Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

<p>Abstract</p> <p>Background</p> <p>Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008.</p> <p>Results</p> <p>Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes.</p> <p>Conclusions</p> <p>The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation and visualization of contacts and rapid cross simulation analysis for knowledge discovery. Using page compression for the atomic coordinate tables and indexes saves ~36% of disk space without any significant decrease in calculation time and should be considered for other non-transactional databases in MS SQL SERVER 2008.</p

Coding for Security and Reliability in Distributed Systems

This dissertation studies the use of coding techniques to improve the reliability and security of distributed systems. The first three parts focus on distributed storage systems, and study schemes that encode a message into n shares, assigned to n nodes, such that any n - r nodes can decode the message (reliability) and any colluding z nodes cannot infer any information about the message (security). The objective is to optimize the computational, implementation, communication and access complexity of the schemes during the process of encoding, decoding and repair. These are the key metrics of the schemes so that when they are applied in practical distributed storage systems, the systems are not only reliable and secure, but also fast and cost-effective. Schemes with highly efficient computation and implementation are studied in Part I. For the practical high rate case of r ≤ 3 and z ≤ 3, we construct schemes that require only r + z XORs to encode and z XORs to decode each message bit, based on practical erasure codes including the B, EVENODD and STAR codes. This encoding and decoding complexity is shown to be optimal. For general r and z, we design schemes over a special ring from Cauchy matrices and Vandermonde matrices. Both schemes can be efficiently encoded and decoded due to the structure of the ring. We also discuss methods to shorten the proposed schemes. Part II studies schemes that are efficient in terms of communication and access complexity. We derive a lower bound on the decoding bandwidth, and design schemes achieving the optimal decoding bandwidth and access. We then design schemes that achieve the optimal bandwidth and access not only for decoding, but also for repair. Furthermore, we present a family of Shamir's schemes with asymptotically optimal decoding bandwidth. Part III studies the problem of secure repair, i.e., reconstructing the share of a (failed) node without leaking any information about the message. We present generic secure repair protocols that can securely repair any linear schemes. We derive a lower bound on the secure repair bandwidth and show that the proposed protocols are essentially optimal in terms of bandwidth. In the final part of the dissertation, we study the use of coding techniques to improve the reliability and security of network communication. Specifically, in Part IV we draw connections between several important problems in network coding. We present reductions that map an arbitrary multiple-unicast network coding instance to a unicast secure network coding instance in which at most one link is eavesdropped, or a unicast network error correction instance in which at most one link is erroneous, such that a rate tuple is achievable in the multiple-unicast network coding instance if and only if a corresponding rate is achievable in the unicast secure network coding instance, or in the unicast network error correction instance. Conversely, we show that an arbitrary unicast secure network coding instance in which at most one link is eavesdropped can be reduced back to a multiple-unicast network coding instance. Additionally, we show that the capacity of a unicast network error correction instance in general is not (exactly) achievable. We derive upper bounds on the secrecy capacity for the secure network coding problem, based on cut-sets and the connectivity of links. Finally, we study optimal coding schemes for the network error correction problem, in the setting that the network and adversary parameters are not known a priori.</p

Unconventional Warfare in East Tennessee, 1861-1865

Preface: President John F. Kennedy, in a speech to the 1962 graduating class at West Point, mentioned a type of warfare which has become particularly important today. He observed: This is another type of warfare--new in its intensity, ancient in its origin-- war by guerrillas, subversives, insurgents, assassins-- war by ambush instead of combat, by infiltration instead of aggression--seeking victory by eroding and exhausting the enemy instead of engaging him. 1 This study proposes to examine the Civil War in East Tennessee in the light of what we know about unconventional warfare today. As the name unconventional would imply, the records of such activities are scarce. As a result, many of the fact have had to be pieced together from local histories, memoirs, letters, newspaper accounts, and stores told by the descendants of a number of participants. Most of their stores have lost nothing in the retelling over the several generations which have elapsed since the Civil War; verification is impossible. Use of such stories has been limited to assisting the author in attempting to get a feeling for the times. This study will employ some of the terms and ideas which are specifically the tools of the military historian. These are likely to be unfamiliar to the reader not intimately associated with them. Hence it seems advisable to have available definitions of some of the more important terms. Appendix I contains a glossary of these terms which are especially related to unconventional warfare and which will be used in this study. There is still a controversy among historians as to the type of conflict that was fought between 1861 and 1865. But there is no doubt about the fact that it was a war, and, for the purpose of this study, war may be defined as . . . a violent interaction between two organized political groups (governments or otherwise). 2 Warfare is a particular variety of military activity involving specific forces, weapons, or tactics. It need not employ all of a participant\u27s capability, nor is it necessary for that part which is employed to conform to any specific proportion or to be used according to any set pattern. Any war may be fought by using any form of warfare to the degree which each antagonist assumes will result in victory for his particular cause. Unconventional warfare may be defined as that method of warfare used by the indigenous people of an area in opposition to an enemy occupying force.3 The effort is usually supported and directed from outside the zone of conflict by a government friendly to those who are resisting. In unconventional warfare there are three major components: guerrilla activities, evasion and escape, and subversion. The technical requirements of all three have a common basis, and in Appendix II are discussed in detail from the point of view of guerrilla operations. This study is divided into six chapters. In the first, unconventional warfare is related to the Civil War background with attention to the problem of its legitimacy as a method of warfare. In the succeeding three chapters, unconventional warfare, as it unfolded in East Tennessee between 1861 and 1865, is presented in some detail. Chapter two sets the background and ends with Colonel S. P. Carter\u27s raid in early 1861. Chapter three continues the narrative through General Ambrose Burnside\u27s successful occupation of Knoxville in late 1863. The fourth chapter considers the remaining years of the war. Chapter five is devoted to escapes involving East Tennessee throughout the war. The concluding chapter summarizes the war in East Tennessee from the viewpoint of unconventional warfare. I wish to express my sincere thanks to all of those who have helped and encouraged me in this undertaking. My special thanks to Professor LeRoy P. Graf who directed this study and to Professors Stanley J. Folmsbee and Ralph W. Haskins who patiently gave their time and valuable suggestions. However, for the final product I must assume full responsibility

Student Life, May 11, 1917, Vol. 15, No. 32

Weekly student newspaper of Utah State University in Logan.https://digitalcommons.usu.edu/newspapers/1881/thumbnail.jp

The Aroostook Times, June 1, 1910

https://digitalmaine.com/aroostook_times/1236/thumbnail.jp

The Wellesley News (03-12-1942)

https://repository.wellesley.edu/news/2427/thumbnail.jp

Goddard Conference on Mass Storage Systems and Technologies, Volume 1

Copies of nearly all of the technical papers and viewgraphs presented at the Goddard Conference on Mass Storage Systems and Technologies held in Sep. 1992 are included. The conference served as an informational exchange forum for topics primarily relating to the ingestion and management of massive amounts of data and the attendant problems (data ingestion rates now approach the order of terabytes per day). Discussion topics include the IEEE Mass Storage System Reference Model, data archiving standards, high-performance storage devices, magnetic and magneto-optic storage systems, magnetic and optical recording technologies, high-performance helical scan recording systems, and low end helical scan tape drives. Additional topics addressed the evolution of the identifiable unit for processing purposes as data ingestion rates increase dramatically, and the present state of the art in mass storage technology

Fifth NASA Goddard Conference on Mass Storage Systems and Technologies

This document contains copies of those technical papers received in time for publication prior to the Fifth Goddard Conference on Mass Storage Systems and Technologies held September 17 - 19, 1996, at the University of Maryland, University Conference Center in College Park, Maryland. As one of an ongoing series, this conference continues to serve as a unique medium for the exchange of information on topics relating to the ingestion and management of substantial amounts of data and the attendant problems involved. This year's discussion topics include storage architecture, database management, data distribution, file system performance and modeling, and optical recording technology. There will also be a paper on Application Programming Interfaces (API) for a Physical Volume Repository (PVR) defined in Version 5 of the Institute of Electrical and Electronics Engineers (IEEE) Reference Model (RM). In addition, there are papers on specific archives and storage products