Genetic algorithms for DNA sequence assembly (open access)

Genetic algorithms for DNA sequence assembly

This paper describes a genetic algorithm application to the DNA fragment assembly problems. The genetic algorithm uses a random key representation for representing the orderings of fragments. Two different fitness functions, both based on pairwise overlap strengths between fragments, were tested. The paper concludes that the genetic algorithm is a promising method for fragment assembly problems, achieving usable solutions quickly, but that the current fitness functions are flawed and that other representations might be more appropriate.
Date: April 13, 1993
Creator: Parsons, R.; Burks, C. (Los Alamos National Lab., NM (United States)) & Forrest, S. (New Mexico Univ., Albuquerque, NM (United States). Dept. of Computer Science)
System: The UNT Digital Library
Exploring phase space concepts in the forecasting of time series with artificial neural networks (open access)

Exploring phase space concepts in the forecasting of time series with artificial neural networks

The authors study the performance of feedforward artificial neural networks in forecasting future values of several different time series. They explore both short- and long-term prediction of several periodic time series. They find that a significant source of error in long-term prediction of time series is introduced by a phase shift between the network output and the time series. They explore the origin of this phase shift and suggest strategies for minimizing its effect. They find that the phase diagrams of the time series and the neural network forecast contain useful diagnostic information.
Date: September 13, 1993
Creator: Rogers, R. D. & Vemuri, V.
System: The UNT Digital Library
Burst mode FEL with the ETA-III induction linac (open access)

Burst mode FEL with the ETA-III induction linac

Pulses of 140 GHz microwaves have been produced at a 2 kHz rate using the ETA-III induction linac and IMP wiggler. The accelerator was run in bursts of up to 50 pulses at 6 MeV and greater than 2 kA peak current. A feedback timing control system was used to synchronize acceleration voltage pulses with the electron beam, resulting in sufficient reduction of the corkscrew and energy sweep for efficient FEL operation. Peak microwave power for short bursts was in the range 0.5--1.1 GW, which is comparable to the single-pulse peak power of 0.75--2 GW. FEL bursts of more than 25 pulses were obtained.
Date: May 13, 1993
Creator: Lasnier, C. J.; Allen, S. L. & Felker, B.
System: The UNT Digital Library
Refining a triangulation of a planar straight-line graph to eliminate large angles (open access)

Refining a triangulation of a planar straight-line graph to eliminate large angles

Triangulations without large angles have a number of applications in numerical analysis and computer graphics. In particular, the convergence of a finite element calculation depends on the largest angle of the triangulation. Also, the running time of a finite element calculation is dependent on the triangulation size, so having a triangulation with few Steiner points is also important. Bern, Dobkin and Eppstein pose as an open problem the existence of an algorithm to triangulate a planar straight-line graph (PSLG) without large angles using a polynomial number of Steiner points. We solve this problem by showing that any PSLG with {upsilon} vertices can be triangulated with no angle larger than 7{pi}/8 by adding O({upsilon}{sup 2}log {upsilon}) Steiner points in O({upsilon}{sup 2} log{sup 2} {upsilon}) time. We first triangulate the PSLG with an arbitrary constrained triangulation and then refine that triangulation by adding additional vertices and edges. Some PSLGs require {Omega}({upsilon}{sup 2}) Steiner points in any triangulation achieving any largest angle bound less than {pi}. Hence the number of Steiner points added by our algorithm is within a log {upsilon} factor of worst case optimal. We note that our refinement algorithm works on arbitrary triangulations: Given any triangulation, we show how to …
Date: May 13, 1993
Creator: Mitchell, S. A.
System: The UNT Digital Library
Stabilization of the external kink and other MHD issues. Summary report (open access)

Stabilization of the external kink and other MHD issues. Summary report

An MHD workshop entitled ``Stabilization of the External Kink and Other MHD Issues`` was held June 1993. This is a summary report of activities at that workshop, structured to respond to the three questions in the charge (letter from J. Willis). The experimental and theoretical status of these issues, and the R&D needs in each area, are addressed. We discuss the potential impact on the TPX and ITER programs of these issues. The workshop participants came from a broad and diverse range of institutions in the fusion program, including international participants. As a result, we believe the summary here reflects some consensus of the community on these very important program issues, and that the TPX and ITER programs will benefit from these discussions. The title of the workshop was chosen to indicate both our knowledge and our uncertainty of MHD phenomena limiting {beta} and causing disruptions in tokamaks. The purpose was to bring together theorists and experimentalist in order to assess our current understanding of the external kink instability at high {beta}, and to assess the potential for passive or active stabilization of the dominant modes. We also outlined the R&D needed for TPX and other future devices. Not only …
Date: August 13, 1993
Creator: Freidberg, J. P.; Goldston, R. J.; Jardin, S. C.; Neilson, G. H.; Rosenbluth, M. N.; Taylor, T. S. et al.
System: The UNT Digital Library
Genetic algorithms for DNA sequence assembly (open access)

Genetic algorithms for DNA sequence assembly

This paper describes a genetic algorithm application to the DNA fragment assembly problems. The genetic algorithm uses a random key representation for representing the orderings of fragments. Two different fitness functions, both based on pairwise overlap strengths between fragments, were tested. The paper concludes that the genetic algorithm is a promising method for fragment assembly problems, achieving usable solutions quickly, but that the current fitness functions are flawed and that other representations might be more appropriate.
Date: April 13, 1993
Creator: Parsons, R.; Burks, C. & Forrest, S.
System: The UNT Digital Library
Poroelasticity of rock (open access)

Poroelasticity of rock

Poroelasticity is the theoretical framework used to describe the coupled processes which occur when a fluid bearing porous material is deformed by a stress field. The theoretical basis for the treatment of problems in poroelasticity has been derived in an extensive body of work over the last fifty years, most notably by Biot. Many of Biot`s successors have attempted to find relationships between the physical properties of the material to be analyzed and the Biot coefficients. Our approach to this problem has both theoretical and experimental components. The general theoretical objective is to produce estimates of the Biot coefficients which are more realistic e.g.. are not limited by assumptions which preclude their use for real earth materials. Experiments are designed to measure the coefficients (or parameters which are directly related to them) which have not been measured as yet to provide new insight for improving the theory of poroelasticity. The experimental program is designed to determine the mechanical and transport properties of a well characterized set of synthetic and natural sandstones from static to ultrasonic frequencies.
Date: May 13, 1993
Creator: Bonner, B. P.; Berge, P. A.; Berryman, J. G. & Wang, H. F.
System: The UNT Digital Library
Industrial alliances (open access)

Industrial alliances

The United States is emerging from the Cold War era into an exciting, but challenging future. Improving the economic competitiveness of our Nation is essential both for improving the quality of life in the United States and maintaining a strong national security. The research and technical skills used to maintain a leading edge in defense and energy now should be used to help meet the challenge of maintaining, regaining, and establishing US leadership in industrial technologies. Companies recognize that success in the world marketplace depends on products that are at the leading edge of technology, with competitive cost, quality, and performance. Los Alamos National Laboratory and its Industrial Partnership Center (IPC) has the strategic goal to make a strong contribution to the nation`s economic competitiveness by leveraging the government`s investment at the Laboratory: personnel, infrastructure, and technological expertise.
Date: September 13, 1993
Creator: Adams, K. V.
System: The UNT Digital Library
Experience with performance based training of nuclear criticality safety engineers (open access)

Experience with performance based training of nuclear criticality safety engineers

For non-reactor nuclear facilities, the U.S. Department of Energy (DOE) does not require that nuclear criticality safety engineers demonstrate qualification for their job. It is likely, however, that more formalism will be required in the future. Current DOE requirements for those positions which do have to demonstrate qualification indicate that qualification should be achieved by using a systematic approach such as performance based training (PBT). Assuming that PBT would be an acceptable mechanism for nuclear criticality safety engineer training in a more formal environment, a site-specific analysis of the nuclear criticality safety engineer job was performed. Based on this analysis, classes are being developed and delivered to a target audience of newer nuclear criticality safety engineers. Because current interest is in developing training for selected aspects of the nuclear criticality safety engineer job, the analysis is incompletely developed in some areas.
Date: July 13, 1993
Creator: Taylor, R. G.
System: The UNT Digital Library