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GPU-accelerated on-the-fly nonadiabatic dynamics is enabled by interfacing the linearized semiclassical dynamics approach with the TeraChem electronic structure program. We describe the computational workflow of the "PySCES" code interface, a Python code for semiclassical dynamics with on-the-fly electronic structure, including parallelization over multiple GPU nodes. We showcase the abilities of this code and present timings for two benchmark systems: fulvene solvated in acetonitrile and a charge transfer system in which a photoexcited zinc-phthalocyanine donor transfers charge to a fullerene acceptor through multiple electronic states on an ultrafast timescale. Our implementation paves the way for an efficient semiclassical approach to model the nonadiabatic excited state dynamics of complex molecules, materials, and condensed phase systems. [ABSTRACT FROM AUTHOR]

CuGBasis is a free and open-source CUDA®/Python library for efficient computation of scalar, vector, and matrix quantities crucial for the post-processing of electronic structure calculations. CuGBasis integrates high-performance Graphical Processing Unit (GPU) computing with the ease and flexibility of Python programming, making it compatible with a vast ecosystem of libraries. We showcase its utility as a Python library and demonstrate its seamless interoperability with existing Python software to gain chemical insight from quantum chemistry calculations. Leveraging GPU-accelerated code, cuGBasis exhibits remarkable performance, making it highly applicable to larger systems or large databases. Our benchmarks reveal a 100-fold performance gain compared to alternative software packages, including serial/multi-threaded Central Processing Unit and GPU implementations. This paper outlines various features and computational strategies that lead to cuGBasis's enhanced performance, guiding developers of GPU-accelerated code. [ABSTRACT FROM AUTHOR]

The Journal of Chemical Physics has released a special issue focused on software for atomistic machine learning. This issue aims to address the lack of journals dedicated to publishing scientific software papers. The collection of papers in this issue provides insight into the tools and goals of software implementations in the field of atomistic machine learning. The articles cover a range of topics, including machine-learning interatomic potentials, sampling, dataset repositories, workflows, and auxiliary tooling and analysis. The article concludes by emphasizing the importance of software implementations in the field and encourages further submissions on relevant topics. [Extracted from the article]

PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density. [ABSTRACT FROM AUTHOR]

A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program's environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree–Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. This package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications. [ABSTRACT FROM AUTHOR]

We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software application to design custom coarse-grained (CG) models, as well as pre-defined models of polyelectrolytes, peptides, and globular proteins in the Extensible Simulation Package for Research on Soft Matter (ESPResSo). The Python interface of ESPResSo offers a flexible framework, capable of building custom CG models from scratch. As a downside, building CG models from scratch is prone to mistakes, especially for newcomers in the field of CG modeling, or for molecules with complex architectures. The pyMBE module builds CG models in ESPResSo using a hierarchical bottom-up approach, providing a robust tool to automate the setup of CG models and helping new users prevent common mistakes. ESPResSo features the constant pH (cpH) and grand-reaction (G-RxMC) methods, which have been designed to study chemical reaction equilibria in macromolecular systems with many reactive species. However, setting up these methods for systems, which contain several types of reactive groups, is an error-prone task, especially for beginners. The pyMBE module enables the automatic setup of cpH and G-RxMC simulations in ESPResSo, lowering the barrier for newcomers and opening the door to investigate complex systems not studied with these methods yet. To demonstrate some of the applications of pyMBE, we showcase several case studies where we successfully reproduce previously published simulations of charge-regulating peptides and globular proteins in bulk solution and weak polyelectrolytes in dialysis. The pyMBE module is publicly available as a GitHub repository (https://github.com/pyMBE-dev/pyMBE), which includes its source code and various sample and test scripts, including the ones that we used to generate the data presented in this article. [ABSTRACT FROM AUTHOR]

Sire is a Python/C++ library that is used both to prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of many other programs and libraries. This empowers researchers to use sire to write a single script that can, for example, load a molecule from a PDBx/mmCIF file via Gemmi, perform SMARTS searches via RDKit, parameterize molecules using BioSimSpace, run GPU-accelerated molecular dynamics via OpenMM, and then display the resulting dynamics trajectory in a NGLView Jupyter notebook 3D molecular viewer. This functionality is built on by BioSimSpace, which uses sire's molecular information engine to interconvert with programs such as GROMACS, NAMD, Amber, and AmberTools for automated molecular parameterization and the running of molecular dynamics, metadynamics, and alchemical free energy workflows. Sire comes complete with a powerful molecular information search engine, plus trajectory loading and editing, analysis, and energy evaluation engines. This, when combined with an in-built computer algebra system, gives substantial flexibility to researchers to load, search for, edit, and combine molecular information from multiple sources and use that to drive novel algorithms by combining functionality from other programs. Sire is open source (GPL3) and is available via conda and at a free Jupyter notebook server at https://try.openbiosim.org. Sire is supported by the not-for-profit OpenBioSim community interest company. [ABSTRACT FROM AUTHOR]

Grid is a free and open-source Python library for constructing numerical grids to integrate, interpolate, and differentiate functions (e.g., molecular properties), with a strong emphasis on facilitating these operations in computational chemistry and conceptual density functional theory. Although designed, maintained, and released as a stand-alone Python library, Grid was originally developed for molecular integration, interpolation, and solving the Poisson equation in the HORTON and ChemTools packages. Grid is designed to be easy to use, extend, and maintain; this is why we use Python and adopt many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. We leverage popular scientific packages, such as NumPy and SciPy, to ensure high efficiency and optimized performance in grid development. This article is the official release note of the Grid library showcasing its unique functionality and scope. [ABSTRACT FROM AUTHOR]

Wavelets and multiwavelets have lately been adopted in quantum chemistry to overcome challenges presented by the two main families of basis sets: Gaussian atomic orbitals and plane waves. In addition to their numerical advantages (high precision, locality, fast algorithms for operator application, linear scaling with respect to system size, to mention a few), they provide a framework that narrows the gap between the theoretical formalism of the fundamental equations and the practical implementation in a working code. This realization led us to the development of the Python library called VAMPyR (Very Accurate Multiresolution Python Routines). VAMPyR encodes the binding to a C++ library for multiwavelet calculations (algebra and integral and differential operator application) and exposes the required functionality to write a simple Python code to solve, among others, the Hartree–Fock equations, the generalized Poisson equation, the Dirac equation, and the time-dependent Schrödinger equation up to any predefined precision. In this study, we will outline the main features of multiresolution analysis using multiwavelets and we will describe the design of the code. A few illustrative examples will show the code capabilities and its interoperability with other software platforms. [ABSTRACT FROM AUTHOR]

HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade. [ABSTRACT FROM AUTHOR]

We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe–Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn–Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW. [ABSTRACT FROM AUTHOR]

TurboGenius is an open-source Python package designed to fully control ab initio quantum Monte Carlo (QMC) jobs using a Python script, which allows one to perform high-throughput calculations combined with TurboRVB [Nakano et al. J. Phys. Chem. 152, 204121 (2020)]. This paper provides an overview of the TurboGenius package and showcases several results obtained in a high-throughput mode. For the purpose of performing high-throughput calculations with TurboGenius, we implemented another open-source Python package, TurboWorkflows, that enables one to construct simple workflows using TurboGenius. We demonstrate its effectiveness by performing (1) validations of density functional theory (DFT) and QMC drivers as implemented in the TurboRVB package and (2) benchmarks of Diffusion Monte Carlo (DMC) calculations for several datasets. For (1), we checked inter-package consistencies between TurboRVB and other established quantum chemistry packages. By doing so, we confirmed that DFT energies obtained by PySCF are consistent with those obtained by TurboRVB within the local density approximation (LDA) and that Hartree–Fock (HF) energies obtained by PySCF and Quantum Package are consistent with variational Monte Carlo energies obtained by TurboRVB with the HF wavefunctions. These validation tests constitute a further reliability check of the TurboRVB package. For (2), we benchmarked the atomization energies of the Gaussian-2 set, the binding energies of the S22, A24, and SCAI sets, and the equilibrium lattice parameters of 12 cubic crystals using DMC calculations. We found that, for all compounds analyzed here, the DMC calculations with the LDA nodal surface give satisfactory results, i.e., consistent either with high-level computational or with experimental reference values. [ABSTRACT FROM AUTHOR]

Many-body dispersion (MBD) is a powerful framework to treat van der Waals (vdW) dispersion interactions in density-functional theory and related atomistic modeling methods. Several independent implementations of MBD with varying degree of functionality exist across a number of electronic structure codes, which both limits the current users of those codes and complicates dissemination of new variants of MBD. Here, we develop and document libMBD, a library implementation of MBD that is functionally complete, efficient, easy to integrate with any electronic structure code, and already integrated in FHI-aims, DFTB+, VASP, Q-Chem, CASTEP, and Quantum ESPRESSO. libMBD is written in modern Fortran with bindings to C and Python, uses MPI/ScaLAPACK for parallelization, and implements MBD for both finite and periodic systems, with analytical gradients with respect to all input parameters. The computational cost has asymptotic cubic scaling with system size, and evaluation of gradients only changes the prefactor of the scaling law, with libMBD exhibiting strong scaling up to 256 processor cores. Other MBD properties beyond energy and gradients can be calculated with libMBD, such as the charge-density polarization, first-order Coulomb correction, the dielectric function, or the order-by-order expansion of the energy in the dipole interaction. Calculations on supramolecular complexes with MBD-corrected electronic structure methods and a meta-review of previous applications of MBD demonstrate the broad applicability of the libMBD package to treat vdW interactions. [ABSTRACT FROM AUTHOR]

Predictive atomistic simulations are increasingly employed for data intensive high throughput studies that take advantage of constantly growing computational resources. To handle the sheer number of individual calculations that are needed in such studies, workflow management packages for atomistic simulations have been developed for a rapidly growing user base. These packages are predominantly designed to handle computationally heavy ab initio calculations, usually with a focus on data provenance and reproducibility. However, in related simulation communities, e.g., the developers of machine learning interatomic potentials (MLIPs), the computational requirements are somewhat different: the types, sizes, and numbers of computational tasks are more diverse and, therefore, require additional ways of parallelization and local or remote execution for optimal efficiency. In this work, we present the atomistic simulation and MLIP fitting workflow management package wfl and Python remote execution package ExPyRe to meet these requirements. With wfl and ExPyRe, versatile atomic simulation environment based workflows that perform diverse procedures can be written. This capability is based on a low-level developer-oriented framework, which can be utilized to construct high level functionality for user-friendly programs. Such high level capabilities to automate machine learning interatomic potential fitting procedures are already incorporated in wfl, which we use to showcase its capabilities in this work. We believe that wfl fills an important niche in several growing simulation communities and will aid the development of efficient custom computational tasks. [ABSTRACT FROM AUTHOR]

Accurate and explainable artificial-intelligence (AI) models are promising tools for accelerating the discovery of new materials. Recently, symbolic regression has become an increasingly popular tool for explainable AI because it yields models that are relatively simple analytical descriptions of target properties. Due to its deterministic nature, the sure-independence screening and sparsifying operator (SISSO) method is a particularly promising approach for this application. Here, we describe the new advancements of the SISSO algorithm, as implemented into SISSO++, a C++ code with Python bindings. We introduce a new representation of the mathematical expressions found by SISSO. This is a first step toward introducing "grammar" rules into the feature creation step. Importantly, by introducing a controlled nonlinear optimization to the feature creation step, we expand the range of possible descriptors found by the methodology. Finally, we introduce refinements to the solver algorithms for both regression and classification, which drastically increase the reliability and efficiency of SISSO. For all these improvements to the basic SISSO algorithm, we not only illustrate their potential impact but also fully detail how they operate both mathematically and computationally. [ABSTRACT FROM AUTHOR]

Spherical harmonics provide a smooth, orthogonal, and symmetry-adapted basis to expand functions on a sphere, and they are used routinely in physical and theoretical chemistry as well as in different fields of science and technology, from geology and atmospheric sciences to signal processing and computer graphics. More recently, they have become a key component of rotationally equivariant models in geometric machine learning, including applications to atomic-scale modeling of molecules and materials. We present an elegant and efficient algorithm for the evaluation of the real-valued spherical harmonics. Our construction features many of the desirable properties of existing schemes and allows us to compute Cartesian derivatives in a numerically stable and computationally efficient manner. To facilitate usage, we implement this algorithm in sphericart, a fast C++ library that also provides C bindings, a Python API, and a PyTorch implementation that includes a GPU kernel. [ABSTRACT FROM AUTHOR]

Simulation has become an essential component of designing and developing scientific experiments. The conventional procedural approach to coding simulations of complex experiments is often error-prone, hard to interpret, and inflexible, making it hard to incorporate changes such as algorithm updates, experimental protocol modifications, and looping over experimental parameters. We present mmodel, a Python framework designed to accelerate the writing of experimental simulation packages. mmodel uses a graph-theory approach to represent the experiment steps and can rewrite its own code to implement modifications, such as adding a loop to vary simulation parameters systematically. The framework aims to avoid duplication of effort, increase code readability and testability, and decrease development time. [ABSTRACT FROM AUTHOR]

Machine-learning (ML)-based interatomic potentials are increasingly popular in material modeling, enabling highly accurate simulations with thousands and millions of atoms. However, the performance of machine-learned potentials depends strongly on the choice of hyperparameters—that is, of those parameters that are set before the model encounters data. This problem is particularly acute where hyperparameters have no intuitive physical interpretation and where the corresponding optimization space is large. Here, we describe an openly available Python package that facilitates hyperparameter optimization across different ML potential fitting frameworks. We discuss methodological aspects relating to the optimization itself and to the selection of validation data, and we show example applications. We expect this package to become part of a wider computational framework to speed up the mainstream adaptation of ML potentials in the physical sciences. [ABSTRACT FROM AUTHOR]

Identifying a reduced set of collective variables is critical for understanding atomistic simulations and accelerating them through enhanced sampling techniques. Recently, several methods have been proposed to learn these variables directly from atomistic data. Depending on the type of data available, the learning process can be framed as dimensionality reduction, classification of metastable states, or identification of slow modes. Here, we present mlcolvar, a Python library that simplifies the construction of these variables and their use in the context of enhanced sampling through a contributed interface to the PLUMED software. The library is organized modularly to facilitate the extension and cross-contamination of these methodologies. In this spirit, we developed a general multi-task learning framework in which multiple objective functions and data from different simulations can be combined to improve the collective variables. The library's versatility is demonstrated through simple examples that are prototypical of realistic scenarios. [ABSTRACT FROM AUTHOR]

In the past few decades, there has been a significant focus on computational methods for periodic systems. In some of these works, various considerations were outlined to establish and categorize algorithms for designing periodic discrete‐time state‐space systems. In a recent work, a direct algorithm was proposed to obtain low‐dimensional realizations from a proper lifted system in state‐space form. This algorithm, which lies in a category often called "fast" algorithms, takes advantage on the structure of lifted representations being highly efficient. In a 1993 work by Ching‐An Lin and Chwan‐Wen King, another direct algorithm was proposed that appears to be quite similar to the algorithm outlined recently. These two algorithms generate state‐space periodic realizations that are both uniform, meaning that the dimension of the state remains constant at each time instant. The algorithms proposed in these two works require both a rank test applied to two different types of matrices, Kℓ$$ {K}_{\ell } $$ and ℓM$$ {}^{\ell }M $$, respectively (in chronologic order). Although the former algorithm establishes an upper bound for the state dimension à priori, by determining the maximum rank of the matrices Kℓ$$ {K}_{\ell } $$, the latter obtains an upper bound à posteriori, based on the rank of matrices ℓM$$ {}^{\ell }M $$. In this work, we proved that these matrices Kℓ$$ {K}_{\ell } $$ and ℓM$$ {}^{\ell }M $$ have the same rank for all ℓ$$ \ell $$, and we use this information to revise the latter algorithm and assess whether it represents an improvement. The algorithm presented as well its modified versions that were coded using the Python programming language. Surprisingly, the revised algorithm did not demonstrate any significant improvement in terms of computational efficiency. [ABSTRACT FROM AUTHOR]

Recently, wireless body area network (WBAN) becomes a hot research topic in the advanced healthcare system. The WBAN plays a vital role in monitoring the physiological parameters of the human body with sensors. The sensors are small in size, and it has a small-sized battery with limited life. Hence, the energy is limited in the multi-hop routing process. The patient data is collected by the sensor, and the data are transmitted with high energy consumption. It causes failure in the data transmission path. To avoid this, the data transmission process should be optimized. This paper presents an advanced authentication and energy-efficient routing protocol (AAERP) for optimal routing paths in WBAN. Patients' data are aggregated from the WBAN through the IoMT devices in the initial stage. To secure the patient's private data, a hybrid mechanism of the elliptic curve cryptosystem (ECC) and Paillier cryptosystem is proposed for the data encryption process. Data security is improved by authenticating the data before transmission using an encryption algorithm. Before the routing process, the data encryption approach converts the original plain text data into ciphertext data. This encryption approach assists in avoiding intrusions in the network system. The encrypted data are optimally routed with the help of the teamwork optimization algorithm (TOA) approach. The optimal path selection using this optimization technique improves the effectiveness and robustness of the system. The experimental setup is performed by using Python software. The efficacy of the proposed model is evaluated by solving parameters like network lifetime, network throughput, residual energy, success rate, number of packets received, number of packets sent, and number of packets dropped. The performance of the proposed model is measured by comparing the obtained results with several existing models. [ABSTRACT FROM AUTHOR]

Content-based image retrieval (CBIR) systems are vital for managing the large volumes of data produced by medical imaging technologies. They enable efficient retrieval of relevant medical images from extensive databases, supporting clinical diagnosis, treatment planning, and medical research.This study aims to enhance CBIR systems’ effectiveness in medical image analysis by introducing the VisualSift Ensembling Integration with Attention Mechanisms (VEIAM). VEIAM seeks to improve diagnostic accuracy and retrieval efficiency by integrating robust feature extraction with dynamic attention mechanisms.VEIAM combines Scale-Invariant Feature Transform (SIFT) with selective attention mechanisms to emphasize crucial regions within medical images dynamically. Implemented in Python, the model integrates seamlessly into existing medical image analysis workflows, providing a robust and accessible tool for clinicians and researchers.The proposed VEIAM model demonstrated an impressive accuracy of 97.34% in classifying and retrieving medical images. This performance indicates VEIAM’s capability to discern subtle patterns and textures critical for accurate diagnostics.By merging SIFT-based feature extraction with attention processes, VEIAM offers a discriminatively powerful approach to medical image analysis. Its high accuracy and efficiency in retrieving relevant medical images make it a promising tool for enhancing diagnostic processes and supporting medical research in CBIR systems. [ABSTRACT FROM AUTHOR]

This article presents an investment recommender system based on an Adaptive Neuro-Fuzzy Inference System (ANFIS) and pre-trained weights from a Multimodal Neural Network (MNN). The model is designed to support the investment process for the customers and takes into consideration seven factors to implement the proposed investment system model through the customer or potential investor data set. The system takes input from a web-based questionnaire that collects data on investors' preferences and investment goals. The data is then preprocessed and clustered using ETL tools, JMP, MATLAB, and Python. The ANFIS-based recommender system is designed with three inputs and one output and trained using a hybrid approach over three epochs with 188 data pairs and 18 fuzzy rules. The system's performance is evaluated using metrics such as RMSE, accuracy, precision, recall, and F1-score. The system is also designed to incorporate expert feedback and opinions from investors to customize and improve investment recommendations. The article concludes that the proposed ANFIS-based investment recommender system is effective and accurate in generating investment recommendations that meet investors' preferences and goals. [ABSTRACT FROM AUTHOR]

Data-driven models that act as surrogates for computationally costly 3D topology optimization techniques are very popular because they help alleviate multiple time-consuming 3D finite element analyses during optimization. In this study, one such 3D CNN-based surrogate model for the topology optimization of Schoen's gyroid triply periodic minimal surface unit cell is investigated. Gyroidlike unit cells are designed using a voxel algorithm and homogenization-based topology optimization codes in MATLAB. A few such optimization data are used as input-output for supervised learning of the topology-optimization process via the 3D CNN model in Python code. These models could then be used to instantaneously predict the optimized unit cell geometry for any topology parameters. The high accuracy of the model was demonstrated by a low mean square error metric and a high Dice coefficient metric. The model has the major disadvantage of running numerous costly topology optimization runs but has the advantages that the trained model can be reused for different cases of TO and that the methodology of the accelerated design of 3D metamaterials can be extended for designing any complex, computationally costly problems of metamaterials with multi-objective properties or multiscale applications. The main purpose of this paper is to provide the complete associated MATLAB and PYTHON codes for optimizing the topology of any cellular structure and predicting new topologies using deep learning for educational purposes. [ABSTRACT FROM AUTHOR]

Natural products are molecules that fulfil a range of important ecological functions. Many natural products have been exploited for pharmaceutical and agricultural applications. In contrast to many other specialised metabolites, the products of modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) systems can often (partially) be predicted from the DNA sequence of the biosynthetic gene clusters. This is because the biosynthetic pathways of NRPS and PKS systems adhere to consistent rulesets. These universal biosynthetic rules can be leveraged to generate biosynthetic models of biosynthetic pathways. While these principles have been largely deciphered, software that leverages these rules to automatically generate visualisations of biosynthetic models has not yet been developed. To enable high-quality automated visualisations of natural product biosynthetic pathways, we developed RAIChU (Reaction Analysis through Illustrating Chemical Units), which produces depictions of biosynthetic transformations of PKS, NRPS, and hybrid PKS/NRPS systems from predicted or experimentally verified module architectures and domain substrate specificities. RAIChU also boasts a library of functions to perform and visualise reactions and pathways whose specifics (e.g., regioselectivity, stereoselectivity) are still difficult to predict, including terpenes, ribosomally synthesised and posttranslationally modified peptides and alkaloids. Additionally, RAIChU includes 34 prevalent tailoring reactions to enable the visualisation of biosynthetic pathways of fully maturated natural products. RAIChU can be integrated into Python pipelines, allowing users to upload and edit results from antiSMASH, a widely used BGC detection and annotation tool, or to build biosynthetic PKS/NRPS systems from scratch. RAIChU's cluster drawing correctness (100%) and drawing readability (97.66%) were validated on 5000 randomly generated PKS/NRPS systems, and on the MIBiG database. The automated visualisation of these pathways accelerates the generation of biosynthetic models, facilitates the analysis of large (meta-) genomic datasets and reduces human error. RAIChU is available at https://github.com/BTheDragonMaster/RAIChU and https://pypi.org/project/raichu. Scientific contribution RAIChU is the first software package capable of automating high-quality visualisations of natural product biosynthetic pathways. By leveraging universal biosynthetic rules, RAIChU enables the depiction of complex biosynthetic transformations for PKS, NRPS, ribosomally synthesised and posttranslationally modified peptide (RiPP), terpene and alkaloid systems, enhancing predictive and analytical capabilities. This innovation not only streamlines the creation of biosynthetic models, making the analysis of large genomic datasets more efficient and accurate, but also bridges a crucial gap in predicting and visualising the complexities of natural product biosynthesis. [ABSTRACT FROM AUTHOR]

Canopy imaging offers a non-destructive, efficient way to objectively measure canopy size, detect stress symptoms, and assess pigment concentrations. While it is faster and easier than traditional destructive methods, manual image analysis, including segmentation and evaluation, can be time-consuming. To make imaging more widely accessible, it's essential to reduce the cost of imaging systems and automate the analysis process. We developed a low-cost imaging system with automated analysis using an embedded microcomputer equipped with a monochrome camera and a filter for a total hardware cost of ~USD 500. Our imaging system takes images under blue, green, red, and infrared light, as well as chlorophyll fluorescence. The system uses a Python-based program to collect and analyze images automatically. The multi-spectral imaging system separates plants from the background using a chlorophyll fluorescence image, which is also used to quantify canopy size. The system then generates normalized difference vegetation index (NDVI, "greenness") images and histograms, providing quantitative, spatially resolved information. We verified that these indices correlate with leaf chlorophyll content and can easily add other indices by installing light sources with the desired spectrums. The low cost of the system can make this imaging technology widely available. [ABSTRACT FROM AUTHOR]

In situ wavefront sensing plays a critical role in the delivery of high‐quality beams for X‐ray experiments. X‐ray speckle‐based techniques stand out among other in situ techniques for their easy experimental setup and various data acquisition modes. Although X‐ray speckle‐based techniques have been under development for more than a decade, there are still no user‐friendly software packages for new researchers to begin with. Here, we present an open‐source Python package, spexwavepy, for X‐ray wavefront sensing using speckle‐based techniques. This Python package covers a variety of X‐ray speckle‐based techniques, provides plenty of examples with real experimental data and offers detailed online documentation for users. We hope it can help new researchers learn and apply the speckle‐based techniques for X‐ray wavefront sensing to synchrotron radiation and X‐ray free‐electron laser beamlines. [ABSTRACT FROM AUTHOR]

The herein proposed Python package pflacco provides a set of numerical features to characterize single-objective continuous and constrained optimization problems. Thereby, pflacco addresses two major challenges in the area of optimization. Firstly, it provides the means to develop an understanding of a given problem instance, which is crucial for designing, selecting, or configuring optimization algorithms in general. Secondly, these numerical features can be utilized in the research streams of automated algorithm selection and configuration. While the majority of these landscape features are already available in the R package flacco, our Python implementation offers these tools to an even wider audience and thereby promotes research interests and novel avenues in the area of optimization. [ABSTRACT FROM AUTHOR]

This article discusses the use of 3D camera systems and accompanying software in physics instruction. The authors describe a Python program that can track and analyze the momentum of a midair collision between two playground balls. The program is freely available for instructors and can be used in student lab settings or as an instructor-led exercise. The article provides detailed information on the camera system used, the data collection and analysis process, and the results obtained. The authors conclude that the use of 3D cameras and tracking software expands the possibilities for physics experiments and enhances students' understanding of complex systems. [Extracted from the article]

• Temporary continuous observation task using non-customized constellation is studied. • A hybrid method for multi-satellite scheduling and task planning is proposed. • A joint simulation software system is developed via STK and Python. • The proposed technique has higher efficiency and target adaptability. This paper put forward a method to address the problem, of how to select multiple satellites from a given heterogeneous constellation and plan their tasks to implement a temporary mission for ground or aerial targets successive observation, while hardly affecting the constellation's original mission as much as possible. First, considering the observation geometric constraints of the satellite on the target, an observability analysis model for effective observation of the satellite on the target is established to characterize the observable spatio-temporal scope. Considering the time-length requirement of sustained observation on the target, a multi-satellite-to-target sustained observation model is constructed for the scheduling of satellites. Second, to address the problem of selecting task satellites in a given heterogeneous constellation, a mathematical model for task planning is established to maximize observation benefits and minimize task burdens. Third, a hybrid method of multi-satellite scheduling and task planning is designed with fault tolerance, based on dynamic programming and an improved contract network protocol algorithm. Next, a joint simulation software system is established through the secondary development of STK and Python, which includes satellite-target observability analysis, task satellite selection, task allocation and planning, and full process visible demonstration functions. Finally, simulation cases verified the effectiveness and superiority of the proposed technique. [ABSTRACT FROM AUTHOR]

The Adaptative neuro-fuzzy inference system (ANFIS) has shown great potential in processing practical data from control, prediction, and inference applications, reflecting advantages in both high performance and system interpretability as a result of the hybridization of neural networks and fuzzy systems. Matlab has been a prevalent platform that allows to utilize and deploy ANFIS conveniently. On the other hand, due to the recent popularity of machine learning and deep learning, which are predominantly Python-based, implementations of ANFIS in Python have attracted recent attention. Although there are a few Python-based ANFIS implementations, none of them are directly compatible with scikit-learn, one of the most frequently used libraries in machine learning. As such, this paper proposes Scikit-ANFIS, a novel scikit-learn compatible Python implementation for ANFIS by adopting a uniform format such as fit() and predict() functions to provide the same interface as scikit-learn. Our Scikit-ANFIS is designed in a user-friendly way to not only manually generate a general fuzzy system and train it with the ANFIS method but also to automatically create an ANFIS fuzzy system. We also provide four kinds of representative cases to show that Scikit-ANFIS represents a valuable addition to the scikit-learn compatible Python software that supports ANFIS fuzzy reasoning. Experimental results on four datasets show that our Scikit-ANFIS outperforms recent Python-based implementations while achieving parallel performance to ANFIS in Matlab, a standard implementation officially realized by Matlab, which indicates the performance advantages and application convenience of our software. [ABSTRACT FROM AUTHOR]

Poland has experienced a remarkable growth in renewable energy adoption, notably in photovoltaic (PV) solar systems. The majority of installations are prosumer PV micro-installations, exceeding predicted capacity targets outlined in the Energy Policy of Poland until 2040. Despite the significant growth in installed PV capacity, there is still a lack of comprehensive research focusing on fast assessment of energy generation capacity for solar PV micro-systems. This study aims to address this gap by providing a comprehensive analysis of energy production potential across different configurations and locations in Poland. Using geocoding techniques, solar irradiation data from PVGIS database and pvlib-python library, a methodology was developed to rapidly estimate energy generation from 1 kWp solar PV systems. Results reveal spatial disparities in energy yield from solar PV micro installations in Poland, influenced by factors such as geographical location and panel orientation and inclination. Recognizing that the presented energy indicators provide valuable initial parameters for determining solar PV system power output, this data can serve as a critical reference point for stakeholders, assisting them in estimating potential energy generation capacities in different regions of Poland. [ABSTRACT FROM AUTHOR]

In the real world, one of the most common problems in project management is the unpredictability of resources and timelines. An efficient way to resolve uncertainty problems and overcome such obstacles is through an extended fuzzy approach, often known as neutrosophic logic. Our rigorous proposed model has led to the creation of an advanced technique for computing the triangular single-valued neutrosophic number. This innovative approach evaluates the inherent uncertainty in project durations of the planning phase, which enhances the potential significance of the decision-making process in the project. Our proposed method, for the first time in the neutrosophic set literature, not only solves existing problems but also introduces a new set of problems not yet explored in previous research. A comparative study using Python programming was conducted to examine the effectiveness of responsive and adaptive planning, as well as their differences from other existing models such as the classical critical path problem and the fuzzy critical path problem. The study highlights the use of neutrosophic logic in handling complex projects by illustrating an innovative dynamic programming framework that is robust and flexible, according to the derived results, and sets the stage for future discussions on its scalability and application across different industries. [ABSTRACT FROM AUTHOR]

In a company, inventory management is crucial due to the significant impact on various aspects of the business. Similarly, the Indonesian water supply company (PDAM) requires effective inventory management to ensure the supply of liquid aluminum sulfate chemicals. The probabilistic statistical inventory control (SIC) model is commonly used for inventory management. However, previous research on chemical inventory models in PDAMs often relied on simple linear regression to forecast demand data, which fails to capture the inherent volatility in demand. Therefore, this research aimed to predict demand data using the seasonal autoregressive integrated moving average (SARIMA) method and determine the optimal policy for supplying liquid aluminum sulfate chemicals. The results showed that the best demand forecasting model was SARIMA (2,1,2) (1,1,0)12 with a mean absolute percentage error (MAPE) value of 8.19%. The finding of the optimal inventory policy showed a safety stock value of 11,922.35 kg, a reorder point value of 49,511.20 kg, and an order quantity of 21,526.59 kg, leading to a total cost of IDR 11,132,034,145.45. The sensitivity test also showed that variations in lead time, price, μ, and σ parameters directly influence changes in total cost, reorder point, and safety stock. These calculations were conducted using Minitab and Python software. [ABSTRACT FROM AUTHOR]

This article aims to examine a novel combined power and refrigeration system, using renewable and waste heat sources suitable for low-temperature applications. The present system is an integrated Kalina cycle and ejector refrigeration system to generate power and refrigeration simultaneously. To improve the vapour generation, the separator vapour fraction is used as a decision variable. Relative irreversibility and efficiency defect as two important parameters considered in this system for an investigation to identify the weaker components. The combined system generates power and refrigeration with two different mediums by the incorporation of the heat exchanger at the turbine exhaust. The novel system's energy and conventional exergy evaluation are carried out through Python Software. The optimum values of decision variables: turbine concentration, separator vapour fraction, entrainment ratio, expander ratio, split ratio and turbine concentration are identified using Python software from an opted range of variables. The maximum value of net power output, first law efficiency for power generation system, combined system, second law efficiency for power generation system, combined system, refrigeration effect and coefficient of performance are obtained as 113 kW, 8.85%, 11.83%, 93.44%, 81.29%, 38.07% and 0.118, respectively, at higher separator vapour fraction. Among the components considered in the combined power generation system, the condenser and LTRGN account for the higher exergy destruction rate of 30.41% and 25.53%. The coefficient of performance is maximized at a higher value of the refrigeration effect. The turbine pressure at the inlet is increased with increments in turbine work on choosing the higher value of the expander ratio. The higher exergetic value components are not emphasized to focus on improvement. [ABSTRACT FROM AUTHOR]

We present ichor, an open‐source Python library that simplifies data management in computational chemistry and streamlines machine learning force field development. Ichor implements many easily extensible file management tools, in addition to a lazy file reading system, allowing efficient management of hundreds of thousands of computational chemistry files. Data from calculations can be readily stored into databases for easy sharing and post‐processing. Raw data can be directly processed by ichor to create machine learning‐ready datasets. In addition to powerful data‐related capabilities, ichor provides interfaces to popular workload management software employed by High Performance Computing clusters, making for effortless submission of thousands of separate calculations with only a single line of Python code. Furthermore, a simple‐to‐use command line interface has been implemented through a series of menu systems to further increase accessibility and efficiency of common important ichor tasks. Finally, ichor implements general tools for visualization and analysis of datasets and tools for measuring machine‐learning model quality both on test set data and in simulations. With the current functionalities, ichor can serve as an end‐to‐end data procurement, data management, and analysis solution for machine‐learning force‐field development. [ABSTRACT FROM AUTHOR]

Here, a deterministic algorithm is proposed, that is capable of constructing a common supercell between two similar crystalline surfaces without scanning all possible cases. Using the complex plane, the 2D lattice is defined as the 2D complex vector. Then, the relationship between two surfaces becomes the eigenvector–eigenvalue relation where an operator corresponds to a transformation matrix. It is shown that this transformation matrix can be directly determined from the lattice parameters and rotation angle of the two given crystalline surfaces with O(log Nmax) time complexity, where Nmax is the maximum index of repetition matrix elements. This process is much faster than the conventional brute force approach (O(Nmax4)$O(N_{\mathrm{max}}^4)$). By implementing the method in Python code, experimental 2D heterostructures and their moiré patterns and additionally find new moiré patterns that have not yet been reported are successfully generated. According to the density functional theory (DFT) calculations, some of the new moiré patterns are expected to be as stable as experimentally‐observed moiré patterns. Taken together, it is believed that the method can be widely applied as a useful tool for designing new heterostructures with interesting properties. [ABSTRACT FROM AUTHOR]

Gaussian processes provide probabilistic surrogates for various applications including classification, uncertainty quantification, and optimization. Using a gradient‐enhanced covariance matrix can be beneficial since it provides a more accurate surrogate relative to its gradient‐free counterpart. An acute problem for Gaussian processes, particularly those that use gradients, is the ill‐conditioning of their covariance matrices. Several methods have been developed to address this problem for gradient‐enhanced Gaussian processes but they have various drawbacks such as limiting the data that can be used, imposing a minimum distance between evaluation points in the parameter space, or constraining the hyperparameters. In this paper a diagonal preconditioner is applied to the covariance matrix along with a modest nugget to ensure that the condition number of the covariance matrix is bounded, while avoiding the drawbacks listed above. The method can be applied with any twice‐differentiable kernel and when there are noisy function and gradient evaluations. Optimization results for a gradient‐enhanced Bayesian optimizer with the Gaussian kernel are compared with the use of the preconditioning method, a baseline method that constrains the hyperparameters, and a rescaling method that increases the distance between evaluation points. The Bayesian optimizer with the preconditioning method converges the optimality, that is, the ℓ2$$ {\ell}_2 $$ norm of the gradient, an additional 5 to 9 orders of magnitude relative to when the baseline method is used and it does so in fewer iterations than with the rescaling method. The preconditioning method is available in the open source Python library GpGradPy, which can be found at https://github.com/marchildon/gpgradpy/tree/paper_precon. [ABSTRACT FROM AUTHOR]

This study was carried out with the aim of applying Condorcet and Borda scoring algorithms based on Game Theory (GT) to determine flood points and Flood Susceptibility Mapping (FSM) based on Machine Learning Algorithms (MLA) including Random Forest (RF), Support Vector Regression (SVR), Support Vector Machine (SVM), and K-Nearest Neighbors (KNN) in the Cheshmeh-Kileh watershed, Iran. Therefore, first, FS conditioning factors including Aspect (As), Elevation (El), Euclidean distance (Euc), Forest (F), NDVI, Precipitation (P), Plan Curvature (PlC), Profile Curvature (PrC), Residential (Re), Rangeland (Rl), Slope (Sl), Stream Power Index (SPI), Topographic Position Index (TPI), and Topographic Wetness Index (TWI) were quantified in each Sub-Watershed (SW). Based on this, flood and non-flood points were identified based on both GT algorithms. In the following, MLAs including Random Forest (RF), Support Vector Regression (SVR), Support Vector Machines (SVM), and K-Nearest Neighbors (KNN) were used for the distributional mapping of FS. Finally, based on optimal conjunct approaches, FS maps were presented in the study watershed. Based on the results, among the conjunct algorithms in FS classification, RF-Condorcet and RF-Borda models were selected as the most optimal MLA-GT hybrid models. The upstream SWs were highly susceptible. Also, the effectiveness of NDVI and forest conditioning factors in each classification approach was high. The similarity of SW prioritization based on Condorcet algorithm with RF-Condorcet algorithm was about 86.70%. Meanwhile, the degree of similarity in RF-Borda conjunct algorithm was around 73.33%. These results showed that Condorcet algorithm had an optimal classification compared to Borda scoring algorithm. [ABSTRACT FROM AUTHOR]

Efficient and accurate classification of DNA barcode data is crucial for large‐scale fungal biodiversity studies. However, existing methods are either computationally expensive or lack accuracy. Previous research has demonstrated the potential of deep learning in this domain, successfully training neural networks for biological sequence classification. We introduce the MycoAI Python package, featuring various deep learning models such as BERT and CNN tailored for fungal Internal Transcribed Spacer (ITS) sequences. We explore different neural architecture designs and encoding methods to identify optimal models. By employing a multi‐head output architecture and multi‐level hierarchical label smoothing, MycoAI effectively generalizes across the taxonomic hierarchy. Using over 5 million labelled sequences from the UNITE database, we develop two models: MycoAI‐BERT and MycoAI‐CNN. While we emphasize the necessity of verifying classification results by AI models due to insufficient reference data, MycoAI still exhibits substantial potential. When benchmarked against existing classifiers such as DNABarcoder and RDP on two independent test sets with labels present in the training dataset, MycoAI models demonstrate high accuracy at the genus and higher taxonomic levels, with MycoAI‐CNN being the fastest and most accurate. In terms of efficiency, MycoAI models can classify over 300,000 sequences within 5 min. We publicly release the MycoAI models, enabling mycologists to classify their ITS barcode data efficiently. Additionally, MycoAI serves as a platform for developing further deep learning‐based classification methods. The source code for MycoAI is available under the MIT Licence at https://github.com/MycoAI/MycoAI. [ABSTRACT FROM AUTHOR]

Ceilometers are used routinely at aerodromes worldwide to derive the height and sky coverage fraction of cloud layers. This information, possibly combined with direct observations by human observers, contributes to the production of meteorological aerodrome reports (METARs). Here, we present ampycloud, a new algorithm, and its associated Python package for automatic processing of ceilometer data with the aim of determining the sky coverage fraction and base height of cloud layers above aerodromes. The ampycloud algorithm was developed at the Swiss Federal Office of Meteorology and Climatology (MeteoSwiss) as part of the AMAROC (AutoMETAR/AutoReport rOund the Clock) program to help in the fully automatic production of METARs at Swiss civil aerodromes. ampycloud is designed to work with no direct human supervision. The algorithm consists of three distinct, sequential steps that rely on agglomerative clustering methods and Gaussian mixture models to identify distinct cloud layers from individual cloud base hits reported by ceilometers. The robustness of the ampycloud algorithm stems from the first processing step, which is simple and reliable. It constrains the two subsequent processing steps that are more sensitive but also better suited to handling complex cloud distributions. The software implementation of the ampycloud algorithm takes the form of an eponymous, pip-installable Python package developed on GitHub and made publicly accessible. [ABSTRACT FROM AUTHOR]

Background: Emergency department (ED) crowding is a major patient safety concern and has a negative impact on healthcare systems and healthcare providers. We hypothesized that it would be feasible to control crowding by employing a multifaceted approach consisting of systematically fast-tracking patients who are mostly not in need of a hospital stay as assessed by an initial nurse and treated by decision competent physicians. Methods: Data from 120,901 patients registered in a secondary care ED from the 4tth quarter of 2021 to the 1st quarter of 2024 was drawn from the electronic health record's data warehouse using the SAP Web Intelligence tool and processed in the Python programming language. Crowding was compared before and after ED transformation from a uniform department into a high flow (α) and a low flow (β) section with patient placement in gurneys/chairs or beds, respectively. Patients putatively not in need of hospitalization were identified by nurse, placed in in the α setting and assessed and treated by decision competent physicians. Incidence of crowding, number of patients admitted per day and readmittances within 72 h following ED admission before and after changes were determined. Values are number of patients, mean ± SEM and mean differences with 95% CIs. Statistical significance was ascertained using Student's two tailed t-test for unpaired values. Results: Before and after ED changes crowding of 130% amounted to 123.8 h and 19.3 h in the latter. This is a difference of -104.6 ± 23.9 h with a 95% CI of -159.9 to -49.3, Δ% -84 (p = 0.002). There was the same amount of patients / day amounting to 135.8 and 133.5 patients / day Δ% = -1.7 patients 95% CI -6.3 to 1.6 (p = 0.21). There was no change in readmittances within 72 h before and after changes amounting to 9.0% versus 9.5%, Δ% = 0.5, 95%, CI -0.007 to 1.0 (p > 0.052). Conclusion: It appears feasible to abate crowding with unchanged patient admission and without an increase in readmittances by fast-track assessment and treatment of patients who are not in need of hospitalization. [ABSTRACT FROM AUTHOR]

Three-dimensional printing has become a fast-growing industry. The first phase of this technology is the design of a 3D object to personalize it and optimize its production. This paper explores the procedural generation of the 3D model. The article aims to present the method of procedurally generating 3D objects in Python. Procedural content generation is the automated creation of content using algorithms. Most often, as part of procedural generation, a small number of input parameters and pseudo-random processes are used to generate content that will meet the requirements. The programming techniques for object customization in Python optimize the manufacturing process. Moreover, procedural generation speeds up the model design, and if developers use 3D scanning methods and artificial intelligence, production can be personalized, which is in line with the concept of Industry 4.0. [ABSTRACT FROM AUTHOR]

Two hypotheses divide experts on determining the effective properties of composite materials using multi–scale homogenization methods. The first hypothesis states that multi-scale homogenization methods can ensure the direct determination of effective properties, at the macro level, of composite materials from a single representation of the medium at the lowest possible scale that allows for a good representation of all heterogeneities. The second hypothesis states that the determination cannot be ensured directly from a single scale but rather through multistep homogenization where each step represents the medium at a different scale from the lowest to the macroscale. To answer this question, a rigorous study is carried out; it includes calculating the two effective elastic properties, bulk, and shear moduli of three phases of a multi–layered sphere composite model by studying three phases. A multistep homogenization method is used to determine the effective properties of the composite and the obtained results are compared with those of the direct homogenization. Two different studies are considered: the first is based on an analytical model and the second on the numerical homogenization based on finite element calculation. To consider the effect of some influential parameters, several situations are treated by the combination of the variation of the volume fractions of the three phases and their property contrasts. The analytical calculations are performed using the Python 3.10 commercial software. It could be concluded that the effective elastic properties obtained either by the multistep or by the direct homogenization show no significant difference. [ABSTRACT FROM AUTHOR]

Simulation software like ANSYS, COMSOL, and SimScale excel at modeling heat transfer phenomena, but their extensive functionalities necessitate a deep understanding, making them less suitable and too expensive for use in educational settings below the post-secondary level in Singapore, where the current curriculum does not demand such advanced capabilities. To provide a more accessible and cost-effective solution, this work introduces a novel universal Python code designed to simplify the understanding of 2D steady-state heat transfer on irregular shapes, utilizing only Microsoft Excel and Python. The developed code employs the Gauss–Seidel iteration method within a full multigrid framework, applying the relevant nodal finite-difference equations based on the node type within a 2D irregular shape delineated by a 65 × 65 mesh in Excel. The generated contour plots from these simulations are meticulously compared with those produced by ANSYS to validate accuracy. The comparison reveals that the results from the Python code closely align with those from ANSYS, showing only minor differences. Consequently, the Python code emerges as a viable and simplified alternative for conducting 2D steady-state heat transfer simulations, making it a valuable tool for educational purposes, bridging the gap between complex simulation software and the educational needs of students in Singapore. [ABSTRACT FROM AUTHOR]