Brief Biosketch

Total Page:16

File Type:pdf, Size:1020Kb

Brief Biosketch Brief Biosketch I obtained a BSc (Hons’) and MSc (Thesis) degree in Biochemistry & Molecular Biology from the Rajshahi University. Then I joined as a research assistant in Protein Chemistry lab in the Rajshahi University for 1 year with Dr. Nurul Absar, Professor of the department of Biochemistry & Molecular Biology, Rajshahi University. In the meanwhile, I then encouraged to join as a Consultant Biochemist in Clinical Biochemistry lab at Anwer Khan Modern Medical College and Hospital Ltd, Dhanmondi, Dhaka. After 4 years, I then motivated to join at Primeasia University as a lecturer of Biochemistry and I am continuing service for 5 years. I then take up a senior lectureship at Primeasia University. In case of broad sense of research; I have established collaborative infectious diseases research lab with Dhaka Hospital Ltd, Dhaka, Bangladesh. I also made inter-office memorandum, Department of Pharmacy and Department of Microbiology for doing research at standard level. From this collaborative research works, we have published more than 20 articles in peer- reviewed journals and more than 08 conference abstracts from 2012 to 2017. As an Investigator, I supervised 27 and more students at the level of BSc (Hons’) final year research/training program from 2012 to 2017. At present; as a Research Fellow (Non-Degree) at Institute of Biological Science in Rajshahi University from April 2017 to date, I am doing research on “Identification of Novel Anticancer Polysaccharides from Edible Mushrooms and the Molecular Mechanisms Underlying Anti-tumor Activity in Human Cancer Cell Lines” with Professor Dr. Md. Matiar Rahman. In dry lab research activities; I am self-educated on Bioinformatics and Computer Aided Drug Design (CADD) and through the utilization of LigPlot+, Gaussian, VMD, NAMD, WebMO, GabEdit, AutoDock Vina, ZincDatabase, PDB, ChemDraw, JsMolEditor, and Molegro Molecular Viewer, to find out the novel inhibitors of HIV Protease and Aromatase for the treating of AIDS and Breast Cancer. A group of students has been working with me on drug discovery in Silico methods of infectious diseases like Hepatitis, TORCH infection, COPD, HIV, TB and Cancers. I am well-educated on data analysis and interpretations by SPSS 21 (IBM), STATA 13, MS- Excell, GrapPad Prism 5 and R (a certificate honored from HarvardedX, an online learning initiative of Harvard University through edX). As an Assistant proctor, I had been partaking in different administrative activities at Primeasia University from January, 2015 to March 2017. I am also honored member of Cultural Club, Anti- Narcotic Committee, Departmental Self-Assessment Committee, Research Evaluation Committee, and CADD Center at Primeasia University. Curriculum Vitae PERSONAL INFORMATION Md. Moyen Uddin PK Research Fellow (Non-Degree) Institute of Biological Science, University of Rajshahi, Bangladesh. +8801941607515 , 01749-038083 Sex : Male | Date of birth: 21/07/1981 | Nationality: Bangladeshi RESEARCH INTERESTS Protein Chemistry; Cell Biology; Molecular Immunology; Neurobiology; Bioinformatics; Molecular basis of diseases, Radiation Genetics; Computer Aided Drug Design; Medicinal Chemistry; WORK EXPERIENCES April 2017 - Present Research Fellow, Institute of Biological Science, University of Rajshahi, Bangladesh, www.ru.ac.bd January 2016 – March 2017 Senior Lecturer , Department of Biochemistry, Primeasia University, Dhaka-1213, Bangladesh, www.primeasia.edu.bd February 2012 – December Lecturer, Department of Biochemistry, Primeasia University, Dhaka-1213, 2015 Bangladesh January 2008 – December Consultant Biochemistry, Department of Clinical Laboratory, Anwer Khan 2011 Medical College & Hospital Ltd. Dhaka-1207, Bangladesh July 2007 – December Research Assistant, Protein Research Laboratory, Dept. of Biochemistry & 2007 Molecular Biology, Rajshahi University, Bangladesh EDUCATIONS Jan 2004 – Dec 2004 MSc (Thesis) st (Exam. Held in 2006) First Class (1 position) Department of Biochemistry & Molecular Biology, Rajshahi University, Bangladesh Thesis title Characterizations of TTX from Puffer Fish Tetraodon Cutcutia. Jan 2000 – Dec 2003 BSc (Hon’s) st (Exam. Held in 2004) First Class (1 position) Department of Biochemistry & Molecular Biology, Rajshahi University, Bangladesh 1996 – 1997 Higher Secondary Certificate (HSC) (Exam. Held in 1998) First Division Science Group, N S Govt. College, Natore, Bangladesh 1994 – 1995 Secondary School Certificate (SSC) (Exam. Held in 1996) First Division Science Group, Sadhanpur High School, Bangladesh RESEARCH EXPERIENCES AND TECHNICAL SKILLS Molecular Biology: Agarose gel electrophoresis and SDS-PAGE for DNA isolation Real time PCR (Smart Cycler version 2) Inverted Fluorescence Microscope (Avert A1, Germany), Bright field microscope, Phase contrast microscope (Avert A1, Germany). Restriction enzyme digestion and DNA recombinant synthesis, Plasmid DNA culture in E. coli and extraction (mini-prep), and ELISA Protein Chemistry: SDS-PAGE for Protein isolation and Western blot Gel filtration chromatography (GFC) Thin layer chromatography (TLC) Affinity chromatography (AC) Western Blotting Analytical Chemistry: Infra-red (IR) Spectroscopy, NMR, GC-MS, and HPLC + Computer Aided Drug LigPlot , Gaussian, VMD, NAMD, WebMO, GabEdit, AutoDock Vina, Design: ZincDatabase, PDB, ChemDraw, JsMolEditor, Amber, SwissParam, (CADD) SwissModel, Pocketome, iScreen, X-score, cQSAR, SwissADME Bioinformatics: DNA Star Lasergene, MEGA 5.1 beta, BLAST, ExPASy, MD5 checksum calculator, Sequin, NCBI, PDB, ClustalW/W2/Omega, Phylogeny.fr, Pymol. Statistical R (a certificate honored from HarvardedX, an online learning initiative Analysis of Harvard University through edX), GraphPad prism 6, SPSS Tools version 21, SPSS AMOS version 22 , and STATA 13 COMMUNICATION Excellent verbal and written communication skill gained through teaching SKILLS undergrad students and co-ordinating several student outreach programs. Experienced at giving presentations to large audiences. ORGANISATIONAL / ▪ Member, research evaluation committee, Dept. of Biochemistry, Primeasia MANAGERIAL SKILLS University (PAU); ▪ Member of infectious diseases research unit of Biomedical Research Centre, PAU; ▪ Member of research group, Department of Pharmacy, PAU; Bangladesh; ▪ Member of diagnostic research unit, Dhaka Hospital Ltd., Bangladesh; ▪ Member, Departmental Self-Assessment Committee, PAU; Bangladesh ▪ Member, Anti-Narcotic Committee, Primeasia University, Bangladesh. ▪ Member ,Cultural Committee, Primeasia University, Bangladesh; ▪ Assistant Proctor, Primeasia University, Bangladesh; PERSONAL SKILLS Mother tongue(s) Bengali Other language(s) English Self-assessment UNDERSTANDING SPEAKING WRITING Spoken Spoken Listening Reading interaction production English C2 C2 B2 B2 C2 Levels: A1/2: Basic user - B1/2: Independent user - C1/2 Proficient user Common European Framework of Reference for Languages PUBLICATIONS 1-27 1. M Moyen Uddin PK, Istiaque Saon (2018). Molecular Docking of CXCR4 Antagonists for treating AIDS at Entry Level of HIV. Review at Drug Discovery Today. 2. M Moyen Uddin PK, Mohammad Sayful Islam et al (2018). Genotoxicity of Binary Combinations of Ganoderma Lucidum and Pleurotus Ostreatus-Edible Mushrooms. Accepted in Journal of Global Pharma Technology, Manuscript ID:5009022018JGPT , Scopus Indexed 3. M Moyen Uddin PK et al (2018). Optimization of Extraction of Antioxidant Polysaccharide from Pleurotus ostreatus (Jacq.) P. Kumm. Review at International food research journal. 4. M Moyen Uddin PK et al (2018). Enzyme Inhibitory and Antioxidant Activity of Binary Combinations of Two Edible Mushrooms of Ganoderma lucidum and Pleurotus ostreatus. Accepted at Tropical Journal of Natural Product Research 5. M Moyen Uddin PK et al (2018). Maximal in vitro Efficacy of Extracts of Ganoderma lucidum in Reducing Free Radicals Formation. Review at FAHAD Journal 6. Akter MS, M Moyen Uddin PK, et al (2018). Antioxidant activity and cytotoxicity of Moringa oleifera leaves grown in Bangladesh. World Journal of Science and Engineering (WJSE) 3 (1) 87- 99. 7. Fazlay Rabbi, M Moyen Uddin PK et al (2016). Hepatitis B Vireamia in Hepatitis B Surface Antigenemic Patients in Bangladesh. Am. J. Biomed. Sci. 2016, 8(4), 288-296; doi: 10.5099/aj160400288 8. Kaniz Fatema, M Moyen Uddin PK et al (2016). An Epidemiological Study of Antibiotic Resistance of Salmonella typhi and Salmonella paratyphi - A from Clinical Samples in Dhaka City. Journal of Applied Life Sciences International, 2394-1103,Vol.: 8, Issue.: 4 9. M Moyen Uddin PK et al. Scattering of Rubella IgG Titer in Cytomegalovirus IgG SeroPositive Adult Women in Bangladesh. American Journal of Virology 2015, 4 (1): 12.15 DOI: 10.3844/ajvsp.2015.12.15 10. M Moyen Uddin PK (2015): Role of USP 18 in Immune Response to Chronic Viral Infection. J Med Microb Diagn 4: 189. 11. M Moyen Uddin PK, Abdul Halim, Y Kabir. Risk factors of being acute hepatitis b surface antigenemia in Bangladeshi adult patients. The american journal of innovative research and applied sciences. 2015; 1(8): xx-xx. 12. M Moyen Uddin PK, Abu Mohammad Azmal Morshed et al. Prevalence of Herpes Simplex Virus Infection among Adults Citizens of Dhaka, Bangladesh. J Blood Disord Transfus 2015, S5:1 http://dx.doi.org/10.4172/2155- 9864.1000S5-003. 13. Moyen Uddin PK*, N Absar et al. Hepatitis B Viral Load (HBV-DNA) With Age and Sex Stratifications in Bangladeshi People. J Med Microb Diagn, 2014; 3: 144. doi:10.4172/2161-0703.1000144 14. M Moyen Uddin PK and Abu Mohammad Azmal Morshed*: Predominance
Recommended publications
  • User Guide of Computational Facilities
    Physical Chemistry Unit Departament de Quimica User Guide of Computational Facilities Beta Version System Manager: Marc Noguera i Julian January 20, 2009 Contents 1 Introduction 1 2 Computer resources 2 3 Some Linux tools 2 4 The Cluster 2 4.1 Frontend servers . 2 4.2 Filesystems . 3 4.3 Computational nodes . 3 4.4 User’s environment . 4 4.5 Disk space quota . 4 4.6 Data Backup . 4 4.7 Generation of SSH keys for automatic SSH login . 4 4.8 Submitting jobs to the cluster . 5 4.8.1 Typical queue system commands . 6 4.8.2 HomeMade scripts . 6 4.8.3 Create your own submit script . 6 4.8.4 Submitting Parallel Calculations . 7 5 Available Software 9 5.1 Chemisty software . 9 5.2 Development Software . 10 5.3 How to use the software . 11 5.4 Non-default environments . 11 6 Your Linux Workstation 11 6.1 Disk space on your workstation . 12 6.2 Workstation Data Backup . 12 6.3 Running virtual Windows XP . 13 6.3.1 The Windows XP Environment . 13 6.4 Submitting calculations to your dekstop . 13 6.5 Network dependent structure . 14 7 Your WindowsXP Workstation 14 7.1 Workstation Data Backup . 14 8 Frequently asked questions 14 1 Introduction This User Guide is aimed to the standard user of the computer facilities in the ”Unitat de Quimica Fisica” in the Universitat Autnoma de Barcelona. It is not assumed that you have a knowledge of UNIX/Linux. However, you are 1 encouraged to take a close look to the linux guides that will be pointed out.
    [Show full text]
  • 3D-Printing Models for Chemistry
    3D-Printing Models for Chemistry: A Step-by-Step Open-Source Guide for Hobbyists, Corporate ProfessionAls, and Educators and Student in K-12 and Higher Education Poster Elisabeth Grace Billman-Benveniste+, Jacob Franz++, Loredana Valenzano-Slough+* +Department of Chemistry, Michigan Technological University, ++Department of Mechanical Engineering, Michigan Technological University *Corresponding Author References 1. “LulzBot TAZ 5.” LulzBot, 14 Aug. 2018, www.lulzbot.com/store/printers/lulzbot-taz-5 2. Gaussian 16, Revision B.01, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, A. V.; Bloino, J.; Janesko, B. G.; Gomperts, R.; Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, A. F.; Sonnenberg, J. L.; Williams-Young, D.; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.; Petrone, A.; Henderson, T.; Ranasinghe, D.; ZakrzeWski, V. G.; Gao, J.; Rega, N.; Zheng, G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; HasegaWa, J.; Ishida, M.; NakaJima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Throssell, K.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Keith, T. A.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.; Cammi, R.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Farkas, O.; Foresman, J. B.; Fox, D. J. Gaussian, Inc., Wallingford CT, 2016. 3.
    [Show full text]
  • Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens
    International Journal of Molecular Sciences Review Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens Anna Helena Mazurek 1 , Łukasz Szeleszczuk 1,* , Thomas Simonson 2 and Dariusz Maciej Pisklak 1 1 Chair and Department of Physical Pharmacy and Bioanalysis, Department of Physical Chemistry, Medical Faculty of Pharmacy, University of Warsaw, Banacha 1 str., 02-093 Warsaw Poland; [email protected] (A.H.M.); [email protected] (D.M.P.) 2 Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91-120 Palaiseau, France; [email protected] * Correspondence: [email protected]; Tel.: +48-501-255-121 Received: 21 July 2020; Accepted: 1 September 2020; Published: 3 September 2020 Abstract: In this review, applications of various molecular modelling methods in the study of estrogens and xenoestrogens are summarized. Selected biomolecules that are the most commonly chosen as molecular modelling objects in this field are presented. In most of the reviewed works, ligand docking using solely force field methods was performed, employing various molecular targets involved in metabolism and action of estrogens. Other molecular modelling methods such as molecular dynamics and combined quantum mechanics with molecular mechanics have also been successfully used to predict the properties of estrogens and xenoestrogens. Among published works, a great number also focused on the application of different types of quantitative structure–activity relationship (QSAR) analyses to examine estrogen’s structures and activities. Although the interactions between estrogens and xenoestrogens with various proteins are the most commonly studied, other aspects such as penetration of estrogens through lipid bilayers or their ability to adsorb on different materials are also explored using theoretical calculations.
    [Show full text]
  • Application of Molecular Dynamics Simulation to Small Systems
    40 Application of Molecular Dynamics Simulation to Small Systems Víctor M. Rosas-García and Isabel Sáenz-Tavera Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, N. L. México 1. Introduction The study of chemical behavior includes answering questions as ’which isomer is the most stable?’, ’which relative orientation is the most favorable for such-and-such interaction?’, ’which conformer is the global minimum?’, ’what are the lowest energy configurations and their relative energies?’. The answer to these questions–and many others–depends on the ability to find and study a variety of configurations of the system of interest. Recently, (Atilgan, 2007) briefly reviewed the use of molecular dynamics simulation for conformational search in the process of drug design, concluding that its use could reduce the errors in estimating binding affinities and finding more viable conformations. In addition, (Corbeil, 2009) considered the need to include ring flexibility in the conformational searches used in flexible docking. Most of the flexible docking algorithms skip searching for conformations in rings, even though a protein may stabilize a conformation other than the most stable one. The need for a tool to examine the diverse configurations of the constituent particles of a system becomes obvious even as we consider relatively small systems (10-100 atoms). Finding by hand all the conformers of cyclohexane is feasible and maybe even instructive; this is somewhat more complex when doing morpholine and even something as small as an eight-membered heterocycle can be prohibitively complex to analyze by manipulating molecular models by hand. One of the methods available to the researcher to tackle this kind of problem is Molecular Dynamics (MD) simulation.
    [Show full text]
  • Open Source Molecular Modeling
    Accepted Manuscript Title: Open Source Molecular Modeling Author: Somayeh Pirhadi Jocelyn Sunseri David Ryan Koes PII: S1093-3263(16)30118-8 DOI: http://dx.doi.org/doi:10.1016/j.jmgm.2016.07.008 Reference: JMG 6730 To appear in: Journal of Molecular Graphics and Modelling Received date: 4-5-2016 Accepted date: 25-7-2016 Please cite this article as: Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes, Open Source Molecular Modeling, <![CDATA[Journal of Molecular Graphics and Modelling]]> (2016), http://dx.doi.org/10.1016/j.jmgm.2016.07.008 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Open Source Molecular Modeling Somayeh Pirhadia, Jocelyn Sunseria, David Ryan Koesa,∗ aDepartment of Computational and Systems Biology, University of Pittsburgh Abstract The success of molecular modeling and computational chemistry efforts are, by definition, de- pendent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. 1. Introduction What is Open Source? Free and open source software (FOSS) is software that is both considered \free software," as defined by the Free Software Foundation (http://fsf.org) and \open source," as defined by the Open Source Initiative (http://opensource.org).
    [Show full text]
  • A Virtual Alternative to Molecular Model Sets
    Phankingthongkum and Limpanuparb BMC Res Notes (2021) 14:66 BMC Research Notes https://doi.org/10.1186/s13104-021-05461-7 RESEARCH NOTE Open Access A virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software Siripreeya Phankingthongkum and Taweetham Limpanuparb* Abstract Objective: The application of molecular graphics software as a simple and free alternative to molecular model sets for introductory-level chemistry learners is presented. Results: Based on either Avogadro or IQmol, we proposed four sets of tasks for students, building basic molecular geometries, visualizing orbitals and densities, predicting polarity of molecules and matching 3D structures with bond- line structures. These topics are typically covered in general chemistry for frst-year undergraduate students. Detailed step-by-step procedures are provided for all tasks for both programs so that instructors and students can adopt one of the two programs in their teaching and learning as an alternative to molecular model sets. Keywords: Chemical education, Molecular model, General chemistry, Molecular graphics software Introduction at high price. With open-source licensing, the cost and Te use of molecular model has been recommended to availability of the software is no longer an issue. be part of the curriculum to enhance spatial thinking in Most molecular graphics programs allow users to con- students of chemistry [1]. Physical molecular model sets struct, edit and visualize molecules in 3D, and hence, are are usually employed in an introductory-level chemistry viable alternatives to conventional teaching materials. laboratory [2]. Other similar teaching tools [3–45] vary Te issue here is therefore how to bring these dynamic greatly in terms of cost, ease of use, required amount of and interactive visualization programs as scafolding time and suitability for relevant topics in chemistry.
    [Show full text]
  • (Bio-)Chemical Tools and Visualization Software for Computational Science
    UvA-DARE (Digital Academic Repository) Highlights of (bio-)chemical tools and visualization software for computational science Dubbeldam, D.; Vreede, J.; Vlugt, T.J.H.; Calero, S. DOI 10.1016/j.coche.2019.02.001 Publication date 2019 Document Version Final published version Published in Current Opinion in Chemical Engineering License Article 25fa Dutch Copyright Act Link to publication Citation for published version (APA): Dubbeldam, D., Vreede, J., Vlugt, T. J. H., & Calero, S. (2019). Highlights of (bio-)chemical tools and visualization software for computational science. Current Opinion in Chemical Engineering, 23, 1-13. https://doi.org/10.1016/j.coche.2019.02.001 General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:01 Oct 2021 Available online at www.sciencedirect.com ScienceDirect Highlights of (bio-)chemical tools and visualization software for computational science 1 1 2 David Dubbeldam , Jocelyne Vreede , Thijs JH Vlugt and 3 Sofia Calero Computational chemistry uses computer simulation to assist in There are hundreds of chemical software packages avail- solving chemical problems.
    [Show full text]
  • Polarized-Unpolarized Ground State of Small Polycyclic Aromatic Hydrocarbons
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Repositorio Institucional de la Universidad de Alicante Polarized-unpolarized ground state of small polycyclic aromatic hydrocarbons E. San-Fabián and F. Moscardó Departamento de Química Física, Unidad Asociada del Consejo Superior de Investigaciones Científicas and Instituto Universitario de Materiales, Universidad de Alicante. San Vicente del Raspeig, Alicante 03690, Spain. (Dated: September 22, 2014) Do polyacenes, circumacenes, periacenes, nanographenes and graphene nanoribbons show a spin polarized ground state? In this work, we present mono-determinantal (Hartree-Fock and Density Functional Theory types), and multi-determinantal calculations ( Møller-Plesset and Coupled Cluster), for several families of un- saturated organic molecules (n-Acenes, n-Periacenes and n-Circumacenes). All HF calculations and many DFT show a spin-polarized (antiferromagnetic) ground state, in agreement with previous calculations. Nevertheless, the multi-determinantal calculations, carried out with perturbative and variational wavefunctions, show that the more stable state is obtained starting from the unpolarized Hartree-Fock wavefunction. The trend of the stabilisation of wavefunctions (polarized or unpolarized) with respect to exchange and cor- relation potentials, and to the number of benzene rings, has been analysed. A study of the spin (<S^2>) and the spin density on the carbon atoms has also been carried out. Key words: Spin-polarized states; DFT calculations; MP3; CCSD. 2 I. INTRODUCTION. Graphene nanoribbons have been the focus of much research both from experimental and theoretical points of view (See for example ref. [1] and their references), and their magnetic properties have motivated the interest in the study of other small polycyclic aromatic hydrocarbons (PAH).
    [Show full text]
  • Visualization of Molecular Structure: the State of the Art
    Eurographics Conference on Visualization (EuroVis) (2015) STAR – State of The Art Report R. Borgo, F. Ganovelli, and I. Viola (Editors) Visualization of Molecular Structure: The State of the Art B. Kozlíkováy1, M. Kroney2, N. Lindow3, M. Falk4, M. Baaden5, D. Baum3, I. Viola6;7, J. Parulek7, and H.-C. Hege3 1Masaryk University, Czech Republic 2Visualization Research Center, University of Stuttgart, Germany 3Zuse Institute Berlin, Germany 4Immersive Visualization Group, Linköping University, Sweden 5Laboratoire de Biochimie Théorique, UPR 9080 CNRS, France 6Institute of Computer Graphics and Algorithms, Vienna University of Technology, Austria 7Department of Informatics, University of Bergen, Norway Abstract Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualization techniques for molecular structures, strategies for efficient display in terms of image quality and frame rate, then it covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures. Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling—Curve, surface, solid, and object representations 1.
    [Show full text]
  • A MOLECULAR DYNAMICS STUDY of N-A-S-H GEL with VARIOUS Si/Al RATIOS
    4th International RILEM conference on Microstructure Related Durability of Cementitious Composites (Microdurability2020) A MOLECULAR DYNAMICS STUDY OF N-A-S-H GEL WITH VARIOUS Si/Al RATIOS Yun Chen (1,2), Jorge S. Dolado (3,4), Suhong Yin (2), Qijun Yu (2), Albina Kostiuchenko (1), Zhenming Li (1), Guang Ye (1,5) (1) Section of Materials and Environment, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Delft 2628CN, The Netherlands (2) School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, Guangdong, China (3) Centro de Física de Materiales CFM (CSIC-UPV/EHU), 20018 San Sebastián/Donostia, Spain (4) Donostial International Physics Center (DIPC), 20018, San Sebastián/Donostia, Spain (5) Magnel Laboratory for Concrete Research, Department of Structural Engineering, Ghent University, Ghent, Belgium Abstract The understanding of sodium aluminosilicate hydrate (N-A-S-H) gel is still limited due to its complex and amorphous structure. Recently, molecular dynamics simulation has provided a unique opportunity to better understand the structure of N-A-S-H gel from nanoscale. In this work, the N-A-S-H gel structure was obtained by simulating the polymerization of Si and Al monomers by molecular dynamics. The simulated polymerization process is in good agreement with the experimental results especially in terms of the reaction rate of Si and Al species. The atomic structural features of the N-A-S-H gel were analyzed in terms of bond length and bond n angle information, simulated X-ray diffraction (XRD) and Q distribution. A significant finding is the existence of pentacoordinate Al in all simulated N-A-S-H structures, indicating that pentacoordinate Al in geopolymer does not only come from raw material.
    [Show full text]
  • User Guide of Computational Facilities
    Physical Chemistry Unit, Departament de Química User Guide of Computational Facilities An User Guide for the standard user of the computer facilities in the ”Unitat de Química Física” in the Universitat Autònoma de Barcelona Marc Noguera i Julián and Carles Acosta i Silva 23/02/2011 Table Of Contents 1 Introduction ................................................................................................................................ 4 2 Computer resources ................................................................................................................... 4 3 Some Linux tools ........................................................................................................................ 5 4 The Cluster ................................................................................................................................. 6 4.1 Frontend servers ................................................................................................................. 6 4.2 Filesystems .......................................................................................................................... 6 4.3 Computational nodes .......................................................................................................... 7 4.4 User’s environment ............................................................................................................. 9 4.5 Disk space quota ................................................................................................................. 9 4.6
    [Show full text]
  • WHAT INFLUENCE WOULD a CLOUD BASED SEMANTIC LABORATORY NOTEBOOK HAVE on the DIGITISATION and MANAGEMENT of SCIENTIFIC RESEARCH? by Samantha Kanza
    UNIVERSITY OF SOUTHAMPTON Faculty of Physical Sciences and Engineering School of Electronics and Computer Science What Influence would a Cloud Based Semantic Laboratory Notebook have on the Digitisation and Management of Scientific Research? by Samantha Kanza Thesis for the degree of Doctor of Philosophy 25th April 2018 UNIVERSITY OF SOUTHAMPTON ABSTRACT FACULTY OF PHYSICAL SCIENCES AND ENGINEERING SCHOOL OF ELECTRONICS AND COMPUTER SCIENCE Doctor of Philosophy WHAT INFLUENCE WOULD A CLOUD BASED SEMANTIC LABORATORY NOTEBOOK HAVE ON THE DIGITISATION AND MANAGEMENT OF SCIENTIFIC RESEARCH? by Samantha Kanza Electronic laboratory notebooks (ELNs) have been studied by the chemistry research community over the last two decades as a step towards a paper-free laboratory; sim- ilar work has also taken place in other laboratory science domains. However, despite the many available ELN platforms, their uptake in both the academic and commercial worlds remains limited. This thesis describes an investigation into the current ELN landscape, and its relationship with the requirements of laboratory scientists. Market and literature research was conducted around available ELN offerings to characterise their commonly incorporated features. Previous studies of laboratory scientists examined note-taking and record-keeping behaviours in laboratory environments; to complement and extend this, a series of user studies were conducted as part of this thesis, drawing upon the techniques of user-centred design, ethnography, and collaboration with domain experts. These user studies, combined with the characterisation of existing ELN features, in- formed the requirements and design of a proposed ELN environment which aims to bridge the gap between scientists' current practice using paper lab notebooks, and the necessity of publishing their results electronically, at any stage of the experiment life cycle.
    [Show full text]