john JACK - Academia.edu (original) (raw)
Papers by john JACK
Metal Finishing, 2000
Hardness has been defined simply as the resistance to penetration. In order to measure this resis... more Hardness has been defined simply as the resistance to penetration. In order to measure this resistance to penetration a testing machine is used to push a specific indenter into the test material with a specified force, and either the depth of penetration or the area of the "footprint" left by the indenter is used to derive a hardness "number." Hardness as measured by indentation is not a single fundamental property but a combination of properties, and the contribution of each to the hardness number varies with the material and the type of test. Variously shaped indenters have been developed and are in use in different industries. The hardness number varies with the size and shape of the indenter and the force used, among other variables, which results in several different hardness scales. The metalworking industry uses several with one or more of the many Rockwell scales being among the more common. Unless the coatings are extremely thick Rockwell methods cannot be used for plated parts. The results of hardness testing of plated coatings have been the subject of disagreements for several years. Standardized methods such as ASTM E 384 (Standard Test Method for Microhardness of Materials), which had been developed to measure the hardness of solid materials, were found to need certain modifications to be adapted to relatively thinly plated coatings. This problem was recognized with ASTM B 578 (Standard Test Method for Microhardness of Electroplated Coatings). The term microhardness is used to describe hardness as measured with small indenters and ~omparatively lower forces. (Some have proposed that microhardness would be more accurately described as microindentation.) Generally, the term microhardness is used for hardness testing when the forced used is 1,000 grams or less.
Genome Research, 2014
The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenc... more The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Com...
Abstract: AERODYNAMICS OF SLENDER BODIES AT MACH NUMBER OF 3.12 AND REYNOLDS NUMBERS FROM 2X106 T... more Abstract: AERODYNAMICS OF SLENDER BODIES AT MACH NUMBER OF 3.12 AND REYNOLDS NUMBERS FROM 2X106 TO 15X106. V-AERODYNAMIC LOAD DISTRIBUTIONS FOR A SERIES OF FOUR BOATTAILED BODIES
Botanical Gazette, 1893
The witch hazel, Haimzazelis Virginiczna L., and the seaside alder, Alngs; naritima Muhl., differ... more The witch hazel, Haimzazelis Virginiczna L., and the seaside alder, Alngs; naritima Muhl., differ from these in only requiring one season of growth from the flower to the ripe fruit, for although the blossoming takes place in the autumn, the young ovary makes little or no ...
The ideas expressed in this work pertain to biochemical modeling. We explore our technique, the N... more The ideas expressed in this work pertain to biochemical modeling. We explore our technique, the Nondeterministic Waiting Time algorithm, for modeling molecular signaling cascades. The algorithm is presented with pseudocode along with an explanation of its implementation. The entire source code can be found in the Appendices. This algorithm builds on earlier work from the lab of Dr. Andrei Paun, the advisor for this dissertation. We discuss several important extensions including: (i) a heap with special maintenance functions for sorting reaction waiting times, (ii) a nondeterminstic component for handling reaction competition, and (iii) a memory enhancement allowing slower reactions to compete with faster reactions. Several example systems are provided for comparisons between modeling with systems of ordinary differential equations, the Gillespie Algorithm, and our Nondeterministic Waiting Time algorithm. Our algorithm has a unique ability to exhibit behavior similar to the solutions to systems of ordinary differential equations for certain models and parameter choices, but it also has the nondeterministic component which yields results similar stochastic methods (e.g., the Gillespie Algorithm). Next, we turn our attention to the Fas-mediated apoptotic signaling cascade. Fas signaling has important implications in the research of cancer, autoimmune and neurodegenerative disorders. We provide an exhaustive account of results from the Nondeterminstic Waiting Time algorithm in comparison to solutions to the system iii iv of ordinary differential equations described by another modeling group. Our work with the Fas pathway led us to explore a new model, focusing on the effects of HIV-1 proteins on the Fas signaling cascade. There is extensive information in the literature on the effects of the HIV-1 proteins on this pathway. The model described in this work represents the first attempt ever made in modeling Fas-induced apoptosis in lantently infected T cells. There are several extensions for the Fas model discussed at the end of the work. Calcium signaling would be an interesting avenue to investigate, building on some recent results reported in the literature. For the HIV model, there are several extensions discussed. We also suggest a new direction for the Nondeterministic Waiting Time algorithm exploring parallelization options.
Applied Optics, 1968
A new experimental technique is developed to determine simultaneously the total hemispherical emi... more A new experimental technique is developed to determine simultaneously the total hemispherical emittance, solar absorptance, and absorptance-emittance ratio for metals at cryogenic temperatures. The method compares the temperature response of thin metal samples to a sinusoidal perturbation of an imposed radiant intensity. Emittance data are presented for aluminum, copper, and 304 stainless steel over the temperature range of 150 to 500 K. From the data, the applicability of the cyclic radiant intensity method is evaluated, and the problems associated with extending the method to temperatures below 150 K are discussed.
We present the Nondeterministic Waiting Time algorithm. Our technique for the simulation of bioch... more We present the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells.
Metal Finishing, 2000
Hardness has been defined simply as the resistance to penetration. In order to measure this resis... more Hardness has been defined simply as the resistance to penetration. In order to measure this resistance to penetration a testing machine is used to push a specific indenter into the test material with a specified force, and either the depth of penetration or the area of the "footprint" left by the indenter is used to derive a hardness "number." Hardness as measured by indentation is not a single fundamental property but a combination of properties, and the contribution of each to the hardness number varies with the material and the type of test. Variously shaped indenters have been developed and are in use in different industries. The hardness number varies with the size and shape of the indenter and the force used, among other variables, which results in several different hardness scales. The metalworking industry uses several with one or more of the many Rockwell scales being among the more common. Unless the coatings are extremely thick Rockwell methods cannot be used for plated parts. The results of hardness testing of plated coatings have been the subject of disagreements for several years. Standardized methods such as ASTM E 384 (Standard Test Method for Microhardness of Materials), which had been developed to measure the hardness of solid materials, were found to need certain modifications to be adapted to relatively thinly plated coatings. This problem was recognized with ASTM B 578 (Standard Test Method for Microhardness of Electroplated Coatings). The term microhardness is used to describe hardness as measured with small indenters and ~omparatively lower forces. (Some have proposed that microhardness would be more accurately described as microindentation.) Generally, the term microhardness is used for hardness testing when the forced used is 1,000 grams or less.
Genome Research, 2014
The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenc... more The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Com...
Abstract: AERODYNAMICS OF SLENDER BODIES AT MACH NUMBER OF 3.12 AND REYNOLDS NUMBERS FROM 2X106 T... more Abstract: AERODYNAMICS OF SLENDER BODIES AT MACH NUMBER OF 3.12 AND REYNOLDS NUMBERS FROM 2X106 TO 15X106. V-AERODYNAMIC LOAD DISTRIBUTIONS FOR A SERIES OF FOUR BOATTAILED BODIES
Botanical Gazette, 1893
The witch hazel, Haimzazelis Virginiczna L., and the seaside alder, Alngs; naritima Muhl., differ... more The witch hazel, Haimzazelis Virginiczna L., and the seaside alder, Alngs; naritima Muhl., differ from these in only requiring one season of growth from the flower to the ripe fruit, for although the blossoming takes place in the autumn, the young ovary makes little or no ...
The ideas expressed in this work pertain to biochemical modeling. We explore our technique, the N... more The ideas expressed in this work pertain to biochemical modeling. We explore our technique, the Nondeterministic Waiting Time algorithm, for modeling molecular signaling cascades. The algorithm is presented with pseudocode along with an explanation of its implementation. The entire source code can be found in the Appendices. This algorithm builds on earlier work from the lab of Dr. Andrei Paun, the advisor for this dissertation. We discuss several important extensions including: (i) a heap with special maintenance functions for sorting reaction waiting times, (ii) a nondeterminstic component for handling reaction competition, and (iii) a memory enhancement allowing slower reactions to compete with faster reactions. Several example systems are provided for comparisons between modeling with systems of ordinary differential equations, the Gillespie Algorithm, and our Nondeterministic Waiting Time algorithm. Our algorithm has a unique ability to exhibit behavior similar to the solutions to systems of ordinary differential equations for certain models and parameter choices, but it also has the nondeterministic component which yields results similar stochastic methods (e.g., the Gillespie Algorithm). Next, we turn our attention to the Fas-mediated apoptotic signaling cascade. Fas signaling has important implications in the research of cancer, autoimmune and neurodegenerative disorders. We provide an exhaustive account of results from the Nondeterminstic Waiting Time algorithm in comparison to solutions to the system iii iv of ordinary differential equations described by another modeling group. Our work with the Fas pathway led us to explore a new model, focusing on the effects of HIV-1 proteins on the Fas signaling cascade. There is extensive information in the literature on the effects of the HIV-1 proteins on this pathway. The model described in this work represents the first attempt ever made in modeling Fas-induced apoptosis in lantently infected T cells. There are several extensions for the Fas model discussed at the end of the work. Calcium signaling would be an interesting avenue to investigate, building on some recent results reported in the literature. For the HIV model, there are several extensions discussed. We also suggest a new direction for the Nondeterministic Waiting Time algorithm exploring parallelization options.
Applied Optics, 1968
A new experimental technique is developed to determine simultaneously the total hemispherical emi... more A new experimental technique is developed to determine simultaneously the total hemispherical emittance, solar absorptance, and absorptance-emittance ratio for metals at cryogenic temperatures. The method compares the temperature response of thin metal samples to a sinusoidal perturbation of an imposed radiant intensity. Emittance data are presented for aluminum, copper, and 304 stainless steel over the temperature range of 150 to 500 K. From the data, the applicability of the cyclic radiant intensity method is evaluated, and the problems associated with extending the method to temperatures below 150 K are discussed.
We present the Nondeterministic Waiting Time algorithm. Our technique for the simulation of bioch... more We present the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells.