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Application of Proteomics and Lipid Studies in Environmental Biotechnology

Description: The overview of changes in protein levels or states in response to a growth condition, stress, mutation or metabolic engineering is invaluable in understanding the physiology of a microbial system. The lipid profile of the cell is similarly a valuable diagnostic of the cellular response and health, especially in context of survival in a fluctuating environment. To obtain comprehensive cellular models, post-transcriptional cell wide surveys at the levels of proteins and lipids are required. Both these fields have been greatly bolstered by the development of high throughput methods using mass spectrometry. Multiple strategies now exist for the identification of proteins, and numerous workflows to quantify protein abundance have also been developed. Cellular profiling such as these allows us to assess the potential of a microbial system for environmental applications such as bioremediation and bio-energy.
Date: August 12, 2008
Creator: Mukhopadhyay, Aindrila
Partner: UNT Libraries Government Documents Department

Discovering and validating biological hypotheses from coherent patterns in functional genomics data

Description: The area of transcriptomics analysis is among the more established in computational biology, having evolved in both technology and experimental design. Transcriptomics has a strong impetus to develop sophisticated computational methods due to the large amounts of available whole-genome datasets for many species and because of powerful applications in regulatory network reconstruction as well as elucidation and modeling of cellular transcriptional responses. While gene expression microarray data can be noisy and comparisons across experiments challenging, there are a number of sophisticated methods that aid in arriving at statistically and biologically significant conclusions. As such, computational transcriptomics analysis can provide guidance for analysis of results from newer experimental technologies. More recently, search methods have been developed to identify modules of genes, which exhibit coherent expression patterns in only a subset of experimental conditions. The latest advances in these methods allow to integrate multiple data types anddatasets, both experimental and computational, within a single statistical framework accounting for data confidence and relevance to specific biological questions. Such frameworks provide a unified environment for the exploration of specific biological hypothesis and for the discovery of coherent data patterns along with the evidence supporting them.
Date: August 12, 2008
Creator: Joachimiak, Marcin Pawel
Partner: UNT Libraries Government Documents Department

Focussing the view on Nature's water-splitting catalyst

Description: About 3 billion years ago Nature invented a catalyst that splits water with highefficiency into molecular oxygen and hydrogen equivalents (protons and electrons). This reaction is energetically driven by sun light and the active centre contains relatively cheap and abundant metals: manganese and calcium. This biological system therefore forms the paradigm for all man made attempts for direct solar fuel production and several studies are underway to determine the electronic and geometric structures of this catalyst. In this report we briefly summarize the problems and the current status of these efforts, and propose a DFT-based strategy for obtaining a reliable high resolution structure of this unique catalyst that includes both the inorganic core and the first ligand sphere.
Date: January 1, 2008
Creator: Messinger, Johannes & Yano, Junko
Partner: UNT Libraries Government Documents Department

On the Jarzynski relation for dissipative quantumdynamics

Description: In this note, we will discuss how to compactly express the Jarzynski identity for an open quantum system with dissipative dynamics. In quantum dynamics we must avoid explicitly measuring the work directly, which is tantamount to continuously monitoring the state of the system, and instead measure the heat ?ow from the environment. These measurements can be concisely represented with Hermitian map superoperators, which provide a convenient and compact representations of correlation functions and sequential measurements of quantum systems.
Date: October 30, 2008
Creator: Crooks, Gavin E
Partner: UNT Libraries Government Documents Department

On thermodynamic and microscopic reversibility

Description: The word 'reversible' has two (apparently) distinct applications in statistical thermodynamics. A thermodynamically reversible process indicates an experimental protocol for which the entropy change is zero, whereas the principle of microscopic reversibility asserts that the probability of any trajectory of a system through phase space equals that of the time reversed trajectory. However, these two terms are actually synonymous: a thermodynamically reversible process is microscopically reversible, and vice versa.
Date: July 12, 2011
Creator: Crooks, Gavin E.
Partner: UNT Libraries Government Documents Department

THE ATTENUATED RADON TRANSFORM: APPLICATION TO SINGLE-PHOTON EMISSION COMPUTED TOMOGRAPHY IN THE PRESENCE OF A VARIABLE ATTENUATING MEDIUM

Description: The properties of the attenuated Radon transform and its application to single-photon emission computed tomography (ECT) are analyzed in detail. In nuclear medicine and biological research, the objective of ECT is to describe quantitatively the position and strengths of internal sources of injected radiopharmaceuticals and radionuclides where the attenuation between the sources and detector is unknown. The problem is mathematically and practically quite different from well-known methods in transmission computed tomography (TCT) where only the attenuation is unknown. A mathematical structure using function theory and the theory of linear operators on Hilbert spaces is developed to better understand the spectral properties of the attenuated Radon transform. The continuous attenuated Radon transform is reduced to a matrix operator for discrete angular and lateral sampling, and the reconstruction problem reduces to a system of linear equations. For variable attenuation coefficients frequently found in imaging internal organs, the numerical methods developed in this paper involve iterative techniques of performing the generalized inverse. Its application to nuclear medicine is demonstrated by reconstructions of transverse sections of the brain, heart, and liver.
Date: March 1, 1980
Creator: Gullberg, Grant T.
Partner: UNT Libraries Government Documents Department

A MARKOV MODEL OF THE REPAIR-MISREPAIR PROCESS OF CELL SURVIVAL

Description: The repair-misrepair model of cell survival is formulated mathematically as a Markov process. The nucleus of a cell is described by the status of the lesions that resulted from exposure to radiation. At any time each of these lesions is either unrepaired, misrepaired, or eurepaired. A system of coupled differential equations for the probabilities of zero, one, two, ... unrepaired lesions is derived. The probability of survival of a cell is the probability of zero unrepaired or misrepaired lesions. Solutions for the probability of survival are obtained for four cases: three for lesions associated with the tracks of ionizing particles through the nucleus and one for lesions resulting from X rays and not distributed along tracks. These solutions reduce to simple forms for various limiting cases of the parameters. These limiting solutions bound the range of the probability of survival. It is shown that when the average number of initial lesions per track is varied while the average number of lesions for the nucleus as a whole is held constant, the cells with a higher number of lesions per track (corresponding to higher LET) have a higher probability of survival than those with a lower number. This shows the effect of larger bunches of lesions on fewer tracks. It is known experimentally that when dose is held constant, a higher probability of survival corresponds to lower LET. These contrasting properties imply that the number of lesions per track must increase much less slowly with LET than in direct proportion, and may provide a means of testing the model.
Date: March 1, 1981
Creator: Albright, Norman W.
Partner: UNT Libraries Government Documents Department

Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics

Description: Many interesting divergence measures between conjugate ensembles of nonequilibrium trajectories can be experimentally determined from the work distribution of the process. Herein, we review the statistical and physical significance of several of these measures, in particular the relative entropy (dissipation), Jeffreys divergence (hysteresis), Jensen-Shannon divergence (time-asymmetry), Chernoff divergence (work cumulant generating function), and Renyi divergence.
Date: June 3, 2011
Creator: Crooks, Gavin & Sivak, David
Partner: UNT Libraries Government Documents Department

Crystallization Process of Protein Rv0731c from Mycobacterium Tuberculosis for a Successful Atomic Resolution Crystal Structure at 1.2 Angstrom

Description: Proteins are bio-macromolecules consisting of basic 20 amino acids and have distinct three-dimensional folds. They are essential parts of organisms and participate in every process within cells. Proteins are crucial for human life, and each protein within the body has a specific function, such as antibodies, contractile proteins, enzymes, hormonal proteins, structural proteins, storage proteins and transport proteins. Determining three-dimensional structure of a protein can help researchers discover the remarkable protein folding, binding site, conformation and etc, in order to understand well of protein interaction and aid for possible drug design. The research on protein structure by X-ray protein crystallography carried by Li-Wei Hung's research group in the Physical Bioscience Division at Lawrence Berkeley National Laboratory (LBNL) is focusing on protein crystallography. The research in this lab is in the process of from crystallizing the proteins to determining the three dimensional crystal structures of proteins. Most protein targets are selected from Mycobacterium Tuberculosis. TB (Tuberculosis) is a possible fatal infectious disease. By studying TB target protein can help discover antituberculer drugs, and find treatment for TB. The high-throughput mode of crystallization, crystal harvesting, crystal screening and data collection are applied to the research pipeline (Figure 1). The X-ray diffraction data by protein crystals can be processed and analyzed to result in a three dimensional representation of electron density, producing a detailed model of protein structure. Rv0731c is a conserved hypothetical protein with unknown function from Mycobacterium Tuberculosis. This paper is going to report the crystallization process and brief structure information of Rv0731c.
Date: June 8, 2009
Creator: Zhu, Liang Cong
Partner: UNT Libraries Government Documents Department

Quantum Operation Time Reversal

Description: The dynamics of an open quantum system can be described by a quantum operation: A linear, complete positive map of operators. Here, I exhibit a compact expression for the time reversal of a quantum operation, which is closely analogous to the time reversal of a classical Markov transition matrix. Since open quantum dynamics are stochastic, and not, in general, deterministic, the time reversal is not, in general, an inversion of the dynamics. Rather, the system relaxes toward equilibrium in both the forward and reverse time directions. The probability of a quantum trajectory and the conjugate, time reversed trajectory are related by the heat exchanged with the environment.
Date: March 25, 2008
Creator: Crooks, Gavin E.
Partner: UNT Libraries Government Documents Department

Measuring Thermodynamic Length

Description: Thermodynamic length is a metric distance between equilibrium thermodynamic states. Among other interesting properties, this metric asymptotically bounds the dissipation induced by a finite time transformation of a thermodynamic system. It is also connected to the Jensen-Shannon divergence, Fisher information, and Rao's entropy differential metric. Therefore, thermodynamic length is of central interestin understanding matter out of equilibrium. In this Letter, we will consider how to denethermodynamic length for a small system described by equilibrium statistical mechanics and how to measure thermodynamic length within a computer simulation. Surprisingly, Bennett's classic acceptance ratio method for measuring free energy differences also measures thermodynamic length.
Date: September 7, 2007
Creator: Crooks, Gavin E
Partner: UNT Libraries Government Documents Department

Nanostructured Cobalt Oxide Clusters in Mesoporous Silica as Efficient Oxygen-Evolving Catalysts

Description: The development of integrated artificial photosynthetic systems for the direct conversion of carbon dioxide and water to fuel depends on the availability of efficient and robust catalysts for the chemical transformations. Catalysts need to exhibit turnover frequency (TOF) and density (hence size) commensurate with the solar flux at ground level (1000Wm2, airmass (AM) 1.5)[1]to avoid wasting of incidentsolar photons. For example, a catalyst with a TOF of 100 s1 requires a density of one catalytic site per square nanometer. Catalysts with lower rates or taking up a larger space will require a high-surface-area, nanostructured support that affords tens to hundreds of catalytic sites per square nanometer. Furthermore, catalysts need to operate close to the thermodynamic potential of the redox reaction so that amaximum fraction of the solar photon energy is converted to chemical energy. Stability considerations favor all-inorganic oxide materials, as does avoidance of harsh reaction conditions of pH value or temperature.
Date: January 1, 2009
Creator: Jiao, Feng & Frei, Heinz
Partner: UNT Libraries Government Documents Department

Comment regarding"On the Crooks fluctuation theorem and the Jarzynski equality" [J. Chem. Phys. 129, 091101 (2008)]and"Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics" [J. Chem. Phys. 129, 144113 (2008)]

Description: The incongruous"unexpected inapplicability of the [Crook's fluctuation theorem]" is due to an inexplicable, inappropriate use of inconsistent expressions. The girding is secure.
Date: March 4, 2009
Creator: Crooks, Gavin E
Partner: UNT Libraries Government Documents Department

Syntrophic Degradation of Lactate in Methanogenic Co-cultures

Description: In environments where the amount of the inorganic electron acceptors (oxygen, nitrate, sulfate, sulfur oroxidized metal ions (Fe3+;Mn4+) is insufficient for complete breakdown of organic matter, methane is formed as the major reduced end product. In such methanogenic environments organic acids are degraded by syntrophic associations of fermenting, acetogenic bacteria (e.g., sulfate-reducing bacteria (SRB) as"secondary fermenters") and methanogenic archaea. In these consortia, the conversion of lactate to acetate, CO2 and methane depends on the cooperating activities of both metabolically distinct microbial groups that are tightly linked by the need to maintain the exchanged metabolites (hydrogenandformate) at very low concentrations.
Date: May 17, 2010
Creator: Meyer, Birte & Stahl, David
Partner: UNT Libraries Government Documents Department

In-situ Spectroscopy of Water Oxidation at Ir Oxide Nanocluster Drivenby Visible TiOCr Charge-Transfer Chromophore in Mesoporous Silica

Description: An all-inorganic photocatalytic unit consisting of a binuclear TiOCr charge-transfer chromophore coupled to an Ir oxide nanocluster has been assembled on the pore surface of mesoporous silica AlMCM-41. In situ FT-Raman and EPR spectroscopy of an aqueous suspension of the resulting IrxOy-TiCr-AlMCM-41 powder reveal the formation of superoxide species when exciting the Ti(IV)OCr(III) --> Ti(III)OCr(IV) metal-to-metal charge-transfer chromophore with visible light. Use of H218O confirms that the superoxide species originates from oxidation of water. Photolysis in the absence of persulfate acceptor leads to accumulation of Ti(III) instead. The results are explained by photocatalytic oxidation of water at Ir oxide nanoclusters followed by trapping of the evolving O2 by transient Ti(III) centers to yield superoxide. Given the flexibility to select donor metals with appropriate redox potential, photocatalytic units consisting of a binuclear charge-transfer chromophore coupled to a water oxidation catalyst shown here constitute a step towards thermodynamically efficient visible light water oxidation units.
Date: June 3, 2008
Creator: Frei, Heinz; Han, Hongxian & Frei, Heinz
Partner: UNT Libraries Government Documents Department

Information Dashboards

Description: "A dashboard is a visual interface that provides at-a-glance views into key measures relevant to a particular objective or business process." Key Attributes: Graphical to focus attention on key trends, comparisons and exceptions, Display only relevant data, Inherently contain predefined conclusions. Note: Collecting user requirements is KEYfrom'Excel 2007 Dashboards& Reports for Dummies' by Michael Alexander
Date: April 11, 2008
Creator: Shutkin, Amy; Shutkin, Amy & Shutkin, Amy
Partner: UNT Libraries Government Documents Department

Direct Observation of the Kinetically Relevant Site of CO Hydrogenation on Supported Ru Catalyst at 700 K by Time-Resolved FT-IR Spectroscopy

Description: Time-resolved FT-IR spectra of carbon monoxide hydrogenation over alumina-supported ruthenium particles were recorded on themillisecond time scale at 700 K using pulsed release of CO and a continuous flow of H2/N2 (ratio 0.067 or 0.15, 1 atm total pressure). Adsorbed carbon monoxide was detected along with gas phase products methane (3016 and 1306 cm-1), water (1900 +- 1300 cm-1), and carbon dioxide (2348 cm-1). Aside from adsorbed CO, no other surface species were observed. The rate of formation of methane is 2.5 +- 0.4 s-1 and coincides with the rate of carbon dioxide growth (3.4 +- 0.6 s-1), thus indicating that CH4 and CO2 originate from a common intermediate. The broad band of adsorbed carbon monoxide has a maximum at 2010 cm-1 at early times (36 ms) that shifts gradually to 1960 cm-1 over a period of 3 s as a result of the decreasing surface concentration of CO. Kinetic analysis of the adsorbed carbon monoxide reveals that surface sites absorbing at the high frequency end of the infrared band are temporally linked to gas phase product growth. Specifically, a (linear) CO site at 2026 cm-1 decays with a rate constant of 2.9 +- 0.1 s-1, which coincides with the rise constant of CH4. This demonstrates that the linear CO site at 2026 cm-1 is the kinetically most relevant one for the rate-determining CO dissociation step under reaction conditions at 700 K.
Date: June 4, 2008
Creator: Frei, Heinz; Wasylenko, Walter & Frei, Heinz
Partner: UNT Libraries Government Documents Department

Integrated Ecogenomics Study for Bioremediation of Cr(VI) at Hanford 100H Area

Description: Hexavalent chromium is a widespread contaminant found in groundwater. In order to stimulate microbially mediated Cr(VI)-reduction, a poly-lactate compound was injected into Cr(VI)-contaminated aquifers at site 100H at Hanford. Investigation of bacterial community composition using high-density DNA microarray analysis of 16S rRNA gene products revealed a stimulation of Pseudomonas, Desulfovibrio and Geobacter species amongst others. Enrichment of these organisms coincided with continued Cr(VI) depletion. Functional gene-array analysis of DNA from monitoring well indicated high abundance of genes involved in nitrate-reduction, sulfate-reduction, iron-reduction, methanogenesis, chromium tolerance/reduction. Clone-library data revealed Psedomonas was the dominant genus in these samples. Based on above results, we conducted lab investigations to study the dominant anaerobic culturable microbial populations present at this site and their role in Cr(VI)-reduction. Enrichments using defined anaerobic media resulted in isolation of an iron-reducing, a sulfate-reducing and a nitrate-reducing isolate among several others. Preliminary 16S rDNA sequence analysis identified the isolates as Geobacter metallireducens, Pseudomonas stutzeri and Desulfovibrio vulgaris species respectively. The Pseudomonas isolate utilized acetate, lactate, glycerol and pyruvate as alternative carbon sources, and reduced Cr(VI). Anaerobic washed cell suspension of strain HLN reduced almost 95?M Cr(VI) within 4 hr. Further, with 100?M Cr(VI) as sole electron-acceptor, cells grew to 4.05 x 107 /ml over 24 h after an initial lag, demonstrating direct enzymatic Cr(VI) reduction coupled to growth. These results demonstrate that Cr(VI)-immobilization at Hanford 100H site could be mediated by direct microbial metabolism in addition to indirect chemical reduction of Cr(VI) by end-products of microbial activity.
Date: August 12, 2008
Creator: Chakraborty, Romy & Chakraborty, Romy
Partner: UNT Libraries Government Documents Department

Integrated Omics in Systems Biology: The New Frontier for Environmental Biotechnology

Description: Environmental biotechnology encompasses a wide range of characterization, monitoring and control for bioenergy and bioremediation technologies that are based on biological processes. Recent breakthroughs in our understanding of biogeochemical processes and genomics are leading to exciting new and cost effective ways to monitor and manipulate the environment and potentially produce bioenergy fuels as we also cleanup the environment. Indeed, our ability to sequence an entire microbial genome in just a few hours is leading to similar breakthroughs in characterizing proteomes, metabolomes, phenotypes, and fluxes for organisms, populations, and communities. Understanding and modeling functional microbial community structure and stress responses in subsurface environments has tremendous implications for our fundamental understanding of biogeochemistry and the potential for making biofuel breakthroughs. Monitoring techniques that inventory and monitor terminal electron acceptors and electron donors, enzyme probes that measure functional activity in the environment, functional genomic microarrays, phylogenetic microarrays, metabolomics, proteomics, and quantitative PCR are also being rapidly adapted for studies in environmental biotechnology. Integration of all of these new high throughput techniques using the latest advances in bioinformatics and modeling will enable break-through science in environmental biotechnology. A review of these techniques with examples from field studies and lab simulations will be discussed.
Date: August 12, 2008
Creator: Hazen, Terry C.
Partner: UNT Libraries Government Documents Department

Controlled Assembly of Heterobinuclear Sites on Mesoporous Silica: Visible Light Charge-Transfer Units with Selectable Redox Properties

Description: Mild synthetic methods are demonstrated for the selective assembly of oxo-bridged heterobinuclear units of the type TiOCrIII, TiOCoII, and TiOCeIII on mesoporous silica support MCM-41. One method takes advantage of the higher acidity and, hence, higher reactivity of titanol compared to silanol OH groups towards CeIII or CoII precursor. The procedure avoids the customary use of strong base. The controlled assembly of the TiOCr system exploits the selective redox reactivity of one metal towards another (TiIII precursor reacting with anchored CrVI centers). The observed selectivity for linking a metal precursor to an already anchored partner versus formation of isolated centers ranges from a factor of six (TiOCe) to complete (TiOCr, TiOCo). Evidence for oxo bridges and determination of the coordination environment of each metal centers is based on K-edge EXAFS (TiOCr), L-edge absorption spectroscopy (Ce), and XANES measurements (Co, Cr). EPR, optical, FT-Raman and FT-IR spectroscopy furnish additional details on oxidation state and coordination environment of donor and acceptor metal centers. In the case of TiOCr, the integrity of the anchored group upon calcination (350 oC) and cycling of the Cr oxidation state is demonstrated. The binuclear units possess metal-to-metal charge-transfer transitions that absorb deep in the visible region. The flexible synthetic method for assembling the units opens up the use of visible light charge transfer pumps featuring donor or acceptor metals with selectable redox potential.
Date: June 4, 2008
Creator: Frei, Heinz; Han, Hongxian & Frei, Heinz
Partner: UNT Libraries Government Documents Department

Where Water is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster from X-ray Spectroscopy

Description: Light-driven oxidation of water to dioxygen in plants, algae and cyanobacteria iscatalyzed within photosystem II (PS II) by a Mn4Ca cluster. Although the cluster has been studied by many different methods, the structure and the mechanism have remained elusive. X-ray absorption and emission spectroscopy and EXAFS studies have been particularly useful in probing the electronic and geometric structure, and the mechanism of the water oxidation reaction. Recent progress, reviewed here, includes polarized X-ray absorption spectroscopy measurements of PS II single crystals. Analysis of those results has constrained the Mn4Ca cluster geometry to a setof three similar high-resolution structures. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 Angstrom-resolution X-ray structures or other previously proposed models. The differences between the models derived from X-rayspectroscopy and crystallography are predominantly because of damage to the Mn4Ca cluster by X-rays under the conditions used for structure determination by X-ray crystallography. X-ray spectroscopy studies are also used for studying the changes in the structure of the Mn4Ca catalytic center as it cycles through the five intermediate states known as the Si-states (i=0-4). The electronic structure of the Mn4Ca cluster has been studied more recently using resonant inelastic X-ray scattering spectroscopy (RIXS), in addition to the earlier X-ray absorption and emission spectroscopy methods. These studies are revealing that the assignment of formaloxidation states is overly simplistic. A more accurate description should consider the charge density on the Mn atoms that includes the covalency of the bonds and delocalization of the charge over the cluster. The geometric and electronic structure of the Mn4Ca cluster in the S-states derived from X-ray spectroscopy are leading to a detailed understanding of the mechanism of the O-O bond formation during the photosynthetic water splitting process.
Date: October 24, 2007
Creator: Yano, Junko; Yano, Junko & Yachandra, Vittal K.
Partner: UNT Libraries Government Documents Department

Empirical Evaluation of a New Method for Calculating Signal to Noise Ratio (SNR) for Microarray Data Analysis

Description: Signal-to-noise-ratio (SNR) thresholds for microarray data analysis were experimentally determined with an oligonucleotide array that contained perfect match (PM) and mismatch (MM) probes based upon four genes from Shewanella oneidensis MR-1. A new SNR calculation, called signal to both standard deviations ratio (SSDR) was developed, and evaluated along with other two methods, signal to standard deviation ratio (SSR), and signal to background ratio (SBR). At a low stringency, the thresholds of SSR, SBR, and SSDR were 2.5, 1.60 and 0.80 with oligonucleotide and PCR amplicon as target templates, and 2.0, 1.60 and 0.70 with genomic DNA as target templates. Slightly higher thresholds were obtained at the high stringency condition. The thresholds of SSR and SSDR decreased with an increase in the complexity of targets (e.g., target types), and the presence of background DNA, and a decrease in the composition of targets, while SBR remained unchanged under all situations. The lowest percentage of false positives (FP) and false negatives (FN) was observed with the SSDR calculation method, suggesting that it may be a better SNR calculation for more accurate determination of SNR thresholds. Positive spots identified by SNR thresholds were verified by the Student t-test, and consistent results were observed. This study provides general guidance for users to select appropriate SNR thresholds for different samples under different hybridization conditions.
Date: March 6, 2008
Creator: Zhou, Jizhong; He, Zhili & Zhou, Jizhong
Partner: UNT Libraries Government Documents Department

Far-from-equilibrium measurements of thermodynamic length

Description: Thermodynamic length is a path function that generalizes the notion of length to the surface of thermodynamic states. Here, we show how to measure thermodynamic length in far-from-equilibrium experiments using the work fluctuation relations. For these microscopic systems, it proves necessary to define the thermodynamic length in terms of the Fisher information. Consequently, the thermodynamic length can be directly related to the magnitude of fluctuations about equilibrium. The work fluctuation relations link the work and the free energy change during an external perturbation on a system. We use this result to determine equilibrium averages at intermediate points of the protocol in which the system is out-of-equilibrium. This allows us to extend Bennett's method to determine the potential of mean force, as well as the thermodynamic length, in single molecule experiments.
Date: November 5, 2008
Creator: Feng, Edward H. & Crooks, Gavin E.
Partner: UNT Libraries Government Documents Department

RADIATION CHEMISTRY OF HEAVY PARTICLE TRACKS. I. GENERAL CONSIDERATIONS

Description: The radiation chemistry of heavy particle tracks in dilute aqueous solution is considered in a unified manner. Emphasis is on the physical and chemical phenomena which are involved rather than on the construction of models to be used in actual calculations although the latter problem is discussed. A differential segment of a heavy particle track is composed of two parts which we call 'core' and 'penumbra'; elementary considerations show that all properties of such a differential track can be uniquely specified in terms of a two-parameter system, and we choose energy per nucleon (E) and atomic number (Z) as independent parameters. The nature of heavy-particle track processes varies with the magnitude of the energy deposit (LET), and we discuss three categories of track problems, for low-, intermediate-, and high-LET cases, respectively. Scavenger reactions normally terminate radical recombination in a track, and for heavy particle tracks we find a criterion involving the scavenger concentration for a convenient separation of core and penumbra into essentially noninteracting parts which can be treated independently. Problems of the core expansion in the three regions are considered and it is found that a versatile model can be constructed on concepts previously introduced by Ganguly and Magee. A model for the penumbra, based on the authors electron track theory, is presented and discussed.
Date: March 1, 1980
Creator: Magee, J.L. & Chatterjee, A.
Partner: UNT Libraries Government Documents Department