Genomics and Proteomics Based Security Protocols for Secure Network Architectures
Total Page：16
File Type：pdf, Size：1020Kb
Genomics and Proteomics Based Security Protocols for Secure Network Architectures Harry Cornel Shaw B.S. in Computer Science, August 1993, University of Maryland University College M.S. in Electrical Engineering, January 2006, The George Washington University A Dissertation submitted to The Faculty of The School of Engineering and Applied Science of The George Washington University in partial satisfaction of the requirements for the degree of Doctor of Philosophy May 19, 2013 Dissertation directed by Hermann J. Helgert Professor of Engineering and Applied Science The School of Engineering and Applied Science of The George Washington University certifies that Harry Cornel Shaw has passed the Final Examination for the degree of Doctor of Philosophy as of March 20, 2013. This is the final and approved form of the dissertation. Genomics and Proteomics Based Security Protocols for Secure Network Architectures Harry C. Shaw Dissertation Research Committee: Hermann J. Helgert, Professor of Engineering and Applied Science, Dissertation Director Murray Loew, Professor of Engineering and Applied Science Committee Member John J. Hudiburg, NASA/Goddard Space Flight Center, Exploration and Space Communications Division Mission Systems Engineer Committee Member Tian Lan, Assistant Professor of Engineering and Applied Science Committee Member Sayed Hussein, Professional Lecturer, Department of Electrical and Computer Engineering, The George Washington University Committee Member ii Copyright 2013 by Harry C. Shaw All rights reserved iii Dedication I dedicate this research to my mother Mary Alice, my wife, Debbie, my sister, Renee and all my friends and colleagues that have supported me through this long ordeal. The GSFC Space Network Project, which has supported me and without their support, this achievement would not have been possible. Ron Miller supported my research at the very outset. I was then lucky enough to end up working for Ted Sobchak who made it possible for me to get to the finish line. Michelle Hamilton and Paula Tidwell without whose support I literally could not have continued in graduate school. The entire Space Network project staff, which helped me in so many ways I will probably never completely know the extent of their support. I dedicate this effort to Diane Rawlings, Taliha Brock, Patricia Gregory, Cathy Barclay, Pat Boldosser, Andre Fortin, Yen Wong, Ron Zaleski, Darryl Lakins, Anne Kosloski, Haleh Safavi (who commiserated with me on a regular basis), Tim Rykowski, Jeff Lubelczyk, Phil Liebrecht, Jeff Volosin, Mary Ann Esfandiari and John Hudiburg, Keiji Tasaki, and Roger Flaherty. At the White Sands Complex: Don Shinners, Mike Bielucki, Markland Benson, Bert Ransom, Dan Hein and Richard Von Wolfe. My trio of supervisors: Lakesha Bates, Miriam Wennersten, Lavida Cooper and the Electrical Engineering Division Chief, Janet Barth. I also dedicate this effort to my good friends Polly at JPL, Barbara, and Ernie for doing what good friends always do. iv Acknowledgement I would like to acknowledge the support of my advisor, Herman Helgert and the committee members Murray Loew, John Hudiburg, Tian Lan, and Sayed Hussein. Dr. Hussein spent many hours with me working on this activity and I very much appreciate his efforts as well as the efforts of the entire committee. I would like to acknowledge the support of the NASA Space Communications and Navigation Program Office for their support and encouragement in my academic efforts. v Abstract Genomics and Proteomics Based Security Protocols for Secure Network Architectures Network security is a vital component of the design of any network. There are five main requirements to be addressed in developing a secure network: Authentication, confidentiality, data integrity, non-repudiation, and access control. In vivo, biomolecular cellular systems of gene expression authenticate themselves through various means such as transcription factors and promoter sequences. These factors also enforce access control. They have means of retaining confidentiality of the meaning of genome sequences through processes such as control of protein expression. They are capable of establishing data integrity and non-repudiation through transcriptional and translational controls. A suite of genomics and proteomics based authentication and confidentiality protocols will be demonstrated that augment traditional network security approaches with concepts from molecular biology via the regulation of gene expression. These protocols are agnostic to their implementation and can be incorporated into any existing network security protocol (Secure http, SSL, TLS, IPSec, etc.) or any future network security strategy. The protocols can be implemented for implementing web-based security strategies, digital signatures, digital rights management, and general purpose encryption for data in motion or data at rest. These protocols will provide new challenges for network attackers by forcing them to work in both the information security domain and the molecular biology domain. Although no security strategy is without vulnerabilities, the intent of this work is to vi present a completely new set of problems for network attackers. vii Table of Contents Dedication…….. .............................................................................................................. iv Acknowledgement ............................................................................................................ v Abstract……….. .............................................................................................................. vi Table of Contents .......................................................................................................... viii List of Figures… ........................................................................................................... xvii List of Tables…. .......................................................................................................... xxiii CHAPTER 1 INTRODUCTION ............................................................................................ 1 1.1 Security Elements in the Electronic and Biological Domains .......................... 1 1.2 Natural sources of security concepts and architectures. ................................... 2 1.3 Problem Statement ........................................................................................... 3 1.3.1 Weak points with the current security approaches ................................. 4 1.3.1.1 Cryptanalysis techniques are very strong and improve with increases in computing capability ......................... 4 1.3.1.2 Protocols for performing authentication are vulnerable to social engineering. .................................................................. 6 1.3.1.3 Certificate Authorities (CA) are vulnerable to identity impersonation ................................................................................................ 6 1.3.1.4 Useful lifetime of cryptographic codes is unpredictable ............. 8 1.3.1.5 Network vulnerability due to lax security implementation.......... 9 1.4 Proposed Solution via the research goals........................................................ 10 1.5 Organization of the Dissertation ..................................................................... 12 viii CHAPTER 2 PREVIOUS WORK BY OTHER RESEARCHERS ............................................. 13 2.1 Genomic approaches that are not targeted for biological instantiation ........... 13 2.1.1 DNA Cryptography and the central dogma .......................................... 13 2.1.2 DNA computing and Elliptic Curve Cryptography .............................. 14 2.1.3 Other DNA encryption systems in the literature................................... 14 2.2 Genomic approaches that are targeted for biological instantiation ................. 16 2.2.1 Cryptography on the basis of separation by gel electrophoresis........... 16 2.2.2 DNA Watermarks via coding in synonymous codons .......................... 16 2.3 Relationship between the currently published approaches and the current research. .......................................................................... 17 CHAPTER 3 KEY CONCEPTS FROM BIOLOGY UTILIZED IN THE DISSERTATION ........... 17 3.1 Short summary of the organization of DNA ................................................... 17 3.1.1 Eukaryotic DNA organization .............................................................. 17 3.1.2 Prokaryotic DNA organization ............................................................. 18 3.2 Gene Transcription and Translation ................................................................ 19 3.3 Patterns of gene expression ............................................................................. 20 3.3.1 Selection of gene expression processes from prokaryotic or eukaryotic groups .......................................................................... 22 3.4 Organization of genes in the eukaryotes ......................................................... 23 3.4.1 DNA Nomenclature in the dissertation ................................................. 27 3.5 Transcription and the General Transcription Machinery of the Eukaryotic Nucleus ........................................................................ 28 3.5.1 Additional regulatory sequences and their functions of interest. .......... 30 ix 3.5.1 Processes of Transcription .................................................................... 31 3.6 Translation of Eukaryotic messenger