The Hopfield model and its role in the development of synthetic biology

Neural network models make extensive use of concepts coming from physics and engineering. How do scientists justify the use of these concepts in the representation of biological systems? How is evidence for or against the use of these concepts produced in the application and manipulation of the models? It will be shown in this article that neural network models are evaluated differently depending on the scientific context and its modeling practice. In the case of the Hopfield model, the different modeling practices related to theoretical physics and neurobiology played a central role for how the model was received and used in the different scientific communities. In theoretical physics, where the Hopfield model has its roots, mathematical modeling is much more common and established than in neurobiology which is strongly experiment driven. These differences in modeling practice contributed to the development of the new field of synthetic biology which introduced a third type of model which combines mathematical modeling and experimenting on biological systems and by doing so mediates between the different modeling practices

Effects of Communication Protocol Stack Offload on Parallel Performance in Clusters

The primary research objective of this dissertation is to demonstrate that the effects of communication protocol stack offload (CPSO) on application execution time can be attributed to the following two complementary sources. First, the application-specific computation may be executed concurrently with the asynchronous communication performed by the communication protocol stack offload engine. Second, the protocol stack processing can be accelerated or decelerated by the offload engine. These two types of performance effects can be quantified with the use of the degree of overlapping Do and degree of acceleration Daccs. The composite communication speedup metrics S_comm(Do, Daccs) can be used in order to quantify the combined effects of the protocol stack offload. This dissertation thesis is validated empirically. The degree of overlapping Do, the degree of acceleration Daccs, and the communication speedup Scomm characteristic of the system configurations under test are derived in the course of experiments performed for the system configurations of interest. It is shown that the proposed metrics adequately describe the effects of the protocol stack offload on the application execution time. Additionally, a set of analytical models of the networking subsystem of a PC-based cluster node is developed. As a result of the modeling, the metrics Do, Daccs, and Scomm are obtained. The models are evaluated as to their complexity and precision by comparing the modeling results with the measured values of Do, Daccs, and Scomm. The primary contributions of this dissertation research are as follows. First, the metric Daccs and Scomm are introduced in order to complement the Do metric in its use for evaluation of the effects of optimizations in the networking subsystem on parallel performance in clusters. The metrics are shown to adequately describe CPSO performance effects. Second, a method for assessing performance effects of CPSO scenarios on application performance is developed and presented. Third, a set of analytical models of cluster node networking subsystems with CPSO capability is developed and characterised as to their complexity and precision of the prediction of the Do and Daccs metrics

Aerospace medicine and biology: A continuing bibliography with indexes, supplement 162, January 1977

This bibliography lists 189 reports, articles, and other documents introduced into the NASA scientific and technical information system in December 1976

The Nornir run-time system for parallel programs using Kahn process networks on multi-core machines – A flexible alternative to MapReduce

Even though shared-memory concurrency is a paradigm frequently used for developing parallel applications on small- and middle-sized machines, experience has shown that it is hard to use. This is largely caused by synchronization primitives which are low-level, inherently non-deterministic, and, consequently, non-intuitive to use. In this paper, we present the Nornir run-time system. Nornir is comparable to well-known frameworks such as MapReduce and Dryad that are recognized for their efficiency and simplicity. Unlike these frameworks, Nornir also supports process structures containing branches and cycles. Nornir is based on the formalism of Kahn process networks, which is a shared-nothing, message-passing model of concurrency. We deem this model a simple and deterministic alternative to shared-memory concurrency. Experiments with real and synthetic benchmarks on up to 8 CPUs show that performance in most cases scales almost linearly with the number of CPUs, when not limited by data dependencies. We also show that the modeling flexibility allows Nornir to outperform its MapReduce counterparts using well-known benchmarks. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited

Experimental analysis of computer system dependability

This paper reviews an area which has evolved over the past 15 years: experimental analysis of computer system dependability. Methodologies and advances are discussed for three basic approaches used in the area: simulated fault injection, physical fault injection, and measurement-based analysis. The three approaches are suited, respectively, to dependability evaluation in the three phases of a system's life: design phase, prototype phase, and operational phase. Before the discussion of these phases, several statistical techniques used in the area are introduced. For each phase, a classification of research methods or study topics is outlined, followed by discussion of these methods or topics as well as representative studies. The statistical techniques introduced include the estimation of parameters and confidence intervals, probability distribution characterization, and several multivariate analysis methods. Importance sampling, a statistical technique used to accelerate Monte Carlo simulation, is also introduced. The discussion of simulated fault injection covers electrical-level, logic-level, and function-level fault injection methods as well as representative simulation environments such as FOCUS and DEPEND. The discussion of physical fault injection covers hardware, software, and radiation fault injection methods as well as several software and hybrid tools including FIAT, FERARI, HYBRID, and FINE. The discussion of measurement-based analysis covers measurement and data processing techniques, basic error characterization, dependency analysis, Markov reward modeling, software-dependability, and fault diagnosis. The discussion involves several important issues studies in the area, including fault models, fast simulation techniques, workload/failure dependency, correlated failures, and software fault tolerance

Resident research associateships. Postdoctoral and senior research awards: Opportunities for research at the Jet Propulsion Laboratory

Opportunities for research as part of NASA-sponsored programs at the JPL cover: Earth and space sciences; systems; telecommunications science and engineering; control and energy conversion; applied mechanics; information systems; and observational systems. General information on applying for an award for tenure as a guest investigator, conditions, of the award, and details of the application procedure are provided