capture complex multi-body phenomena such as the hydrophobic effect. As the hydrophobic effect primarily manifests itself due to the nonpolar solute affecting the nearby hydrogen bonding network in water, capturing such effects using a simple one CG site or "bead" water model is a challenge. In this work, we systematically test the ability of CG one site water models for capturing critical features of the solvent environment around a hydrophobe as well as the potential of mean force (PMF) of neopentane association. We study two bottom-up models: a simple pairwise (SP) force-matched water model constructed using the multiscale coarse-graining method and the Bottom-Up Many-Body Projected Water (BUMPer) model, which has implicit three-body correlations. We also test the top-down monatomic (mW) and the Machine Learned mW (ML-mW) water models. The mW models perform well in capturing structural correlations but not the energetics of the PMF. BUMPer outperforms SP in capturing structural correlations and also gives an accurate PMF in contrast to the two mW models. Our study highlights the importance of including three-body interactions in CG water models, either explicitly or implicitly, while in general highlighting the applicability of bottom-up CG water models for studying hydrophobic effects in a quantitative fashion. This assertion comes with a caveat, however, regarding the accuracy of the enthalpy–entropy decomposition of the PMF of hydrophobe association. [ABSTRACT FROM AUTHOR]

In public libraries, especially those in rural settings, it is important that every dime of library funding is leveraged effectively into serving the community. As part of a year-long project beginning in January 2023, we are evaluating item-level cost-effectiveness for each circulating item housed at the public library in Lakeville, Indiana. Through the use of big(ish) data, some custom Python scripting, and machine learning algorithms we hope to answer: How much money is saved by library patrons through their use of the public library's physical collection? How much money is saved by the community through the operation of a public library based on the use of the circulating collection? And are there any non-obvious traits which make an item or title a more or less cost-effective circulating asset? In this column, I will describe the scripts, share initial findings, discuss challenges, and investigate next steps. [ABSTRACT FROM AUTHOR]