ZHUOFAN SHEN Chemistry, Shanghai New York University 1555# Century Avenue, Pudong New Area, Shanghai Phone: +86 15370073076 Email: Zs1605@Nyu.Edu

ZHUOFAN SHEN Chemistry, Shanghai New York University 1555# Century Avenue, Pudong New Area, Shanghai Phone: +86 15370073076 Email: [email protected] EDUCATION ShanghaiTech University, Shanghai, China Sep 2016-July 2020 Bachelor of School of Physical Science and Technology, Class Rank: 1/107 GPA 3.9/4.0 University of California, Berkeley, California, US Aug 2018-Jun 2019 Visiting Undergraduate Student Program（exchange program） GPA 4.0/4.0 Padova University Summer School, Padova, Italy July 2017-Aug 2017 International Summer Student Program, three weeks WORK Shanghai New York University, Shanghai, China Aug 2020-July 2021(expected) Research associate RESEARCH Theoretical computation and simulation of hydrated electron Jun 2019-Present Advisor: Prof. William James Glover (New York University, Shanghai, China) • Investigated the structure and properties of hydrated electron by calculating Resonance Raman Spectra based on mixed quantum classical simulations. Caught the science of the redshift of RR by analyzing the Hydrogen bond forming • Studied on QM/MM Molecular Dynamics, and developed a new approach to separate QM and MM particles from mixing during the long timescale simulations • Investigated the properties of hydrated electron at excited stated by Ab Initio Molecular Dynamics. Theoretical computation using CCSD method Nov 2018-Jun 2019 Advisor: Prof. Eric Neuscamman (University of California, Berkeley, USA) • Studied and practiced with the computational chemistry software Molpro. Got familiar with Linux systems and High-Performance Computing. Artificial photosynthesis by electrochemical method System Apr 2017-Aug 2018 Advisor: Prof. Bolin Lin (ShanghaiTech University, Shanghai, China) • Did research on seeking for a suitable metal material to synthesize functional electrode, which can convert carbon dioxide (CO2) into ethylene and other recyclable materials with the method of electrochemical reduction of CO2. HONORS Outstanding graduate by ShanghaiTech University Jun 2020 2019 Scholarship of Shanghai City – Top 3 students from ShanghaiTech University Dec 2019 President’s Scholarship (top 2%) by ShanghaiTech University Nov 2017, Nov 2018, Nov 2019 ShanghaiTech University Outstanding Student Nov 2018 2017 Amgen International Exchange Scholarship Jun 2017 SKILLS Programming languages: Python, Shell Softwares: Molpro, Terachem, Q-chem, Amber Wet-Lab Skills: Electrochemical workstation, GC, HPLC, NMR, IR spectroscopy, UV-Vis spectroscopy EXTRACURRICULAR ACTIVITIES Social practice in Ningbo Aug 2017 • Investigated the steering and survival status of the labor force in the Hangzhou Bay New District of Ningbo. • Visited and interviewed the local rural residents and companies to understand their living status and wrote a report with suggestions to improve their living status. VOLUNTEER SERVICE Charity national music Orchestra of Suzhou, Traditional Flute Player Sep 2011- Feb 2013 .

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Supporting Information
Electronic Supplementary Material (ESI) for RSC Advances. This journal is © The Royal Society of Chemistry 2020 Supporting Information How to Select Ionic Liquids as Extracting Agent Systematically? Special Case Study for Extractive Denitrification Process Shurong Gaoa,b,c,*, Jiaxin Jina,b, Masroor Abroc, Ruozhen Songc, Miao Hed, Xiaochun Chenc,* a State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, North China Electric Power University, Beijing, 102206, China b Research Center of Engineering Thermophysics, North China Electric Power University, Beijing, 102206, China c Beijing Key Laboratory of Membrane Science and Technology & College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China d Office of Laboratory Safety Administration, Beijing University of Technology, Beijing 100124, China * Corresponding author, Tel./Fax: +86-10-6443-3570, E-mail: [email protected], [email protected] 1 COSMO-RS Computation COSMOtherm allows for simple and efficient processing of large numbers of compounds, i.e., a database of molecular COSMO files; e.g. the COSMObase database. COSMObase is a database of molecular COSMO files available from COSMOlogic GmbH & Co KG. Currently COSMObase consists of over 2000 compounds including a large number of industrial solvents plus a wide variety of common organic compounds. All compounds in COSMObase are indexed by their Chemical Abstracts / Registry Number (CAS/RN), by a trivial name and additionally by their sum formula and molecular weight, allowing a simple identification of the compounds. We obtained the anions and cations of different ILs and the molecular structure of typical N-compounds directly from the COSMObase database in this manuscript.
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Popular GPU-Accelerated Applications
LIFE & MATERIALS SCIENCES GPU-ACCELERATED APPLICATIONS | CATALOG | AUG 12 LIFE & MATERIALS SCIENCES APPLICATIONS CATALOG Application Description Supported Features Expected Multi-GPU Release Status Speed Up* Support Bioinformatics BarraCUDA Sequence mapping software Alignment of short sequencing 6-10x Yes Available now reads Version 0.6.2 CUDASW++ Open source software for Smith-Waterman Parallel search of Smith- 10-50x Yes Available now protein database searches on GPUs Waterman database Version 2.0.8 CUSHAW Parallelized short read aligner Parallel, accurate long read 10x Yes Available now aligner - gapped alignments to Version 1.0.40 large genomes CATALOG GPU-BLAST Local search with fast k-tuple heuristic Protein alignment according to 3-4x Single Only Available now blastp, multi cpu threads Version 2.2.26 GPU-HMMER Parallelized local and global search with Parallel local and global search 60-100x Yes Available now profile Hidden Markov models of Hidden Markov Models Version 2.3.2 mCUDA-MEME Ultrafast scalable motif discovery algorithm Scalable motif discovery 4-10x Yes Available now based on MEME algorithm based on MEME Version 3.0.12 MUMmerGPU A high-throughput DNA sequence alignment Aligns multiple query sequences 3-10x Yes Available now LIFE & MATERIALS& LIFE SCIENCES APPLICATIONS program against reference sequence in Version 2 parallel SeqNFind A GPU Accelerated Sequence Analysis Toolset HW & SW for reference 400x Yes Available now assembly, blast, SW, HMM, de novo assembly UGENE Opensource Smith-Waterman for SSE/CUDA, Fast short
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Benchmarking and Application of Density Functional Methods In
BENCHMARKING AND APPLICATION OF DENSITY FUNCTIONAL METHODS IN COMPUTATIONAL CHEMISTRY by BRIAN N. PAPAS (Under Direction the of Henry F. Schaefer III) ABSTRACT Density Functional methods were applied to systems of chemical interest. First, the effects of integration grid quadrature choice upon energy precision were documented. This was done through application of DFT theory as implemented in five standard computational chemistry programs to a subset of the G2/97 test set of molecules. Subsequently, the neutral hydrogen-loss radicals of naphthalene, anthracene, tetracene, and pentacene and their anions where characterized using five standard DFT treatments. The global and local electron affinities were computed for the twelve radicals. The results for the 1- naphthalenyl and 2-naphthalenyl radicals were compared to experiment, and it was found that B3LYP appears to be the most reliable functional for this type of system. For the larger systems the predicted site specific adiabatic electron affinities of the radicals are 1.51 eV (1-anthracenyl), 1.46 eV (2-anthracenyl), 1.68 eV (9-anthracenyl); 1.61 eV (1-tetracenyl), 1.56 eV (2-tetracenyl), 1.82 eV (12-tetracenyl); 1.93 eV (14-pentacenyl), 2.01 eV (13-pentacenyl), 1.68 eV (1-pentacenyl), and 1.63 eV (2-pentacenyl). The global minimum for each radical does not have the same hydrogen removed as the global minimum for the analogous anion. With this in mind, the global (or most preferred site) adiabatic electron affinities are 1.37 eV (naphthalenyl), 1.64 eV (anthracenyl), 1.81 eV (tetracenyl), and 1.97 eV (pentacenyl). In later work, ten (scandium through zinc) homonuclear transition metal trimers were studied using one DFT 2 functional.
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A Summary of ERCAP Survey of the Users of Top Chemistry Codes
A survey of codes and algorithms used in NERSC chemical science allocations Lin-Wang Wang NERSC System Architecture Team Lawrence Berkeley National Laboratory We have analyzed the codes and their usages in the NERSC allocations in chemical science category. This is done mainly based on the ERCAP NERSC allocation data. While the MPP hours are based on actually ERCAP award for each account, the time spent on each code within an account is estimated based on the user’s estimated partition (if the user provided such estimation), or based on an equal partition among the codes within an account (if the user did not provide the partition estimation). Everything is based on 2007 allocation, before the computer time of Franklin machine is allocated. Besides the ERCAP data analysis, we have also conducted a direct user survey via email for a few most heavily used codes. We have received responses from 10 users. The user survey not only provide us with the code usage for MPP hours, more importantly, it provides us with information on how the users use their codes, e.g., on which machine, on how many processors, and how long are their simulations? We have the following observations based on our analysis. (1) There are 48 accounts under chemistry category. This is only second to the material science category. The total MPP allocation for these 48 accounts is 7.7 million hours. This is about 12% of the 66.7 MPP hours annually available for the whole NERSC facility (not accounting Franklin). The allocation is very tight. The majority of the accounts are only awarded less than half of what they requested for.
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Porting the DFT Code CASTEP to Gpgpus
Porting the DFT code CASTEP to GPGPUs Toni Collis [email protected] EPCC, University of Edinburgh CASTEP and GPGPUs Outline • Why are we interested in CASTEP and Density Functional Theory codes. • Brief introduction to CASTEP underlying computational problems. • The OpenACC implementation http://www.nu-fuse.com CASTEP: a DFT code • CASTEP is a commercial and academic software package • Capable of Density Functional Theory (DFT) and plane wave basis set calculations. • Calculates the structure and motions of materials by the use of electronic structure (atom positions are dictated by their electrons). • Modern CASTEP is a re-write of the original serial code, developed by Universities of York, Durham, St. Andrews, Cambridge and Rutherford Labs http://www.nu-fuse.com CASTEP: a DFT code • DFT/ab initio software packages are one of the largest users of HECToR (UK national supercomputing service, based at University of Edinburgh). • Codes such as CASTEP, VASP and CP2K. All involve solving a Hamiltonian to explain the electronic structure. • DFT codes are becoming more complex and with more functionality. http://www.nu-fuse.com HECToR • UK National HPC Service • Currently 30- cabinet Cray XE6 system – 90,112 cores • Each node has – 2×16-core AMD Opterons (2.3GHz Interlagos) – 32 GB memory • Peak of over 800 TF and 90 TB of memory http://www.nu-fuse.com HECToR usage statistics Phase 3 statistics (Nov 2011 - Apr 2013) Ab initio codes (VASP, CP2K, CASTEP, ONETEP, NWChem, Quantum Espresso, GAMESS-US, SIESTA, GAMESS-UK, MOLPRO) GS2NEMO ChemShell 2%2% SENGA2% 3% UM Others 4% 34% MITgcm 4% CASTEP 4% GROMACS 6% DL_POLY CP2K VASP 5% 8% 19% http://www.nu-fuse.com HECToR usage statistics Phase 3 statistics (Nov 2011 - Apr 2013) 35% of the Chemistry software on HECToR is using DFT methods.
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The Molpro Quantum Chemistry Package
The Molpro Quantum Chemistry package Hans-Joachim Werner,1, a) Peter J. Knowles,2, b) Frederick R. Manby,3, c) Joshua A. Black,1, d) Klaus Doll,1, e) Andreas Heßelmann,1, f) Daniel Kats,4, g) Andreas Köhn,1, h) Tatiana Korona,5, i) David A. Kreplin,1, j) Qianli Ma,1, k) Thomas F. Miller, III,6, l) Alexander Mitrushchenkov,7, m) Kirk A. Peterson,8, n) Iakov Polyak,2, o) 1, p) 2, q) Guntram Rauhut, and Marat Sibaev 1)Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany 2)School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom 3)School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom 4)Max-Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany 5)Faculty of Chemistry, University of Warsaw, L. Pasteura 1 St., 02-093 Warsaw, Poland 6)Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States 7)MSME, Univ Gustave Eiffel, UPEC, CNRS, F-77454, Marne-la- Vallée, France 8)Washington State University, Department of Chemistry, Pullman, WA 99164-4630 1 Molpro is a general purpose quantum chemistry software package with a long devel- opment history. It was originally focused on accurate wavefunction calculations for small molecules, but now has many additional distinctive capabilities that include, inter alia, local correlation approximations combined with explicit correlation, highly efficient implementations of single-reference correlation methods, robust and efficient multireference methods for large molecules, projection embedding and anharmonic vibrational spectra.
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Ab Initio Theoretical Chemical Kinetics
Ab Initio Theoretical Chemi ca l Kine tics CEFRC Summer School Princeton June, 2010 Stephen J. Klippenstein Ab Initio Theoretical Chemical Kinetics Stephen J. Klippenstein James A. Miller Lawrence B. Harding Yuri Georgievskii Outline 1. Overview of Ab Initio Transition State Theory a) Transition State Theory (TST) b) Introduction to Electronic Structure Theory c) Multireference Electronic Structure Theory 2. Ab Initio TST for Different Classes of Reaction a) Tight TST for Reactions with Barriers b) TST for Radical-Radical Reactions c) Multiple Transition States and Dynamics 3. Pressure Dependent Kinetics a) Single Well Reactions b) Multiple Well Time Dependent Master Equation c) Examples Review Articles The Current Status of Transition State Theory Donald G. Truhlar, Bruce C. Garrett, and Stephen J. Klippenstein J. Phys. Chem. (Centennial Issue) 100, 12771-12800 (1996). RRKM Theory and Its Implementation Stephen J. Klippenstein, in Comprehensive Chemical Kinetics, 39, 55, (2003). Modeling the Kinetics of Bimolecular Reactions Antonio Fernandez Ramos, James A. Miller, Stephen J. Klippenstein, and Donald G. Truhlar, Chem. Rev., 106, 4518-4584 (2006). Predictive Theory for Hydrogen Atom-Hydrocarbon Radical Association Kinetics Lawrence B. Harding, Yuri Georgievskii, and Stephen J. Klippenstein J. Phys. Chem. A, feature article, 109, 4646-4656 (2005). Predictive Theory for the Association Kinetics of Two Alkyl Radicals Stephen J. Klippenstein, Yuri Georgievskii, and Lawrence B. Harding Phys. Chem. Chem. Phys., invited article, 8, 1133-1147 (2006). Master Equation Methods in Gas Phase Chemical Kinetics James A. Miller and Stephen J. Klippenstein J. Phys. Chem. A, feature article, 110, 10528-10544 (2006). Ab Initio Methods for Reactive Potential Surfaces Lawrence B.
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1 Advances in Electronic Structure Theory: Gamess a Decade Later Mark S. Gordon and Michael W. Schmidt Department of Chemistry A
ADVANCES IN ELECTRONIC STRUCTURE THEORY: GAMESS A DECADE LATER MARK S. GORDON AND MICHAEL W. SCHMIDT DEPARTMENT OF CHEMISTRY AND AMES LABORATORY, IOWA STATE UNIVERSITY, AMES, IA 50011 Abstract. Recent developments in advanced quantum chemistry and quantum chemistry interfaced with model potentials are discussed, with the primary focus on new implementations in the GAMESS electronic structure suite of programs. Applications to solvent effects and surface science are discussed. 1. Introduction The past decade has seen an extraordinary growth in novel new electronic structure methods and creative implementations of these methods. Concurrently, there have been important advances in “middleware”, software that enables the implementation of efficient electronic structure algorithms. Combined with continuing improvements in computer and interconnect hardware, these advances have extended both the accuracy of computations and the sizes of molecular systems to which such methods may be applied. The great majority of the new computational chemistry algorithms have found their way into one or more broadly distributed electronic structure packages. Since this work focuses on new features of the GAMESS (General Atomic and Molecular Electronic Structure System1) suite of codes, it is important at the outset to recognize the many other packages that offer both similar and complementary features. These include ACES2 CADPAC3, DALTON4, GAMESS-UK5, HYPERCHEM6, JAGUAR7, MOLCAS8 MOLPRO9, NWChem10, PQS11, PSI312, Q-Chem13, SPARTAN14, TURBOMOLE15, and UT-Chem16. Some1,3,4,10 of these packages are distributed at no cost to all, or to academic users, while others are commercial packages, but all are generally available to users without restriction or constraint. Indeed, the developers of these codes frequently collaborate to share features, a practice that clearly benefits all of their users.
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FIESTA: the Filipino Initiative on Electronic Structure Theory and Applications
FIESTA: the Filipino Initiative on Electronic Structure Theory and Applications Han Ung Lee, Hayan Lee and Wilfredo Credo Chung* Department of Chemistry, De La Salle University – Manila, 2401 Taft Avenue, Manila, 1004 Philippines *E-mail: [email protected] FIESTA—the Filipino Initiative on Electronic Structure Theory and Applications—a new computational chemistry software is developed. The new software is capable of doing ground- state self-consistent field (SCF) single-point restricted Hartree-Fock (RHF) calculation of polyelectronic and polyatomic systems using the Slater-type orbital basis set STO-3G. The new program implements well-known quantum mechanical theories for practical calculations. FIESTA is written using two programming languages, namely C and FORTRAN. It is accurate and user-friendly. It runs efficiently under the Linux operating system and is able to reproduce the energies calculated using well-established standard quantum chemical software products Gaussian, Firefly and Molpro. To our knowledge, FIESTA is the first and only molecular modeling software developed in the Philippines to date. The software will be extended to calculate the properties of systems such as atoms, molecules, ions and formula units using more sophisticated basis sets and quantum mechanical techniques. Computational chemistry is used for precise gas-phase system properties such as the electronic chemical predictions and refined simulations of energy, orbital energies, nuclear repulsion energy chemical processes with the use of computer and the total energy. programs. Computational data may not yield the At present, there is a good deal of computational exact experimental value from measurements, but it chemistry softwares available. Most of them can predict chemical phenomena qualitatively, and require a commercial license.
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Computational Chemistry: a Practical Guide for Applying Techniques to Real-World Problems
Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems. David C. Young Copyright ( 2001 John Wiley & Sons, Inc. ISBNs: 0-471-33368-9 (Hardback); 0-471-22065-5 (Electronic) COMPUTATIONAL CHEMISTRY COMPUTATIONAL CHEMISTRY A Practical Guide for Applying Techniques to Real-World Problems David C. Young Cytoclonal Pharmaceutics Inc. A JOHN WILEY & SONS, INC., PUBLICATION New York . Chichester . Weinheim . Brisbane . Singapore . Toronto Designations used by companies to distinguish their products are often claimed as trademarks. In all instances where John Wiley & Sons, Inc., is aware of a claim, the product names appear in initial capital or all capital letters. Readers, however, should contact the appropriate companies for more complete information regarding trademarks and registration. Copyright ( 2001 by John Wiley & Sons, Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic or mechanical, including uploading, downloading, printing, decompiling, recording or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without the prior written permission of the Publisher. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 605 Third Avenue, New York, NY 10158-0012, (212) 850-6011, fax (212) 850-6008, E-Mail: PERMREQ @ WILEY.COM. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold with the understanding that the publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional person should be sought.
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Wmpack –Version 1.0
1 MANUAL WMPack –version 1.0 Yan Zhao State Key Laboratory of Silicate Materials for Architectures, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070, People’s Republic of China Donald G. Truhlar Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, MN 55455-0431 Program Version: 1.0 Program Version Date: Oct 11, 2018 Manual Version Date: Oct 25, 2018 Copyright 2018 Abstract: WMPack is a computer program for generating input files and computing electronic energies by the WMS, W2X, W3X, and W3X-L multilevel methods. To use the WMS or W2X method in WMPack, one needs the Molpro program, and to use the W3X or W3X-L method in WMPack , one needs the Molpro and MRCC programs. 2 Table of Contents 1. Introduction .............................................................................................................................. 3 2. References for the WMPack Program ...................................................................................... 4 3. General Program Description ................................................................................................... 6 4. Theoretical Background .............................................................................................................. 7 4.1 Basis Sets .............................................................................................................................. 7 4.2 Methodology and Theory of WMS ......................................................................................
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What Is the Price of Open-Source Software? 8 9 Anna I
The Journal of Physical Chemistry Letters This document is confidential and is proprietary to the American Chemical Society and its authors. Do not copy or disclose without written permission. If you have received this item in error, notify the sender and delete all copies. What is the Price of Open -Source Software? Journal: The Journal of Physical Chemistry Letters Manuscript ID: jz-2015-01258h Manuscript Type: Viewpoint Date Submitted by the Author: 13-Jun-2015 Complete List of Authors: Krylov, Anna; University of Southern California, Dept. of Chemistry Herbert, John; The Ohio State University, Chemistry Furche, Filipp; University of California, Irvine, Chemistry Head-Gordon, Martin; University of California, Berkeley, Chemistry Knowles, Peter; Cardiff University, School of Chemistry Lindh, Roland; Chemistry - Ångström Laboratory, Theoretical Chemistry Manby, Frederick; University of Bristol, School of Chemistry Pulay, Peter; University of Arkansas, Chemistry and Biochemistry Skylaris, Chris-Kriton; University of Southampton, Werner, Hans-Joachim; Universitaet Stuttgart, Institut fuer Theoretische Chemie ACS Paragon Plus Environment Page 1 of 6 The Journal of Physical Chemistry Letters 1 2 3 4 5 6 7 What is the price of open-source software? 8 9 Anna I. Krylov,1∗ John M. Herbert,2† Filipp Furche,3 10 Martin Head-Gordon,4 Peter J. Knowles,5 Roland Lindh,6 Frederick R. Manby,7 11 8 9 10 12 Peter Pulay, Chris-Kriton Skylaris, and Hans-Joachim Werner 13 14 1Dept. of Chemistry, University of Southern California, Los Angeles, California, USA 15 2Dept. of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA 16 3Dept. of Chemistry, University of California, Irvine, California, USA 17 4 18 Dept.
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