UNE Postgraduate Conference 2017
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Free and Open Source Software for Computational Chemistry Education
Free and Open Source Software for Computational Chemistry Education Susi Lehtola∗,y and Antti J. Karttunenz yMolecular Sciences Software Institute, Blacksburg, Virginia 24061, United States zDepartment of Chemistry and Materials Science, Aalto University, Espoo, Finland E-mail: [email protected].fi Abstract Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. We point out the existence of a variety of free and open source software (FOSS) packages for computational chemistry that offer a wide range of functionality all the way from approximate semiempirical calculations with tight- binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. By their very definition, FOSS packages allow usage for whatever purpose by anyone, meaning they can also be used in industrial applications without limitation. Also, FOSS software has no limitations to redistribution in source or binary form, allowing their easy distribution and installation by third parties. Many FOSS scientific software packages are available as part of popular Linux distributions, and other package managers such as pip and conda. Combined with the remarkable increase in the power of personal devices—which rival that of the fastest supercomputers in the world of the 1990s—a decentralized model for teaching computational chemistry is now possible, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device 1 (BYOD) scheme. In addition to the programs’ use for various applications, open access to the programs’ source code also enables comprehensive teaching strategies, as actual algorithms’ implementations can be used in teaching. -
A DATA-ORIENTED NETWORK ARCHITECTURE Doctoral Dissertation
TKK Dissertations 140 Espoo 2008 A DATA-ORIENTED NETWORK ARCHITECTURE Doctoral Dissertation Teemu Koponen Helsinki University of Technology Faculty of Information and Natural Sciences Department of Computer Science and Engineering TKK Dissertations 140 Espoo 2008 A DATA-ORIENTED NETWORK ARCHITECTURE Doctoral Dissertation Teemu Koponen Dissertation for the degree of Doctor of Science in Technology to be presented with due permission of the Faculty of Information and Natural Sciences for public examination and debate in Auditorium T1 at Helsinki University of Technology (Espoo, Finland) on the 2nd of October, 2008, at 12 noon. Helsinki University of Technology Faculty of Information and Natural Sciences Department of Computer Science and Engineering Teknillinen korkeakoulu Informaatio- ja luonnontieteiden tiedekunta Tietotekniikan laitos Distribution: Helsinki University of Technology Faculty of Information and Natural Sciences Department of Computer Science and Engineering P.O. Box 5400 FI - 02015 TKK FINLAND URL: http://cse.tkk.fi/ Tel. +358-9-4511 © 2008 Teemu Koponen ISBN 978-951-22-9559-3 ISBN 978-951-22-9560-9 (PDF) ISSN 1795-2239 ISSN 1795-4584 (PDF) URL: http://lib.tkk.fi/Diss/2008/isbn9789512295609/ TKK-DISS-2510 Picaset Oy Helsinki 2008 AB ABSTRACT OF DOCTORAL DISSERTATION HELSINKI UNIVERSITY OF TECHNOLOGY P. O. BOX 1000, FI-02015 TKK http://www.tkk.fi Author Teemu Koponen Name of the dissertation A Data-Oriented Network Architecture Manuscript submitted 09.06.2008 Manuscript revised 12.09.2008 Date of the defence 02.10.2008 Monograph X Article dissertation (summary + original articles) Faculty Information and Natural Sciences Department Computer Science and Engineering Field of research Networking Opponent(s) Professor Jon Crowcroft Supervisor Professor Antti Ylä-Jääski Instructor(s) Dr. -
Defence Week Premium Edition
ISSUE 562 NEWS | INTELLIGENCE | BUSINESS OPPORTUNITIES | EVENTS DEFENCE WEEK PREMIUM EDITION PTE Levi Wauchope of NORFORCE’s Darwin squadron supporting COL Papalitsas at the summit. ABC NEWS: ALEX TIGHE The north is getting busier IN THIS ISSUE The north is getting busier 1 Ewen Levick | Darwin NZ brings in updated procurement rules 4 ADM’s seventh annual Northern Australia Defence The Pacific slip up? 5 summit took place in Darwin this week, attract- Penten partners with CSIRO ing close to 200 delegates and a range of speakers on cyber defences 8 to discuss growing changes to the military and Jeumont Electric tapped for Attack class propulsion 10 industry outlook for Australia’s north. New seminars to boost This year’s highlights included NT Chief Minister opportunities for SMEs 11 Michael Gunner, RFSG Commander Colonel John Forthcoming Events 13 Papalitsas, Defence Export Advocate David Johnston, Marine Corps Attaché Lieutenant Colonel Robert Burrell, US Force Posture Initiative Director Brigadier Mark Brewer, Defence’s Director of US Alliance Policy Mikaela James, and former Minister for Defence Christopher Pyne. Minister Gunner opened proceedings with an overview of Darwin and the NT’s strategic value for Australia, including as an ingress and egress for power projec- tion on and around the Australian continent. “I am here to support the case for the north, highlighting our significance as a www.australiandefence.com.au | Defence Week Premium 25 OCTOBER 2019 | ISSUE 562 | 1 ADM’s Defence Week Premium Edition This publication is copyright and may not be reproduced in whole or part without the permission of the publisher. -
Computational Chemistry
G UEST E DITORS’ I NTRODUCTION COMPUTATIONAL CHEMISTRY omputational chemistry has come of chemical, physical, and biological phenomena. age. With significant strides in com- The Nobel Prize award to John Pople and Wal- puter hardware and software over ter Kohn in 1998 highlighted the importance of the last few decades, computational these advances in computational chemistry. Cchemistry has achieved full partnership with the- With massively parallel computers capable of ory and experiment as a tool for understanding peak performance of several teraflops already on and predicting the behavior of a broad range of the scene and with the development of parallel software for efficient exploitation of these high- end computers, we can anticipate that computa- tional chemistry will continue to change the scientific landscape throughout the coming cen- tury. The impact of these advances will be broad and encompassing, because chemistry is so cen- tral to the myriad of advances we anticipate in areas such as materials design, biological sci- ences, and chemical manufacturing. Application areas Materials design is very broad in scope. It ad- dresses a diverse range of compositions of matter that can better serve structural and functional needs in all walks of life. Catalytic design is one such example that clearly illustrates the promise and challenges of computational chemistry. Al- most all chemical reactions of industrial or bio- chemical significance are catalytic. Yet, catalysis is still more of an art (at best) or an empirical fact than a design science. But this is sure to change. A recent American Chemical Society Sympo- sium volume on transition state modeling in catalysis illustrates its progress.1 This sympo- sium highlighted a significant development in the level of modeling that researchers are em- 1521-9615/00/$10.00 © 2000 IEEE ploying as they focus more and more on the DONALD G. -
Network‐Based Approaches for Pathway Level Analysis
Network-Based Approaches for Pathway UNIT 8.25 Level Analysis Tin Nguyen,1 Cristina Mitrea,2 and Sorin Draghici2,3 1Department of Computer Science and Engineering, University of Nevada, Reno, Nevada 2Department of Computer Science, Wayne State University, Detroit, Michigan 3Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan Identification of impacted pathways is an important problem because it allows us to gain insights into the underlying biology beyond the detection of differ- entially expressed genes. In the past decade, a plethora of methods have been developed for this purpose. The last generation of pathway analysis methods are designed to take into account various aspects of pathway topology in order to increase the accuracy of the findings. Here, we cover 34 such topology-based pathway analysis methods published in the past 13 years. We compare these methods on categories related to implementation, availability, input format, graph models, and statistical approaches used to compute pathway level statis- tics and statistical significance. We also discuss a number of critical challenges that need to be addressed, arising both in methodology and pathway repre- sentation, including inconsistent terminology, data format, lack of meaningful benchmarks, and, more importantly, a systematic bias that is present in most existing methods. C 2018 by John Wiley & Sons, Inc. Keywords: systems biology r pathway r topology r gene network r survey r pathway analysis How to cite this article: Nguyen, T., Mitrea, C., & Draghici, S. (2018). Network-based approaches for pathway level analysis. Current Protocols in Bioinformatics, 61, 8.25.1–8.25.24. doi: 10.1002/cpbi.42 INTRODUCTION this gap is the fact that living organisms are With rapid advances in high-throughput complex systems whose emerging phenotypes technologies, various kinds of genomic are the results of multiple complex interactions data have become prevalent in most of taking place on various metabolic and signal- biomedical research. -
Architecture of Low Duty-Cycle Mechanisms Nadjib Aitsaadi, Paul Muhlethaler, Mohamed-Haykel Zayani
Architecture of low duty-cycle mechanisms Nadjib Aitsaadi, Paul Muhlethaler, Mohamed-Haykel Zayani To cite this version: Nadjib Aitsaadi, Paul Muhlethaler, Mohamed-Haykel Zayani. Architecture of low duty-cycle mecha- nisms. 2014. hal-01068788 HAL Id: hal-01068788 https://hal.archives-ouvertes.fr/hal-01068788 Submitted on 26 Sep 2014 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. GETRF delivrable 4: Architecture of low duty-cycle mechanisms Nadjib Aitsaadi, Paul M¨uhlethaler, Mohamed-Haykel Zayani Hipercom Project-Team Inria Paris-Rocquencourt February 2014 1 Contents 1 Introduction 4 2 Principlesofthearchitecture 5 2.1 Routingprotocols......................... 5 2.2 MACrendezvousprotocols. 6 2.2.1 Sender-oriented rendezvous algorithm . 6 2.2.2 Receiver-oriented rendezvous algorithms . 9 2.3 Building a low duty-cycle protocol in multihop wireless networks 9 3 Descriptionofourcontributions 10 3.1 Receiver-orientedproposal . 10 3.1.1 Description ........................ 10 3.1.2 Analyticalmodel . 12 3.1.3 Simulationresults. 15 3.2 Sender-orientedproposal . 24 3.2.1 Description ........................ 24 3.2.2 Analyticalmodel . 27 3.2.3 Simulationresults. 28 3.3 Comparisonanddiscussion . 32 4 Conclusion 34 2 3 1 Introduction A Wireless Sensor Network (WSN) is composed of sensor nodes deployed within an area to monitor predefined phenomena (e.g. -
Outstanding 50 LGBTI Leaders
2018 Outstanding 50 LGBTI Leaders In 2016, Deloitte released Australia’s first list of 50 LGBTI Executives, with the purpose of providing visible business role models to LGBTI Australians of all ages. This year, Deloitte is collaborating with Google to celebrate our Outstanding 50 LGBTI Leaders of 2018. Together, we are extremely proud to be recognising the many role models in business, beyond traditional large corporate organisations. We have taken an inclusive approach to include remarkable leaders from the public sector, government and small to medium-sized businesses alongside those in traditional corporate roles. For more on our Outstanding 50 LGBTI leaders of 2018 please visit www.deloitte.com/au/out50 2018 #out50 03 04 Message from Cindy Hook 08 Feyi Akindoyeni 46 Virginia Lovett 11 Dean Allright 49 Denise Lucero 06 Message from Jason Pellegrino 14 Andrew Barr MLA 50 Graeme Mason 15 Simone Bartley 51 Matthew McCarron 08 Profiles and interviews 16 Mark Baxter 52 Jennifer Morris 20 Nicole Brennan 53 Jude Munro AO 84 Our alumni 21 Councillor Tony Briffa JP 54 Rachel Nicolson 24 David Brine 55 Steve Odell 89 Diversity and inclusion 25 John Caldwell 56 Lisa Paul AO PSM 27 Magali De Castro 57 Luke Pellegrini 30 Emma Dunch 61 Neil Pharaoh 31 Cathy Eccles 62 Janet Rice 32 Luci Ellis 63 Anthony Schembri 33 Tiziano Galipo 64 Tracy Smart 34 Mark Gay 65 Dean Smith 35 Alasdair Godfrey 66 Jarther Taylor 36 Dr Cassandra Goldie 67 Michael Tennant 37 Matthew Groskorth 68 Amy Tildesley 39 Manda Hatter 69 Sam Turner 40 Jane Hill 74 Tea Uglow 41 Dawn Hough 75 Louis Vega 42 Steve Jacques 76 Tess Walsh 43 Leigh Johns OAM 79 Benjamin Wash 44 David Jones 80 Lisa Watts Contents 45 Jason Laufer 83 Penny Wong 04 2018 #out50 2018 #out50 05 Message from Cindy Hook, Chief involvement in bringing this next list of Executive Officer, Deloitte Australia: One of dynamic LGBTI Leaders into the public eye. -
Lesson 5: Web Based E Commerce Architecture
E-COMMERCE LESSON 5: WEB BASED E COMMERCE ARCHITECTURE Topic: other over the internet. This protocol is called the Hypertext Transfer · Introduction Protocol (HTTP). · Web System Architecture Uniform Resource Locator · Generation Of Dynamic Web Pages To identify web pages, an addressing scheme is needed. Basically, a Web page is given an address called a Uniform Resource Locator · Cookies (URL). At the application level, this URL · Summary provides the unique address for a web page, which can be treated · Exercise as an internet resource. The general format for a URL is as follows: Objectives protocol://domain_name:port/directory/resource After this lecture the students will be able to: The protocol defines the protocol being used. Here are some · Understand web based E Commerce architecture examples: All of you might have understood that web system together with · http: hypertext transfer protocol the internet forms the basic infrastructure for supporting E · https: secure hypertext transfer protocol Commerce. In this lecture we will discuss in detail what are the · ftp: file transfer protocol components a web bases system is consist of assuming that you have a knowledge of basic network architecture of the internet · telnet: telnet protocol for accessing a remote host (i.e. Layered model of the Internet) The domain_name, port, directory and resource specify the domain Web System Architecture name of the destined computer, the port number of the connection, the corresponding directory of the resource and the Figure 5.1 gives the general architecture of a web-based ecommerce requested resource, respectively. system. For example, the URL of the welcome page (main.html) of our Basically, it consists of the following components: VBS may be writ-ten as http://www.vbs.com/welcome/ · Web browser: It is the client interface. -
Reviewed Article International Journal of Gender, Sexuality and Law
Reviewed Article International Journal of Gender, Sexuality and Law “There are only two genders – male and female…”1 An Analysis of Online Responses to Tasmania Removing ‘Gender’ from Birth Certificates Louise Richardson-Self2 Abstract This article details and analyses some of the public online response to the Tasmanian Government’s decision to make the recording of gender on birth certificates an opt-in process. Tasmania is the first jurisdiction in Australia to make such a change, which aims to simplify the legal processes involved in affirming a person’s gender identity (including agender and non-binary status). The data set is comprised of comments posted on Facebook in response to The Australian newspaper’s coverage of this event; The Australian is Australia’s only truly national daily broadsheet. This article argues that the effect of this overwhelmingly negative ciscentric response, as revealed by the aesthetic of this digital social space, is the generation of an impression of Australians as trans- (and intersex-) averse. This risks undermining the basic good of assurance that transgender and intersex people ought to have: an assurance that they can inhabit public spaces and be treated with dignity and respect (cf. Waldron). To prevent this kind of hostile response in the future, we must find a way to communicate and make resonant to the general public what queer and feminist theorists have been arguing for quite some time: that sex and gender are not synonymous and that both gender and sex are social constructs. Keywords Birth Certificates; Online Comments; Hate Speech; LGBTI Issues; Cissexism Biography Dr Louise Richardson-Self is a feminist philosopher and Lecturer in Philosophy and Gender Studies at the University of Tasmania. -
Research on Network Architecture of the E-Commerce Platform and Optimization of the System Performance
Send Orders for Reprints to [email protected] 2266 The Open Cybernetics & Systemics Journal, 2015, 9, 2266-2271 Open Access Research on Network Architecture of the E-commerce Platform and Optimization of the System Performance Zhanwei Chen* College of Computer Science and Technology, Zhoukou Normal University, Zhoukou 466001, Henan, China Abstract: With the rapid development of computer technology, especially the rapid development of network technology and the acceleration of global economic integration, electronic commerce has been used more and more widely. This also puts forward a new standard for the enterprise application computer to business activities. On one hand, we should take into account the advanced nature of the electronic commerce platform, on the other hand, we should make the existing business system of the enterprise more smoothly into the new business platform. Aiming at the problem of resource bot- tleneck in current e-commerce system, the application model of grid based electronic commerce system is put forward to be based on the application background of grid technology. How to make full use of the existing software and hardware resources, to obtain the largest data processing capacity has become an important part of the electronic commerce plat- form application system. Keywords: Electronic commerce, framework, grid, system optimization. 1. INTRODUCTION network transactions and online electronic payment and a variety of business activities, trading activities, financial With the rapid development of economic globalization activities and comprehensive service activities without the and the rapid development of Internet technology, e- meeting between the buyers and sellers, in a wide range of commerce which is a new business model has been the commercial and trading activities around the world, in the world's attention and recognition. -
NIST Computational Chemistry Comparison and Benchmark Database
NIST Computational Chemistry Comparison and Benchmark Database A website which compares computed and experimental ideal-gas thermochemical properties http://srdata.nist.gov/cccbdb Russell D. Johnson III Computational Chemistry Group, NIST http://www.nist.gov/compchem How good is that ab initio calculation? For predicting enthalpies. For predicting geometries. For predicting vibrational frequencies. For this molecule. For these molecules. http://srdata.nist.gov/cccbdb CCCBDB Contents • 680 molecules • Enthalpies of formation, Entropies, Geometries, Vibrational frequencies • Experimental values • Computed values • Comparisons • Auxiliary information http://srdata.nist.gov/cccbdb Properties • Energetics – Enthalpies of formation – Atomization enthalpies – Reaction enthalpies – Barriers to Internal Rotation • Entropies – Heat Capacities – Integrated Heat Capacities http://srdata.nist.gov/cccbdb More Properties • Geometries – Bond lengths and angles – Rotational Constants – Moments of Inertia • Vibrational Frequencies – Intensities – Zero point energies http://srdata.nist.gov/cccbdb Even More Properties • Electrostatics – Dipole Moments – Quadrupole Moments – Polarizabilities – Charges • Mulliken •ESP • ChelpG http://srdata.nist.gov/cccbdb Molecules in CCCBDB • Small, gas-phase • Mostly < 7 heavy atoms - hexane • Mostly no atoms with atomic number >17 (chlorine). A dozen Br-containing molecules. • 90 diatomics, 574 polyatomics • 469 organic molecules, – 125 hydrocarbons – 145 CHO species – 16 amides http://srdata.nist.gov/cccbdb Experimental -
Arxiv:2103.15954V1 [Cs.CV] 29 Mar 2021 Better Performing Architectures
DiNTS: Differentiable Neural Network Topology Search for 3D Medical Image Segmentation Yufan He1 Dong Yang2 Holger Roth2 Can Zhao2 Daguang Xu2 1Johns Hopkins University 2NVIDIA Abstract 0.1 0.9 휷 0.9 0.1 ퟏ Search Discretization 0.8 0.8 휷ퟐ Recently, neural architecture search (NAS) has been ap- 0.1 0.1 plied to automatically search high-performance networks 0.1 0.1 Gap 휷ퟑ 0.9 0.9 for medical image segmentation. The NAS search space 0.1 0.1 usually contains a network topology level (controlling con- 휷ퟏ+휷ퟐ+휷ퟑ=1 Continuous Model Discrete Model nections among cells with different spatial scales) and a cell level (operations within each cell). Existing meth- Figure 1. Limitations of existing differentiable topology search ods either require long searching time for large-scale 3D formulation. E.g. in Auto-DeepLab [21], each edge in the topol- image datasets, or are limited to pre-defined topologies ogy search space is given a probability β. The probabilities of in- (such as U-shaped or single-path) . In this work, we fo- put edges to a node sum to one, which means only one input edge cus on three important aspects of NAS in 3D medical image for each node would be selected. A single-path discrete model (red segmentation: flexible multi-path network topology, high path) is extracted from the continuous searched model. This can result in a large “discretization gap” between the feature flow of search efficiency, and budgeted GPU memory usage. A the searched continuous model and the final discrete model.