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2020 AIChE Annual Meeting

作者： Achar, Siddarth Johnson, J. Karl Computational Modeling and Simulation Program University of Pittsburgh United States Department of Chemical Engineering University of Pittsburgh United States

ISBN: (纸本)9780816911141

Standard density functional theory (DFT) molecular dynamic (MD) simulations are prohibitively expensive in terms ofcompute time and memory requirements when the size of the physical system is larger than several hundred *** alternate approach is to develop a deep learning neural network potential that can accurately reproduce DFTenergies within an error of several 10s of meVs. Neural network potentials thus allow large-scale MD simulations formuch longer times than can be achieved with DFT-MD, but with comparable accuracy. We have used the recentlypublished DeePMD [1] formalism to develop potentials for systems relevant to modeling proton transport onfunctionalized graphane. We have used DFT-MD calculations for small structures of graphane and graphanol astraining data to build reliable machine-learned potentials. Apart from energies and forces, vibrational and thermalproperties such as phonon dispersion relations and thermal expansion coefficients from DFT-MD were used to validatethe accuracy of our trained DeePMD potentials. Our goal is to develop a machine learning potential that is able toaccurately predict proton conduction on graphanol in the complete absence of water. Previous DFT calculations haveshown that graphanol a promising candidate for anhydrous proton exchange membrane applications [2]. We seek toidentify large-scale and long-time proton hopping behavior for this system through the use of machine learningpotentials. © 2020 American Institute of Chemical Engineers. All rights reserved.

关键词： Density functional theory

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Evidence-based Practice of Chinese Medicine in Physical Rehabilitation Science

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Chinese Journal of Integrative Medicine 2013年第10期19卷 723-729页

作者： Arthur de Sá Ferreira Laboratory of Computational Simulation and Modeling in Rehabilitation Program of Rehabilitation ScienceCentro Universitario Augusto MottaRio de JaneiroRJBrazil(21041-021) Department of Physical Therapy UniversidadeSalgado de OliveiraNiteróiRJBrazil(21041-021)

Chinese medicine is among other traditional medical systems practiced either as a coadjutant intervention to Greek medicine or as the unique therapeutic intervention for illness prevention, treatment or rehabilitation. The complete spectrum from that traditional system includes acupuncture and moxibustion, herbal and food therapy, massage therapy （tuina）, physical exercises （taijiquan）, and breathing exercises （qigong）. In this article, it is presented several randomized controlled trials and systematic reviews on the application of all therapeutic modalities from Chinese medicine in the physical rehabilitation scenario. The discussed studies encompasses both ＂positive＂ and ＂negative＂ results of Chinese medicine intervention for disabilities due to illnesses of the nervous, musculoskeletal or cardiovascular systems. Additionally, the importance of the personalized approach for Chinese medicineand rehabilitation is emphasized together with the need for reproducible methods for pattern differentiation and intervention selection. Chinese medicine resources are recognized as promising methods for therapeutic rehabilitation and can be incorporated into the rehabilitation science. The wide variety of therapeutic resources explains why Chinese medicine is currently a multidisciplinary practice for health protection and promotion, early diagnosis and treatment as well as rehabilitation with roles in the public health care system.

关键词： rehabilitation physical therapy Chinese medicine

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The impact of the resolution of the identity approximate integral method on modern ab initio algorithm development

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THEORETICAL CHEMISTRY ACCOUNTS 1997年第1-4期97卷 158-163页

作者： Kendall, RA Fruchtl, HA High Performance Computational Chemistry Group Theory Modeling and Simulation Program Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory P.O. Box 999 MSIN K1-90 Richland WA 99352-0999 USA US

The computation of the two-electron four-center integrals over gaussian basis functions is a significant component of the overall work of many ab initio methods used today, Improvements in the computational efficiency of the base algorithms have provided significant impact, Somewhat overlooked are methods that provide approximations to these integrals and their implementation in application software. A partial review of approximate integral techniques focused on the resolution of the identity (RI) four-center, two-electron integral approximation is given. The past and current uses of the RI algorithms are presented along with possibilities for further exploitation of the technology.

关键词： resolution identity ab initio algorithm integral

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Promoting integrative medicine by computerization of traditional Chinese medicine for scientific research and clinical practice: The SuiteTCM Project

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Journal of Integrative Medicine 2013年第2期11卷 135-139页

作者： Arthur de Sá Ferreira Laboratory of Computational Simulation and Modeling in Rehabilitation Post-graduation Program of Rehabilitation Science Augusto Motta University Center

BACKGROUND： Chinese and contemporary Western medical practices evolved on different cultures and historical contexts and, therefore, their medical knowledge represents this cultural divergence. Computerization of traditional Chinese medicine （TCM） is being used to promote the integrative medicine to manage, process and integrate the knowledge related to TCM anatomy, physiology, semiology, pathophysiology, and therapy. METHODS： We proposed the development of the SuiteTCM software, a collection of integrated computational models mainly derived from epidemiology and statistical sciences for computerization of Chinese medicine scientific research and clinical practice in all levels of prevention. The software includes components for data management （DataTCM）, simulation of cases （SimTCM）, analyses and validation of datasets （SciTCM）, clinical examination and pattern differentiation （DiagTCM, TongueTCM, and PulseTCM）, intervention selection （AcuTCM, HerbsTCM, and DietTCM）, management of medical records （ProntTCM）, epidemiologic investigation of sampled data （ResearchTCM）, and medical education, training, and assessment （StudentTCM）. DISCUSSION： The SuiteTCM project is expected to contribute to the ongoing development of integrative medicine and the applicability of TCM in worldwide scientific research and health care. The SuiteTCM 1.0 runs on Windows XP or later and is freely available for download as an executable application.

关键词： traditional Chinese medicine evidence-based practice computer-assisted decision making

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Broadening the scope of nanopublications

Broadening the scope of nanopublications

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10th International Conference on The Semantic Web: Semantics and Big Data, ESWC 2013

作者： Kuhn, Tobias Barbano, Paolo Emilio Nagy, Mate Levente Krauthammer, Michael Department of Pathology Yale University New Haven United States Department of Sociology Particular of Modeling and Simulation ETH Zurich Switzerland Department of Mathematics Yale University United States Program for Computational Biology and Bioinformatics Yale University United States

ISBN: (纸本)9783642382871

In this paper, we present an approach for extending the existing concept of nanopublications-tiny entities of scientific results in RDF representation-to broaden their application range. The proposed extension uses English sentences to represent informal and underspecified scientific claims. These sentences follow a syntactic and semantic scheme that we call AIDA (Atomic, Independent, Declarative, Absolute), which provides a uniform and succinct representation of scientific assertions. Such AIDA nanopublications are compatible with the existing nanopublication concept and enjoy most of its advantages such as information sharing, interlinking of scientific findings, and detailed attribution, while being more flexible and applicable to a much wider range of scientific results. We show that users are able to create AIDA sentences for given scientific results quickly and at high quality, and that it is feasible to automatically extract and interlink AIDA nanopublications from existing unstructured data sources. To demonstrate our approach, a web-based interface is introduced, which also exemplifies the use of nanopublications for non-scientific content, including meta-nanopublications that describe other nanopublications. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Semantics

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Chinese Medicine Pattern Differentiation and Its Implications for Clinical Practice

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Chinese Journal of Integrative Medicine 2011年第11期17卷 818-823页

作者： Arthur Sá Ferreira Agnaldo José Lopes Laboratory of Computational Modeling and Simulation in Rehabilitation Program of Rehabilitation Science Augusto Motta University Laboratory of Cardiopulmonar Analysis Rehabilitation Science Postgraduation Program Augusto Motta University Laboratory of Respiratory Physiology State University of Rio de Janeiro

Chinese medicine practitioners apply the differentiation reasoning for decision-making. The wide scope of Chinese medicine intervention provides coverage of methods and techniques with applications to primary, secondary and tertiary levels of prevention. The rapid evolution of mathematical and computational techniques allowed the implementation of several models for pattern differentiation that were tested for several physiologic systems. Concurrently, it is argued that pattern differentiation might improve the efficacy of either traditional or conventional medical interventions. This article reviewed the influence of pattern differentiation into clinical practice organized by medical field： general pattern differentiation; genitourinary （recurrent cystitis）; cardiovascular （coronary heart disease; arterial hypertension; angina pectoris）; neurology （stroke）; surgery; metabolic （diabetes mellitus）; hepatic （cirrhosis）; gastrointestinal （chronic superficial gastritis）; orthopedic （low back pain; rheumatoid arthritis; cervical spondylosis; elbow arthritis）; oncology （gastric mucosal dysplasia; lung cancer）; gynecologic and obstetric manifestations （nausea and vomiting）. The reviewed studies presented achievements that have contributed to the integration of Chinese medicine and evidence-based medicine in the treatment of many mild and severe diseases. Target diseases considered as major public health problems were also investigated and the results are promising regarding the possibility to treat guided by pattern differentiation.

关键词： Chinese medicine-syndrome differentiation Chinese medicine preventive medicine rehabilitation "health care delivery"

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Antimalarial artemisinins derivatives study: Molecular modeling and multivariate analysis (PCA, HCA, KNN, SIMCA and SDA)

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Journal of computational and Theoretical Nanoscience 2015年第10期12卷 3443-3458页

作者： Macdo, Williams Jorge C. Braga, Francinaldo Sarges Santos, César Freitas Da Silva Costa, Josivan De Melo, Geraldo Souza De Mello, Marcello Neiva Sousa, Daniele Salgado Carvalho, José Carlos T. Do Socorro Barros Brasil, Davi Dos Santos, Cleydson Breno R. Laboratory of Molecular Modeling and Simulation System Federal Rural University of Amaznia Campus Capanema-Centro Rua João Pessoa 121 Capanema Pará Brazil Laboratory of Modeling and Computational Chemistry Federal University of Amapá Macapá Amapá Brazil Postgraduate Program in Pharmaceutical Sciences Federal University of Amapá Macapá Amapá Brazil Laboratory of Drug Research School of Pharmaceutical Sciences Federal University of Amapá Macapá Amapá Brazil Institute of Technology Federal University of Pará Belém-Pará-Amazon Brazil

A set of 20 artemisinins compounds with antimalarial activity against clone D-6 strains of Plasmodium falciparum, mefloquine resistant but chloroquine sensitive, were studied through quantum chemistry and multivariate analysis. The geometry optimization of structures was done with the Hartree-Fock (HF) theory and 6-31G∗basis set. Maps of molecular electrostatic potential (MEP) and molecular docking were used to investigate interaction between ligands and receptor (heme). The chemometrics methods employed was Principal Component Analysis (PCA), Hierarquical Cluster Analysis (HCA), K-Nearest Neighbor (KNN), Soft Independent modeling of Class Analogy (SIMCA) and Stepwise Discriminant Analisis (SDA) were employed to select most important descriptors, related to obtain possible relationships for two compounds classes with activity antimalarial. A predictive model was done with a set of 20 compounds artemisinin derivatives with known activity experimental by PCA, HCA, KNN, SIMCA and SDA classification methods. Four descriptors were responsible for separation between origin two class inactives and actives compounds: HOMO (highest occupied molecular orbital), QC3 (charge on atom carbon 3), logP (logarithm of the partition coefficient) and HATS7v (leverage-weighted autocorrelation of lag7/weighted by atomic Van der Waals Volume). The model proposed may follow the results of the MEP maps and docking molecular. Copyright © 2015 American Scientific Publishers.

关键词： Principal component analysis

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Combined Deep Learning and Classical Potential Approach for modeling Diffusion in UiO-66

Combined Deep Learning and Classical Potential Approach for ...

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2023 AIChE Annual Meeting

作者： Achar, Siddarth K. Wardzala, Jacob J. Bernasconi, Leonardo Zhang, Linfeng Johnson, J. Karl Department of Chemical & Petroleum Engineering University of Pittsburgh PittsburghPA15261 United States Computational Modeling & Simulation Program University of Pittsburgh PittsburghPA15260 United States Center for Research Computing Department of Chemistry University of Pittsburgh PittsburghPA15260 United States DP Technology Beijing100080 China AI for Science Institute Beijing100080 China

modeling of diffusion of adsorbates through porous materials with atomistic molecular dynamics (MD) can be a challenging task if the flexibility of the adsorbent needs to be included. This is because potentials need to be developed that accurately account for the motion of the adsorbent in response to the presence of adsorbate molecules. In this work, we show that it is possible to use accurate machine learning atomistic potentials for metal−organic frameworks in concert with classical potentials for adsorbates to accurately compute diffusivities though a hybrid potential approach. As a proof-of-concept, we have developed an accurate deep learning potential (DP) for UiO-66, a metal− organic framework, and used this DP to perform hybrid potential simulations, modeling diffusion of neon and xenon through the crystal. The adsorbate−adsorbate interactions were modeled with Lennard−Jones (LJ) potentials, the adsorbent−adsorbent interactions were described by the DP, and the adsorbent−adsorbate interactions used LJ cross-interactions. Thus, our hybrid potential allows for adsorbent−adsorbate interactions with classical potentials but models the response of the adsorbent to the presence of the adsorbate through near-DFT accuracy DPs. This hybrid approach does not require refitting the DP for new adsorbates. We calculated self-diffusion coefficients for Ne in UiO-66 from DFT-MD, our hybrid DP/LJ approach, and from two different classical potentials for UiO-66. Our DP/LJ results are in excellent agreement with DFT-MD. We modeled diffusion of Xe in UiO-66 with DP/LJ and a classical potential. Diffusion of Xe in UiO-66 is about a factor of 30 slower than that of Ne, so it is not computationally feasible to compute Xe diffusion with DFT-MD. Our hybrid DP−classical potential approach can be applied to other MOFs and other adsorbates, making it possible to use an accurate DP generated from DFT simulations of an empty adsorbent in concert with existing classical potentials for ads

关键词： Molecular dynamics

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Facile Anhydrous Proton Transport on Hydroxyl Functionalized Graphane

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Physical Review Letters 2017年第18期118卷 186101-186101页

作者： Abhishek Bagusetty Pabitra Choudhury Wissam A. Saidi Bridget Derksen Elizabeth Gatto J. Karl Johnson Computational Modeling and Simulation Program University of Pittsburgh Pittsburgh Pennsylvania 15260 USA Department of Chemical and Petroleum Engineering University of Pittsburgh Pittsburgh Pennsylvania 15261 USA Department of Chemical Engineering New Mexico Tech Socorro New Mexico 87801 USA Department of Mechanical and Materials Science University of Pittsburgh Pittsburgh Pennsylvania 15261 USA

Graphane functionalized with hydroxyl groups is shown to rapidly conduct protons under anhydrous conditions through a contiguous network of hydrogen bonds. Density functional theory calculations predict remarkably low barriers to diffusion of protons along a 1D chain of surface hydroxyls. Diffusion is controlled by the local rotation of hydroxyl groups, a mechanism that is very different from that found in 1D water wires in confined nanopores or in bulk water. The proton mean square displacement in the 1D chain was observed to follow Fickian diffusion rather than the expected single-file mobility. A charge analysis reveals that the charge on the proton is essentially equally shared by all hydrogens bound to oxygens, effectively delocalizing the proton.

关键词： Anomalous diffusion Graphene Membrane structures

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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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