Publications

Proposed for publication in IEEE Engineering in Medicine and Biology Magazine.

May, Elebeoba E.; Johnston, Anna M.

Abstract not provided.

May, Elebeoba E.; Johnston, Anna M.; Watson, Jean-Paul W.; Hart, William E.; Rintoul, Mark D.

We have found that developing a computational framework for reconstructing error control codes for engineered data and ultimately for deciphering genetic regulatory coding sequences is a challenging and uncharted area that will require advances in computational technology for exact solutions. Although exact solutions are desired, computational approaches that yield plausible solutions would be considered sufficient as a proof of concept to the feasibility of reverse engineering error control codes and the possibility of developing a quantitative model for understanding and engineering genetic regulation. Such evidence would help move the idea of reconstructing error control codes for engineered and biological systems from the high risk high payoff realm into the highly probable high payoff domain. Additionally this work will impact biological sensor development and the ability to model and ultimately develop defense mechanisms against bioagents that can be engineered to cause catastrophic damage. Understanding how biological organisms are able to communicate their genetic message efficiently in the presence of noise can improve our current communication protocols, a continuing research interest. Towards this end, project goals include: (1) Develop parameter estimation methods for n for block codes and for n, k, and m for convolutional codes. Use methods to determine error control (EC) code parameters for gene regulatory sequence. (2) Develop an evolutionary computing computational framework for near-optimal solutions to the algebraic code reconstruction problem. Method will be tested on engineered and biological sequences.

Cooper, Arlin C.; Cooper, Arlin C.; Johnston, Anna M.

The Unique Signal is a key constituent of Enhanced Nuclear Detonation Safety (ENDS). Although the Unique Signal approach is well prescribed and mathematically assured, there are numerous unsolved mathematical problems that could help assess the risk of deviations from the ideal approach. Some of the mathematics-based results shown in this report are: 1. The risk that two patterns with poor characteristics (easily generated by inadvertent processes) could be combined through exclusive-or mixing to generate an actual Unique Signal pattern has been investigated and found to be minimal (not significant when compared to the incompatibility metric of actual Unique Signal patterns used in nuclear weapons). 2. The risk of generating actual Unique Signal patterns with linear feedback shift registers is minimal, but the patterns in use are not as invulnerable to inadvertent generation by dependent processes as previously thought. 3. New methods of testing pair-wise incompatibility threats have resulted in no significant problems found for the set of Unique Signal patterns currently used. Any new patterns introduced would have to be carefully assessed for compatibility with existing patterns, since some new patterns under consideration were found to be deficient when associated with other patterns in use. 4. Markov models were shown to correspond to some of the engineered properties of Unique Signal sequences. This gives new support for the original design objectives. 5. Potential dependence among events (caused by a variety of communication protocols) has been studied. New evidence has been derived of the risk associated with combined communication of multiple events, and of the improvement in abnormal-environment safety that can be achieved through separate-event communication.

May, Elebeoba E.; May, Elebeoba E.; Johnston, Anna M.; Hart, William E.; Watson, Jean-Paul W.; Pryor, Richard J.; Rintoul, Mark D.

A fundamental challenge for all communication systems, engineered or living, is the problem of achieving efficient, secure, and error-free communication over noisy channels. Information theoretic principals have been used to develop effective coding theory algorithms to successfully transmit information in engineering systems. Living systems also successfully transmit biological information through genetic processes such as replication, transcription, and translation, where the genome of an organism is the contents of the transmission. Decoding of received bit streams is fairly straightforward when the channel encoding algorithms are efficient and known. If the encoding scheme is unknown or part of the data is missing or intercepted, how would one design a viable decoder for the received transmission? For such systems blind reconstruction of the encoding/decoding system would be a vital step in recovering the original message. Communication engineers may not frequently encounter this situation, but for computational biologists and biotechnologist this is an immediate challenge. The goal of this work is to develop methods for detecting and reconstructing the encoder/decoder system for engineered and biological data. Building on Sandia's strengths in discrete mathematics, algorithms, and communication theory, we use linear programming and will use evolutionary computing techniques to construct efficient algorithms for modeling the coding system for minimally errored engineered data stream and genomic regulatory DNA and RNA sequences. The objective for the initial phase of this project is to construct solid parallels between biological literature and fundamental elements of communication theory. In this light, the milestones for FY2003 were focused on defining genetic channel characteristics and providing an initial approximation for key parameters, including coding rate, memory length, and minimum distance values. A secondary objective addressed the question of determining similar parameters for a received, noisy, error-control encoded data set. In addition to these goals, we initiated exploration of algorithmic approaches to determine if a data set could be approximated with an error-control code and performed initial investigations into optimization based methodologies for extracting the encoding algorithm given the coding rate of an encoded noise-free and noisy data stream.

Johnston, Anna M.

The moduli used in RSA (see [5]) can be generated by many different sources. The generator of that modulus (assuming a single entity generates the modulus) knows its factorization. They would have the ability to forge signatures or break any system based on this moduli. If a moduli and the RSA parameters associated with it were generated by a reputable source, the system would have higher value than if the parameters were generated by an unknown entity. So for tracking, security, confidence and financial reasons it would be beneficial to know who the generator of the RSA modulus was. This is where digital marking comes in. An RSA modulus ia digitally marked, or digitally trade marked, if the generator and other identifying features of the modulus (such as its intended user, the version number, etc.) can be identified and possibly verified by the modulus itself. The basic concept of digitally marking an RSA modulus would be to fix the upper bits of the modulus to this tag. Thus anyone who sees the public modulus can tell who generated the modulus and who the generator believes the intended user/owner of the modulus is.

Journal of Cryptology

Johnston, Anna M.

Finding a q{sup th} root in GF(p), where p and q are prunes, q is large and q{sup 2} divides (p{minus}1) is a difficult problem equivalent to the discrete logarithm problem using an element of order q as the base. This paper describes an authenticated key exchange algorithm utilizing this hard problem.