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The Molecular Sciences Software Institute
The Molecular Sciences Software Institute T. Daniel Crawford, Cecilia Clementi, Robert Harrison, Teresa Head-Gordon, Shantenu Jha*, Anna Krylov, Vijay Pande, and Theresa Windus http://molssi.org S2I2 HEP/CS Workshop at NCSA/UIUC 07 Dec, 2016 1 Outline • Space and Scope of Computational Molecular Sciences. • “State of the art and practice” • Intellectual drivers • Conceptualization Phase: Identifying the community and needs • Bio-molecular Simulations (BMS) Conceptualization • Quantum Mechanics/Chemistry (QM) Conceptualization • Execution Phase. • Structure and Governance Model • Resource Distribution • Work Plan 2 The Molecular Sciences Software Institute (MolSSI) • New project (as of August 1st, 2016) funded by the National Science Foundation. • Collaborative effort by Virginia Tech, Rice U., Stony Brook U., U.C. Berkeley, Stanford U., Rutgers U., U. Southern California, and Iowa State U. • Total budget of $19.42M for five years, potentially renewable to ten years. • Joint support from numerous NSF divisions: Advanced Cyberinfrastructure (ACI), Chemistry (CHE), Division of Materials Research (DMR), Office of Multidisciplinary Activities (OMA) • Designed to serve and enhance the software development efforts of the broad field of computational molecular science. 3 Computational Molecular Sciences (CMS) • The history of CMS – the sub-fields of quantum chemistry, computational materials science, and biomolecular simulation – reaches back decades to the genesis of computational science. • CMS is now a “full partner with experiment”. • For an impressive array of chemical, biochemical, and materials challenges, our community has developed simulations and models that directly impact: • Development of new chiral drugs; • Elucidation of the functionalities of biological macromolecules; • Development of more advanced materials for solar-energy storage, technology for CO2 sequestration, etc. -
Design, Communication & Collaboration in Immersive Virtual
International Journal of Design Computing: Vol 4/2002: Special Issue on Designing Virtual Worlds Design, Communication & Collaboration in Immersive Virtual Environments MARC AUREL SCHNABEL & THOMAS KVAN Department of Architecture The University of Hong Kong, Hong Kong, China [email protected], [email protected] Please use IE 5.5+ and Quicktime. http://www.arch.usyd.edu.au/kcdc/journal/vol4/schnabel/index.html 19/07/2005 International Journal of Design Computing: Vol 4/2002: Special Issue on Designing Virtual Worlds Abstract | Introduction | Experiments | Tasks | Results | Discussion | Conclusion | Acknowledgements | References Abstract Virtual Environments (VE) are increasingly offered as environments for design. Using VE to visualize ideas from the initial steps of design, the architect is challenged to deal with perception of space, solid and void, without translations to and from a two dimensional media. From this new ability, we might expect new forms of design expression. The goal of our study was to identify how designers use and communicate early design ideas by using immersive three-dimensional VEs. We set-up a series of experiments including navigation- and perception-tasks, designing in immersive VE, transcription of design, remote communication between design partners and controlled observations. We explored initial intentions of three-dimensional (3D) immersive design schemes, textual descriptions and collaborations within immersive VE. This article describes the outcome of creation, interpretation and communication of architectural design, by using a 3D maze together with text-based communication in a series of collaborative design experiments. We conducted the first successful attempt of a Joint Design Studio, which uses immersive VE as tool of design and communication between remote partners. -
A Command-Line Interface for Analysis of Molecular Dynamics Simulations
taurenmd: A command-line interface for analysis of Molecular Dynamics simulations. João M.C. Teixeira1, 2 1 Previous, Biomolecular NMR Laboratory, Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain 2 DOI: 10.21105/joss.02175 Current, Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Software Canada • Review Summary • Repository • Archive Molecular dynamics (MD) simulations of biological molecules have evolved drastically since its application was first demonstrated four decades ago (McCammon, Gelin, & Karplus, 1977) and, nowadays, simulation of systems comprising millions of atoms is possible due to the latest Editor: Richard Gowers advances in computation and data storage capacity – and the scientific community’s interest Reviewers: is growing (Hospital, Battistini, Soliva, Gelpí, & Orozco, 2019). Academic groups develop most of the MD methods and software for MD data handling and analysis. The MD analysis • @amritagos libraries developed solely for the latter scope nicely address the needs of manipulating raw data • @luthaf and calculating structural parameters, such as: MDAnalysis (Gowers et al., 2016; Michaud- Agrawal, Denning, Woolf, & Beckstein, 2011); (McGibbon et al., 2015); (Romo, Submitted: 03 March 2020 MDTraj LOOS Published: 02 June 2020 Leioatts, & Grossfield, 2014); and PyTraj (Hai Nguyen, 2016; Roe & Cheatham, 2013), each with its advantages and drawbacks inherent to their implementation strategies. This diversity License enriches the field with a panoply of strategies that the community can utilize. Authors of papers retain copyright and release the work The MD analysis software libraries widely distributed and adopted by the community share under a Creative Commons two main characteristics: 1) they are written in pure Python (Rossum, 1995), or provide a Attribution 4.0 International Python interface; and 2) they are libraries: highly versatile and powerful pieces of software that, License (CC BY 4.0). -
The Application of Virtual Reality in Art Design
International Conference on Education Technology, Management and Humanities Science (ETMHS 2015) The Application of Virtual Reality in Art Design: A New Approach 1, a CHEN Dalei 1 School of Art, Henan Institute of Education, Zhengzhou 450046,China a [email protected] Keywords: Virtual Reality; Art Design; 3D Modeling Abstract. As virtual reality technology matures and popular, it is gradually applied in art design. Virtual reality is constructed by high-tech means of the artificial environment. How best to achieve the user in the virtual world of realistic experience, has become a new research hotspot. In view of the present virtual reality technology and virtual aesthetics can improve the effect of the simulation are faced with the problem, in this paper, the study of virtual reality in art and design. Put forward the integration of technology and art technique can improve the virtual reality visual properties and the degree of match user requirements, improve the effect of the simulation. Introduction In recent years, along with the development of network and multimedia technology, virtual reality technology matures and popularization, the virtual reality technology is gradually applied in art design [1]. Virtual reality, art design is accompanied by virtual reality technology and the popularization of computer application technology and related form of audio-visual design new topic, it used the computer virtual reality technology and integrate images, sound, animation, video and other multimedia means, through the creation and performance of virtual objects with virtual space, information is a new way to display and form, make the information more intuitive, efficient delivery. As people gradually understand and attention to this kind of art and design, its application and development are also more and more widely and rapidly [2-3]. -
(2) Patent Application Publication (10) Pub. No.: US 2016/0370971 A1 HACKETT Et Al
US 20160370971A1 (19) United States (2) Patent Application Publication (10) Pub. No.: US 2016/0370971 A1 HACKETT et al. (43) Pub. Date: Dec. 22, 2016 (54) DRESS FORM FOR THREE-DIMENSIONAL G06T 19/00 (2006.01) DRAWING INSIDE VIRTUAL REALITY G{}6F 3/0484 (2006.01) ENVIRONMENT G06T 15/1() (2006.01) G06T 13/20 (2006.01) (71) Applicant: GOOGLE INC., Mountain View, CA (52) U.S. CI. (US) CPC ........... G06F 3/04815 (2013.01); G06T 15/10 e (2013.01); G06T 13/20 (2013.01); G06T (72) Inventors: Patrick Ryan HACKETT, San 19/006 (2013.01); G06F 3/04842 (2013.01); Francisco, CA (US); Clayton G06F 3/04845 (2013.01); G06F 3/0482 Woodward BAVOR, JR., Atherton, CA (2013.01) (US); Andrey DORONICHEV, San Francisco, CA (US) (57) ABSTRACT (21) Appl. No.: 14/859,167 Systems and methods are described for producing a repre (22) Filed: Sep. 18, 2015 sentation of a display of a three-dimensional virtual reality environment and defining a dress form object within the Related U.S. Application Data virtual reality environment. The virtual reality environment (60) Provisional application No. 62/052,338, filed on Sep. is configured to receive interactive commands from at least 18, 2014. 5- -- ~5 one input device coupled to a computing device and asso s ciated with a user. Fabric movement simulations are gener Publication Classification ated by animating the dress form object according to con figured animation data and displayed in the virtual reality (51) Int. Cl. environment. The display being may be generated in G{}6F 3/0481 (2006.01) response to receiving a movement pattern indicating move G{}6F 3/0482 (2006.01) ment of the dress form object. -
In Human-Computer Interaction Published, Sold and Distributed By: Now Publishers Inc
Full text available at: http://dx.doi.org/10.1561/1100000067 Communicating Personal Genomic Information to Non-experts: A New Frontier for Human-Computer Interaction Orit Shaer Wellesley College, Wellesley, MA, USA [email protected] Oded Nov New York University, USA [email protected] Lauren Westendorf Wellesley College, Wellesley, MA, USA [email protected] Madeleine Ball Open Humans Foundation, Boston, MA, USA [email protected] Boston — Delft Full text available at: http://dx.doi.org/10.1561/1100000067 Foundations and Trends R in Human-Computer Interaction Published, sold and distributed by: now Publishers Inc. PO Box 1024 Hanover, MA 02339 United States Tel. +1-781-985-4510 www.nowpublishers.com [email protected] Outside North America: now Publishers Inc. PO Box 179 2600 AD Delft The Netherlands Tel. +31-6-51115274 The preferred citation for this publication is O. Shaer, O. Nov, L. Wstendorf, and M. Ball. Communicating Personal Genomic Information to Non-experts: A New Frontier for Human-Computer Interaction. Foundations and Trends R in Human-Computer Interaction, vol. 11, no. 1, pp. 1–62, 2017. R This Foundations and Trends issue was typeset in LATEX using a class file designed by Neal Parikh. Printed on acid-free paper. ISBN: 978-1-68083-254-9 c 2017 O. Shaer, O. Nov, L. Wstendorf, and M. Ball 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, mechanical, photocopying, recording or otherwise, without prior written permission of the publishers. Photocopying. In the USA: This journal is registered at the Copyright Clearance Cen- ter, Inc., 222 Rosewood Drive, Danvers, MA 01923. -
Sparse Tangibles
Demos and Posters TEI 2016, February 14-17, 2016, Eindhoven, the Netherlands Sparse Tangibles: Collaborative Exploration of Gene Networks using Active Tangibles and Interactive Tabletops Ahmed Sabbir Arif1, Roozbeh Manshaei1, Sean Delong1, Brien East1, Matthew Kyan3, Ali Mazalek1,2 Synaesthetic Media Laboratory Electrical Engineering & Computer Science3 Ryerson University1 Georgia Institute of York University Toronto, Ontario Technology2 Toronto, Ontario Canada Atlanta, GA, USA Canada {asariF, roozbeh.manshaei, sean.delong, beast, mazalek}@ryerson.ca, [email protected] ABSTRACT fail to work with big data sets or fail to provide the support We present Sparse Tangibles, a tabletop and active tangible- for custom query construction. Most of these solutions are based framework to support cross-platForm, collaborative also system-dependent (that is, do not work with all gene network exploration using a Web interFace. It uses operating systems), require the installation of proprietary smartwatches as active tangibles to allow query construction soFtware, or demand high processing power. Furthermore, on- and oFF-the-table. We expand their interaction vocabulary almost all present solutions are desktop-based, which using inertial sensors and a custom case. We also introduce hinders collaborative exploration and generally limits the a new metric for measuring the “conFidence level” of protein users to smaller screens. and genetic interactions. Three expert biologists evaluated the system and Found it fun, useFul, easy to use, and ideal for We Formed an interdisciplinary team oF six to address these collaborative explorations. issues. Apart From two HCI researchers and an engineer, the group consists oF three expert biomedical/signal processing Author Keywords engineers, whom we identiFy as potential users oF the Systems biology; biomedical engineering; sparse network; system. -
EPSRC Service Level Agreement with STFC for Computational Science Support
CoSeC Computational Science Centre for Research Communities EPSRC Service Level Agreement with STFC for Computational Science Support FY 2016/17 Report and Update on FY 2017/18 Work Plans This document contains the 2016/17 plans, 2016/17 summary reports, and 2017/18 plans for the programme in support of CCP and HEC communities delivered by STFC and funded by EPSRC through a Service Level Agreement. Notes in blue are in-year updates on progress to the tasks included in the 2016/17 plans. Text highlighted in yellow shows changes to the draft 2017/18 plans that we submitted in January 2017. Contents CCP5 – Computer Simulation of Condensed Phases .......................................................................... 4 CCP5 – 2016 / 17 Plans (1 April 2016 – 31 March 2017) ...................................................... 4 CCP5 – Summary Report (1 April 2016 – 31 March 2017) .................................................... 7 CCP5 –2017 / 18 Plans (1 April 2017 – 31 March 2018) ....................................................... 8 CCP9 – Electronic Structure of Solids .................................................................................................. 9 CCP9 – 2016 / 17 Plans (1 April 2016 – 31 March 2017) ...................................................... 9 CCP9 – Summary Report (1 April 2016 – 31 March 2017) .................................................. 11 CCP9 – 2017 / 18 Plans (1 April 2017 – 31 March 2018) .................................................... 12 CCP-mag – Computational Multiscale -
Immersive Experience Impact on Students' Understanding of Design
Paper ID #10069 Immersive Experience Impact on Students’ Understanding of Design Ms. Antonette T. Cummings P.E., Purdue University Antonette Cummings is a Ph.D. student in Engineering Education at Purdue University. She holds an M.S. in Mechanical Engineering from the University of Texas at Austin. Dr. Carla B. Zoltowski, Purdue University, West Lafayette Carla B. Zoltowski, Ph.D., is Co-Director of the EPICS Program at Purdue University. She received her B.S. and M.S. in electrical engineering and Ph.D. in engineering education, all from Purdue University. She has served as a lecturer in Purdue’s School of Electrical and Computer Engineering. Dr. Zoltowski’s academic and research interests include human-centered design learning and assessment, service-learning, ethical reasoning development and assessment, leadership, and assistive technology. Ms. Ming-Chien Hsu, Purdue University, West Lafayette Ming-Chien Hsu is a doctoral candidate of Engineering Education at Purdue University. She was an elec- trical engineer working on semiconductor devices before stepping into the realm of education research. Her current research explores and characterizes learning experiences in engineering such as design and interdisciplinary learning. Dr. Monica E Cardella, Purdue University, West Lafayette Monica Cardella is an Associate Professor of Engineering Education at Purdue University. She teaches design to first-year engineering students at Purdue as well as an upper-level design course for seniors and graduate students. Her research focuses on the development of engineering thinking skills (operational- ized as design thinking, mathematical thinking, and the interplay between the two) in children as young as 4 years old as well as older ”children” (i.e. -
Designing Reality-Based Interfaces for Experiential Bio-Design
Pers Ubiquit Comput DOI 10.1007/s00779-013-0752-1 ORIGINAL ARTICLE Designing reality-based interfaces for experiential bio-design Orit Shaer • Consuelo Valdes • Sirui Liu • Kara Lu • Kimberly Chang • Wendy Xu • Traci L. Haddock • Swapnil Bhatia • Douglas Densmore • Robert Kincaid Received: 16 December 2012 / Accepted: 15 February 2013 Ó Springer-Verlag London 2013 Abstract Reality-based interfaces (RBIs) such as table- design process for enhancing college-level science educa- top and tangible user interfaces draw upon ideas from tion through reality-based interaction, (2) reflections on the embodied cognition to offer a more natural, intuitive, and design, implementation, and validation of two case stud- accessible form of interaction that reduces the mental effort ies—RBIs for learning synthetic biology, and (3) discus- required to learn and operate computational systems. sion of opportunities and challenges for advancing learning However, to date, little research has been devoted to of college-level sciences through next-generation investigating the strengths and limitations of applying interfaces. reality-based interaction for promoting learning of complex scientific concepts at the college level. We propose that Keywords Reality-based interaction Multi-touch Á Á RBIs offer unique opportunities for enhancing college- Bioinformatics Collaborative learning level science education. This paper presents three main Synthetic biologyÁ Á contributions: (1) design considerations and participatory O. Shaer (&) C. Valdes S. Liu K. Lu K. Chang W. Xu 1 Introduction Wellesley College,Á 106 CentralÁ St.,Á Wellesley,Á MA, USAÁ e-mail: [email protected] Over the past two decades, human–computer interaction C. Valdes (HCI) research has generated a broad range of interaction e-mail: [email protected] styles that move beyond the desktop into new physical and S. -
EXTENDED REALITY for DESIGN Online Option Short Course Extended Reality for Design Online Option 02
SHORT COURSES EXTENDED REALITY FOR DESIGN Online Option Short Course eXtended Reality for Design Online Option 02 General Introduction Over the past 80 years Istituto Marangoni has grown and developed alongside the thriving Italian fashion and design scenario. Through an exciting curriculum aimed to develop practical, creative, business and management skills which are subject spe- cific, and relevant to the international fashion, design or art industries, Istituto Marangoni short courses prepare students in the principles of subjects such as Fashion Design, Accessories and Footwear Design, Fashion Styling, Fashion Business and Com- munication, Visual and Multimedia Design, Interior Design, Product Design, Art Management and Art Curation. 1. Certification Attained Istituto Marangoni Certificate Course Information 2. General info: • Duration: 6 Weeks (3 days per week) • Total Hours: 45 • Course Delivery mode: full online • Lesson Duration: 2h30 3. Short Course Description This is a short introductory course to fast track the working knowledge and practical skills in extended reality (XR) technology. This new wave of mass media offers unlimited freedom to create products and artwork without the limitations of space and re- sources and allows for a more human design process (avoiding code, keyboards and years of training). With a special focus on experimenting with hands-on practical skills that can be used straight away, this course equips partici- pants with the tools to start building ideas in 3D space. Focusing on Virtual Reality and Augmented Reality, each class covers a new topic with take away exercises and homework to practice and present for feedback from the experienced lecturer. Students also discover ways to create 3D models, floorplans and visual concepts in 3D using readily available tools to build virtual worlds, capture real world objects, share their work to new audiences and visualise ideas to create exciting new experiences. -
A Reader in Themed and Immersive Spaces
A READER IN THEMED AND IMMERSIVE SPACES A READER IN THEMED AND IMMERSIVE SPACES Scott A. Lukas (Ed.) Carnegie Mellon: ETC Press Pittsburgh, PA Copyright © by Scott A. Lukas (Ed.), et al. and ETC Press 2016 http://press.etc.cmu.edu/ ISBN: 978-1-365-31814-6 (print) ISBN: 978-1-365-38774-6 (ebook) Library of Congress Control Number: 2016950928 TEXT: The text of this work is licensed under a Creative Commons Attribution-NonCommercial-NonDerivative 2.5 License (http://creativecommons.org/licenses/by-nc-nd/2.5/) IMAGES: All images appearing in this work are property of the respective copyright owners, and are not released into the Creative Commons. The respective owners reserve all rights. Contents Part I. 1. Introduction: The Meanings of Themed and Immersive Spaces 3 Part II. The Past, History, and Nostalgia 2. The Uses of History in Themed Spaces 19 By Filippo Carlà 3. Pastness in Themed Environments 31 By Cornelius Holtorf 4. Nostalgia as Litmus Test for Themed Spaces 39 By Susan Ingram Part III. The Constructs of Culture and Nature 5. “Wilderness” as Theme 47 Negotiating the Nature-Culture Divide in Zoological Gardens By Jan-Erik Steinkrüger 6. Flawed Theming 53 Center Parcs as a Commodified, Middle-Class Utopia By Steven Miles 7. The Cultures of Tiki 61 By Scott A. Lukas Part IV. The Ways of Design, Architecture, Technology, and Material Form 8. The Effects of a Million Volt Light and Sound Culture 77 By Stefan Al 9. Et in Chronotopia Ego 83 Main Street Architecture as a Rhetorical Device in Theme Parks and Outlet Villages By Per Strömberg 10.