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Application of Hartree-Fock Method for modeling of Bioactive Molecules Using SAR and QSPR

computational Molecular Bioscience 2014年第1期4卷 1-24页

作者： Cleydson B. R. Santos Cleison C. Lobato Francinaldo S. Braga Sílvia S. S. Morais Cesar F. Santos Caio P. Fernandes Davi S. B. Brasil Lorane I. S. Hage-Melim Williams J. C. Macêdo José C. T. Carvalho Laboratory of Modeling and Computational Chemistry Federal University of Amap&#225 Macap&#225 Brazil Laboratory of Modeling and Computational Chemistry Federal University of Amap&#225 Macap&#225 Brazil Laboratory of Drug Research School of Pharmaceutical Sciences Federal University of Amap&#225 Macap&#225 Brazil Laboratory of Modeling and Computational Chemistry Federal University of Amap&#225 Macap&#225 Brazil Institute of Technology Federal University of Par&#225 Bel&#233m Brazil Laboratory of Modeling and Computational Chemistry Federal University of Amap&#225 Macap&#225 Brazil Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE Campus Universit&#225rio Marco Zero Macap&#225 Brazil Laboratory of Modeling and Computational Chemistry Federal University of Amap&#225 Macap&#225 Brazil Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE Campus Universit&#225rio Marco Zero Macap&#225 Brazil Laboratory of Drug Research School of Pharmaceutical Sciences Federal University of Amap&#225 Macap&#225 Brazil Laboratory of Modeling and Computational Chemistry Federal University of Amap&#225 Macap&#225 Brazil Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE Campus Universit&#225rio Marco Zero Macap&#225 Brazil Laboratory of Drug Research School of Pharmaceutical Sciences Federal University of Amap&#225 Macap&#225 Brazil Laboratory of Statistical and Computational Modeling University of the State of Amap&#225 Macap&#225 Brazil

The central importance of quantum chemistry is to obtain solutions of the Schr?dinger equation for the accurate determination of the properties of atomic and molecular systems that occurred from the calculation of wave functions accurate for many diatomic and polyatomic molecules, using Self Consistent Field method (SCF). The application of quantum chemical methods in the study and planning of bioactive compounds has become a common practice nowadays. From the point of view of planning it is important to note, when it comes to the use of molecular modeling, a collective term that refers to methods and theoretical modeling and computational techniques to mimic the behavior of molecules, not intend to reach a bioactive molecule simply through the use of computer programs. The choice of method for energy minimization depends on factors related to the size of the molecule, parameters of availability, stored data and computational resources. Molecular models generated by the computer are the result of mathematical equations that estimate the positions and properties of the electrons and nuclei, the calculations exploit experimentally, the characteristics of a structure, providing a new perspective on the molecule. In this work we show that studies of Highest Occupied Molecular Orbital Energy (HOMO), Low Unoccupied Molecular Orbital Energy (LUMO) and Map of molecular electrostatic potential (MEP) using Hatree-Fock method with different basis sets (HF/3-21G*, HF/3-21G**, HF/6-31G, HF/6-31G*, HF/6-31G** and HF/6-311G), that are of great importance in modern chemistry, biochemistry, molecular biology, and other fields of knowledge of health sciences. In order to obtain a significant correlation, it is essential that the descriptors are used appropriately. Thus, the quantum chemical calculations are an attractive source of new molecular descriptors that can, in principle, express all the geometrical and electronic properties of molecules and their interactions with biological

关键词： Molecular modeling Meps Maps Orbital Frontier Quantum Chemical Methods

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Mechanical properties study of plasma treated epoxy-base post in dual-material systems 2nd

Mechanical properties study of plasma treated epoxy-base pos...

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2nd International Conference on Applied Physics and Material Applications, ICAPMA 2015

作者： Sangprasert, Waleepan Lee, Vannajan Sanghiran Yavirach, Piriya Boonyawan, Dheerawan Nimmanpipug, Piyarat Program of Chemistry Faculty of Science and Technology Chiang Rai Rajabhat University Chiang Rai57100 Thailand Computational Simulation and Modeling Laboratory Department of Chemistry Faculty of Science Chiang Mai University Chiang Mai50200 Thailand Thailand Center of Excellence in Physics Bangkok10400 Thailand Department of Chemistry Faculty of Science University of Malaya Kuala Lumpur50603 Malaysia Department of Prosthodontic Faculty of Dentistry Chiang Mai University Chiang Mai50200 Thailand Department of Physics Faculty of Science Chiang Mai University Chiang Mai50200 Thailand

ISBN: (纸本)9783038356837

Improvement of adhesion between epoxy based post and composite resin core materials by low temperature plasma is an on-going dental material development. To systematically investigate the effects of surface change on the material's chemical and mechanical properties, three series of two component materials, epoxy/urethane dimethacrylate (UDMA), epoxy/polyethylene (PE), and epoxy/poly(methylmethacrylate) (PMMA), were compared with dental epoxy based post/composite resin core. Each dual-materials system was modeled at an atomistic level. A molecular dynamics (MD) method with COMPASS force field was employed to simulate the most probable functionalization and the materials physical properties changes. Material surface modification was modeled and optimized using quantum calculations based on experimental characterization. To validate calculation results, the effect of plasma treatment on the mechanical properties of the dental post materials were examined by tensile pull out test. © 2016 Trans Tech Publications, Switzerland.

关键词： Molecular dynamics

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A simulator for underwater unmanned vehicles and cable-like flexible structures

A simulator for underwater unmanned vehicles and cable-like ...

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OCEANS

作者： Marcos Vinicius Scholl Sebastião C. P. Gomes Carlos Rodrigues Rocha Graduate Program in Computational Modeling Federal University of Rio Grande - FURG Rio Grande-RS Brazil Federal Institute of Education Science and Technology of Rio Grande do Sul Rio Grande Campus Rio Grande-RS Brazil

A graphical tool to qualitative analysis of underwater unmanned vehicles and cable-like flexible structures is presented. The software provides a realistic virtual environment where the dynamic behavior of different u... 详细信息

ISBN: (纸本)9781509064298;9780692946909

关键词： Vehicle dynamics Underwater cables Dynamics Mathematical model Software Unmanned vehicles Numerical simulation

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Homogenisation for the monodomain model in the presence of microscopic fibrotic structures

arXiv

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arXiv 2020年

作者： Lawson, Brodie A.J. dos Santos, Rodrigo Weber Turner, Ian W. Bueno-Orovio, Alfonso Burrage, Pamela Burrage, Kevin Centre for Data Science Queensland University of Technology QLD Australia ARC Centre of Excellence for Mathematical and Statistical Frontiers Queensland University of Technology QLD Australia Graduate Program on Computational Modeling Universidade de Juiz de Fora Minas Gerais Brazil Department of Computer Science University of Oxford Oxfordshire United Kingdom

MSC Codes 35B27computational models in cardiac electrophysiology are notorious for long runtimes, restricting the numbers of nodes and mesh elements in the numerical discretisations used for their solution. This makes it particularly challenging to incorporate structural heterogeneities on small spatial scales, preventing a full understanding of the critical arrhythmogenic effects of conditions such as cardiac fibrosis. In this work, we explore the technique of homogenisation by volume averaging for the inclusion of non-conductive micro-structures into larger-scale cardiac meshes with minor computational overhead. Importantly, our approach is not restricted to periodic patterns, enabling homogenised models to represent, for example, the intricate patterns of collagen deposition present in different types of fibrosis. We first highlight the importance of appropriate boundary condition choice for the closure problems that define the parameters of homogenised models. Then, we demonstrate the technique’s ability to correctly upscale the effects of fibrotic patterns with a spatial resolution of 10 µm into much larger numerical mesh sizes of 100-250 µm. The homogenised models using these coarser meshes correctly predict critical pro-arrhythmic effects of fibrosis, including slowed conduction, source/sink mismatch, and stabilisation of re-entrant activation patterns. As such, this approach to homogenisation represents a significant step towards whole organ simulations that unravel the effects of microscopic cardiac tissue heterogeneities. © 2020, CC BY.

关键词： Heart

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The Fisher Geometry and Geodesics of the Multivariate Normals, without Differential Geometry

arXiv

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arXiv 2023年

作者： Lawson, Brodie A.J. Burrage, Kevin Mengersen, Kerrie Santos, Rodrigo Weber dos Centre for Data Science Queensland University of Technology Australia School of Mathematical Sciences Queensland University of Technology Australia ARC Centre of Excellence for Plant Success in Nature and Agriculture Australia Department of Computer Science University of Oxford United Kingdom Graduate Program in Computational Modeling Universidade Federal de Juiz de Fora Brazil

Choosing the Fisher information as the metric tensor for a Riemannian manifold provides a powerful yet fundamental way to understand statistical distribution families. Distances along this manifold become a compelling measure of statistical distance, and paths of shorter distance improve sampling techniques that leverage a sequence of distributions in their operation. Unfortunately, even for a distribution as generally tractable as the multivariate normal distribution, this information geometry proves unwieldy enough that closed-form solutions for shortest-distance paths or their lengths remain unavailable outside of limited special cases. In this review we present for general statisticians the most practical aspects of the Fisher geometry for this fundamental distribution family. Rather than a differential geometric treatment, we use an intuitive understanding of the covariance-induced curvature of this manifold to unify the special cases with known closed-form solution and review approximate solutions for the general case. We also use the multivariate normal information geometry to better understand the paths or distances commonly used in statistics (annealing, Wasserstein). Given the unavailability of a general solution, we also discuss the methods used for numerically obtaining geodesics in the space of multivariate normals, identifying remaining challenges and suggesting methodological *** Codes 62B11 (primary), 62-02, 62-08 (secondary) © 2023, CC BY.

关键词： Geometry

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An Improved Approach for Semantic Segmentation of Fundus Lesions using R2U-Net 46

An Improved Approach for Semantic Segmentation of Fundus Les...

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46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2024

作者： Pereira, Alejandro Santos, Carlos Aguiar, Marilton Welfer, Daniel Dias, Marcelo De Menezes, Rafaela Ferreira, Paulo Roberto Rossi, Fábio D'Ornellas, Marcos Haygert, Carlos Jesus Kazienko, Juliano Comim, Fabio Hoppe, Aurélio Weber, Juliano Tavares, Leandro Guths, Leonardo Guerra, Rodrigo Federal University of Pelotas - UFPel Postgraduate Program in Computing Pelotas Brazil Science and Technology Farroupilha - IFFar Federal Institute of Education Alegrete Brazil Federal University of Santa Maria - Ufsm Department of Applied Computing Santa Maria Brazil Federal University of Santa Maria - Ufsm Department of Clinical Medicine Santa Maria Brazil Federal University of Santa Maria - Ufsm Industrial Technical College Santa Maria Brazil Federal University of Minas Gerais - Ufmg Department of Clinical Medicine Belo Horizonte Brazil Regional University of Blumenau - Furb Department of Information Systems and Computing Blumenau Brazil Science and Technology Farroupilha - IFFar Federal Institute of Education Santo Ângelo Brazil Federal University of Rio Grande do Sul - Ufrgs Postgraduate Program in Computing Porto Alegre Brazil Federal University of Rio Grande - Furg Center of Computational Sciences Rio Grande Brazil

ISBN: (纸本)9798350371499

Diabetic Retinopathy (DR) is a microvascular complication related to diabetes that affects approximately 33% of individuals with this condition and, if not detected and treated early, can lead to irreversible vision loss. Fundus lesions such as Hard and Soft Exudates, Hemorrhages, and Microaneurysms typically identify DR. The development of computational methods to segment these lesions plays a fundamental role in the early diagnosis of the disease. This paper proposes a new approach that uses an R2U-Net combined with data augmentation techniques for segmenting fundus lesions. We trained, adjusted, and evaluated the proposed work in the DDR dataset, achieving an accuracy of 99.87% and a mean Intersection over Union (mIoU) equal 59.69%. Furthermore, we assessed it in the IDRiD dataset, achieving an mIoU of 49.92%. The results obtained in the experiments highlight the potential contribution of the model in the lesion annotations for creating new DR datasets, which is essential given the scarcity of annotations in publicly available datasets. © 2024 IEEE.

关键词： Semantic Segmentation

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Molecular Docking and Evaluation of Antileishmania Activity of a Ruthenium Complex with Epiisopiloturine and Nitric Oxide

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Journal of Biosciences and Medicines 2020年第5期8卷 42-53页

作者： Joabe Lima Araújo Ruan Sousa Bastos Gardênia Taveira Santos Michel Muálem de Moraes Alves Kayo Alves Figueiredo Lucas Aires de Sousa Ionara Nayana Gomes Passos Fernando Aécio de Amorim Carvalho Francisco das Chagas Alves Lima Jefferson Almeida Rocha Postgraduate Program in Nanoscience and Nanobiotechnology Department of Genetics and Morphology University of Brasília Brasília DF Brazil Research Group in Natural Sciences and Biotechnology Department of Natural Sciences/Chemistry Federal University of Maranhao Grajaú MA Brazil Research Group in Medicinal Chemistry and Biotechnology QUIMEBIO Federal University of Maranhao Sao Bernardo MA Brazil Postgraduate Program in Medicinal Chemistry and Molecular Modeling Federal University of Pará Belém PA Brazil Department of Nursing State University of Maranhao Colinas MA Brazil Department of Veterinary Morphophysiology Federal University of Piauí Teresina PI Brazil Department of Health Federal Institute of Education Science and Technology of Piauí Teresina PI Brazil Postgraduate Program in Materials Science Center for Social Sciences Health and Technology Federal University of Maranhao Imperatriz MA Brazil Department of Biochemistry and Pharmacology Federal University of Piauí Teresina PI Brazil Department of Chemistry Quantum Computational Chemistry Laboratory Federal University of Piauí Teresina PI Brazil

Leishmaniasis is an infectious disease that affects both animals and humans, caused by flagellated parasites belonging to the genus Leishmania. The disease is estimated to reach about 700,000 to 1 million people, causing the deaths of 20 to 30,000 individuals annually. Thus, the present study aims to perform molecular docking tests and evaluation of antileishmania activity in vitro of a ruthenium complex with epiisopiloturine and nitric oxide. AutoDockTools-1.5.6 software was used to perform molecular docking tests. Molecular targets were considered rigid, and Epiruno2 considered flexible. The genetic algorithm Lamarckian (AGL) with global search and pseudo-Solis and Wets with local search were the methods adopted in the docking. The most promising results of molecular interaction were achieved in the targets Pteridine reductase and UDP-glucose Pyrophosphorylase with rates of -10.68 Kcal·mol-1 and -10.51 Kcal·mol-1, respectively. This demonstrates that Epiruno2 has molecular affinity with the targets of L. major. In vitro assays prove the antileishmania activity of the complex in the face of promastigote forms with inhibition of growth, concluding through this study that the Epiruno2 complex has antileishmania activity.

关键词： Molecular Docking Simulation Neglected Diseases Leishmania major

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Analyzing dominance move (MIP-DoM) indicator for multi- And many-objective optimization

arXiv

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arXiv 2020年

作者： do Val Lopes, Claudio Lucio Martins, Flávio Vinícius Cruzeiro Wanner, Elizabeth Fialho Deb, Kalyanmoy Postgraduate Program in Mathematical and Computational Modeling CEFET-MG Brazil Computer Department Centro Federal de Educação Tecnológica de Minas Gerais 30510-000 Brazil Computer Department Centro Federal de Educação Tecnológica de Minas Gerais 30510-000 Brazil Department of Computer Science and Engineering Michigan State University East LansingMI48824 United States

—Dominance move (DoM) is a binary quality indicator that can be used in multi-objective and many-objective optimization to compare two solution sets obtained from different algorithms. The DoM indicator can differentiate the sets for certain important features, such as convergence, spread, uniformity, and cardinality. DoM does not use any reference, and it has an intuitive and physical meaning, similar to the -indicator, and calculates the minimum total move of members of one set so that all elements in another set are to be dominated or identical to at least one member of the first set. Despite the aforementioned properties, DoM is hard to calculate, particularly in higher dimensions. There is an efficient and exact method to calculate it in a bi-objective case only. This work proposes a novel approach to calculate DoM using a mixed integer programming (MIP) approach, which can handle sets with three or more objectives and is shown to overcome the -indicator’s information loss. Experiments, in the bi-objective space, are done to verify the model’s correctness. Furthermore, other experiments, using 3, 5, 10, 15, 20, 25 and 30-objective problems are performed to show how the model behaves in higher-dimensional cases. Algorithms, such as IBEA, MOEA/D, NSGA-III, NSGA-II, and SPEA2 are used to generate the solution sets (however any other algorithms can also be used with the proposed MIP-DoM indicator). Further extensions are discussed to handle certain idiosyncrasies with some solution sets and also to improve the quality indicator and its use for other situations. Copyright © 2020, The Authors. All rights reserved.

关键词： Multiobjective optimization

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Theoretical insights into the chemical bonding, electronic structure, and spectroscopic properties of the lanarkite Pb2SO5 structure

arXiv

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arXiv 2023年

作者： Fabris, Guilherme S.L. Ferrer, Mateus M. Sambrano, Julio R. Almeida, Cláudio R.R. Paskocimas, Carlos A. La Porta, Felipe A. Graduate Program in Materials Science and Engineering Technological Development Center Universidade Federal de Pelotas RS Pelotas96010-610 Brazil Modeling and Molecular Simulation Group São Paulo State University Bauru São Paulo17033-360 Brazil Department of Materials Engineering Federal University of Rio Grande do Norte RN Natal59078-970 Brazil Postgraduate Program in Science and Engineering of Materials Federal University of Rio Grande do Norte RN Natal59078-970 Brazil Federal University of Technology - Paraná Nanotechnology and Computational Chemistry Laboratory Avenida dos Pioneiros 3131 CEP PR Londrina86036-370 Brazil State University of Londrina Post-Graduation Program in Chemistry Rodovia Celso Garcia Cid 445 km 380 CEP PR Londrina86057-970 Brazil

Lanarkite is a mineral formed by a combination of lead, sulphur, and oxygen atoms arranged in the general chemical formula Pb2SO5 (PSO) that crystallises with monoclinic symmetry (belonging to the C2/m space group, No. 12). This mineral was first discovered in Lanarkshire, Scotland and was named after its location. PSO has a unique structure comprising alternating penta-coordinated lead [PbO5] and tetra-coordinated sulphur [SO4] clusters. This lanarkite-type structure has recently attracted significant scientific interest and has been the focus of the superconducting material research community. However, its chemistry needs to be explored further. This article presents a comprehensive investigation on the chemical bonding, electronic structure, and spectroscopic properties of the lanarkite-type PSO structure from a computational perspective. Thus, different functionals in the DFT (e.g., PBE, PBE0, PBESOL, PBESOL0, BLYP, WC1LYP37, and B3LYP) were assessed to accurately predict their fundamental properties. All the DFT calculations were performed using a triple-zeta valence plus polarisation basis set. Among all the DFT functionals tested in this study, PBE showed the best agreement with the experimental data available in the literature. Our results also reveal that the [PbO5] clusters are formed with three Pb–O bond lengths, with values of about 2.32, 2.59, and 2.84 Å, respectively, while the [SO4] clusters have the same S–O bond length of 1.57 Å. We performed a complete topological analysis of this system to comprehend these structural differences. Additionally, the PSO structure has an indirect band gap energy of 2.9 eV and an effective mass ratio (mℎ∗ /me∗) of about 0.415 (using PBE calculations) which may, in principle, indicate a low recombination of electron-hole pairs in the lanarkite structure. Therefore, we believe that a detailed understanding of their electronic structures, spectroscopic properties as well as their chemical bonding is critically important

关键词： Lead compounds

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Estimation of the main air pollutants from different biomasses under combustion atmospheres by artificial neural networks

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Chemosphere 2024年 352卷 141484页

作者： Monteiro, Thalyssa Oliveira Alves, Pedro Augusto Araújo da Silva de Almeida Nava Barradas Filho, Alex Oliveira Villa-Vélez, Harvey Alexander Cruz, Glauber Postgraduate Program in Mechanical Engineering (PPGMEC) Department of Mechanics and Materials Federal Institute of Education Science and Technology of Maranhão (IFMA) Maranhão São Luís Brazil Postgraduate Program in Computer Science and Computational Mathematics (PPG-CCMC) Department of Computer Science University of São Paulo (USP) São Carlos São Paulo Brazil Data Analysis and Artificial Intelligence Laboratory (DARTi) Department of Computational Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil Department of Chemical Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil Processes and Thermal Systems Laboratory (LPSisTer) Department of Mechanical Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil

The production of biofuels to be used as bioenergy under combustion processes generates some gaseous emissions (CO, CO2, NOx, SOx, and other pollutants), affecting living organisms and requiring careful assessments. H... 详细信息

The production of biofuels to be used as bioenergy under combustion processes generates some gaseous emissions (CO, CO₂, NO_x, SO_x, and other pollutants), affecting living organisms and requiring careful assessments. However, obtaining such information experimentally for data evaluation is costly and time-consuming and its in situ obtaining for regional biomasses (e.g., those from Northeast Brazil (NEB) is still a major challenge. This paper reports on the application of artificial neural networks (ANNs) for the prediction of the main air pollutants (CO, CO₂, NO, and SO₂) produced during the direct biomass combustion (N₂/O₂:80/20%) with the use of ultimate analysis (carbon, hydrogen, nitrogen, sulfur, and oxygen). 116 worldwide biomasses were used as input data, which is a relevant alternative to overcome the lack of experimental resources in NEB and obtain such information. Cross-validation was conducted with k-fold to optimize the ANNs and performance was analyzed with the use of statistical errors for accuracy assessments. The results showed an acceptable statistical performance for all architectures of ANNs, with 0.001–12.41% MAPE, 0.001–5.82 mg Nm⁻³ MAE, and 0.03–52.30 mg Nm⁻³ RMSE, highlighting the high precision of the emissions studied. On average, the differences between predicted and real values for CO, CO₂, NO, and SO₂ emissions from NEB biomasses were approximately 0.01%, 10⁻⁶%, 0.14%, and 0.05%, respectively. Pearson coefficient provided consistent results of concentration of the ultimate analysis in relation to the emissions studied and effectiveness of the test set in the developed models. © 2024 Elsevier Ltd

关键词： Brazilian northeastern Environmental statistics Evaluation metrics Gaseous emissions Predictive models Thermoconversion

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