Development of Chemoinformatic Tools to Enumerate Functional Groups in Molecules for Organic Aerosol Characterization G
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Wannier90 As a Community Code: New
IOP Journal of Physics: Condensed Matter Journal of Physics: Condensed Matter J. Phys.: Condens. Matter J. Phys.: Condens. Matter 32 (2020) 165902 (25pp) https://doi.org/10.1088/1361-648X/ab51ff 32 Wannier90 as a community code: new 2020 features and applications © 2020 IOP Publishing Ltd Giovanni Pizzi1,29,30 , Valerio Vitale2,3,29 , Ryotaro Arita4,5 , Stefan Bl gel6 , Frank Freimuth6 , Guillaume G ranton6 , JCOMEL ü é Marco Gibertini1,7 , Dominik Gresch8 , Charles Johnson9 , Takashi Koretsune10,11 , Julen Ibañez-Azpiroz12 , Hyungjun Lee13,14 , 165902 Jae-Mo Lihm15 , Daniel Marchand16 , Antimo Marrazzo1 , Yuriy Mokrousov6,17 , Jamal I Mustafa18 , Yoshiro Nohara19 , 4 20 21 G Pizzi et al Yusuke Nomura , Lorenzo Paulatto , Samuel Poncé , Thomas Ponweiser22 , Junfeng Qiao23 , Florian Thöle24 , Stepan S Tsirkin12,25 , Małgorzata Wierzbowska26 , Nicola Marzari1,29 , Wannier90 as a community code: new features and applications David Vanderbilt27,29 , Ivo Souza12,28,29 , Arash A Mostofi3,29 and Jonathan R Yates21,29 Printed in the UK 1 Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 CM Lausanne, Switzerland 2 Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom 10.1088/1361-648X/ab51ff 3 Departments of Materials and Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom 4 RIKEN -
Accelerating Molecular Docking by Parallelized Heterogeneous Computing – a Case Study of Performance, Quality of Results
solis vasquez, leonardo ACCELERATINGMOLECULARDOCKINGBY PARALLELIZEDHETEROGENEOUSCOMPUTING–A CASESTUDYOFPERFORMANCE,QUALITYOF RESULTS,ANDENERGY-EFFICIENCYUSINGCPUS, GPUS,ANDFPGAS Printed and/or published with the support of the German Academic Exchange Service (DAAD). ACCELERATINGMOLECULARDOCKINGBYPARALLELIZED HETEROGENEOUSCOMPUTING–ACASESTUDYOF PERFORMANCE,QUALITYOFRESULTS,AND ENERGY-EFFICIENCYUSINGCPUS,GPUS,ANDFPGAS at the Computer Science Department of the Technische Universität Darmstadt submitted in fulfilment of the requirements for the degree of Doctor of Engineering (Dr.-Ing.) Doctoral thesis by Solis Vasquez, Leonardo from Lima, Peru Reviewers Prof. Dr.-Ing. Andreas Koch Prof. Dr. Christian Plessl Date of the oral exam October 14, 2019 Darmstadt, 2019 D 17 Solis Vasquez, Leonardo: Accelerating Molecular Docking by Parallelized Heterogeneous Computing – A Case Study of Performance, Quality of Re- sults, and Energy-Efficiency using CPUs, GPUs, and FPGAs Darmstadt, Technische Universität Darmstadt Date of the oral exam: October 14, 2019 Please cite this work as: URN: urn:nbn:de:tuda-tuprints-92886 URL: https://tuprints.ulb.tu-darmstadt.de/id/eprint/9288 This document is provided by TUprints, The Publication Service of the Technische Universität Darmstadt https://tuprints.ulb.tu-darmstadt.de This work is licensed under a Creative Commons “Attribution-ShareAlike 4.0 In- ternational” license. ERKLÄRUNGENLAUTPROMOTIONSORDNUNG §8 Abs. 1 lit. c PromO Ich versichere hiermit, dass die elektronische Version meiner Disserta- tion mit der schriftlichen Version übereinstimmt. §8 Abs. 1 lit. d PromO Ich versichere hiermit, dass zu einem vorherigen Zeitpunkt noch keine Promotion versucht wurde. In diesem Fall sind nähere Angaben über Zeitpunkt, Hochschule, Dissertationsthema und Ergebnis dieses Versuchs mitzuteilen. §9 Abs. 1 PromO Ich versichere hiermit, dass die vorliegende Dissertation selbstständig und nur unter Verwendung der angegebenen Quellen verfasst wurde. -
Universid Ade De Sã O Pa
A hardware/software codesign for the chemical reactivity of BRAMS Carlos Alberto Oliveira de Souza Junior Dissertação de Mestrado do Programa de Pós-Graduação em Ciências de Computação e Matemática Computacional (PPG-CCMC) UNIVERSIDADE DE SÃO PAULO DE SÃO UNIVERSIDADE Instituto de Ciências Matemáticas e de Computação Instituto Matemáticas de Ciências SERVIÇO DE PÓS-GRADUAÇÃO DO ICMC-USP Data de Depósito: Assinatura: ______________________ Carlos Alberto Oliveira de Souza Junior A hardware/software codesign for the chemical reactivity of BRAMS Master dissertation submitted to the Instituto de Ciências Matemáticas e de Computação – ICMC- USP, in partial fulfillment of the requirements for the degree of the Master Program in Computer Science and Computational Mathematics. FINAL VERSION Concentration Area: Computer Science and Computational Mathematics Advisor: Prof. Dr. Eduardo Marques USP – São Carlos August 2017 Ficha catalográfica elaborada pela Biblioteca Prof. Achille Bassi e Seção Técnica de Informática, ICMC/USP, com os dados fornecidos pelo(a) autor(a) Souza Junior, Carlos Alberto Oliveira de S684h A hardware/software codesign for the chemical reactivity of BRAMS / Carlos Alberto Oliveira de Souza Junior; orientador Eduardo Marques. -- São Carlos, 2017. 109 p. Dissertação (Mestrado - Programa de Pós-Graduação em Ciências de Computação e Matemática Computacional) -- Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, 2017. 1. Hardware. 2. FPGA. 3. OpenCL. 4. Codesign. 5. Heterogeneous-computing. I. Marques, Eduardo, orient. II. Título. Carlos Alberto Oliveira de Souza Junior Um coprojeto de hardware/software para a reatividade química do BRAMS Dissertação apresentada ao Instituto de Ciências Matemáticas e de Computação – ICMC-USP, como parte dos requisitos para obtenção do título de Mestre em Ciências – Ciências de Computação e Matemática Computacional. -
Estimation of Hydrolysis Rate Constants of Carboxylic Acid Ester and Phosphate Ester Compounds in Aqueous Systems from Molecular Structure by SPARC
Estimation of Hydrolysis Rate Constants of Carboxylic Acid Ester and Phosphate Ester Compounds in Aqueous Systems from Molecular Structure by SPARC R E S E A R C H A N D D E V E L O P M E N T EPA/600/R-06/105 September 2006 Estimation of Hydrolysis Rate Constants of Carboxylic Acid Ester and Phosphate Ester Compounds in Aqueous Systems from Molecular Structure by SPARC By S. H. Hilal Ecosystems Research Division National Exposure Research Laboratory Athens, Georgia U.S. Environmental Protection Agency Office of Research and Development Washington, DC 20460 NOTICE The information in this document has been funded by the United States Environmental Protection Agency. It has been subjected to the Agency's peer and administrative review, and has been approved for publication. Mention of trade names of commercial products does not constitute endorsement or recommendation for use. ii ABSTRACT SPARC (SPARC Performs Automated Reasoning in Chemistry) chemical reactivity models were extended to calculate hydrolysis rate constants for carboxylic acid ester and phosphate ester compounds in aqueous non- aqueous and systems strictly from molecular structure. The energy differences between the initial state and the transition state for a molecule of interest are factored into internal and external mechanistic perturbation components. The internal perturbations quantify the interactions of the appended perturber (P) with the reaction center (C). These internal perturbations are factored into SPARC’s mechanistic components of electrostatic and resonance effects. External perturbations quantify the solute-solvent interactions (solvation energy) and are factored into H-bonding, field stabilization and steric effects. These models have been tested using 1471 reliable measured base, acid and general base-catalyzed carboxylic acid ester hydrolysis rate constants in water and in mixed solvent systems at different temperatures. -
PDF Hosted at the Radboud Repository of the Radboud University Nijmegen
PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/75818 Please be advised that this information was generated on 2018-07-08 and may be subject to change. SULFATION VIA SULFITE AND SULFATE DIESTERS AND SYNTHESIS OF BIOLOGICALLY RELEVANT ORGANOSULFATES Een wetenschappelijke proeve op het gebied van de Natuurwetenschappen, Wiskunde en Informatica Proefschrift ter verkrijging van de graad van doctor aan de Radboud Universiteit Nijmegen op gezag van de rector magnificus prof. mr. S. C. J. J. Kortmann, volgens besluit van het college van decanen in het openbaar te verdedigen op vrijdag 9 oktober 2009 om 13:00 uur precies door Martijn Huibers geboren op 21 november 1978 te Arnhem Promotor: Prof. dr. Floris P. J. T. Rutjes Copromotor: Dr. Floris L. van Delft Manuscriptcommissie: Prof. dr. ir. Jan C. M. van Hest Prof. dr. Binne Zwanenburg Dr. Martin Ostendorf (Schering‐Plough) Paranimfen: Laurens Mellaard Eline van Roest Het in dit proefschrift beschreven onderzoek is uitgevoerd in het kader van het project “Use of sulfatases in the production of sulfatated carbohydrates and steroids”. Dit project is onderdeel van het Integration of Biosynthesis and Organic Synthesis (IBOS) programma, wat deel uitmaakt van het Advanced Chemical Technologies for Sustainability (ACTS) platform van de Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO). Cofinancierders zijn Schering‐Plough en Syncom. ISBN/EAN: 978‐94‐90122‐51‐5 Drukkerij: Gildeprint Drukkerijen, Enschede Omslagfoto: Martijn Huibers i.s.m. Maarten van Roest Omslagontwerp: Martijn Huibers en Gildeprint Drukkerijen Vermelding van een citaat (onderaan kernpagina's 1 tot en met 112) betekent niet per se dat de auteur van dit proefschrift zich daarbij aansluit, maar dat de uitspraak interessant is, prikkelend is, en/of betrekking heeft op de wetenschap in het algemeen of dit promotieonderzoek in het bijzonder. -
GREEN BOOK 4 Alkyl Benzoates CIR EXPERT PANEL MEETING
GREEN BOOK 4 Alkyl Benzoates CIR EXPERT PANEL MEETING AUGUST 30-31, 2010 July 30, 2010 MEMORANDUM To: CIR Expert Panel and Liaisons From: Lillian C. Becker, M.S. Scientific Analyst and Writer Subject: Draft Report for C12-15 Alkyl Benzoate and related Alkyl Benzoates The Cosmetic Ingredient Review (CIR) announced the Scientific Literature Review (SLR) for alkyl benzoates in June, 2010. C12-15 alkyl benzoate is the lead ingredient of this safety assessment. Related alkyl benzoate ingredients are included. CIR has been informed that a comprehensive dossier on the C12-15 alkyl benzoates being prepared for the European REACH program will be completed and provided to CIR in late September or early October. The Panel should review the Draft Report and decide: 1) if it is reasonable to include the other listed ingredients with C12-15 alkyl benzoate in this report and 2) whether any additional data are needed in order to reach a safety conclusion for C12-15 alkyl benzoates and the related ingredients. If no additional data are required, then the Panel may issue a Tentative Report. Alternatively, the Panel may choose to table the report to await the receipt of the dossier mentioned above. CIR Panel Book Page 1 CIR Panel Book Page 2 History of Alkyl Benzoates June, 2010 – SLR issued. August, 2010 - CIR Panel Book Page 3 Search Strategy for Benzoates EXPORATORY SEARCH: PUBMED: “alkyl benzoate” – 7 hits, 1 useful; CAS No. – 0 hits. Internet (Dogpile) – “alkyl benzoate” ‐ 1 MSDS FULL SEARCH: PUBMED: “lauryl alcohol” – 53 hits, 6 ordered. Learned that Valerie was doing this ingredient. -
(12) United States Patent (10) Patent No.: US 8,895,679 B2 Havinka (45) Date of Patent: *Nov
US008895679B2 (12) United States Patent (10) Patent No.: US 8,895,679 B2 Havinka (45) Date of Patent: *Nov. 25, 2014 (54) CATALYST COMPOSITIONS AND METHODS (Continued) OF MAKING AND USING SAME (71) Applicant: Chevron Phillips Chemical Company Primary Examiner — Rip A Lee LP, The Woodlands, TX (US) (74) Attorney, Agent, or Firm — Conley Rose, P.C.; Rodney (72) Inventor: Mark L. Hlavinka, Bartlesville, OK B. Carroll; Cheryl L. Huseman (US) (57) ABSTRACT (73) Assignee: Chevron Phillips Chemical Company LP, The Woodlands, TX (US) An imine phenol compound having Structure I: (*) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 77 days. Structure I This patent is Subject to a terminal dis claimer. (21) Appl. No.: 13/660,857 (22) Filed: Oct. 25, 2012 (65) Prior Publication Data R3 US 2014/O121343 A1 May 1, 2014 wherein O and N represent oxygen and nitrogen respectively; (51) Int. Cl. R comprises a halogen, a hydrocarbyl group, or a Substituted C08F 4/64 (2006.01) hydrocarbyl group; R and R can each independently be CSF 4/52 (2006.01) hydrogen, a halogen, a hydrocarbyl group, or a substituted so G'gif7 (2006.01) hydrocarbyl group; and Q is a donor group. A method com USPC ........... 526/161; 526/172; 526/160; 526/126; prising contacting a catalyst composition with a monomer 526/127; 526/129; 526/130; 556/51; 502/103; under conditions suitable for the formation of a polymer 502/104: 502/118: 502/119; 502/120 wherein the catalyst composition comprises a metal Saltcom (58) Field of Classification Search plex of an imine (bis)phenolate compound, a solid oxide, and USPC ............. -
WO 2019/060485 Al 28 March 2019 (28.03.2019) W 1P O PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2019/060485 Al 28 March 2019 (28.03.2019) W 1P O PCT (51) International Patent Classification: Published: C07F 7/08 (2006.0 1) C07F 7/12 (2006.0 1) — with international search report (Art. 21(3)) (21) International Application Number: — before the expiration of the time limit for amending the PCT/US2018/051859 claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) (22) International Filing Date: 20 September 2018 (20.09.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 17192237.0 20 September 2017 (20.09.2017) 18177922.4 15 June 2018 (15.06.2018) (71) Applicant: MOMENTIVE PERFORMANCE MATERIALS INC. [US/US]; 260 Hudson River Road, Waterford, NY 12188 (US). (72) Inventors: AUNER, Norbert; Auf der Piatt 5 1, 61479 Glashutten (DE). SANTOWSKI, Tobias; Im Ellenbugel 28, 63505 Langenselbold (DE). STURM, Alexander, G.; Im Munchfeld 27, 55 122 Mainz (DE). (74) Agent: DILWORTH, Peter, G. et al; Dilworth & Bar- rese, LLP, 1000 Woodbury Road, Suite 405, Woodbury, NY 11797 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available) : AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
Door 2.0 - Comprehensive Mapping of Drosophila Melanogaster Odorant Responses
DoOR 2.0 - Comprehensive Mapping of Drosophila melanogaster Odorant Responses Daniel Münch1,* and C. Giovanni Galizia1 1Neurobiology, University of Konstanz, 78457 Konstanz, Germany *[email protected] Supplementary Figures & Tables Or47b overlap 5 Or47b overlap 3 Or47b Dweck LTK: 0.25; n: 178 LTK: 3.4; n: 218 LTK: 33.12; n: 43 0.5 0.5 0.5 0.0 0.0 0.0 DoOR response −0.5 −0.5 −0.5 odorants ab4B all ab4B geosmin LTK: −1.53; n: 182 LTK: 89.35; n: 181 0.5 0.5 0.0 0.0 DoOR response −0.5 −0.5 odorants (a) model: inv.sigmoid model: inv.asympOff model: sigmoid n = 12 n = 10 n = 16 MD = 0.093643 MD = 0.140333 MD = 0.052509 merged_data merged_data Hallem.2004.EN 0.0 0.4 0.8 0.0 0.4 0.8 0.0 0.4 0.8 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.4 0.8 Hallem.2006.EN Pelz.2005.Or47bnmr Hallem.2004.WT model: inv.linear model: inv.linear n = 44 n = 3 MD = 0.124972 MD = 0.027766 merged_data merged_data 0.0 0.5 1.0 0.0 0.5 1.0 1.5 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.4 0.8 Muench.2015.AntGC1 Dweck.2015b.WT (b) Figure S1: Related to Figure3. Merging two narrowly tuned responding units with different merge-specifications. -
Open Chemoinformatic Resources to Explore the Structure, Properties and Chemical Space of Molecules
RSC Advances REVIEW View Article Online View Journal | View Issue Open chemoinformatic resources to explore the structure, properties and chemical space of Cite this: RSC Adv.,2017,7,54153 molecules a ab a Mariana Gonzalez-Medina,´ J. Jesus´ Naveja, Norberto Sanchez-Cruz´ a and Jose´ L. Medina-Franco * New technologies are shaping the way drug discovery data is analyzed and shared. Open data initiatives and web servers are assisting the analysis of the large amounts of data that we are now able to produce. The final goal is to accelerate the process of moving from new data to useful information that could lead to Received 27th October 2017 treatments for human diseases. This review discusses open chemoinformatic resources to analyze the Accepted 21st November 2017 diversity and coverage of the chemical space of screening libraries and to explore structure–activity DOI: 10.1039/c7ra11831g relationships of screening data sets. Free resources to implement workflows and representative web- rsc.li/rsc-advances based applications are emphasized. Future directions in this field are also discussed. Creative Commons Attribution 3.0 Unported Licence. 1. Introduction connections between biological activities, ligands and proteins.3 During the past few years, there has been an important increase Herein we review representative chemoinformatic tools in open data initiatives to promote the availability of free essential to explore the structure, chemical space and properties research-based tools and information.1 While there is still some of molecules. The review is focused on recent and representative resistance to open data in some chemistry and drug discovery free web-based applications. -
Development of an Atmospheric Chemistry Model Coupled to the PALM Model System 6.0: Implementation and First Applications
https://doi.org/10.5194/gmd-2020-286 Preprint. Discussion started: 25 September 2020 c Author(s) 2020. CC BY 4.0 License. Development of an atmospheric chemistry model coupled to the PALM model system 6.0: Implementation and first applications Basit Khan1, Sabine Banzhaf2, Edward C. Chan2,3, Renate Forkel1, Farah Kanani-Sühring4,7, Klaus Ketelsen5, Mona Kurppa6, Björn Maronga4,10, Matthias Mauder1, Siegfried Raasch4, Emmanuele Russo2,8,9, Martijn Schaap2, and Matthias Sühring4 1Institute of Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen, 82467, Germany 2Freie Universität Berlin (FUB), Institute of Meteorology, TrUmF 3Institute for Advanced Sustainability Studies (IASS), Potsdam 4Leibniz University Hannover (LUH), Institute of Meteorology and Climatology 5Independent Software Consultant 6University of Helsinki 7Harz Energie GmbH & Co. KG, Goslar, Germany 8Climate and Environmental Physics, Physics Institute, University of Bern, Sidlerstrasse 5, 3012, Bern, Switzerland 9Oeschger Centre for Climate Change Research, University of Bern, Hochschulstrasse 4, 3012, Bern, Switzerland 10University of Bergen, Geophysical Institute, Bergen, Norway Correspondence: Basit Khan ([email protected]) Abstract. In this article we describe the implementation of an online-coupled gas-phase chemistry model in the turbulence resolving PALM model system 6.0. The new chemistry model is part of the PALM-4U components (read: PALM for you; PALM for urban applications) which are designed for application of PALM model in the urban environment (Maronga et al., 2020). The 5 latest version of the Kinetic PreProcessor (KPP, 2.2.3), has been utilised for the numerical integration of gas-phase chemical reactions. A number of tropospheric gas-phase chemistry mechanisms of different complexity have been implemented ranging from the photostationary state to more complex mechanisms such as CBM4, which includes major pollutants namely O3, NO, NO2, CO, a simplified VOC chemistry and a small number of products. -
A Consistent Cheminformatics Framework for Automated Virtual Screening
A consistent cheminformatics framework for automated virtual screening Cumulative Dissertation to receive the degree Dr. rer. nat. at the Faculty of Mathematics, Informatics and Natural Sciences University of Hamburg submitted to the Department of Informatics of the University of Hamburg Sascha Urbaczek born in Mannheim Hamburg, August 2014 1. Reviewer: Prof. Dr. Matthias Rarey 2. Reviewer: JProf. Dr. Tobias Schwabe 3. Reviewer: Prof. Dr. Andreas Hildebrandt Date of thesis defense: 23.01.2015 F¨urmeine Lena Acknowledgements At this point, I would like to acknowledge the people who supported and encouraged me during my doctoral thesis. First and foremost, I extend my sincere gratitude to my supervisor Prof. Matthias Rarey for entrusting me with this interesting research project and providing guidance and support every step of the way. I also thank the Beiersdorf AG for funding the project and Dr. Inken Groth and Prof. Stefan Heuser in particular for their constant support as well as their great interest in my work. Furthermore, I thank the BiosolveIT GmbH for the productive working relationship during and especially after my time at the Center for Bioinformatics. As for the current and former colleagues from the Center of Bioinformatics (which are far too many to list here); I am grateful to have had the opportunity to work in such a remarkably pleasant and productive environment. I really appreciate everyone's hard work and dedication during these (very successful) last years. In particular I owe a great deal of gratitude to Dr. Tobias Lippert from whom I learned a lot and who has become a very dear friend to me.