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Software News and Updates MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations

JOURNAL OF COMPUTATIONAL CHEMISTRY 2011年第10期32卷 2319-2327页

作者： Michaud-Agrawal, Naveen Denning, Elizabeth J. Woolf, Thomas B. Beckstein, Oliver Johns Hopkins Sch Med Dept Biophys Baltimore MD 21205 USA Univ Maryland Sch Pharm Dept Pharmaceut Chem Baltimore MD 21201 USA Johns Hopkins Sch Med Dept Physiol Baltimore MD 21205 USA Univ Oxford Dept Biochem Oxford OX1 3QU England

MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://***. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2319-2327, 2011

关键词： molecular dynamics simulations analysis proteins object-oriented design software membrane systems python programming language

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Charged Silicon Nitride Films: Field-Effect Passivation of Silicon Solar Cells and a Novel Characterization Method through Lifetime Measurements

Charged Silicon Nitride Films: Field-Effect Passivation of S...

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作者： Yang, Qun Arizona State University

学位级别：M.S.

Silicon (Si) solar cells are the dominant technology used in the Photovoltaics industry. Field-effect passivation by means of electrostatic charges stored in an overlying insulator on a silicon solar cell has been proven to be a significantly efficient way to reduce effective surface recombination velocity and increase minority carrier lifetime. Silicon nitride (SiNx) films have been extensively used as passivation layers. The capability to store charges makes SiNx a promising material for excellent feild effect passivation. In this work, symmetrical Si/SiO2/SiNx stacks are developed to study the effect of charges in SiNx films. SiO 2 films work as barrier layers. Corona charging technique showed the ability to inject charges into the SiNx films in a short time. Minority carrier lifetimes of the Czochralski (CZ) Si wafers increased significantly after either positive or negative charging. A fast and contactless method to characterize the charged overlying insulators on Si wafer through lifetime measurements is proposed and studied in this work, to overcome the drawbacks of capacitance-voltage (CV) measurements such as time consuming, induction of contanmination and hysteresis effect, etc. Analytical simulations showed behaviors of inverse lifetime (Auger corrected) vs. minority carrier density curves depend on insulator charge densities (N f). From the curve behavior, the Si surface condition and region of Nf can be estimated. When the silicon surface is at high strong inversion or high accumulation, insulator charge density (Nf) or surface recombination velocity parameters (Sn0 and Sp0) can be determined from the slope of inverse lifetime curves, if the other variable is known. If S n0 and Sp0 are unknown, Nf values of different samples can be compared as long as all have similar Sn0 and Sp0 values. Using the saturation current density (J 0) and intercept fit extracted from the lifetime measurement, the bulk lifetime can be calculated. Therefore, this method is fea

关键词： Biochemistry Bioinformatics Molecular biology Chromatic Acclimation Next-generation sequencing Photosynthesis Phycoerythrin Protein crystallography python programming language

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Harnessing Artificial Neural Networks for Financial Analysis of Investments in a Shower Heat Exchanger

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ENERGIES 2024年第14期17卷

作者： Kordana-Obuch, Sabina Starzec, Mariusz Piotrowska, Beata Rzeszow Univ Technol Dept Infrastruct & Water Management Al Powstancow Warszawy 6 PL-35959 Rzeszow Poland

This study focused on assessing the financial efficiency of investing in a horizontal shower heat exchanger. The analysis was based on net present value (NPV). The research also examined the possibility of using artificial neural networks and SHapley Additive exPlanation (SHAP) analysis to assess the profitability of the investment and the significance of individual parameters affecting the NPV of the project related to installing the heat exchanger in buildings. Comprehensive research was conducted, considering a wide range of input parameters. As a result, 1,215,000 NPV values were obtained, ranging from EUR -1996.40 to EUR 36,933.83. Based on these values, artificial neural network models were generated, and the one exhibiting the highest accuracy in prediction was selected (R-2 approximate to 0.999, RMSE approximate to 57). SHAP analysis identified total daily shower length and initial energy price as key factors influencing the profitability of the shower heat exchanger. The least influential parameter was found to be the efficiency of the hot water heater. The research results can contribute to improving systems for assessing the profitability of investments in shower heat exchangers. The application of the developed model can also help in selecting appropriate technical parameters of the system to achieve maximum financial benefits.

关键词： net present value (NPV) waste heat recovery machine learning multilayer perceptron SHAP analysis python programming language

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Automatic assessment of object oriented programming assignments with unit testing in python and a real case assignment

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COMPUTER APPLICATIONS IN ENGINEERING EDUCATION 2023年第5期31卷 1321-1338页

作者： Climent, Laura Arbelaez, Alejandro Univ Autonoma Madrid UAM Dept Ingn Informat Madrid Spain

In this paper, we focus on developing automatic assessment (AA) for a topic that has some difficulties in its practical assessment: object oriented programming (OOP). For evaluating that the OOP principles have been correctly applied to a real application, we use unit testing. In this paper, we focus on prioritizing that the students understand and apply correctly complex OOP principles and that they design properly the classes (including their relationships). In addition, we focus on the python programming language rather than the typical previous works' focus in this area. Thus, we present a real case study of a practical assignment, in which the students have to implement characters for a video game. This assignment has the particularities and advantages that it is incremental and that it applies all four OOP principles within a single assignment. We also present its solution with the UML class diagram description. Furthermore, we provide unit testing for this case study and give general advice for generalizing the unit tests to other real case scenarios. Finally, we corroborate the effectiveness of our approach with positive student evaluations.

关键词： automatic assessment object oriented programming python programming language unit testing

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PyFREC: Software for Forster electronic coupling evaluation in molecular fragments

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JOURNAL OF COMPUTATIONAL CHEMISTRY 2016年第19期37卷 1847-1854页

作者： Kosenkov, Dmytro Dmytro Kosenkov Monmouth Univ Dept Chem & Phys 400 Cedar Ave West Long Branch NJ 07764 USA

Electronic couplings are crucial for understanding exciton dynamics and associated energy transfer in artificial and natural chromophores. The proposed PyFREC (python FRagment Electronic Coupling) software enables evaluation of electronic couplings based on the Forster model. PyFREC features the decomposition of electronic couplings, obtained through quantum chemical calculations, into the orientation and dipole strength components. Furthermore, the variation method to evaluate energies of coupled electronic excited states and delocalization of electronic excitations is implemented in the software. PyFREC has been tested on the S22 benchmark dataset of non-covalent complexes and water clusters. (c) 2016 Wiley Periodicals, Inc.

关键词： Forster resonance energy transfer fragmentation methods exciton coupling python programming language

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Efficiency and accuracy of GPU-parallelized Fourier spectral methods for solving phase-field models

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COMPUTATIONAL MATERIALS SCIENCE 2023年 228卷

作者： Boccardo, A. D. Tong, M. Leen, S. B. Tourret, D. Segurado, J. Univ Galway Coll Sci & Engn Sch Engn Mech Engn Univ Rd Galway H91 HX31 Ireland Univ Galway I Form Adv Mfg Res Ctr Univ Rd Galway H91 HX31 Ireland IMDEA Mat Inst C Er Kandel 2 Getafe 28906 Madrid Spain Univ Politecn Madrid Dept Mat Sci ETSI Caminos C Prof Aranguren 3 Madrid 28040 Spain

Phase-field models are widely employed to simulate microstructure evolution during processes such as solidification or heat treatment. The resulting partial differential equations, often strongly coupled together, may be solved by a broad range of numerical methods, but this often results in a high computational cost, which calls for advanced numerical methods to accelerate their resolution. Here, we quantitatively test the efficiency and accuracy of semi-implicit Fourier spectral-based methods, implemented in python programming language and parallelized on a graphics processing unit (GPU), for solving a phase-field model coupling Cahn-Hilliard and Allen-Cahn equations. We compare computational performance and accuracy with a standard explicit finite difference (FD) implementation with similar GPU parallelization on the same hardware. For a similar spatial discretization, the semi-implicit Fourier spectral (FS) solvers outperform the FD resolution as soon as the time step can be taken 5 to 6 times higher than afforded for the stability of the FD scheme. The accuracy of the FS methods also remains excellent even for coarse grids, while that of FD deteriorates significantly. Therefore, for an equivalent level of accuracy, semi-implicit FS methods severely outperform explicit FD, by up to 4 orders of magnitude, as they allow much coarser spatial and temporal discretization.

关键词： Phase-field model Fourier spectral method python programming language Graphic processing unit

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Computing the number of perfumes that constitute the gandharnava and kacchaputa of Varahamihira

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INDIAN JOURNAL OF HISTORY OF SCIENCE 2021年第2期56卷 85-92页

作者： Chauthaiwale, Shriram Deopujari, Jayant Chauthaiwale, Atharva Amolakchand Coll Math Yavatmal Maharashtra India Govt India Minist AYUSH Natl Commiss Indian Syst Med New Delhi India SLACK Technol Pune Maharashtra India

The sixth-century Indian scholar Varahamihira elaborated on the processes for the preparation of perfumes in the 'gandhayukti' chapter of the Brhatsamhita. He adapted the combinatorial analysis and magic square structure for arriving at the possible number of perfumes from the set of specified substances. This attempt is an excellent example of the multidisciplinary thought process of the Indian scholars in general and Varahamihira in particular. This paper focuses on the verses under the captions 'gandharnava' and 'kacchaputa'. In the first case, four substances are selected from sixteen, and the chosen four are permuted with the pre-defined proportions. In the second case, selected substances are placed in a 4 x 4 magic square. The claims by Varahamihira and the same amended by the commentator Bhattotpala for the number of perfumes are verified here. The constraints imposed by Varahamihira in the first case on the proportions of the two substances are considered. The correct number for the possible perfumes is determined mathematically in the first case and by the specially designed computer program in the second case. Valid lists of perfumes with ingredients obtained as the output are attached in the form of web links in the first case, and the same is placed in the Appendix for the second case.

关键词： Bhattotpala Gandharnava Kacchaputa Permutations and combinations python programming language Varahamihira

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Drone Elevation Control Based on python-Unity Integrated Framework for Reinforcement Learning Applications

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DRONES 2023年第4期7卷

作者： Abbass, Mahmoud Abdelkader Bashery Kang, Hyun-Soo Chungbuk Natl Univ Sch Elect & Comp Engn Dept Informat & Commun Engn Cheongju 28644 South Korea Helwan Univ Dept Mech Power Engn Cairo 11772 Egypt

Reinforcement learning (RL) applications require a huge effort to become established in real-world environments, due to the injury and break down risks during interactions between the RL agent and the environment, in the online training process. In addition, the RL platform tools (e.g., python OpenAI's Gym, Unity ML-Agents, PyBullet, DART, MoJoCo, RaiSim, Isaac, and AirSim), that are required to reduce the real-world challenges, suffer from drawbacks (e.g., the limited number of examples and applications, and difficulties in implementation of the RL algorithms, due to difficulties with the programing language). This paper presents an integrated RL framework, based on python-Unity interaction, to demonstrate the ability to create a new RL platform tool, based on making a stable user datagram protocol (UDP) communication between the RL agent algorithm (developed using the python programing language as a server), and the simulation environment (created using the Unity simulation software as a client). This python-Unity integration process, increases the advantage of the overall RL platform (i.e., flexibility, scalability, and robustness), with the ability to create different environment specifications. The challenge of RL algorithms' implementation and development is also achieved. The proposed framework is validated by applying two popular deep RL algorithms (i.e., Vanilla Policy Gradient (VPG) and Actor-Critic (A2C)), on an elevation control challenge for a quadcopter drone. The validation results for these experimental tests, prove the innovation of the proposed framework, to be used in RL applications, because both implemented algorithms achieve high stability, by achieving convergence to the required performance through the semi-online training process.

关键词： reinforcement learning agent simulation platform python programming language Unity simulation software UDP communication protocol Vanilla Policy Gradient algorithm Actor-Critic algorithm

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On lazy evaluation as a tool to optimize the efficiency of large scale numerical simulations in python

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Procedia Computer Science 2010年第1期1卷 2145-2153页

作者： L. Gross A. Amirbekyan J. Fenwick L. Gao A. Mohajeri H. Muhlhaus Earth Systems Science Computational Center School of Earth Sciences The University of Queensland St. Lucia QLD 4072 Australia

Scientists working on mathematical models want to concentrate on the design of models. They pay little attention to numerical methods such as the finite element method (FEM), their implementation and parallelization. The escript module in python provides an environment in which scientists can define new models using a language of partial differential equation (PDE) and spatial functions which is natural for the formulation of continuous models. This approach defines a high level of abstraction from the underlying data structures and frees modelers from issues of optimized implementation and parallelization. In its current implementation escript evaluates expressions which define PDE coefficients immediately for all nodes or elements of an FEM mesh. In the paper we will demonstrate that for complex rheologies such as the Drucker–Prager plasticity model, the memory requirements for this strategy are the limiting factor for scaling up the mesh size. The python module is backed by an escript C++ library where the processing is performed. We will discuss an new extension to the PDE coefficient handling provided by this C++ library which uses a lazy evaluation technique and will demonstrate the efficiency of this new extension in terms of compute time and memory usage for a practical engineering application, namely the simulation of elastic-plastic, saturated porous media.

关键词： python programming language Partial differential equations Finite element methods

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Evaluating the Effective Factors of Hospital Rooms on Patients' Recovery Using the Data Mining Method

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HERD-HEALTH ENVIRONMENTS RESEARCH & DESIGN JOURNAL 2022年第1期15卷 97-114页

作者： Nikabadi, S. Zabihi, H. Shahcheraghi, A. Islamic Azad Univ Dept Architecture Sci & Res Branch Tehran Iran Islamic Azad Univ Dept Urban Dev Sci & Res Branch Tehran Iran

Objectives: This study aims to investigate the effective environmental factors of hospital rooms in patients' recovery through data mining techniques. Background: Previous studies have shown the positive effect of the interior environment of the hospitals on patients' recovery. The methods of these studies were mainly based on the evidence and patients' perception while hospital environments are associated with a large amount of data that make them an appropriate case for data mining studies. But data mining studies in hospitals mainly focused on medical and management purposes rather than evaluating the interior environment condition. Methods: We analyzed the hospital information system data of a hospital using python programming language and some of its libraries. Preprocessing and eliminating the outliers, labeling and clustering of diseases, data visualization and analysis, final evaluation, and concluding were done using the knowledge discovery in databases process. Results: Pearson coefficient value for rooms' area was .5 and, respectively, for the distance from the ward entrance and nursing station were .75 and .70. The chi(2) values for the variables of room types, location, and occupation were 24.62, 18.98, and 21.53, respectively, and for the beds' location was 0.12. Conclusions: The results confirmed the correlation of the length of stay with the room types, location, and occupation, distance from the nursing station and ward entrance and also showed a moderate correlation with the rooms' area. However, no evidence was found about the relationship between the beds' location in rooms and patients' length of hospital stay.

关键词： data mining hospital information system hospital room features length of stay python programming language

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