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Biological physics

Description: Major goals of biological physics are the understanding of biological systems in physical terms and the study of concepts and laws of complex systems.
Date: September 24, 1998
Partner: UNT Libraries Government Documents Department

Radiological Sciences Department: Quarterly Progress Report Research and Development Activities for October - December, 1951

Description: A report which is the ninth report of the research and development activities of the radiological sciences department, Hanford Works, which includes some items charged to control but include for for general interest.
Date: November 1, 1951
Creator: Parker, H. M.
Partner: UNT Libraries Government Documents Department

Health Physics Division Annual Progress Report: Period Ending June 30, 1976

Description: Annual report for the Oak Ridge National Laboratory Health Physics Division including sections on medical physics and internal dosimetry; chemical physics and spectroscopy; biological and radiation physics; assessment technology; emergency technology; analytic dosimetry and education group; theses, papers, publications, and lectures; and miscellaneous staff activities.
Date: October 1976
Creator: Oak Ridge National Laboratory. Health Physics Division.
Partner: UNT Libraries Government Documents Department

Nanoporous microbead supported bilayers: stability, physical characterization, and incorporation of functional transmembrane proteins.

Description: The introduction of functional transmembrane proteins into supported bilayer-based biomimetic systems presents a significant challenge for biophysics. Among the various methods for producing supported bilayers, liposomal fusion offers a versatile method for the introduction of membrane proteins into supported bilayers on a variety of substrates. In this study, the properties of protein containing unilamellar phosphocholine lipid bilayers on nanoporous silica microspheres are investigated. The effects of the silica substrate, pore structure, and the substrate curvature on the stability of the membrane and the functionality of the membrane protein are determined. Supported bilayers on porous silica microspheres show a significant increase in surface area on surfaces with structures in excess of 10 nm as well as an overall decrease in stability resulting from increasing pore size and curvature. Comparison of the liposomal and detergent-mediated introduction of purified bacteriorhodopsin (bR) and the human type 3 serotonin receptor (5HT3R) are investigated focusing on the resulting protein function, diffusion, orientation, and incorporation efficiency. In both cases, functional proteins are observed; however, the reconstitution efficiency and orientation selectivity are significantly enhanced through detergent-mediated protein reconstitution. The results of these experiments provide a basis for bulk ionic and fluorescent dye-based compartmentalization assays as well as single-molecule optical and single-channel electrochemical interrogation of transmembrane proteins in a biomimetic platform.
Date: March 1, 2007
Creator: Davis, Ryan W.; Brozik, James A.; Brozik, Susan Marie; Cox, Jason M.; Lopez, Gabriel P.; Barrick, Todd A. et al.
Partner: UNT Libraries Government Documents Department

Protein Microarrays--Without a Trace

Description: Many experimental approaches in biology and biophysics, as well as applications in diagnosis and drug discovery, require proteins to be immobilized on solid supports. Protein microarrays, for example, provide a high-throughput format to study biomolecular interactions. The technique employed for protein immobilization is a key to the success of these applications. Recent biochemical developments are allowing, for the first time, the selective and traceless immobilization of proteins generated by cell-free systems without the need for purification and/or reconcentration prior to the immobilization step.
Date: April 5, 2007
Creator: Camarero, J A
Partner: UNT Libraries Government Documents Department


Description: The 2010 Gordon Conference on Single-Molecule Approaches to Biology focuses on cutting-edge research in single-molecule science. Tremendous technical developments have made it possible to detect, identify, track, and manipulate single biomolecules in an ambient environment or even in a live cell. Single-molecule approaches have changed the way many biological problems are addressed, and new knowledge derived from these approaches continues to emerge. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of biomolecular machines: what they do, how they work individually, how they work together, and finally, how they work inside live cells. The burgeoning use of single-molecule methods to elucidate biological problems is a highly multidisciplinary pursuit, involving both force- and fluorescence-based methods, the most up-to-date advances in microscopy, innovative biological and chemical approaches, and nanotechnology tools. This conference seeks to bring together top experts in molecular and cell biology with innovators in the measurement and manipulation of single molecules, and will provide opportunities for junior scientists and graduate students to present their work in poster format and to exchange ideas with leaders in the field. A number of excellent poster presenters will be selected for short oral talks. Topics as diverse as single-molecule sequencing, DNA/RNA/protein interactions, folding machines, cellular biophysics, synthetic biology and bioengineering, force spectroscopy, new method developments, superresolution imaging in cells, and novel probes for single-molecule imaging will be on the program. Additionally, the collegial atmosphere of this Conference, with programmed discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings in the beauty of the Il Ciocco site in Tuscany, provides an avenue for scientists from different disciplines to interact and brainstorm and promotes cross-disciplinary collaborations directed toward compelling biological problems.
Date: July 9, 2010
Creator: Moerner, Professor William
Partner: UNT Libraries Government Documents Department

New developments for the site-specific attachment of protein to surfaces

Description: Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physical adsorption. However, since these interactions are weak, the molecules can get denatured or dislodged, thus causing loss of signal. They also result in random attachment of the protein to the surface. Site-specific covalent attachment of proteins onto surfaces, on the other hand, leads to molecules being arranged in a definite, orderly fashion and uses spacers and linkers to help minimize steric hindrances between the protein surface. This work reviews in detail some of the methods most commonly used as well as the latest developments for the site-specific covalent attachment of protein to solid surfaces.
Date: May 12, 2005
Creator: Camarero, J A
Partner: UNT Libraries Government Documents Department

Electronic Spectroscopy & Dynamics

Description: The Gordon Research Conference (GRC) on Electronic Spectroscopy and Dynamics was held at Colby College, Waterville, NH from 07/19/2009 thru 07/24/2009. The Conference was well-attended with participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. The GRC on Electronic Spectroscopy & Dynamics showcases some of the most recent experimental and theoretical developments in electronic spectroscopy that probes the structure and dynamics of isolated molecules, molecules embedded in clusters and condensed phases, and bulk materials. Electronic spectroscopy is an important tool in many fields of research, and this GRC brings together experts having diverse backgrounds in physics, chemistry, biophysics, and materials science, making the meeting an excellent opportunity for the interdisciplinary exchange of ideas and techniques. Topics covered in this GRC include high-resolution spectroscopy, biological molecules in the gas phase, electronic structure theory for excited states, multi-chromophore and single-molecule spectroscopies, and excited state dynamics in chemical and biological systems.
Date: June 8, 2010
Creator: Mark Maroncelli, Nancy Ryan Gray
Partner: UNT Libraries Government Documents Department

Evolution on folding landscapes in combinatorial structures

Description: In this paper the authors investigate the evolution of molecular structures by random point mutations. They will consider two types of molecular structures: (a) (RNA) secondary structures, and (b) random structures. In both cases structure consists of: (1) a contact graph, and (2) a family of relations imposed on its adjacent vertices. The vertex set of the contact graph is simply the set of all indices of a sequence, and its edges are the bonds. The corresponding relations associated with the edges are viewed as secondary base pairing rules and tertiary interaction rules respectively. Mapping of sequences into secondary and random structures are modeled and analyzed. Here, the set of all sequences that map into a particular structure is modeled as a random graph in the sequence space, the so called neutral network and they study how neutral networks are embedded in sequence space. A basic replication of deletion experiment reveals how effective secondary and random structures can be searched by random point mutations and to what extent the structure effects the dynamics of this optimization process. In particular the authors can report a nonlinear relation between the fraction of tertiary interactions in random structures, and the times taken for a population of sequences to find a high fitness target random structure.
Date: November 1, 1997
Creator: Fraser, S.M. & Reidys, C.M.
Partner: UNT Libraries Government Documents Department

Visualization of Information Spaces with VxInsight

Description: VxInsight provides a visual mechanism for browsing, exploring and retrieving information from a database. The graphical display conveys information about the relationship between objects in several ways and on multiple scales. In this way, individual objects are always observed within a larger context. For example, consider a database consisting of a set of scientific papers. Imagine that the papers have been organized in a two dimensional geometry so that related papers are located close to each other. Now construct a landscape where the altitude reflects the local density of papers. Papers on physics will form a mountain range, and a different range will stand over the biological papers. In between will be research reports from biophysics and other bridging disciplines. Now, imagine exploring these mountains. If we zoom in closer, the physics mountains will resolve into a set of sub-disciplines. Eventually, by zooming in far enough, the individual papers become visible. By pointing and clicking you can learn more about papers of interest or retrieve their full text. Although physical proximity conveys a great deal of information about the relationship between documents, you can also see which papers reference which others, by drawing lines between the citing and cited papers. For even more information, you can choose to highlight papers by a particular researcher or a particular institution, or show the accumulation of papers through time, watching some disciplines explode and other stagnate. VxInsight is a general purpose tool, which enables this kind of interaction with wide variety of relational data: documents, patents, web pages, and financial transactions are just a few examples. The tool allows users to interactively browse, explore and retrieve information from the database in an intuitive way.
Date: December 1, 2000
Creator: Wylie, B.N.; Boyack, K.W.; Davidson, G.S. & Johnson, D.K.
Partner: UNT Libraries Government Documents Department

Final Report: 8th International Symposium on NCT for Cancer, May 15, 1998 - May 15, 1999

Description: The 8th International Symposium on Neutron Capture Therapy for Cancer (8th ISNCTC) was held in La Jolla, CA on Sept. 13-18, 1998. This biennial meeting of the International Society for Neutron Capture Therapy (ISNCT) was hosted by Society President M.F. Hawthorne (UCLA Dept. of Chemistry and Biochemistry). The Symposium brought together scientists (300 registrants from 21 countries) from diverse fields to report the latest developments in NCT. Topics of the 275 papers presented (30 plenary lectures, 81 oral presentations, and 164 posters) included the physics of neutron sources, chemistry of tumor-targeting agents, dosimetry, radiobiological studies, and clinical applications.
Date: September 1, 1999
Creator: Hawthorne, M.F.
Partner: UNT Libraries Government Documents Department

6th International Conference on Biophysics & Synchrotron Radiation. Final report

Description: The 6th International Conference on Biophysics and Synchrotron Rdiation was held at the Advanced Photon Source, Argonne National Laboratory, from August 4-8, 1998, with pre-conference activities on August 3. Over 300 attendees and 65 presenters participated in the conference that was collaboratively hosted by the University of Chicago, Center for Advanced Radiation Sources and the Advanced Photon Source.
Date: August 3, 1999
Creator: Moffat, Keith
Partner: UNT Libraries Government Documents Department

Comparison of the bioavailability of elemental waste laden soils using in vivo and in vitro analytical methodology and refinement of exposure/dose models. 1998 annual progress report

Description: 'The authors hypotheses are: (1) the more closely the synthetic, in vitro, extractant mimics the extraction properties of the human digestive bio-fluids, the more accurate will be the estimate of an internal dose; (2) performance can be evaluated by in vivo studies with a rat model and quantitative examination of a mass balance, calculation and dose estimates from model simulations for the in vitro and in vivo system; and (3) the concentration of the elements Pb, Cd, Cr and selected Radionuclides present in the bioavailable fraction obtained with a synthetic extraction system will be a better indicator of contaminant ingestion from a contaminated soil because it represents the portion of the mass which can yield exposure, uptake and then the internal dose to an individual. As of April 15, 1998, they have made significant progress in the development of a unified approach to the examination of bioavailability and bioaccessibility of elemental contamination of soils for the ingestion route of exposure. This includes the initial characterization of the soil, in vitro measurements of bioaccessibility, and in vivo measurements of bioavailability. They have identified the basic chemical and microbiological characteristics of waste laden soils. These have been used to prioritize the soils for potential mobility of the trace elements present in the soil. Subsequently they have employed a mass balance technique, which for the first time tracked the movement and distribution of elements through an in vitro or in vivo experimental protocol to define the bioaccessible and the bioavailable fractions of digested soil. The basic mass balance equation for the in vitro system is: MT = MSGJ + MIJ + MR. where MT is the total mass extractable by a specific method, MSGJ, is the mass extracted by the saliva and the gastric juices, MIJ is the mass extracted by the intestinal ...
Date: June 1, 1998
Creator: Lioy, P.J.; Gallo, M.; Georgopoulos, P.; Tate, R. & Buckley, B.
Partner: UNT Libraries Government Documents Department

A Molecular Theory for Gatekeeper Proteins

Description: Predicting the behavior of ion channel proteins is important for understanding biological effects of drugs and toxins. These problems involve steady state transport of ions through very small (1-2 atoms wide) pores. FY99 LDRD funding was used to begin investigations of ion channel proteins using a molecular theory approach. Much of our efforts involved establishing the soundness of the approach by direct comparison with grand canonical molecular dynamics simulations of simple model systems. In addition, several dimensional ion channel models have been implemented to demonstrate the viability of the approach, The seed funding provided by this LDRD grant resulted in 50K of DOWOBER funds for FY99, an invitation to submit a full length 0(500K) proposal for consideration to DOWOBER, and start a larger LDRD effort in computational biophysics beginning in FY00.
Date: November 1, 1999
Partner: UNT Libraries Government Documents Department

Comparison of the bioavailability of elemental waste laden soils using in vivo and in vitro analytical methodology and refinement of exposure/dose model. 1997 annual progress report

Description: 'The bioavailability study has made significant progress in developing in vitro methodology, and the authors have completed the time course in vivo studies. The in vitro studies have been conducted to establish the major digestive variables of concern and the values to be used in application of both the saliva/gastric juice and intestinal fluid components of a synthetic digestive extraction. In vitro and in vivo experiments have been conducted on the 575 urn particle fraction of a soil sample collected in a Jersey City State Park. Five Jersey City soil samples were first characterized for physical and chemical characteristics. Based upon the composition of the five soils, one was selected for use in the first series of experiments. The second set of in vivo studies are to be conducted on a standard NIST Montana soil. It has already been examined for bioaccessibility and availability with the in vitro methodology. A sample has been collected in Bayonne to obtain an urban background soil. Surficial soil samples have been acquired from the Savannah River Site of the DOE. These are not radioactive but are contaminated with heavy metals, e.g. arsenic, and are being analyzed by both the in vivo and in vitro methodology. During this past summer a second set of soil samples were collected at Savannah River Site. These contain levels of both heavy metals and radionuclides. Recently, a special extraction laboratory has been constructed at EOHSI, with resources made available from the organization. It will handle the extraction and measurement of the radio activity of the soil, and extracts obtained by the in vivo techniques. It is anticipated that the SRS samples collected this summer will be available for analysis in both the in vivo and in vitro systems this fall. The initial characterization will be for soil, physical and ...
Date: January 1, 1997
Creator: Gailo, M.; Georgopoulos, P.; Lioy, P.J. & Roy, A.
Partner: UNT Libraries Government Documents Department

Improved radiation dosimetry/risk estimates to facilitate environmental management of plutonium contaminated sites. 1998 annual progress report

Description: 'The objective of this research is to evaluate distributions of possible alpha radiation doses to the lung, bone, and liver and associated health-risk distributions for plutonium (Pu) inhalation-exposure scenarios relevant to environmental management of PuO{sub 2}-contaminated sites. Currently available dosimetry/risk models do not apply to exposure scenarios where, at most, a small number of highly radioactive PuO{sub 2} particles are inhaled (stochastic exposure [SE] paradigm). For the SE paradigm, risk distributions are more relevant than point estimates of risk. The focus of the research is on the SE paradigm and on high specific activity, alpha-emitting (HSA-aE) particles such as 238 PuO{sub 2} . The scientific goal is to develop a stochastic respiratory tract dosimetry/risk computer model for evaluating the desired absorbed dose distributions and associated health-risk distributions, for Department of Energy (DOE) workers and members of the public. This report summarizes results after 1 year of a 2-year project.'
Date: June 1, 1998
Creator: Scott, B.R.
Partner: UNT Libraries Government Documents Department

Radiation Leukemogenesis: Applying Basic Science of Epidemiological Estimates of Low Dose Risks and Dose-Rate Effects

Description: The next stage of work has been to examine more closely the A-bomb leukemia data which provides the underpinnings of the risk estimation of CML in the above mentioned manuscript. The paper by Hoel and Li (Health Physics 75:241-50) shows how the linear-quadratic model has basic non-linearities at the low dose region for the leukemias including CML. Pierce et. al., (Radiation Research 123:275-84) have developed distributions for the uncertainty in the estimated exposures of the A-bomb cohort. Kellerer, et. al., (Radiation and Environmental Biophysics 36:73-83) has further considered possible errors in the estimated neutron values and with changing RBE values with dose and has hypothesized that the tumor response due to gamma may not be linear. We have incorporated his neutron model and have constricted new A-bomb doses based on his model adjustments. The Hoel and Li dose response analysis has also been applied using the Kellerer neutron dose adjustments for the leukemias. Finally, both Pierce's dose uncertainties and Kellerer neutron adjustments are combined as well as the varying RBE with dose as suggested by Rossi and Zaider and used for leukemia dose-response analysis. First the results of Hoel and Li showing a significantly improved fit of the linear-quadratic dose response by the inclusion of a threshold (i.e. low-dose nonlinearity) persisted. This work has been complete for both solid tumor as well as leukemia for both mortality as well as incidence data. The results are given in the manuscript described below which has been submitted to Health Physics.
Date: November 1, 1998
Creator: Hoel, D. G.
Partner: UNT Libraries Government Documents Department

2004 Sensory Transduction in Microorganisms Gordon Research Conference-January 11-16, 2004

Description: Research into the mechanisms involved in the sensing and responses of microorganisms to changes in their environment is currently very active in a large number of laboratories in the US, Europe, Japan, and Israel. A wide range of eukaryotic and prokaryotic species are being studies with regard to their sensing of chemical changes, light and redox signal and intercellular signaling, leading either to changes in motile behavior, gene expression or development. It has become increasingly apparent that the mechanisms involved in development have application in higher organisms while the sensing systems in bacteria are involved in a very wide range of physiological traits, from pathogenicity, through to biofilm formation. This is an area where a wide range of state of the art tools have been used and developed over the past few decades. Approaches include behavioral studies, electro-physiology, genetics, molecular biology, structural biology, biophysics and single molecule microscopy, immunocytochemistry and molecular and mathematical modeling, all of this helped by the large number of bacterial and eukaryotic microbial genome sequences now available. The central goal of this meeting is to bring together investigators using this wide range of approaches and different systems to compare data, share ideas and approaches and seeks to understand the fundamental principles underlying these responses.
Date: January 7, 2005
Creator: Storm, Judith Armitage Carlyle
Partner: UNT Libraries Government Documents Department