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Sample records for physics chemistry biology

  1. Physical and Biological Modes of Thought in the Chemistry of Linus Pauling

    NASA Astrophysics Data System (ADS)

    Nye, Mary Jo

    No figure in modern chemistry better exemplifies than Linus Pauling (1901-1994) the intersections of the scientific disciplines of chemistry, physics, and biology nor the roles of physical and biological modes of thought in the 'central science' of chemistry.

  2. Exemplary Programs in Physics, Chemistry, Biology, and Earth Science.

    ERIC Educational Resources Information Center

    Yager, Robert E., Ed.

    The 1982 Search for Excellence in Science Education project has identified 50 exemplary programs in physics, chemistry, biology, and earth science. Descriptions of four of these programs and the criteria used in their selection are presented. The first section reviews the direction established by Project Synthesis in searching for exemplary…

  3. Biomaterials — where biology, physics, chemistry, engineering and medicine meet

    NASA Astrophysics Data System (ADS)

    Hing, K. A.

    2008-03-01

    The success or failure of an implant material in the body depends on a complex interaction between a synthetic 'foreign body' and the 'host tissue'. These interactions occur at many levels from the sub-microscopic level, where subtle changes in the surface physio-chemistry can substantially alter the nature of the biomaterial-host tissue interface, through the microscopical level (e.g. sensitivity to surface topography) to the macrostructural level (e.g. dependence on scaffold porosity). Thus the factors that control these responses are not only biologically determined but also mechanically, physically and chemically mediated, although identifying where one starts and the other finishes can be difficult. Design of a successful medical device has therefore to call on expertise within a wide range of disciplines. In terms of both investigating the basic science behind the factors which orchestrate a biological response and developing research tools that enable study of these responses. However, a medical device must also meet the economic and practical demands of health care professionals who will ultimately be using it in the clinic. Bone graft substitute materials are used in orthopaedics as an alternative or adjunct to autografting, a practice where the patient 'donates' bone from a healthy site to aid bone repair at a damaged or diseased site. These materials are used in a wide range of procedures from total hip revision to spinal fusion and their evolution over the last 10 years illustrates how an interdisciplinary approach has benefited their development and may lead to further innovation in the future.

  4. Metrology in physics, chemistry, and biology: differing perceptions.

    PubMed

    Iyengar, Venkatesh

    2007-04-01

    The association of physics and chemistry with metrology (the science of measurements) is well documented. For practical purposes, basic metrological measurements in physics are governed by two components, namely, the measure (i.e., the unit of measurement) and the measurand (i.e., the entity measured), which fully account for the integrity of a measurement process. In simple words, in the case of measuring the length of a room (the measurand), the SI unit meter (the measure) provides a direct answer sustained by metrological concepts. Metrology in chemistry, as observed through physical chemistry (measures used to express molar relationships, volume, pressure, temperature, surface tension, among others) follows the same principles of metrology as in physics. The same basis percolates to classical analytical chemistry (gravimetry for preparing high-purity standards, related definitive analytical techniques, among others). However, certain transition takes place in extending the metrological principles to chemical measurements in complex chemical matrices (e.g., food samples), as it adds a third component, namely, indirect measurements (e.g., AAS determination of Zn in foods). This is a practice frequently used in field assays, and calls for additional steps to account for traceability of such chemical measurements for safeguarding reliability concerns. Hence, the assessment that chemical metrology is still evolving.

  5. Analyzing Students' Understanding of Models and Modeling Referring to the Disciplines Biology, Chemistry, and Physics

    ERIC Educational Resources Information Center

    Krell, Moritz; Reinisch, Bianca; Krüger, Dirk

    2015-01-01

    In this study, secondary school students' (N?=?617; grades 7 to 10) understanding of models and modeling was assessed using tasks which explicitly refer to the scientific disciplines of biology, chemistry, and physics and, as a control, to no scientific discipline. The students' responses are interpreted as their biology-, chemistry-, and…

  6. Analysis of High School Physics, Chemistry and Biology Curriculums in Terms of Scientific Literacy Themes

    ERIC Educational Resources Information Center

    Erdogan, Melek Nur; Koseoglu, Fitnat

    2012-01-01

    The purpose of this study is to analyze 9th grade physics, chemistry and biology curriculums, which were implemented by the Ministry of Education since the academic year 2008-2009, in terms of scientific literacy themes and the balance of these themes and also to examine the quality of statements about objectives. Physics, chemistry, and biology…

  7. A Course in Biophysics: An Integration of Physics, Chemistry, and Biology

    ERIC Educational Resources Information Center

    Giancoli, Douglas C.

    1971-01-01

    Describes an interdisciplinary course for advanced undergraduates in the physical and biological sciences. The goal is to understand a living cell from the most basic standpoint possible. The ideas of physics, chemistry, and molecular biology are all essential to the course, which leads to a unified view of the sciences. (PR)

  8. Analyzing Students' Understanding of Models and Modeling Referring to the Disciplines Biology, Chemistry, and Physics

    NASA Astrophysics Data System (ADS)

    Krell, Moritz; Reinisch, Bianca; Krüger, Dirk

    2015-06-01

    In this study, secondary school students' ( N = 617; grades 7 to 10) understanding of models and modeling was assessed using tasks which explicitly refer to the scientific disciplines of biology, chemistry, and physics and, as a control, to no scientific discipline. The students' responses are interpreted as their biology-, chemistry-, and physics-related or general understanding of models and modeling. A subpopulation ( N = 115; one class per grade) was subsequently asked which models they had in mind when answering the tasks referring to biology, chemistry, and physics (open-ended questions). The findings show significant differences between students' biology-, chemistry-, and physics-related understandings of models and modeling. Based on a theoretical framework, the biology-related understanding can be seen as less elaborated than the physics- and chemistry-related understandings. The students' general understanding of models and modeling is located between the biology- and the physics-related understandings. Answers to the open-ended questions indicate that students primarily think about scale and functional models in the context of biology tasks. In contrast, more abstract models (e.g., analogical models, diagrams) were mentioned in relation to chemistry and physics tasks. In sum, the findings suggest that models may be used in a rather descriptive way in biology classes but in a predictive way in chemistry and physics classes. This may explain discipline-specific understandings of models and modeling. Only small differences were found in students' understanding of models and modeling between the different grade levels 7/8 and 9/10.

  9. Topological data analysis: A promising big data exploration tool in biology, analytical chemistry and physical chemistry.

    PubMed

    Offroy, Marc; Duponchel, Ludovic

    2016-03-03

    An important feature of experimental science is that data of various kinds is being produced at an unprecedented rate. This is mainly due to the development of new instrumental concepts and experimental methodologies. It is also clear that the nature of acquired data is significantly different. Indeed in every areas of science, data take the form of always bigger tables, where all but a few of the columns (i.e. variables) turn out to be irrelevant to the questions of interest, and further that we do not necessary know which coordinates are the interesting ones. Big data in our lab of biology, analytical chemistry or physical chemistry is a future that might be closer than any of us suppose. It is in this sense that new tools have to be developed in order to explore and valorize such data sets. Topological data analysis (TDA) is one of these. It was developed recently by topologists who discovered that topological concept could be useful for data analysis. The main objective of this paper is to answer the question why topology is well suited for the analysis of big data set in many areas and even more efficient than conventional data analysis methods. Raman analysis of single bacteria should be providing a good opportunity to demonstrate the potential of TDA for the exploration of various spectroscopic data sets considering different experimental conditions (with high noise level, with/without spectral preprocessing, with wavelength shift, with different spectral resolution, with missing data).

  10. Life as physics and chemistry: A system view of biology.

    PubMed

    Baverstock, Keith

    2013-04-01

    Cellular life can be viewed as one of many physical natural systems that extract free energy from their environments in the most efficient way, according to fundamental physical laws, and grow until limited by inherent physical constraints. Thus, it can be inferred that it is the efficiency of this process that natural selection acts upon. The consequent emphasis on metabolism, rather than replication, points to a metabolism-first origin of life with the adoption of DNA template replication as a second stage development. This order of events implies a cellular regulatory system that pre-dates the involvement of DNA and might, therefore, be based on the information acquired as peptides fold into proteins, rather than on genetic regulatory networks. Such an epigenetic cell regulatory model, the independent attractor model, has already been proposed to explain the phenomenon of radiation induced genomic instability. Here it is extended to provide an epigenetic basis for the morphological and functional diversity that evolution has yielded, based on natural selection of the most efficient free energy transduction. Empirical evidence which challenges the current genetic basis of cell and molecular biology and which supports the above proposal is discussed.

  11. Pre-Service Science Teachers' Pedagogical Content Knowledge in the Physics, Chemistry, and Biology Topics

    ERIC Educational Resources Information Center

    Bektas, Oktay

    2015-01-01

    This study investigated pre-service science teachers' pedagogical content knowledge in the physics, chemistry, and biology topics. These topics were the light and sound, the physical and chemical changes, and reproduction, growth, and evolution. Qualitative research design was utilized. Data were collected from 33 pre-service science teachers…

  12. Biology--Chemistry--Physics, Students' Guide, A Three-Year Sequence, Parts I and II.

    ERIC Educational Resources Information Center

    Scott, Arthur; And Others

    Parts I and II of the students' guide to the three-year integrated biology, chemistry, and physics course being prepared by the Portland Project Committee are contained in this guide. A committee reviewed and selected material developed by the national course improvement groups--Physical Science Study Committee, Chemical Bond Approach, Chemical…

  13. Biology-Chemistry-Physics, Teachers' Guide, a Three-Year Sequence, Parts I and II.

    ERIC Educational Resources Information Center

    Scott, Arthur; And Others

    This is one of two teacher's guides for a three-year integrated biology, chemistry, and physics course being prepared by the Portland Project Committee. This committee reviewed and selected material developed by the national course improvement groups--Physical Science Study Committee, Chemical Bond Approach, Chemical Education Materials Study,…

  14. S.E.A. Lab. Science Experiments and Activities. Marine Science for High School Students in Chemistry, Biology and Physics.

    ERIC Educational Resources Information Center

    Hart, Kathy, Ed.

    A series of science experiments and activities designed for secondary school students taking biology, chemistry, physics, physical science or marine science courses are outlined. Each of the three major sections--chemistry, biology, and physics--addresses concepts that are generally covered in those courses but incorporates aspects of marine…

  15. Physical Chemistry for the Chemical and Biological Sciences (by Raymond Chang)

    NASA Astrophysics Data System (ADS)

    Pounds, Andrew

    2001-05-01

    This book does offer an alternative approach to physical chemistry that is particularly well suited for those who want to pursue a course of study more focused on the biological sciences. It could also be an excellent choice for schools that mainly serve preprofessional programs or for schools that have split physical chemistry tracks to independently serve the B.S. and B.A. degrees. Since the book focuses on single-variable mathematics, schools that require only one year of calculus for their chemistry degree could also think about adopting it. However, in general, the use of the text as a drop-in replacement for physical chemistry for the B.S. degree is questionable owing to its lack of focus on quantum mechanics and its implications for spectroscopy.

  16. Density functional theory across chemistry, physics and biology.

    PubMed

    van Mourik, Tanja; Bühl, Michael; Gaigeot, Marie-Pierre

    2014-03-13

    The past decades have seen density functional theory (DFT) evolve from a rising star in computational quantum chemistry to one of its major players. This Theme Issue, which comes half a century after the publication of the Hohenberg-Kohn theorems that laid the foundations of modern DFT, reviews progress and challenges in present-day DFT research. Rather than trying to be comprehensive, this Theme Issue attempts to give a flavour of selected aspects of DFT.

  17. Essential concepts and underlying theories from physics, chemistry, and mathematics for "biochemistry and molecular biology" majors.

    PubMed

    Wright, Ann; Provost, Joseph; Roecklein-Canfield, Jennifer A; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry, and Mathematics that all Biochemistry or Molecular Biology majors must understand to complete their major coursework. The allied fields working group created a survey to validate foundational concepts from Physics, Chemistry, and Mathematics identified from participant feedback at various workshops. One-hundred twenty participants responded to the survey and 68% of the respondents answered yes to the question: "We have identified the following as the core concepts and underlying theories from Physics, Chemistry, and Mathematics that Biochemistry majors or Molecular Biology majors need to understand after they complete their major courses: 1) mechanical concepts from Physics, 2) energy and thermodynamic concepts from Physics, 3) critical concepts of structure from chemistry, 4) critical concepts of reactions from Chemistry, and 5) essential Mathematics. In your opinion, is the above list complete?" Respondents also delineated subcategories they felt should be included in these broad categories. From the results of the survey and this analysis the allied fields working group constructed a consensus list of allied fields concepts, which will help inform Biochemistry and Molecular Biology educators when considering the ASBMB recommended curriculum for Biochemistry or Molecular Biology majors and in the development of appropriate assessment tools to gauge student understanding of how these concepts relate to biochemistry and molecular biology.

  18. Using Metaphor Theory to Examine Conceptions of Energy in Biology, Chemistry, and Physics

    ERIC Educational Resources Information Center

    Lancor, Rachael

    2014-01-01

    Energy is one of the most important unifying themes in science. Yet the way energy is conceptualized varies depending on context. In this paper, the discourse used to explain the role of energy in systems from biology, chemistry, and physics is examined from the perspective of metaphor theory. Six substance metaphors for energy are identified in…

  19. Biology, Chemistry and Physics Teaching in Ohio: An Analysis of the 1982-1983 School Year.

    ERIC Educational Resources Information Center

    Walter, Franklin B.; And Others

    This study assessed the qualifications of biology, chemistry, and physics teachers, both from the perspective of their initial preparation and with regard to the type of certification they possessed. In particular, the Ohio Department of Education sought to determine what patterns of preparation must be followed at each of Ohio's teacher education…

  20. Essential Concepts and Underlying Theories from Physics, Chemistry, and Mathematics for "Biochemistry and Molecular Biology" Majors

    ERIC Educational Resources Information Center

    Wright, Ann; Provost, Joseph; Roecklein-Canfield, Jennifer A.; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry,…

  1. Job Satisfaction Levels of Secondary School Physics, Chemistry and Biology Teachers

    ERIC Educational Resources Information Center

    Maskan, A. Kadir

    2014-01-01

    The purpose of this study is to determine the job satisfaction levels of the teachers participating in the study and to investigate whether their job satisfaction levels differ with respect to certain variables. The participants of the study were 297 science teachers (physics: 104, chemistry: 105, biology: 87 and 1 N/A) from secondary schools in…

  2. Preservice Teachers' Epistemological Beliefs in Physics, Chemistry, and Biology: A Mixed Study

    ERIC Educational Resources Information Center

    Topcu, Mustafa Sami

    2013-01-01

    The purposes of the study were to assess preservice teachers' domain-specific epistemological beliefs and to investigate whether preservice teachers distinguish disciplinary differences (physics, chemistry, and biology) in domain-specific epistemological beliefs. Mixed-method research design guided the present research. The researcher explored…

  3. Accelerated Integrated Science Sequence (AISS): An Introductory Biology, Chemistry, and Physics Course

    ERIC Educational Resources Information Center

    Purvis-Roberts, Kathleen L.; Edwalds-Gilbert, Gretchen; Landsberg, Adam S.; Copp, Newton; Ulsh, Lisa; Drew, David E.

    2009-01-01

    A new interdisciplinary, introductory science course was offered for the first time during the 2007-2008 school year. The purpose of the course is to introduce students to the idea of working at the intersections of biology, chemistry, and physics and to recognize interconnections between the disciplines. Interdisciplinary laboratories are a key…

  4. Integrated Science as a Preparation for 'A' Level Physics, Chemistry and Biology.

    ERIC Educational Resources Information Center

    Chamberlain, Peter J.

    1985-01-01

    Compared performance in A-level science examinations of students who took an integrated science course (SCISP) with students who studied the separate subjects of physics, chemistry, and biology to 0-level standard. Results show no significant differences between the performance of the two groups. (JN)

  5. The relative role of "A" level chemistry, physics and biology in the medical course.

    PubMed

    Tomilson, R W; Clack, G B; Pettingale, K W; Anderson, J; Ryan, K C

    1977-03-01

    The performance of 209 students in the 2nd MBBS, first clinical year and final MBBS examinations has been compared retrospectively with their grades in chemistry, physics and biology at "A" level. The mean grade has also been determined for students from different social classes and secondary education. Significant differences in marks for biology were found between successful and not so successful students, especially in the pre-clinical part of the course. Significnat differences in marks and significant correlations were also found for physics but not to any great extent for chemistry. The relative role of these three basic sciences in the medical course is discussed. The suggestion is made that there is a need for a re-appraisal of the privleged position of chemistry and an unquestioned science requirement for entry to medical school.

  6. A Profile of Michigan Teachers of High School Biology, Chemistry, and Physics: 1980-1983.

    ERIC Educational Resources Information Center

    Hirsch, Christian R.

    1984-01-01

    Provides a profile of Michigan high school biology, chemistry, and physics teachers for the 1980-81, 1981-82, and 1982-83 school years, including highest degree(s), major(s), minor(s), sex, years of teaching experience, type of certificate, and assignment(s). Also examines possible trends in the staffing of high school science courses in Michigan.…

  7. The Use of Textbooks for Advanced-Level GCE Courses in Physics, Chemistry and Biology by Sixth-Form Students.

    ERIC Educational Resources Information Center

    Newton, D. P.

    1984-01-01

    A survey of sixth-form students to determine the level of A-level textbook use in physics, chemistry, and biology in English schools found that texts are used primarily after the lesson, at the student's discretion, and with great variations between students. Biology texts were used most, and physics texts used least. (MBR)

  8. Research Data in Core Journals in Biology, Chemistry, Mathematics, and Physics.

    PubMed

    Womack, Ryan P

    2015-01-01

    This study takes a stratified random sample of articles published in 2014 from the top 10 journals in the disciplines of biology, chemistry, mathematics, and physics, as ranked by impact factor. Sampled articles were examined for their reporting of original data or reuse of prior data, and were coded for whether the data was publicly shared or otherwise made available to readers. Other characteristics such as the sharing of software code used for analysis and use of data citation and DOIs for data were examined. The study finds that data sharing practices are still relatively rare in these disciplines' top journals, but that the disciplines have markedly different practices. Biology top journals share original data at the highest rate, and physics top journals share at the lowest rate. Overall, the study finds that within the top journals, only 13% of articles with original data published in 2014 make the data available to others.

  9. Research Data in Core Journals in Biology, Chemistry, Mathematics, and Physics

    PubMed Central

    Womack, Ryan P.

    2015-01-01

    This study takes a stratified random sample of articles published in 2014 from the top 10 journals in the disciplines of biology, chemistry, mathematics, and physics, as ranked by impact factor. Sampled articles were examined for their reporting of original data or reuse of prior data, and were coded for whether the data was publicly shared or otherwise made available to readers. Other characteristics such as the sharing of software code used for analysis and use of data citation and DOIs for data were examined. The study finds that data sharing practices are still relatively rare in these disciplines’ top journals, but that the disciplines have markedly different practices. Biology top journals share original data at the highest rate, and physics top journals share at the lowest rate. Overall, the study finds that within the top journals, only 13% of articles with original data published in 2014 make the data available to others. PMID:26636676

  10. Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry.

    PubMed

    Kalay, Ziya

    2011-08-01

    How small can a macroscopic object be made without losing its intended function? Obviously, the smallest possible size is determined by the size of an atom, but it is not so obvious how many atoms are required to assemble an object so small, and yet that performs the same function as its macroscopic counterpart. In this review, we are concerned with objects of intermediate nature, lying between the microscopic and the macroscopic world. In physics and chemistry literature, this regime in-between is often called mesoscopic, and is known to bear interesting and counterintuitive features. After a brief introduction to the concept of mesoscopic systems from the perspective of physics, we discuss the functional aspects of mesoscopic architectures in cell biology, and supramolecular chemistry through many examples from the literature. We argue that the biochemistry of the cell is largely regulated by mesoscopic functional architectures; however, the significance of mesoscopic phenomena seems to be quite underappreciated in biological sciences. With this motivation, one of our main purposes here is to emphasize the critical role that mesoscopic structures play in cell biology and biochemistry.

  11. Enhancing Student Success in Biology, Chemistry, and Physics by Transforming the Faculty Culture

    NASA Astrophysics Data System (ADS)

    Jackson, Howard; Smith, Leigh; Koenig, Kathleen; Beyette, Jill; Kinkle, Brian; Vonderheide, Anne

    We present preliminary results of an effort to enhance undergraduate student success in the STEM disciplines. We explore a multistep approach that reflects recent literature and report initial results by each of the Departments of Biology, Chemistry, and Physics of implementing several change strategies. The central elements of our approach involve identified departmental Teaching and Learning Liaisons, a unique faculty development component by our teaching center, a vertical integration of leadership across department heads, the Dean, and the Provost, and the explicit acknowledgement that change happens locally. Teaching and Learning lunches across the departments have attracted an attendance of ~65% of the faculty. The use of Learning Assistants in classrooms has also increased sharply. Modest changes in the student success rates have been observed. These efforts and others at the decanal and provostal levels promise changes in student success. We acknowledge the financial support of the National Science Foundation through DUE 1544001 and 1431350.

  12. Visual Representations on High School Biology, Chemistry, Earth Science, and Physics Assessments

    NASA Astrophysics Data System (ADS)

    LaDue, Nicole D.; Libarkin, Julie C.; Thomas, Stephen R.

    2015-12-01

    The pervasive use of visual representations in textbooks, curricula, and assessments underscores their importance in K-12 science education. For example, visual representations figure prominently in the recent publication of the Next Generation Science Standards (NGSS Lead States in Next generation science standards: for states, by states. Achieve, Inc. on behalf of the twenty-six states and partners that collaborated on the NGSS, 2013). Although assessments of the NGSS have yet to be developed, most students are currently evaluated on their ability to interpret science visuals. While numerous studies exist on particular visuals, it is unclear whether the same types of visuals are emphasized in all science disciplines. The present study is an evaluation of the similarities and differences of visuals used to assess students' knowledge of chemistry, earth science, living environment (biology), and physics on the New York State Regents examination. Analysis of 266 distinct visual representations categorized across the four content examinations reveals that the frequency and type of visuals vary greatly between disciplines. Diagrams, Graphs, Tables, and Maps are the most prevalent across all science disciplines. Maps, Cartograms, and Time Charts are unique to the Earth Science examination, and Network Diagrams are unique to the living environment (biology) examination. This study identifies which representations are most critical for training students across the science disciplines in anticipation of the implementation and eventual assessment of the NGSS.

  13. Success Factors in Curriculum Innovation: The Case of Mathematics, Physics, Chemistry and Biology in Secondary Education in the Netherlands.

    ERIC Educational Resources Information Center

    Vermeulen, Ard; And Others

    This paper reports on a theoretical and empirical study into curriculum innovation in secondary education in the Netherlands focusing on mathematics, physics, chemistry, and biology. Curriculum specialists, subject specialists, researchers, policy makers, and teachers were interviewed for the study. Results indicate that mathematics had the most…

  14. Practical Work in Biology, Chemistry and Physics at Lower Secondary and General Upper Secondary Schools in Slovenia

    ERIC Educational Resources Information Center

    Sorgo, Andrej; Spernjak, Andreja

    2012-01-01

    Syllabi in the science subjects, biology, chemistry and physics at lower and general upper secondary school are compared in the light of their underlying philosophies, goals, objectives and recognized importance in science teaching. Even though all syllabi were prepared within the same framework, great differences among syllabi concerning…

  15. The Clarinet Reed: AN Introduction to its Biology, Chemistry, and Physics

    NASA Astrophysics Data System (ADS)

    Casadonte, Donald Jay

    Although clarinet reeds have been used for over two-hundred years, there has been little scientific study of the reed, either from a material science or engineering perspective. This document is intended to be the first large-scale study of the clarinet reed covering its biology, chemistry and physics. The reed is made, most often, from cane--Arundo donax. We present a complete atlas of the anatomy of Arundo donax, and examine the role of each of the cellular components in the clarinet reed performance. We examine the three principal chemical components of the processed clarinet reed: cellulose, xylan, and lignin through the use of instrumental analysis. We examine the breakdown pathways of the clarinet reed, and isolate five: (1) decrystallization of the cellulose microstructure, (2) removal of xylan by saliva, (3) plasticization of the reed material due to alkalai attack in saliva, (4) the culturing of a bacterium, Staph Epidermitis, in the cell wall matrix, (5) density changes due to salival coating of the reed. The physics of the reed is examined, and a finite element model of the modal shapes is presented. We present a theoretical treatment of the two modes of excitation of the reed, a low frequency mode (normal playing mode) due to vortex shedding, and a high frequency mode which is associated with reed squeak.

  16. DNA as information: at the crossroads between biology, mathematics, physics and chemistry.

    PubMed

    Cartwright, Julyan H E; Giannerini, Simone; González, Diego L

    2016-03-13

    On the one hand, biology, chemistry and also physics tell us how the process of translating the genetic information into life could possibly work, but we are still very far from a complete understanding of this process. On the other hand, mathematics and statistics give us methods to describe such natural systems-or parts of them-within a theoretical framework. Also, they provide us with hints and predictions that can be tested at the experimental level. Furthermore, there are peculiar aspects of the management of genetic information that are intimately related to information theory and communication theory. This theme issue is aimed at fostering the discussion on the problem of genetic coding and information through the presentation of different innovative points of view. The aim of the editors is to stimulate discussions and scientific exchange that will lead to new research on why and how life can exist from the point of view of the coding and decoding of genetic information. The present introduction represents the point of view of the editors on the main aspects that could be the subject of future scientific debate.

  17. DNA as information: at the crossroads between biology, mathematics, physics and chemistry

    PubMed Central

    2016-01-01

    On the one hand, biology, chemistry and also physics tell us how the process of translating the genetic information into life could possibly work, but we are still very far from a complete understanding of this process. On the other hand, mathematics and statistics give us methods to describe such natural systems—or parts of them—within a theoretical framework. Also, they provide us with hints and predictions that can be tested at the experimental level. Furthermore, there are peculiar aspects of the management of genetic information that are intimately related to information theory and communication theory. This theme issue is aimed at fostering the discussion on the problem of genetic coding and information through the presentation of different innovative points of view. The aim of the editors is to stimulate discussions and scientific exchange that will lead to new research on why and how life can exist from the point of view of the coding and decoding of genetic information. The present introduction represents the point of view of the editors on the main aspects that could be the subject of future scientific debate. PMID:26857674

  18. How and why does the immunological synapse form? Physical chemistry meets cell biology.

    PubMed

    Chakraborty, Arup K

    2002-03-05

    During T lymphocyte (T cell) recognition of an antigen, a highly organized and specific pattern of membrane proteins forms in the junction between the T cell and the antigen-presenting cell (APC). This specialized cell-cell junction is called the immunological synapse. It is several micrometers large and forms over many minutes. A plethora of experiments are being performed to study the mechanisms that underlie synapse formation and the way in which information transfer occurs across the synapse. The wealth of experimental data that is beginning to emerge must be understood within a mechanistic framework if it is to prove useful in developing modalities to control the immune response. Quantitative models can complement experiments in the quest for such a mechanistic understanding by suggesting experimentally testable hypotheses. Here, a quantitative synapse assembly model is described. The model uses concepts developed in physical chemistry and cell biology and is able to predict the spatiotemporal evolution of cell shape and receptor protein patterns observed during synapse formation. Attention is directed to how the juxtaposition of model predictions and experimental data has led to intriguing hypotheses regarding the role of null and self peptides during synapse assembly, as well as correlations between T cell effector functions and the robustness of synapse assembly. We remark on some ways in which synergistic experiments and modeling studies can improve current models, and we take steps toward a better understanding of information transfer across the T cell-APC junction.

  19. The Quantitative and Qualitative Analysis of Cohorts' Early Enrollment in Physics: concurrent with enrollment in mathematics, biology and chemistry

    NASA Astrophysics Data System (ADS)

    Lynch, Robert Bruce Rodes

    Cohorts of 48 entering biological science majors was recruited in the fall of 2007 and again in 2008 and 2009 for the Interdisciplinary Science Experience (ISE). These ISE students enrolled in their own sections of standard courses of physics, chemistry, and biology. In these courses average ISE student out-performed their non-cohort peers by up to a full letter grade. A qualitative analysis of ISE student interviews illuminates the student experience and shows how the ISE students perceived themselves to be different than their non-cohort peers. Quantitative modeling of student performance shows that higher grades are correlated with multiple factors. These factors includes admissions characteristics such as high school GPA, and SAT scores, as well as demographic information. These trends support and elaborate on the selection narratives told by participants. Additionally the quantitative model found that higher student performance is predicted by structural aspects of the ISE program, specifically the timing of course, enrolling as a freshmen in many of their courses, and the sequencing of physics and chemistry courses. There is a statistically significant benefit to student performance in general and organic chemistry courses associated with completing the first quarter of the Physics for Bio-Science majors prior to enrollment. Further the combination of quantitative and qualitative data suggest that there is a epistemological transfer of problem solving skills and outlook from the physics to the chemistry courses.

  20. Towards the virtual artery: a multiscale model for vascular physiology at the physics-chemistry-biology interface.

    PubMed

    Hoekstra, Alfons G; Alowayyed, Saad; Lorenz, Eric; Melnikova, Natalia; Mountrakis, Lampros; van Rooij, Britt; Svitenkov, Andrew; Závodszky, Gábor; Zun, Pavel

    2016-11-13

    This discussion paper introduces the concept of the Virtual Artery as a multiscale model for arterial physiology and pathologies at the physics-chemistry-biology (PCB) interface. The cellular level is identified as the mesoscopic level, and we argue that by coupling cell-based models with other relevant models on the macro- and microscale, a versatile model of arterial health and disease can be composed. We review the necessary ingredients, both models of arteries at many different scales, as well as generic methods to compose multiscale models. Next, we discuss how this can be combined into the virtual artery. Finally, we argue that the concept of models at the PCB interface could or perhaps should become a powerful paradigm, not only as in our case for studying physiology, but also for many other systems that have such PCB interfaces.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

  1. Towards the virtual artery: a multiscale model for vascular physiology at the physics-chemistry-biology interface

    NASA Astrophysics Data System (ADS)

    Hoekstra, Alfons G.; Alowayyed, Saad; Lorenz, Eric; Melnikova, Natalia; Mountrakis, Lampros; van Rooij, Britt; Svitenkov, Andrew; Závodszky, Gábor; Zun, Pavel

    2016-11-01

    This discussion paper introduces the concept of the Virtual Artery as a multiscale model for arterial physiology and pathologies at the physics-chemistry-biology (PCB) interface. The cellular level is identified as the mesoscopic level, and we argue that by coupling cell-based models with other relevant models on the macro- and microscale, a versatile model of arterial health and disease can be composed. We review the necessary ingredients, both models of arteries at many different scales, as well as generic methods to compose multiscale models. Next, we discuss how this can be combined into the virtual artery. Finally, we argue that the concept of models at the PCB interface could or perhaps should become a powerful paradigm, not only as in our case for studying physiology, but also for many other systems that have such PCB interfaces. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

  2. FOREWORD: Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology and Mathematics

    NASA Astrophysics Data System (ADS)

    Kaski, K.; Salomaa, M.

    1990-01-01

    These are Proceedings of the Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology, and Mathematics, held August 25-26, 1989, at Lahti (Finland). The Symposium belongs to an annual series of Meetings, the first one of which was arranged in 1987 at Lund (Sweden) and the second one in 1988 at Kolle-Kolle near Copenhagen (Denmark). Although these Symposia have thus far been essentially Nordic events, their international character has increased significantly; the trend is vividly reflected through contributions in the present Topical Issue. The interdisciplinary nature of Computational Science is central to the activity; this fundamental aspect is also responsible, in an essential way, for its rapidly increasing impact. Crucially important to a wide spectrum of superficially disparate fields is the common need for extensive - and often quite demanding - computational modelling. For such theoretical models, no closed-form (analytical) solutions are available or they would be extremely difficult to find; hence one must rather resort to the Art of performing computational investigations. Among the unifying features in the computational research are the methods of simulation employed; methods which frequently are quite closely related with each other even for faculties of science that are quite unrelated. Computer simulation in Natural Sciences is presently apprehended as a discipline on its own right, occupying a broad region somewhere between the experimental and theoretical methods, but also partially overlapping with and complementing them. - Whichever its proper definition may be, the computational approach serves as a novel and an extremely versatile tool with which one can equally well perform "pure" experimental modelling and conduct "computational theory". Computational studies that have earlier been made possible only through supercomputers have opened unexpected, as well as exciting, novel frontiers equally in mathematics (e.g., fractals

  3. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012)

    NASA Astrophysics Data System (ADS)

    Foffi, G.; Pastore, A.; Piazza, F.; Temussi, P. A.

    2013-08-01

    held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding through an

  4. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

    PubMed

    Foffi, G; Pastore, A; Piazza, F; Temussi, P A

    2013-08-02

    conference held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding

  5. Development of a Core-Course for College Science Majors Combining Material from Introductory Courses in Biology, Chemistry, and Physics-Phase II. Final Report.

    ERIC Educational Resources Information Center

    Pickar, Arnold D.

    Reported is the second phase of the development of a two-year college core science course for science majors. Materials were combined from introductory college courses in biology, chemistry, and physics. A revised lecture and laboratory syllabus was prepared incorporating improvements suggested after a pilot study of the first year course.…

  6. Biological and physical forcing of carbonate chemistry in an upwelling filament off northwest Africa: Results from a Lagrangian study

    NASA Astrophysics Data System (ADS)

    Loucaides, Socratis; Tyrrell, Toby; Achterberg, Eric P.; Torres, Ricardo; Nightingale, Philip D.; Kitidis, Vassilis; Serret, Pablo; Woodward, Malcolm; Robinson, Carol

    2012-09-01

    The Mauritanian upwelling system is one of the most biologically productive regions of the world's oceans. Coastal upwelling transfers nutrients to the sun-lit surface ocean, thereby stimulating phytoplankton growth. Upwelling of deep waters also supplies dissolved inorganic carbon (DIC), high levels of which lead to low calcium carbonate saturation states in surface waters, with potentially adverse effects on marine calcifiers. In this study an upwelled filament off the coast of northwest Africa was followed using drifting buoys and sulphur hexafluoride to determine how the carbonate chemistry changed over time as a result of biological, physical and chemical processes. The initial pHtot in the mixed layer of the upwelled plume was 7.94 and the saturation states of calcite and aragonite were 3.4 and 2.2, respectively. As the plume moved offshore over a period of 9 days, biological uptake of DIC (37 μmol kg-1) reduced pCO2 concentrations from 540 to 410 μatm, thereby increasing pHtot to 8.05 and calcite and aragonite saturation states to 4.0 and 2.7 respectively. The increase (25 μmol kg-1) in total alkalinity over the 9 day study period can be accounted for solely by the combined effects of nitrate uptake and processes that alter salinity (i.e., evaporation and mixing with other water masses). We found no evidence of significant alkalinity accumulation as a result of exudation of organic bases by primary producers. The ongoing expansion of oxygen minimum zones through global warming will likely further reduce the CaCO3 saturation of upwelled waters, amplifying any adverse consequences of ocean acidification on the ecosystem of the Mauritanian upwelling system.

  7. EDITORIAL: Physical Biology

    NASA Astrophysics Data System (ADS)

    Roscoe, Jane

    2004-06-01

    Physical Biology is a new peer-reviewed publication from Institute of Physics Publishing. Launched in 2004, the journal will foster the integration of biology with the traditionally more quantitative fields of physics, chemistry, computer science and other math-based disciplines. Its primary aim is to further the understanding of biological systems at all levels of complexity, ranging from the role of structure and dynamics of a single molecule to cellular networks and organisms. The journal encourages the development of a new biology-driven physics based on the extraordinary and increasingly rich data arising in biology, and provides research directions for those involved in the creation of novel bio-engineered systems. Physical Biology will publish a stimulating combination of full length research articles, communications, perspectives, reviews and tutorials from a wide range of disciplines covering topics such as: Single-molecule studies and nanobiotechnology Molecular interactions and protein folding Charge transfer and photobiology Ion channels; structure, function and ion regulation Molecular motors and force generation Subcellular processes Biological networks and neural systems Modeling aspects of molecular and cell biology Cell-cell signaling and interaction Biological patterns and development Evolutionary processes Novel tools and methods in physical biology Experts in the areas encompassed by the journal's scope have been appointed to the Editorial Scientific Committee and the composition of the Committee will be updated regularly to reflect the developments in this new and exciting field. Physical Biology is free online to everyone in 2004; you are invited to take advantage of this offer by visiting the journal homepage at http://physbio.iop.org This special print edition of Physical Biology is a combination of issues 1 and 2 of this electronic-only journal and it brings together an impressive range of articles in the fields covered, including a popular

  8. Rapid Detection of Biological and Chemical Threat Agents Using Physical Chemistry, Active Detection, and Computational Analysis

    SciTech Connect

    Chung, Myung; Dong, Li; Fu, Rong; Liotta, Lance; Narayanan, Aarthi; Petricoin, Emanuel; Ross, Mark; Russo, Paul; Zhou, Weidong; Luchini, Alessandra; Manes, Nathan; Chertow, Jessica; Han, Suhua; Kidd, Jessica; Senina, Svetlana; Groves, Stephanie

    2007-01-01

    Basic technologies have been successfully developed within this project: rapid collection of aerosols and a rapid ultra-sensitive immunoassay technique. Water-soluble, humidity-resistant polyacrylamide nano-filters were shown to (1) capture aerosol particles as small as 20 nm, (2) work in humid air and (3) completely liberate their captured particles in an aqueous solution compatible with the immunoassay technique. The immunoassay technology developed within this project combines electrophoretic capture with magnetic bead detection. It allows detection of as few as 150-600 analyte molecules or viruses in only three minutes, something no other known method can duplicate. The technology can be used in a variety of applications where speed of analysis and/or extremely low detection limits are of great importance: in rapid analysis of donor blood for hepatitis, HIV and other blood-borne infections in emergency blood transfusions, in trace analysis of pollutants, or in search of biomarkers in biological fluids. Combined in a single device, the water-soluble filter and ultra-sensitive immunoassay technique may solve the problem of early warning type detection of aerosolized pathogens. These two technologies are protected with five patent applications and are ready for commercialization.

  9. Biological Chemistry of Hydrogen Selenide.

    PubMed

    Cupp-Sutton, Kellye A; Ashby, Michael T

    2016-11-22

    There are no two main-group elements that exhibit more similar physical and chemical properties than sulfur and selenium. Nonetheless, Nature has deemed both essential for life and has found a way to exploit the subtle unique properties of selenium to include it in biochemistry despite its congener sulfur being 10,000 times more abundant. Selenium is more easily oxidized and it is kinetically more labile, so all selenium compounds could be considered to be "Reactive Selenium Compounds" relative to their sulfur analogues. What is furthermore remarkable is that one of the most reactive forms of selenium, hydrogen selenide (HSe(-) at physiologic pH), is proposed to be the starting point for the biosynthesis of selenium-containing molecules. This review contrasts the chemical properties of sulfur and selenium and critically assesses the role of hydrogen selenide in biological chemistry.

  10. Biological Chemistry of Hydrogen Selenide

    PubMed Central

    Cupp-Sutton, Kellye A.; Ashby, Michael T.

    2016-01-01

    There are no two main-group elements that exhibit more similar physical and chemical properties than sulfur and selenium. Nonetheless, Nature has deemed both essential for life and has found a way to exploit the subtle unique properties of selenium to include it in biochemistry despite its congener sulfur being 10,000 times more abundant. Selenium is more easily oxidized and it is kinetically more labile, so all selenium compounds could be considered to be “Reactive Selenium Compounds” relative to their sulfur analogues. What is furthermore remarkable is that one of the most reactive forms of selenium, hydrogen selenide (HSe− at physiologic pH), is proposed to be the starting point for the biosynthesis of selenium-containing molecules. This review contrasts the chemical properties of sulfur and selenium and critically assesses the role of hydrogen selenide in biological chemistry. PMID:27879667

  11. PREFACE: Water Interfaces in Physics Chemistry and Biology: a multi-disciplinary approach

    NASA Astrophysics Data System (ADS)

    Bellissent-Funel, Marie-Claire; Dore, John

    2009-07-01

    This 5-day meeting, sponsored by the European Science Foundation (ESF) in partnership with the Fonds zur Förderung der wissenschaftlichen Forschung in Österreich (FWF) was organised by Marie-Claire Bellissent-Funel (Lab. Léon Brillouin (CEA-CNRS), CEA Saclay) and John Dore (School of Physical Sciences, University of Kent). It took place in the Universitatszcentrum (University of Innsbruck), in the ski resort of Obergurgl, Austria, from 8-13 December 2007. The main aim of the meeting was to bring together various groups working on the characteristics of water in a wide range of different conditions, particularly in relation to the difference in behaviour of bulk water and water in close proximity to an interface. Another focus was on the properties of 'solid water' and the free time during the afternoon provided a good opportunity for studying ice interfaces in a different context as the snow conditions were good for ski-ing! An outline of the programme is contained in the PDF file associated with this preface. There was a wide representation encompassing 30 countries and 130 scientists drawn from different science disciplines. Furthermore there was a good range of young scientists, who made an excellent contribution to the poster session. There were, of course, many animated discussions away from the conference room and the feedback forms showed that almost everyone (96%!) felt that they had enjoyed the sessions and had learned something new. There was support for a further conference on this theme in the future. Inevitably, many of the speakers presented information that was in preparation for publication elsewhere and therefore our compilation of some papers in this brief report is not fully representative of the range of topics discussed at the meeting. Further information on specific work reported at the meeting can be obtained by following the author list through the Web of Science or by contacting the authors directly. We report eight short papers from the

  12. Factors associated with computer and Internet technology implementation in biology, chemistry, and physics education in Turkish secondary schools

    NASA Astrophysics Data System (ADS)

    Ozer, Melike

    The main purposes of the research were to identify computer and Internet use by biology, chemistry and physics teachers in Turkish secondary schools and identify factors associated with computer and Internet technology. To this end, survey documents were sent by the Provincial Directorate of National Education to 250 selected schools' administrators for further distribution. Administrators were asked to complete the "Computer and Internet Use: School Survey," and to distribute the "Science Teacher Computer and Internet Use" surveys to the two teachers who teach science class. Surveys were then returned to the General Directorate of Educational Technologies. Research findings showed that computer and Internet use has not occurred effectively. Computers were first introduced to Turkish schools in 1984; unfortunately the current situation of computer and Internet use in science education is not at the projected earlier point in time. Considering the fact that science teachers' participation in technology-related professional development program is higher than other subject teachers, the use of computer and Internet technologies in Turkish secondary schools is still at its early stages. Lack of computer knowledge and not knowing how to integrate computers into education were the major factors reported. With regard to computer and Internet use, a regression model for Turkish schools, which includes access and knowledge, explains a large part of the variance in study results. There was a significant relationship between computer attitude (computer liking, usefulness, and confidence) and computer and Internet use. Although there was a significant negative relationship between Internet and computer uses and the attitudinal component, computer anxiety, it did not deter individuals from expressing a desire to engage in computer use in education.

  13. Combining supramolecular chemistry with biology.

    PubMed

    Uhlenheuer, Dana A; Petkau, Katja; Brunsveld, Luc

    2010-08-01

    Supramolecular chemistry has primarily found its inspiration in biological molecules, such as proteins and lipids, and their interactions. Currently the supramolecular assembly of designed compounds can be controlled to great extent. This provides the opportunity to combine these synthetic supramolecular elements with biomolecules for the study of biological phenomena. This tutorial review focuses on the possibilities of the marriage of synthetic supramolecular architectures and biological systems. It highlights that synthetic supramolecular elements are for example ideal platforms for the recognition and modulation of proteins and cells. The unique features of synthetic supramolecular systems with control over size, shape, valency, and interaction strength allow the generation of structures fitting the demands to approach the biological problems at hand. Supramolecular chemistry has come full circle, studying the biology and its molecules which initially inspired its conception.

  14. Rethinking Undergraduate Physical Chemistry Curricula

    ERIC Educational Resources Information Center

    Miller, Stephen R.

    2016-01-01

    A summary of fundamental changes made to the undergraduate physical chemistry curriculum in the Chemistry Department at Gustavus Adolphus College (beginning in the 2013-2014 academic year) is presented. The yearlong sequence now consists of an introductory semester covering both quantum mechanics and thermodynamics/kinetics, followed by a second…

  15. Physical chemistry and the environment

    SciTech Connect

    Dunning, T.H. Jr.; Garrett, B.C.; Kolb, C.E. Jr.; Shaw, R.W.; Choppin, G.R.; Wagner, A.F.

    1994-08-01

    From the ozone hole and the greenhouse effect to plastics recycling and hazardous waste disposal, society faces a number of issues, the solutions to which require an unprecedented understanding of the properties of molecules. We are coming to realize that the environment is a coupled set of chemical systems, its dynamics determining the welfare of the biosphere and of humans in particular. These chemical systems are governed by fundamental molecular interactions, and they present chemists with an unparalleled challenge. The application of current concepts of molecular behavior and of up-to-date experimental and computational techniques can provide us with insights into the environment that are needed to mitigate past damage, to anticipate the impact of current human activity, and to avoid future insults to the environment. Environmental chemistry encompasses a number of separate, yet interlocking, areas of research. In all of these areas progress is limited by an inadequate understanding of the underlying chemical processes involved. Participation of all chemical approaches -- experimental, theoretical and computational -- and of all disciplines of chemistry -- organic, inorganic, physical, analytical and biochemistry -- will be required to provide the necessary fundamental understanding. The Symposium on ``Physical Chemistry and the Environment`` was designed to bring the many exciting and challenging physical chemistry problems involved in environmental chemistry to the attention of a larger segment of the physical chemistry community.

  16. Collaborative Physical Chemistry Projects Involving Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Whisnant, David M.; Howe, Jerry J.; Lever, Lisa S.

    2000-02-01

    The physical chemistry classes from three colleges have collaborated on two computational chemistry projects using Quantum CAChe 3.0 and Gaussian 94W running on Pentium II PCs. Online communication by email and the World Wide Web was an important part of the collaboration. In the first project, students used molecular modeling to predict benzene derivatives that might be possible hair dyes. They used PM3 and ZINDO calculations to predict the electronic spectra of the molecules and tested the predicted spectra by comparing some with experimental measurements. They also did literature searches for real hair dyes and possible health effects. In the final phase of the project they proposed a synthetic pathway for one compound. In the second project the students were asked to predict which isomer of a small carbon cluster (C3, C4, or C5) was responsible for a series of IR lines observed in the spectrum of a carbon star. After preliminary PM3 calculations, they used ab initio calculations at the HF/6-31G(d) and MP2/6-31G(d) level to model the molecules and predict their vibrational frequencies and rotational constants. A comparison of the predictions with the experimental spectra suggested that the linear isomer of the C5 molecule was responsible for the lines.

  17. Physics and Biology Collaborate to Color the World

    ERIC Educational Resources Information Center

    Liu, Dennis W. C.

    2013-01-01

    To understand how life works, it is essential to understand physics and chemistry. Most biologists have a clear notion of where chemistry fits into their life sciences research and teaching. Although we are physical beings, physics does not always find a place in the biology curriculum. Physics informs and enlightens biology in myriad dimensions,…

  18. Life is physics and chemistry and communication.

    PubMed

    Witzany, Guenther

    2015-04-01

    Manfred Eigen extended Erwin Schroedinger's concept of "life is physics and chemistry" through the introduction of information theory and cybernetic systems theory into "life is physics and chemistry and information." Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language. However, the basics of scientific knowledge changed dramatically within the second half of the 20th century. Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life.

  19. Radiation applications of physical chemistry

    NASA Astrophysics Data System (ADS)

    Talrose, V. L.

    1991-05-01

    Many chemical energy problems have a physical chemistry nature connected with chemical kinetics and thermodynamics. In the USSR, the development in this field is associated with the name of N. N. Semenov, who was involved in a large number of fundamental and applied physical chemistry problems. The new Institute of Energy Problems of Chemical Physics of the USSR Academy of Sciences is dealing with some of them. An overview of the Institute's work on radiation applications is presented. Examples of the use of radiation in the power industry (e.g., in coal gasification), tire production, mechanical joints, metal powder production, and sterilization of pharmaceutical products are given. Methods and problems involved in these applications are discussed and the great potential for extensive utilization is demonstrated.

  20. Ideograms for Physics and Chemistry

    NASA Astrophysics Data System (ADS)

    García Risueño, Pablo; Syropoulos, Apostolos; Vergés, Natàlia

    2016-12-01

    Ideograms (symbols that represent a word or idea) have great communicative value. They refer to concepts in a simple manner, easing the understanding of related ideas. Moreover, ideograms can simplify the often cumbersome notation used in the fields of Physics and physical Chemistry. Nonetheless only a few ideograms- like and - have been defined to date. In this work we propose that the scientific community follows the example of Mathematics—as well as that of oriental languages—and bestows a more important role upon ideograms. To support this thesis we propose ideograms for essential concepts in Physics and Chemistry. They are designed to be intuitive, and their goal is to make equations easier to read and understand. Our symbols are included in a publicly available [InlineEquation not available: see fulltext.]package ( svrsymbols).

  1. Supplemental Instruction in Physical Chemistry I

    ERIC Educational Resources Information Center

    Toby, Ellen; Scott, Timothy P.; Migl, David; Kolodzeji, Elizabeth

    2016-01-01

    Physical chemistry I at Texas A&M University is an upper division course requiring mathematical and analytical skills. As such, this course poses a major problem for many Chemistry, Engineering, Biochemistry and Genetics majors. Comparisons between participants and non-participants in Supplemental Instruction for physical chemistry were made…

  2. Fundamental molecular physics and chemistry, part 1

    NASA Astrophysics Data System (ADS)

    Stehney, A. F.; Inokuti, M.

    1983-12-01

    Scientifically, the work of the program deals with aspects of the physics and chemistry of molecules related to their interactions with photons, electrons, and other external agents. These areas of study were chosen in view of our goals; that is to say, they were chosen so that the eventual outcome of the work meets some of the needs of the US Department of Energy (DOE) and of other government agencies that support the research. First, cross sections for electron and photon interactions with molecules were determined theoretically and experimently, because those cross sections are indispensable for detailed microscopic analyses of the earliest processes of radiation action on any molecular substance, including biological materials. Those analyses in turn provide a sound basis for radiology and radiation dosimetry. Second, the spectroscopy of certain molecules and of small clusters of molecules were studied because this topic is fundamental to the full understanding of atmospheric-pollutant chemistry.

  3. Quantum physics meets biology.

    PubMed

    Arndt, Markus; Juffmann, Thomas; Vedral, Vlatko

    2009-12-01

    Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the past decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world-view of quantum coherences, entanglement, and other nonclassical effects, has been heading toward systems of increasing complexity. The present perspective article shall serve as a "pedestrian guide" to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future "quantum biology," its current status, recent experimental progress, and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena.

  4. Are Biology and Chemistry Out of Order?

    ERIC Educational Resources Information Center

    Gaudin, Felix A.

    1984-01-01

    Discusses advantages and disadvantages of standard high school biology and chemistry course sequences. Relates these sequences to Piagetian developmental levels as well as to David Ausubel's cognitive theory. Suggests that the sequences be reexamined in light of issues considered. (JM)

  5. A Quantum Chemistry Concept Inventory for Physical Chemistry Classes

    ERIC Educational Resources Information Center

    Dick-Perez, Marilu; Luxford, Cynthia J.; Windus, Theresa L.; Holme, Thomas

    2016-01-01

    A 14-item, multiple-choice diagnostic assessment tool, the quantum chemistry concept inventory or QCCI, is presented. Items were developed based on published student misconceptions and content coverage and then piloted and used in advanced physical chemistry undergraduate courses. In addition to the instrument itself, data from both a pretest,…

  6. Quantum physics meets biology

    PubMed Central

    Arndt, Markus; Juffmann, Thomas; Vedral, Vlatko

    2009-01-01

    Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the past decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world-view of quantum coherences, entanglement, and other nonclassical effects, has been heading toward systems of increasing complexity. The present perspective article shall serve as a “pedestrian guide” to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future “quantum biology,” its current status, recent experimental progress, and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena. PMID:20234806

  7. Biological Physics Program at the University of Arizona

    NASA Astrophysics Data System (ADS)

    Visscher, Koen; Brown, Michael F.

    2011-10-01

    Biological Physics studies the physics of life processes by applying the quantitative physical sciences approach to outstanding problems in Biology while also feeding crucial insights back into Physics. The Biological Physics Program is a graduate program with a broad scope, involving Physics, Chemistry and Biochemistry, and Molecular and Cellular Biology faculty members. Graduate work in involves teamwork and collaboration that cuts across the traditional boundaries of academic departments and includes the areas of single molecule biophysics, molecular simulations, and membrane biophysics. The Biological Physics Program offers laboratory rotations and research opportunities in multiple departments and opportunities for research fellowships and awards.

  8. From Artificial Chemistries to Systems Biology

    NASA Astrophysics Data System (ADS)

    Kaleta, Christoph

    Artificial Chemistries abstract from real-world chemistries by reducing them to systems of interacting and reacting molecules. They have been used to study phenomena in a wide array of fields like social and ecological modelling, evolution or chemical computing. Artificial Chemistries are inherently difficult to study and, thus, methods have been proposed to analyze their complexity. This chapter outlines how the concept of chemical organization and software dedicated at their analysis can help to ease this task. The chemical organizations of a reaction network correspond to sets of molecules that can coexist over long periods of (simulation-) time. Thus, they can be used to study the full dynamic behavior a system can exhibit without the need to simulate it in every detail. Due to this appealing property, Chemical Organization Theory has been used in the study of a wide array of systems ranging from Artificial Chemistries to real-world chemistries and biological systems. Especially the analysis of biological systems motivated an integration of the tools dedicated to the study of chemical organizations into an application framework from Systems Biology. The benefit of this integration is that tools from Systems Biology can be used without much effort along with the tools for the computation of chemical organizations and vice versa. Thus, software for the analysis of chemical organizations seamlessly integrates into a framework covering almost any aspect of network design and analysis.

  9. Customized Laboratory Experience in Physical Chemistry

    ERIC Educational Resources Information Center

    Castle, Karen J.; Rink, Stephanie M.

    2010-01-01

    A new physical chemistry laboratory experience has been designed for upper-level undergraduate chemistry majors. Students customize the first 10 weeks of their laboratory experience by choosing their own set of experiments (from a manual of choices) and setting their own laboratory schedule. There are several topics presented in the accompanying…

  10. Physics and Its Interfaces with Medicinal Chemistry and Drug Design

    NASA Astrophysics Data System (ADS)

    Santos, Ricardo N.; Andricopulo, Adriano D.

    2013-08-01

    Medicinal chemistry is a multidisciplinary subject that integrates knowledge from a variety of fields of science, including, but not limited to, chemistry, biology, and physics. The area of drug design involves the cooperative work of scientists with a diverse range of backgrounds and technical skills, trying to tackle complex problems using an integration of approaches and methods. One important contribution to this field comes from physics through studies that attempt to identify and quantify the molecular interactions between small molecules (drugs) and biological targets (receptors), such as the forces that govern the interactions, the thermodynamics of the drug-receptor interactions, and so on. In this context, the interfaces of physics, medicinal chemistry, and drug design are of vital importance for the development of drugs that not only have the right chemistry but also the right intermolecular properties to interact at the macromolecular level, providing useful information about the principles and molecular mechanisms underlying the therapeutic action of drugs. This article highlights some of the most important connections between physics and medicinal chemistry in the design of new drugs.

  11. Integrating Computational Chemistry into the Physical Chemistry Curriculum

    ERIC Educational Resources Information Center

    Johnson, Lewis E.; Engel, Thomas

    2011-01-01

    Relatively few undergraduate physical chemistry programs integrate molecular modeling into their quantum mechanics curriculum owing to concerns about limited access to computational facilities, the cost of software, and concerns about increasing the course material. However, modeling exercises can be integrated into an undergraduate course at a…

  12. From biologically-inspired physics to physics-inspired biology From biologically-inspired physics to physics-inspired biology

    NASA Astrophysics Data System (ADS)

    Kornyshev, Alexei A.

    2010-10-01

    discovery was the 'chemistry' between an enthusiastic biologist (Watson) and physicist (Crick) that helped them to find common language, and as a result discover not only the structure but also the 'function' of DNA. Now we know that the machinery of DNA replication is very complex, promoted by motor proteins such as DNA helicase, polymerase, ligases etc, but the complementary principle of synthesis of two identical DNA molecules on the unwound complimentary single strands as templates remains the same as mentioned in the famous phrase ('It did not escape our attention') of the first Watson-Crick paper. Dogma 4: (Almost literally from a letter from Don Roy Forsdyke, Biochemistry Professor at Queens Ontario). 'Biologists will not read a paper with formulae. The biological literature is vast. Biologists have too many papers to read and too many experiments to make. They will leave aside any reading that looks difficult'. If this is true, and I think it is, we are in big trouble; this brings us to the next dogma. Dogma 5: (Catch 22) It is impossible to publish a serious theoretical paper in a biological journal. Physicists, particularly, theorists need derivations to prove the validity of their findings. But with the derivations in the script, the paper will be rejected. If you still publish it in a physical journal it will not be read by those to whom it is addressed. Dogma 6:Physicists are too ignorant to offer biologists anything useful. Perhaps, some new spectroscopic method or apparatus for force measurement, but that's about it. Leave biology to professionals. Full stop. I make no comments about this extreme point of view, referring the reader to the dispute between Parsegian and Austin, which is still quite relevant today. Next, a pearl of wisdom of a theoretical physicist, Nobel Laureate in Physiology and Medicine, Max Delbrück (Caltech), formulated in his 1949 lecture in Copenhagen, the principles on which organisms of today are based must have been determined by a

  13. Carbonate chemistry in the Mertz Polynya (East Antarctica): Biological and physical modification of dense water outflows and the export of anthropogenic CO2

    NASA Astrophysics Data System (ADS)

    Shadwick, E. H.; Tilbrook, B.; Williams, G. D.

    2014-01-01

    Dense shelf water (DSW) is formed in East Antarctica from enhanced sea-ice production driven by air-sea interaction in coastal polynyas. Cross-shelf export and downslope mixing of this DSW produces Antarctic Bottom Water, contributing to the lower limb of the global overturning circulation. We present biogeochemical observations from the Mertz Polynya region in summer 2007/2008, with additional observations from spring 2001 and winter 1996. The seasonal changes in mixed-layer carbonate chemistry are driven by a combination of air-sea CO2 exchange, biological activity and the formation and melt of sea-ice. The air-sea fluxes in 2008 were ˜15 mmol C m-2 d-1, and net community production, estimated from the summertime surface dissolved inorganic carbon (DIC) deficit, ranged from 0.9 to 1.2 mol C m-2 yr-1. We show that biological modification of carbonate chemistry over the shelf in summer preconditions the DSW outflows from the Adélie Depression. This process appears to supply both organic material, and water depleted in CO2, and with enhanced carbonate saturation state (relative to inflowing water), to coral communities on the slope. We combined model-based transports of exported DSW with the natural and anthropogenic (Cant) carbon concentrations and estimate that the annual outflows of DIC and Cant from the Mertz Polynya range from 320 to 560 Tg C yr-1, and from 3 to 6 Tg Cant yr-1, respectively. The formation and export of dense water from this region, and by extension all similar polynyas around Antarctica, is an effective mechanism for the transfer of anthropogenic carbon into the deep ocean.

  14. Enhancing Interdisciplinary, Mathematics, and Physical Science in an Undergraduate Life Science Program through Physical Chemistry

    PubMed Central

    2009-01-01

    BIO2010 advocates enhancing the interdisciplinary, mathematics, and physical science components of the undergraduate biology curriculum. The Department of Chemistry and Life Science at West Point responded by developing a required physical chemistry course tailored to the interests of life science majors. To overcome student resistance to physical chemistry, students were enabled as long-term stakeholders who would shape the syllabus by selecting life science topics of interest to them. The initial 2 yr of assessment indicates that students have a positive view of the course, feel they have succeeded in achieving course outcome goals, and that the course is relevant to their professional future. Instructor assessment of student outcome goal achievement via performance on exams and labs is comparable to that of students in traditional physical chemistry courses. Perhaps more noteworthy, both student and instructor assessment indicate positive trends from year 1 to year 2, presumably due to the student stakeholder effect. PMID:19255133

  15. The biological inorganic chemistry of zinc ions.

    PubMed

    Krężel, Artur; Maret, Wolfgang

    2016-12-01

    The solution and complexation chemistry of zinc ions is the basis for zinc biology. In living organisms, zinc is redox-inert and has only one valence state: Zn(II). Its coordination environment in proteins is limited by oxygen, nitrogen, and sulfur donors from the side chains of a few amino acids. In an estimated 10% of all human proteins, zinc has a catalytic or structural function and remains bound during the lifetime of the protein. However, in other proteins zinc ions bind reversibly with dissociation and association rates commensurate with the requirements in regulation, transport, transfer, sensing, signalling, and storage. In contrast to the extensive knowledge about zinc proteins, the coordination chemistry of the "mobile" zinc ions in these processes, i.e. when not bound to proteins, is virtually unexplored and the mechanisms of ligand exchange are poorly understood. Knowledge of the biological inorganic chemistry of zinc ions is essential for understanding its cellular biology and for designing complexes that deliver zinc to proteins and chelating agents that remove zinc from proteins, for detecting zinc ion species by qualitative and quantitative analysis, and for proper planning and execution of experiments involving zinc ions and nanoparticles such as zinc oxide (ZnO). In most investigations, reference is made to zinc or Zn(2+) without full appreciation of how biological zinc ions are buffered and how the d-block cation Zn(2+) differs from s-block cations such as Ca(2+) with regard to significantly higher affinity for ligands, preference for the donor atoms of ligands, and coordination dynamics. Zinc needs to be tightly controlled. The interaction with low molecular weight ligands such as water and inorganic and organic anions is highly relevant to its biology but in contrast to its coordination in proteins has not been discussed in the biochemical literature. From the discussion in this article, it is becoming evident that zinc ion speciation is

  16. The Spontaneous Development of Biology from Chemistry

    NASA Astrophysics Data System (ADS)

    Lauterbur, Paul C.

    2008-02-01

    Biology arose as a spontaneous development from the chemistry of the early Earth by Free Energydriven processes that occurred in common environments involving significant populations of systems. Molecular imprinting to matrices is capable of catalysis of polymer formation and reproduction that, in association with self-assembled membranes, could lead to proto-enzymes, proto-ribosomes, and proto-cells. Proto-cells would evolve via processes analogous to Darwinian natural selection. These hypotheses are testable by controlled laboratory experiments. What we call life is the sum of properties of such highly evolved systems.

  17. Gated supramolecular chemistry in hybrid mesoporous silica nanoarchitectures: controlled delivery and molecular transport in response to chemical, physical and biological stimuli.

    PubMed

    Alberti, Sebastián; Soler-Illia, Galo J A A; Azzaroni, Omar

    2015-04-11

    This review presents and discusses recent advances in the emerging field of "gated nanochemistry", outlining the substantial progress made so far. The development of hybrid mesoporous silica with complex tailored pore nanoarchitectures bridges the gap between molecular materials and the requirements of nanodevices for controlled nanoscale chemistry. In the last decade, membranes, particles and thin film porous architectures have been designed, synthesized and selectively modified by molecular, polymeric, organometallic or biologically active groups. The exquisite manipulation of mesopore morphology and interconnection combined with molecular or supramolecular functionalities, and the intrinsic biological compatibility of silica have made these materials a potential platform for selective sensing and drug delivery. The wide répertoire of these hard-soft architectures permit us to envisage sophisticated intelligent nano-systems that respond to a variety of external stimuli such as pH, redox potential, molecule concentration, temperature, or light. Transduction of these stimuli into a predefined response implies exploiting spatial and physico-chemical effects such as charge distribution, steric constraints, equilibria displacements, or local changes in ionic concentration, just to name a few examples. As expected, this "positional mesochemistry" can be only attained through the concerted control of assembly, surface tailoring and, confinement conditions, thus giving birth to a new class of stimuli-responsive materials with modulable transport properties. As a guiding framework the emerging field of "gated nanochemistry" offers methodologies and tools for building up stimuli-sensitive porous architectures equipped with switchable entities whose transport properties can be triggered at will. The gated nanoscopic hybrid materials discussed here not only herald a new era in the integrative design of "smart" drug delivery systems, but also give the reader a perspective of

  18. Surfactant Adsorption: A Revised Physical Chemistry Lab

    ERIC Educational Resources Information Center

    Bresler, Marc R.; Hagen, John P.

    2008-01-01

    Many physical chemistry lab courses include an experiment in which students measure surface tension as a function of surfactant concentration. In the traditional experiment, the data are fit to the Gibbs isotherm to determine the molar area for the surfactant, and the critical micelle concentration is used to calculate the Gibbs energy of micelle…

  19. Playing with Liquid Foams: Learning Physical Chemistry

    ERIC Educational Resources Information Center

    Ritacco, Hernan

    2008-01-01

    Who has never played with soap bubbles? They are so beautiful and amazing, they have a perfect spherical shape and surprising tints. Foams are structures of bubbles of an incredible complexity and they are a perfect system to stimulate students' interest in the chemistry and physics of surface phenomena. In this article I propose a simple…

  20. Solar Energy Project, Activities: Chemistry & Physics.

    ERIC Educational Resources Information Center

    Tullock, Bruce, Ed.; And Others

    This guide contains lesson plans and outlines of science activities which present concepts of solar energy in the context of chemistry and physics experiments. Each unit presents an introduction to the unit; objectives; required skills and knowledge; materials; method; questions; recommendations for further work; and a teacher information sheet.…

  1. PHYSICS AND CHEMISTRY FOR THE AUTOMOTIVE TRADES.

    ERIC Educational Resources Information Center

    WORTHING, ROBERT

    DESIGNED FOR STUDENT USE, THIS MANUAL PRESENTS RELATED INFORMATION AND LABORATORY EXPERIMENTS FOR A 1-YEAR COURSE IN APPLIED PHYSICS AND CHEMISTRY. IT WAS DEVELOPED BY ESSEX COUNTY AUTOMOTIVE TEACHERS. CONTENT HEADINGS ARE -- (1) MATTER AND ITS PROPERTIES (15 EXPERIMENTS), (2) MECHANICS (4 EXPERIMENTS), (3) HEAT (3 EXPERIMENTS), (4) ELECTRICITY (8…

  2. Dilution physics modeling: Dissolution/precipitation chemistry

    SciTech Connect

    Onishi, Y.; Reid, H.C.; Trent, D.S.

    1995-09-01

    This report documents progress made to date on integrating dilution/precipitation chemistry and new physical models into the TEMPEST thermal-hydraulics computer code. Implementation of dissolution/precipitation chemistry models is necessary for predicting nonhomogeneous, time-dependent, physical/chemical behavior of tank wastes with and without a variety of possible engineered remediation and mitigation activities. Such behavior includes chemical reactions, gas retention, solids resuspension, solids dissolution and generation, solids settling/rising, and convective motion of physical and chemical species. Thus this model development is important from the standpoint of predicting the consequences of various engineered activities, such as mitigation by dilution, retrieval, or pretreatment, that can affect safe operations. The integration of a dissolution/precipitation chemistry module allows the various phase species concentrations to enter into the physical calculations that affect the TEMPEST hydrodynamic flow calculations. The yield strength model of non-Newtonian sludge correlates yield to a power function of solids concentration. Likewise, shear stress is concentration-dependent, and the dissolution/precipitation chemistry calculations develop the species concentration evolution that produces fluid flow resistance changes. Dilution of waste with pure water, molar concentrations of sodium hydroxide, and other chemical streams can be analyzed for the reactive species changes and hydrodynamic flow characteristics.

  3. Integrative Biological Chemistry Program Includes the Use of Informatics Tools, GIS and SAS Software Applications

    ERIC Educational Resources Information Center

    D'Souza, Malcolm J.; Kashmar, Richard J.; Hurst, Kent; Fiedler, Frank; Gross, Catherine E.; Deol, Jasbir K.; Wilson, Alora

    2015-01-01

    Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning…

  4. Cultivating the Physical Biology Mindset

    NASA Astrophysics Data System (ADS)

    Phillips, Rob

    2014-03-01

    Biological experiments now regularly result in data that emphasize functional relationships between key parameters such as level of gene expression and number of transcription factors or motor velocity and applied force. This trend towards quantitative dissection of biological problems has been acknowledged explicitly in learned reports such as ``Bio2010'' and the recent NAS report ``A New Biology for the 21st Century.'' These reports repeatedly emphasize the need for a new biology characterized by what one might call ``biological numeracy'' and for overhauling biological education in a way that is consistent with this kind of biological research. In this talk, I will describe my own experience in introducing courses aimed at introducing physical biology both in the lecture hall and in the laboratory. One of the most interesting aspects of the physics-biology interface is the question of what constitutes understanding and here, I will describe my views on the role of polarizing predictions as a test of such understanding with special emphasis on examples from signaling and regulation.

  5. Exploration of fluorine chemistry at the multidisciplinary interface of chemistry and biology.

    PubMed

    Ojima, Iwao

    2013-07-05

    Over the last three decades, my engagement in "fluorine chemistry" has evolved substantially because of the multidisciplinary nature of the research programs. I began my research career as a synthetic chemist in organometallic chemistry and homogeneous catalysis directed toward organic synthesis. Then, I was brought into a very unique world of "fluorine chemistry" in the end of 1970s. I started exploring the interface of fluorine chemistry and transition metal homogeneous catalysis first, which was followed by amino acids, peptides, and peptidomimetics for medicinal chemistry. Since then, I have been exploring the interfaces of fluorine chemistry and multidisciplinary fields of research involving medicinal chemistry, chemical biology, cancer biology, and molecular imaging. This perspective intends to cover my fruitful endeavor in the exploration of fluorine chemistry at the multidisciplinary interface of chemistry and biology in a chronological order to show the evolution of my research interest and strategy.

  6. Amanita muscaria: chemistry, biology, toxicology, and ethnomycology.

    PubMed

    Michelot, Didier; Melendez-Howell, Leda Maria

    2003-02-01

    The fly agaric is a remarkable mushroom in many respects; these are its bearing, history, chemical components and the poisoning that it provokes when consumed. The 'pantherina' poisoning syndrome is characterized by central nervous system dysfunction. The main species responsible are Amanita muscaria and A. pantherina (Amanitaceae); however, some other species of the genus have been suspected for similar actions. Ibotenic acid and muscimol are the active components, and probably, some other substances detected in the latter species participate in the psychotropic effects. The use of the mushroom started in ancient times and is connected with mysticism. Current knowledge on the chemistry, toxicology, and biology relating to this mushroom is reviewed, together with distinctive features concerning this unique species.

  7. Unifying Quantum Physics with Biology

    NASA Astrophysics Data System (ADS)

    Goradia, Shantilal

    2014-09-01

    We find that the natural logarithm of the age of the universe in quantum mechanical units is close to 137. Since science is not religion, it is our moral duty to recognize the importance of this finding on the following ground. The experimentally obtained number 137 is a mystical number in science, as if written by the hand of God. It is found in cosmology; unlike other theories, it works in biology too. A formula by Boltzmann also works in both: biology and physics, as if it is in the heart of God. His formula simply leads to finding the logarithm of microstates. One of the two conflicting theories of physics (1) Einstein's theory of General Relativity and (2) Quantum Physics, the first applies only in cosmology, but the second applies in biology too. Since we have to convert the age of the universe, 13 billion years, into 1,300,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 Planck times to get close to 137, quantum physics clearly shows the characteristics of unifying with biology. The proof of its validity also lies in its ability to extend information system observed in biology.

  8. Physical Chemistry in Practice: Evaluation of DVD Modules

    ERIC Educational Resources Information Center

    Dyer, James U.; Towns, Marcy; Weaver, Gabriela C.

    2007-01-01

    The Physical Chemistry in Practice (PCIP) DVD contains video programs (modules) and experimental data that present the research of scientists working in applications of physical chemistry. The DVD allows students to learn about cutting edge research in physical chemistry while making connections to the theoretical concepts learned in lecture.…

  9. Physical organic chemistry of supramolecular polymers.

    PubMed

    Serpe, Michael J; Craig, Stephen L

    2007-02-13

    Unlike the case of traditional covalent polymers, the entanglements that determine properties of supramolecular polymers are defined by very specific, intermolecular interactions. Recent work using modular molecular platforms to probe the mechanisms underlying mechanical response of supramolecular polymers is reviewed. The contributions of supramolecular kinetics, thermodynamics, and conformational flexibility to supramolecular polymer properties in solutions of discrete polymers, in networks, and at interfaces, are described. Molecule-to-material relationships are established through methods reminiscent of classic physical organic chemistry.

  10. Ultrafast electron microscopy in materials science, biology, and chemistry

    SciTech Connect

    King, Wayne E.; Campbell, Geoffrey H.; Frank, Alan; Reed, Bryan; Schmerge, John F.; Siwick, Bradley J.; Stuart, Brent C.; Weber, Peter M.

    2005-06-01

    The use of pump-probe experiments to study complex transient events has been an area of significant interest in materials science, biology, and chemistry. While the emphasis has been on laser pump with laser probe and laser pump with x-ray probe experiments, there is a significant and growing interest in using electrons as probes. Early experiments used electrons for gas-phase diffraction of photostimulated chemical reactions. More recently, scientists are beginning to explore phenomena in the solid state such as phase transformations, twinning, solid-state chemical reactions, radiation damage, and shock propagation. This review focuses on the emerging area of ultrafast electron microscopy (UEM), which comprises ultrafast electron diffraction (UED) and dynamic transmission electron microscopy (DTEM). The topics that are treated include the following: (1) The physics of electrons as an ultrafast probe. This encompasses the propagation dynamics of the electrons (space-charge effect, Child's law, Boersch effect) and extends to relativistic effects. (2) The anatomy of UED and DTEM instruments. This includes discussions of the photoactivated electron gun (also known as photogun or photoelectron gun) at conventional energies (60-200 keV) and extends to MeV beams generated by rf guns. Another critical aspect of the systems is the electron detector. Charge-coupled device cameras and microchannel-plate-based cameras are compared and contrasted. The effect of various physical phenomena on detective quantum efficiency is discussed. (3) Practical aspects of operation. This includes determination of time zero, measurement of pulse-length, and strategies for pulse compression. (4) Current and potential applications in materials science, biology, and chemistry. UEM has the potential to make a significant impact in future science and technology. Understanding of reaction pathways of complex transient phenomena in materials science, biology, and chemistry will provide fundamental

  11. The Physics of Marine Biology.

    ERIC Educational Resources Information Center

    Conn, Kathleen

    1992-01-01

    Discusses ways in which marine biology can be integrated into the physics classroom. Topics suggested for incorporation include the harmonic motion of ocean waves, ocean currents, the interaction of visible light with ocean water, pressure, light absorption, and sound transfer in water. (MDH)

  12. Integrated Chemistry and Biology for First-Year College Students

    ERIC Educational Resources Information Center

    Abdella, Beth R. J.; Walczak, Mary M.; Kandl, Kim A.; Schwinefus, Jeffrey J.

    2011-01-01

    A three-course sequence for first-year students that integrates beginning concepts in biology and chemistry has been designed. The first two courses that emphasize chemistry and its capacity to inform biological applications are described here. The content of the first course moves from small to large particles with an emphasis on membrane…

  13. Oscillatory multiphase flow strategy for chemistry and biology.

    PubMed

    Abolhasani, Milad; Jensen, Klavs F

    2016-07-19

    Continuous multiphase flow strategies are commonly employed for high-throughput parameter screening of physical, chemical, and biological processes as well as continuous preparation of a wide range of fine chemicals and micro/nano particles with processing times up to 10 min. The inter-dependency of mixing and residence times, and their direct correlation with reactor length have limited the adaptation of multiphase flow strategies for studies of processes with relatively long processing times (0.5-24 h). In this frontier article, we describe an oscillatory multiphase flow strategy to decouple mixing and residence times and enable investigation of longer timescale experiments than typically feasible with conventional continuous multiphase flow approaches. We review current oscillatory multiphase flow technologies, provide an overview of the advancements of this relatively new strategy in chemistry and biology, and close with a perspective on future opportunities.

  14. Exploration of Fluorine Chemistry at the Multidisciplinary Interface of Chemistry and Biology

    PubMed Central

    Ojima, Iwao

    2013-01-01

    Over the last three decades, my engagement in “fluorine chemistry” has evolved substantially, because of the multidisciplinary nature of the research programs. I began my research career as a synthetic chemist in organometallic chemistry and homogeneous catalysis directed toward organic synthesis. Then, I was brought into a very unique world of “fluorine chemistry” in the end of 1970s. I started exploring the interface of fluorine chemistry and transition metal homogeneous catalysis first, which was followed by amino acids, peptides, and peptidomimetics for medicinal chemistry. Since then, I have been exploring the interfaces of fluorine chemistry and multidisciplinary fields of research involving medicinal chemistry, chemical biology, cancer biology and molecular imaging. This perspective intends to cover my fruitful endeavor in the exploration of fluorine chemistry at the multidisciplinary interface of chemistry and biology in a chronological order to show the evolution of my research interest and strategy. PMID:23614876

  15. MIANN models in medicinal, physical and organic chemistry.

    PubMed

    González-Díaz, Humberto; Arrasate, Sonia; Sotomayor, Nuria; Lete, Esther; Munteanu, Cristian R; Pazos, Alejandro; Besada-Porto, Lina; Ruso, Juan M

    2013-01-01

    Reducing costs in terms of time, animal sacrifice, and material resources with computational methods has become a promising goal in Medicinal, Biological, Physical and Organic Chemistry. There are many computational techniques that can be used in this sense. In any case, almost all these methods focus on few fundamental aspects including: type (1) methods to quantify the molecular structure, type (2) methods to link the structure with the biological activity, and others. In particular, MARCH-INSIDE (MI), acronym for Markov Chain Invariants for Networks Simulation and Design, is a well-known method for QSAR analysis useful in step (1). In addition, the bio-inspired Artificial-Intelligence (AI) algorithms called Artificial Neural Networks (ANNs) are among the most powerful type (2) methods. We can combine MI with ANNs in order to seek QSAR models, a strategy which is called herein MIANN (MI & ANN models). One of the first applications of the MIANN strategy was in the development of new QSAR models for drug discovery. MIANN strategy has been expanded to the QSAR study of proteins, protein-drug interactions, and protein-protein interaction networks. In this paper, we review for the first time many interesting aspects of the MIANN strategy including theoretical basis, implementation in web servers, and examples of applications in Medicinal and Biological chemistry. We also report new applications of the MIANN strategy in Medicinal chemistry and the first examples in Physical and Organic Chemistry, as well. In so doing, we developed new MIANN models for several self-assembly physicochemical properties of surfactants and large reaction networks in organic synthesis. In some of the new examples we also present experimental results which were not published up to date.

  16. Communities of Molecules: A Physical Chemistry Module. Teacher's Guide.

    ERIC Educational Resources Information Center

    DeVoe, Howard; Hearle, Robert

    This teacher's guide is designed to provide science teachers with the necessary guidance and suggestions for teaching physical chemistry. The material in this book can be integrated with the other modules in a sequence that helps students see that chemistry is a unified science. Contents include: (1) "Introduction of Physical Chemistry"; (2) "The…

  17. Academic excellence workshops in chemistry and physics

    NASA Astrophysics Data System (ADS)

    Mills, Susan Rose

    In the mid-1970's, Uri Treisman, at the University of California, Berkeley, developed an academic excellence workshop program that had important successes in increasing minority student achievement and persistence in calculus. The present dissertation research is an in-depth study of chemistry and physics workshops at the California State Polytechnic University, Pomona. Data for the first, longitudinal component of this study were obtained by tracking to Spring 1998 all workshop minority students, i.e., Latino, African American, and Native American workshop students, a random sample of non-workshop minority students, and a random sample of non-targeted students, i.e., Anglo and Asian students, enrolled in first-quarter General Chemistry or Physics during specific quarters of 1992 or 1993. Data for the second component were obtained by administering questionnaires, conducting interviews, and observing science students during Fall, 1996. Workshop participation was a significant predictor of first-quarter course grade for minority students in both chemistry and physics, while verbal and mathematics Scholastic Aptitude Test (SAT) scores were not significant predictors of beginning course grade for minority science students. The lack of predictive ability of the SAT and the importance of workshop participation in minority students' beginning science course performance are results with important implications for educators and students. In comparing pre-college achievement measures for workshop and non-targeted students, non-targeted students' mathematics SAT scores were significantly higher than chemistry and physics workshop students' scores. Nonetheless, workshop participation "leveled the field" as workshop and non-targeted students performed similarly in beginning science courses. Positive impacts of workshop participation on achievement, persistence, efficiency, social integration, and self-confidence support the continued and expanded funding of workshop programs

  18. Biological evolution and statistical physics

    NASA Astrophysics Data System (ADS)

    Drossel, Barbara

    2001-03-01

    This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the majority of publications have appeared in biology journals. The review has three parts, which can be read independently. The first part deals with evolution in fitness landscapes and includes Fisher's theorem, adaptive walks, quasispecies models, effects of finite population sizes, and neutral evolution. The second part studies models of coevolution, including evolutionary game theory, kin selection, group selection, sexual selection, speciation, and coevolution of hosts and parasites. The third part discusses models for networks of interacting species and their extinction avalanches. Throughout the review, attention is paid to giving the necessary biological information, and to pointing out the assumptions underlying the models, and their limits of validity.

  19. Physical and biological controls on the carbonate chemistry of coral reef waters: effects of metabolism, wave forcing, sea level, and geomorphology.

    PubMed

    Falter, James L; Lowe, Ryan J; Zhang, Zhenlin; McCulloch, Malcolm

    2013-01-01

    We present a three-dimensional hydrodynamic-biogeochemical model of a wave-driven coral-reef lagoon system using the circulation model ROMS (Regional Ocean Modeling System) coupled with the wave transformation model SWAN (Simulating WAves Nearshore). Simulations were used to explore the sensitivity of water column carbonate chemistry across the reef system to variations in benthic reef metabolism, wave forcing, sea level, and system geomorphology. Our results show that changes in reef-water carbonate chemistry depend primarily on the ratio of benthic metabolism to the square root of the onshore wave energy flux as well as on the length and depth of the reef flat; however, they are only weakly dependent on channel geometry and the total frictional resistance of the reef system. Diurnal variations in pCO(2), pH, and aragonite saturation state (Ω(ar)) are primarily dependent on changes in net production and are relatively insensitive to changes in net calcification; however, net changes in pCO(2), pH, and Ω(ar) are more strongly influenced by net calcification when averaged over 24 hours. We also demonstrate that a relatively simple one-dimensional analytical model can provide a good description of the functional dependence of reef-water carbonate chemistry on benthic metabolism, wave forcing, sea level, reef flat morphology, and total system frictional resistance. Importantly, our results indicate that any long-term (weeks to months) net offsets in reef-water pCO(2) relative to offshore values should be modest for reef systems with narrow and/or deep lagoons. Thus, the long-term evolution of water column pCO(2) in many reef environments remains intimately connected to the regional-scale oceanography of offshore waters and hence directly influenced by rapid anthropogenically driven increases in pCO(2).

  20. Physical and Biological Controls on the Carbonate Chemistry of Coral Reef Waters: Effects of Metabolism, Wave Forcing, Sea Level, and Geomorphology

    PubMed Central

    Falter, James L.; Lowe, Ryan J.; Zhang, Zhenlin; McCulloch, Malcolm

    2013-01-01

    We present a three-dimensional hydrodynamic-biogeochemical model of a wave-driven coral-reef lagoon system using the circulation model ROMS (Regional Ocean Modeling System) coupled with the wave transformation model SWAN (Simulating WAves Nearshore). Simulations were used to explore the sensitivity of water column carbonate chemistry across the reef system to variations in benthic reef metabolism, wave forcing, sea level, and system geomorphology. Our results show that changes in reef-water carbonate chemistry depend primarily on the ratio of benthic metabolism to the square root of the onshore wave energy flux as well as on the length and depth of the reef flat; however, they are only weakly dependent on channel geometry and the total frictional resistance of the reef system. Diurnal variations in pCO2, pH, and aragonite saturation state (Ωar) are primarily dependent on changes in net production and are relatively insensitive to changes in net calcification; however, net changes in pCO2, pH, and Ωar are more strongly influenced by net calcification when averaged over 24 hours. We also demonstrate that a relatively simple one-dimensional analytical model can provide a good description of the functional dependence of reef-water carbonate chemistry on benthic metabolism, wave forcing, sea level, reef flat morphology, and total system frictional resistance. Importantly, our results indicate that any long-term (weeks to months) net offsets in reef-water pCO2 relative to offshore values should be modest for reef systems with narrow and/or deep lagoons. Thus, the long-term evolution of water column pCO2 in many reef environments remains intimately connected to the regional-scale oceanography of offshore waters and hence directly influenced by rapid anthropogenically driven increases in pCO2. PMID:23326411

  1. The Eighth Central European Conference "Chemistry towards Biology": Snapshot.

    PubMed

    Perczel, András; Atanasov, Atanas G; Sklenář, Vladimír; Nováček, Jiří; Papoušková, Veronika; Kadeřávek, Pavel; Žídek, Lukáš; Kozłowski, Henryk; Wątły, Joanna; Hecel, Aleksandra; Kołkowska, Paulina; Koča, Jaroslav; Svobodová-Vařeková, Radka; Pravda, Lukáš; Sehnal, David; Horský, Vladimír; Geidl, Stanislav; Enriz, Ricardo D; Matějka, Pavel; Jeništová, Adéla; Dendisová, Marcela; Kokaislová, Alžběta; Weissig, Volkmar; Olsen, Mark; Coffey, Aidan; Ajuebor, Jude; Keary, Ruth; Sanz-Gaitero, Marta; van Raaij, Mark J; McAuliffe, Olivia; Waltenberger, Birgit; Mocan, Andrei; Šmejkal, Karel; Heiss, Elke H; Diederich, Marc; Musioł, Robert; Košmrlj, Janez; Polański, Jarosław; Jampílek, Josef

    2016-10-17

    The Eighth Central European Conference "Chemistry towards Biology" was held in Brno, Czech Republic, on August 28-September 1, 2016 to bring together experts in biology, chemistry and design of bioactive compounds; promote the exchange of scientific results, methods and ideas; and encourage cooperation between researchers from all over the world. The topics of the conference covered "Chemistry towards Biology", meaning that the event welcomed chemists working on biology-related problems, biologists using chemical methods, and students and other researchers of the respective areas that fall within the common scope of chemistry and biology. The authors of this manuscript are plenary speakers and other participants of the symposium and members of their research teams. The following summary highlights the major points/topics of the meeting.

  2. REFLECTIONS ON PHYSICAL CHEMISTRY: Science and Scientists

    NASA Astrophysics Data System (ADS)

    Jortner, Joshua

    2006-05-01

    This is the story of a young person who grew up in Tel-Aviv during the period of the establishment of the State of Israel and was inspired to become a physical chemist by the cultural environment, by the excellent high-school education, and by having been trained by some outstanding scientists at the Hebrew University of Jerusalem and, subsequently, by the intellectual environment and high-quality scientific endeavor at the University of Chicago. Since serving as the first chairman of the Chemistry Department of the newly formed Tel-Aviv University he has been immersed in research, in the training of young scientists, and in intensive and extensive international scientific collaboration. Together with the members of his "scientific family" he has explored the phenomena of energy acquisition, storage and disposal and structure-dynamics-function relations in large molecules, condensed phase, clusters and biomolecules, and is looking forward to many future adventures in physical chemistry. "What to leave out and what to put in? That's the problem." Hugh Lofting, Doctor Dolittle's Zoo, 1925

  3. Pre-Service Physics and Chemistry Teachers' Conceptual Integration of Physics and Chemistry Concepts

    ERIC Educational Resources Information Center

    Tuysuz, Mustafa; Bektas, Oktay; Geban, Omer; Ozturk, Gokhan; Yalvac, Bugrahan

    2016-01-01

    This study examines the pre-service teachers' opinions about conceptual integration (CI) and their understanding of it. A qualitative phenomenology design was used in the study. Data was collected through in-depth semi-structured interviews comprising ten guiding questions. Three pre-service physics and three pre-service chemistry teachers…

  4. Building bridges between the physical and biological sciences.

    PubMed

    Ninham, B W; Boström, M

    2005-12-16

    This paper attempts to identify major conceptual issues that have inhibited the application of physical chemistry to problems in the biological sciences. We will trace out where theories went wrong, how to repair the present foundations, and discuss current progress toward building a better dialogue.

  5. Biology-inspired AMO physics

    NASA Astrophysics Data System (ADS)

    Mathur, Deepak

    2015-01-01

    This Topical Review presents an overview of increasingly robust interconnects that are being established between atomic, molecular and optical (AMO) physics and the life sciences. AMO physics, outgrowing its historical role as a facilitator—a provider of optical methodologies, for instance—now seeks to partner biology in its quest to link systems-level descriptions of biological entities to insights based on molecular processes. Of course, perspectives differ when AMO physicists and biologists consider various processes. For instance, while AMO physicists link molecular properties and dynamics to potential energy surfaces, these have to give way to energy landscapes in considerations of protein dynamics. But there are similarities also: tunnelling and non-adiabatic transitions occur both in protein dynamics and in molecular dynamics. We bring to the fore some such differences and similarities; we consider imaging techniques based on AMO concepts, like 4D fluorescence microscopy which allows access to the dynamics of cellular processes, multiphoton microscopy which offers a built-in confocality, and microscopy with femtosecond laser beams to saturate the suppression of fluorescence in spatially controlled fashion so as to circumvent the diffraction limit. Beyond imaging, AMO physics contributes with optical traps that probe the mechanical and dynamical properties of single ‘live’ cells, highlighting differences between healthy and diseased cells. Trap methodologies have also begun to probe the dynamics governing of neural stem cells adhering to each other to form neurospheres and, with squeezed light to probe sub-diffusive motion of yeast cells. Strong field science contributes not only by providing a source of energetic electrons and γ-rays via laser-plasma accelerations schemes, but also via filamentation and supercontinuum generation, enabling mainstream collision physics into play in diverse processes like DNA damage induced by low-energy collisions to

  6. Organic First: A Biology-Friendly Chemistry Curriculum

    ERIC Educational Resources Information Center

    Reingold, I. David

    2005-01-01

    In this essay, the author describes to biologists the advantages of organic-first curriculum, on the assumption that few biologists are regular readers of "Journal of Chemistry Education" and therefore are probably unaware of the method for integrating chemistry and biology curricula. The author begins with the assumption that the majority of…

  7. Recent advances in the chemistry and biology of pyridopyrimidines.

    PubMed

    Buron, F; Mérour, J Y; Akssira, M; Guillaumet, G; Routier, S

    2015-05-05

    The interest in pyridopyrimidine cores for pharmaceutical products makes this scaffold a highly useful building block for organic chemistry. These derivatives have found applications in various areas of medicine such as anticancer, CNS, fungicidal, antiviral, anti-inflammatory, antimicrobial, and antibacterial therapies. This review mainly focuses on the progress achieved since 2004 in the chemistry and biological activity of pyridopyrimidines.

  8. Spectroscopy, colorimetry, and biological chemistry in the nineteenth century.

    PubMed Central

    Rinsler, M G

    1981-01-01

    The development of colorimetry and spectroscopy in the nineteenth century is described. An account is given of the application of their techniques to biological chemistry during that period. PMID:7014652

  9. Strontium: Part II. Chemistry, Biological Aspects and Applications.

    ERIC Educational Resources Information Center

    Britton, G. C.; Johnson, C. H.

    1987-01-01

    Reviews basic information on the Chemistry of strontium and its compounds. Explains biological aspects of strontium and its pharmaceutical applications. Highlights industrial application of strontium and its components. (ML)

  10. Modern Physical Chemistry: A Molecular Approach by George H. Duffey

    NASA Astrophysics Data System (ADS)

    Ranck, John P.

    2001-08-01

    The text has been carefully edited; I found no mathematical or typographical errors.

    Literature Cited

    1. Duffey, G. H. Physical Chemistry; McGraw-Hill: New York, 1962.
    2. Barrow, G. M. Physical Chemistry; McGraw-Hill: New York, 1961.
    3. McQuarrie, D. A.; Simon, J. D. Physical Chemistry: A Molecular Approach; University Science Books: Sausalito, CA, 1997.

  11. Time in physics and biology.

    PubMed

    Günther, Bruno; Morgado, Enrique

    2004-01-01

    In contrast with classical physics, particularly with Sir Isaac Newton, where time is a continuous function, generally valid, eternally and evenly flowing as an absolute time dimension, in the biological sciences, time is in essence of cyclical nature (physiological periodicities), where future passes to past through an infinitely thin boundary, the present. In addition, the duration of the present (DP) leads to the so-called 'granulation of time' in living beings, so that by the fusion of two successive pictures of the world, which are not entirely similar, they attain the perception of 'movement,' both in the real world as well as in the sham-movement in the mass media (TV).

  12. Condensed Matter Physics - Biology Resonance

    NASA Astrophysics Data System (ADS)

    Baskaran, G.

    The field of condensed matter physics had its genesis this century and it has had a remarkable evolution. A closer look at its growth reveals a hidden aim in the collective consciousness of the field - a part of the development this century is a kind of warm up exercise to understand the nature of living condensed matter, namely the field of biology, by a growing new breed of scientists in the coming century. Through some examples the vitality of this interaction will be pointed out.

  13. From physical to biological individuation.

    PubMed

    Miquel, Paul-Antoine; Hwang, Su-Young

    2016-10-01

    In this paper, we insist on stressing the epistemic and metaphysical difference between individual and individuation, a distinction originally developed by Gilbert Simondon. Individuation occurs in complex physical systems by the coupling (R1) between the system and its outside conditions. As such the system is not well defined by its sole constituents. Let's characterize (R2) as follows: the system is not entirely defined by its structure at a given time because this structure will change and global emergent properties will appear, as in the paradigmatic example of phase transition. Thus physical individuation is defined both by the coupling of a physical system with its environment (R1) and by its diachronic dynamics taking place (R2). We interpret biological individuation as a second order one, i.e. as a recursive procedure through which physical individuation is also acting on "its own theatre". We represent this procedure like a mapping through which (R1R2) are applied to themselves, so that: RN = (R1R2)(N). We highlight the relation between this assumption and the concept of extended criticality developed by Bailly, Longo and Montévil.

  14. Laboring in the vineyard of physical chemistry.

    PubMed

    Widom, Benjamin

    2011-01-01

    This is an account mostly of what I have seen and worked on in physical chemistry, from my time in graduate school six decades ago to the present. It is a personal story about kinetics, thermodynamics, and statistical mechanics--in which subjects I continue to be educated, thanks to patient instruction by my students and associates. When I had the invitation from Steve Leone to write this article I said "yes" because (a) "yes" is my default setting; (b) it was a great honor to have been invited to do it; and (c) I was too busy at the time to think about what the consequences of saying "yes" would be. I must now do my best to fulfill my promise.

  15. Physical and chemical mechanisms in molecular radiation biology

    SciTech Connect

    Glass, W.A.; Varma, M.N.

    1991-01-01

    Through its Radiological and Chemical Physics Program, the Department of Energy (DOE) has been a primary source of funding for research in radiation physics and radiochemistry, supporting a wide range of explorations of the link between physical, chemical and biological events. This book is a series of articles by authors working within this field, most of whom have been central to the DOE-sponsored research. The opening papers focus on radiological physics; the second section covers radiation chemistry in a discussion that extends from the initial energy transfer to the production of intermediate chemical species and DNA damage. The third section explores the link between the physical and chemical events and the production of biological effects. Finally the book closes with a series of papers on molecular radiation biology.

  16. Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry

    PubMed Central

    Harris, D. Calvin; Jewett, Michael C.

    2014-01-01

    Just as synthetic organic chemistry once revolutionized the ability of chemists to build molecules (including those that did not exist in nature) following a basic set of design rules, cell-free synthetic biology is beginning to provide an improved toolbox and faster process for not only harnessing but also expanding the chemistry of life. At the interface between chemistry and biology, research in cell-free synthetic systems is proceeding in two different directions: using synthetic biology for synthetic chemistry and using synthetic chemistry to reprogram or mimic biology. In the coming years, the impact of advances inspired by these approaches will make possible the synthesis of non-biological polymers having new backbone compositions, new chemical properties, new structures, and new functions. PMID:22483202

  17. Communities of Molecules: A Physical Chemistry Module.

    ERIC Educational Resources Information Center

    DeVoe, Howard

    This book is one in the series of Interdisciplinary Approaches to Chemistry (IAC) designed to help students discover that chemistry is a lively science and actively used to pursue solutions to the important problems of today. It is expected for students to see how chemistry takes place continuously all around and to readily understand the daily…

  18. An Integrated Biology-Chemistry Freshman Laboratory Project in Biotechnology.

    ERIC Educational Resources Information Center

    Schendel, Marilyn Shimizu

    1999-01-01

    Describes a freshman biology laboratory project that uses the polymerase chain reaction to introduce students to the interrelationship between biology and chemistry. Students must develop their own experimental protocol, perform calculations introduced in freshman classes, and evaluate group dynamics. (Author/WRM)

  19. Nationwide Survey of the Undergraduate Physical Chemistry Course

    ERIC Educational Resources Information Center

    Fox, Laura J.; Roehrig, Gillian H.

    2015-01-01

    A nationwide survey of the undergraduate physical chemistry course was conducted to investigate the depth and breadth of content that is covered, how content is delivered, how student understanding is assessed, and the experiences and beliefs of instructors. The survey was administered to instructors of physical chemistry (N = 331) at American…

  20. Chemical biology: Chromatin chemistry goes cellular

    NASA Astrophysics Data System (ADS)

    Fischle, Wolfgang; Schwarzer, Dirk; Mootz, Henning D.

    2015-05-01

    Analysing post-translational modifications of histone proteins as they occur within chromatin is challenging due to their large number and chemical diversity. A major step forward has now been achieved by using split intein chemistry to engineer functionalized histones within cells.

  1. Connecting Biology and Organic Chemistry Introductory Laboratory Courses through a Collaborative Research Project

    ERIC Educational Resources Information Center

    Boltax, Ariana L.; Armanious, Stephanie; Kosinski-Collins, Melissa S.; Pontrello, Jason K.

    2015-01-01

    Modern research often requires collaboration of experts in fields, such as math, chemistry, biology, physics, and computer science to develop unique solutions to common problems. Traditional introductory undergraduate laboratory curricula in the sciences often do not emphasize connections possible between the various disciplines. We designed an…

  2. Connecting biology and organic chemistry introductory laboratory courses through a collaborative research project.

    PubMed

    Boltax, Ariana L; Armanious, Stephanie; Kosinski-Collins, Melissa S; Pontrello, Jason K

    2015-01-01

    Modern research often requires collaboration of experts in fields, such as math, chemistry, biology, physics, and computer science to develop unique solutions to common problems. Traditional introductory undergraduate laboratory curricula in the sciences often do not emphasize connections possible between the various disciplines. We designed an interdisciplinary, medically relevant, project intended to help students see connections between chemistry and biology. Second term organic chemistry laboratory students designed and synthesized potential polymer inhibitors or inducers of polyglutamine protein aggregation. The use of novel target compounds added the uncertainty of scientific research to the project. Biology laboratory students then tested the novel potential pharmaceuticals in Huntington's disease model assays, using in vitro polyglutamine peptide aggregation and in vivo lethality studies in Drosophila. Students read articles from the primary literature describing the system from both chemical and biological perspectives. Assessment revealed that students emerged from both courses with a deeper understanding of the interdisciplinary nature of biology and chemistry and a heightened interest in basic research. The design of this collaborative project for introductory biology and organic chemistry labs demonstrated how the local interests and expertise at a university can be drawn from to create an effective way to integrate these introductory courses. Rather than simply presenting a series of experiments to be replicated, we hope that our efforts will inspire other scientists to think about how some aspect of authentic work can be brought into their own courses, and we also welcome additional collaborations to extend the scope of the scientific exploration.

  3. Is Biology based on Physics?

    NASA Astrophysics Data System (ADS)

    Goradia, Shantilal

    2015-04-01

    The equation on Boltsmann's tomb is S = K log W, giving 137 = 10E60 where 10E60 closely stands for the age of the universe in Plank times. We wish we could add ``137 = 10E60'' on his tomb as a contribution leading physics towards information in biology as explained in our book ``Quantum Consciousness - the Road to Reality.'' (1) We draft our speculation that such a step may explain the underlying physical cause for mutations. Tiny immeasurable and slow changes well beyond the tenth digit of fine structure constant may suffice to change the information system in constituent particles of nucleotides with their external effects forcing changes in the genetic code with successful changes resulting into mutations. (2) Our quantum mechanical published derivation of the strong coupling implies gravity as a cumulative effect of quantum mechanical particles further implying that the universal constant of gravity (G) can not be constant everywhere. (1) and (2) put together should remove Darwin's confusion about the constancy of gravity. Moving planets and Sunstorms should also cause changes in G on earth unnoticeable to mankind, but large enough to have an impact on the internal particles of nucleotides which should implicitly have an external effect on the genetic code per our theory.

  4. Radiation physics, biophysics, and radiation biology

    SciTech Connect

    Hall, E.J.; Zaider, M.

    1993-05-01

    Research at the Center for Radiological Research is a multidisciplenary blend of physics, chemistry and biology aimed at understanding the mechanisms involved in the health problems resulting from human exposure to ionizing radiations. The focus is increased on biochemistry and the application of the techniques of molecular biology to the problems of radiation biology. Research highlights of the program from the past year are described. A mathematical model describing the production of single-strand and double-strand breaks in DNA as a function radiation quality has been completed. For the first time Monte Carlo techniques have been used to obtain directly the spatial distribution of DNA moieties altered by radiation. This information was obtained by including the transport codes a realistic description of the electronic structure of DNA. We have investigated structure activity relationships for the potential oncogenicity of a new generation of bioreductive drugs that function as hypoxic cytotoxins. Experimental and theoretical investigation of the inverse dose rate effect, whereby medium LET radiations actually produce an c effect when the dose is protracted, is now at a point where the basic mechanisms are reasonably understood and the complex interplay between dose, dose rate and radiation quality which is necessary for the effect to be present can now be predicted at least in vitro. In terms of early radiobiological damage, a quantitative link has been established between basic energy deposition and locally multiply damaged sites, the radiochemical precursor of DNA double strand breaks; specifically, the spatial and energy deposition requirements necessary to form LMDs have been evaluated. For the first time, a mechanically understood biological fingerprint'' of high-LET radiation has been established. Specifically measurement of the ratio of inter-to intra-chromosomal aberrations produces a unique signature from alpha-particles or neutrons.

  5. Physics and Chemistry of the Solar Nebula

    NASA Astrophysics Data System (ADS)

    Lunine, Jonathan I.

    The solar system is thought to have begun in a flattened disk of gas and dust referred to traditionally as the solar nebula. Such a construct seems to be a natural product of the collapse of dense parts of giant molecular clouds, the vast star-forming regions that pepper the Milky Way and other galaxies. Gravitational, magnetic and thermal forces within the solar nebula forced a gradual evolution of mass toward the center (where the sun formed) and angular momentum (borne by a small fraction of the mass) toward the outer more distant regions of the disk. This evolution was accompanied by heating and a strong temperature contrast from the hot, inner regions to the cold, more remote parts of the disk. The resulting chemistry in the disk determined the initial distribution of organic matter in the planets; most of the reduced carbon species, in condensed form, were located beyond the asteroid belt (the `outer' solar system). The Earth could have received much of its inventory of pre-biological material from comets and other icy fragments of the process of planetary formation in the outer solar system.

  6. Physics and chemistry of the solar nebula.

    PubMed

    Lunine, J I

    1997-06-01

    The solar system is thought to have begun in a flattened disk of gas and dust referred to traditionally as the solar nebula. Such a construct seems to be a natural product of the collapse of dense parts of giant molecular clouds, the vast star-forming regions that pepper the Milky Way and other galaxies. Gravitational, magnetic and thermal forces within the solar nebula forced a gradual evolution of mass toward the center (where the sun formed) and angular momentum (borne by a small fraction of the mass) toward the outer more distant regions of the disk. This evolution was accompanied by heating and a strong temperature contrast from the hot, inner regions to the cold, more remote parts of the disk. The resulting chemistry in the disk determined the initial distribution of organic matter in the planets; most of the reduced carbon species, in condensed form, were located beyond the asteroid belt (the 'outer' solar system). The Earth could have received much of its inventory of pre-biological material from comets and other icy fragments of the process of planetary formation in the outer solar system.

  7. Analytical Chemistry at the Interface Between Materials Science and Biology

    SciTech Connect

    O'Brien, Janese C.

    2000-09-21

    Likedlessentid sciences, anal~cd chetis~continues toreinvent itself. Moving beyond its traditional roles of identification and quantification, analytical chemistry is now expanding its frontiers into areas previously reserved to other disciplines. This work describes several research efforts that lie at the new interfaces between analytical chemistry and two of these disciplines, namely materials science and biology. In the materials science realm, the search for new materials that may have useful or unique chromatographic properties motivated the synthesis and characterization of electrically conductive sol-gels. In the biology realm, the search for new surface fabrication schemes that would permit or even improve the detection of specific biological reactions motivated the design of miniaturized biological arrays. Collectively, this work represents some of analytical chemistry’s newest forays into these disciplines. The introduction section to this dissertation provides a literature review on several of the key aspects of this work. In advance of the materials science discussion, a brief introduction into electrochemically-modulated liquid chromatography (EMLC) and sol-gel chemistry is provided. In advance of the biological discussions, brief overviews of scanning force microscopy (SFM) and the oxidative chemistry used to construct our biological arrays are provided. This section is followed by four chapters, each of which is presented as a separate manuscript, and focuses on work that describes some of our cross-disciplinary efforts within materials science and biology. This dissertation concludes with a general summary and future prospectus.

  8. Synthetic biology, inspired by synthetic chemistry.

    PubMed

    Malinova, V; Nallani, M; Meier, W P; Sinner, E K

    2012-07-16

    The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell.

  9. Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry.

    PubMed

    Harris, D Calvin; Jewett, Michael C

    2012-10-01

    Just as synthetic organic chemistry once revolutionized the ability of chemists to build molecules (including those that did not exist in nature) following a basic set of design rules, cell-free synthetic biology is beginning to provide an improved toolbox and faster process for not only harnessing but also expanding the chemistry of life. At the interface between chemistry and biology, research in cell-free synthetic systems is proceeding in two different directions: using synthetic biology for synthetic chemistry and using synthetic chemistry to reprogram or mimic biology. In the coming years, the impact of advances inspired by these approaches will make possible the synthesis of nonbiological polymers having new backbone compositions, new chemical properties, new structures, and new functions.

  10. Undergraduates' Views about Biology and Physics

    ERIC Educational Resources Information Center

    Spall, Katie; Barrett, Stephanie; Stanisstreet, Martin; Dickson, Dominic; Boyes, Edward

    2003-01-01

    There is continuing concern about the low enrolment of students on to some undergraduate science courses, especially physics. Here we explore some of the reasons that might underpin this. The views about physics and biology of Year 1 undergraduate students on English, physics and biology programmes of study were compared using a closed-form…

  11. Organic chemistry and biology of the interstellar medium

    NASA Technical Reports Server (NTRS)

    Sagan, C.

    1973-01-01

    Interstellar organic chemistry is discussed as the field of study emerging from the discovery of microwave lines of formaldehyde and of hydrogen cyanide in the interstellar medium. The reliability of molecular identifications and comparisons of interstellar and cometary compounds are considered, along with the degradational origin of simple organics. It is pointed out that the contribution of interstellar organic chemistry to problems in biology is not substantive but analogical. The interstellar medium reveals the operation of chemical processes which, on earth and perhaps on vast numbers of planets throughout the universe, led to the origin of life, but the actual molecules of the interstellar medium are unlikely to play any significant biological role.

  12. Physical Biology : challenges for our second decade

    NASA Astrophysics Data System (ADS)

    Levine, Herbert

    2014-06-01

    understand when the details of proteins and nucleic acids structure and function can be assumed constant when considering the cell. This problem is even more serious as we try to set higher sights and think of cells as constituents of tissue, organ and organism. Trying to understand higher-order biological systems is a bit like trying to play a board game where the pieces and rules are constantly changing, somehow in concert with what is happening at the scale of the game. Others will undoubtedly have their own view of what is really difficult and different about living systems. One of the roles of Physical Biology should therefore be to provide a needed forum to address some of these really difficult questions. Of course, most papers will operate with the safety-setting on, and will use established ideas in physics, either experimental or theoretical, to further our quantitative appreciation of living systems. These papers are without doubt an absolutely necessary part of the field, and we hope that our journal can serve as a home for the best of these. But, my real hope is that we can attract papers that really try to break new ground, that suggest ways in which the living world is not just an extremely messy example of the same phenomena that can be studied in non-biological contexts. Amazingly, this hope is actually shared by many leading biologists. In one of the most influential papers on cancer research in the past decades. Hanahan and Weinberg argue that 'one day, we imagine that cancer biology and treatment—at present, a patchwork quilt of cell biology, genetics, histopathology, biochemistry, immunology, and pharmacology—will become a science with a conceptual structure and logical coherence that rivals that of chemistry or physics.' We should take up the challenge, not just for cancer, and Physical Biology should help. Figuring out exactly how best to do this is now my responsibility, and I look forward to hearing from you and working with all of you, in order

  13. Physical Biology : challenges for our second decade.

    PubMed

    Levine, Herbert

    2014-06-01

    understand when the details of proteins and nucleic acids structure and function can be assumed constant when considering the cell. This problem is even more serious as we try to set higher sights and think of cells as constituents of tissue, organ and organism. Trying to understand higher-order biological systems is a bit like trying to play a board game where the pieces and rules are constantly changing, somehow in concert with what is happening at the scale of the game. Others will undoubtedly have their own view of what is really difficult and different about living systems. One of the roles of Physical Biology should therefore be to provide a needed forum to address some of these really difficult questions. Of course, most papers will operate with the safety-setting on, and will use established ideas in physics, either experimental or theoretical, to further our quantitative appreciation of living systems. These papers are without doubt an absolutely necessary part of the field, and we hope that our journal can serve as a home for the best of these. But, my real hope is that we can attract papers that really try to break new ground, that suggest ways in which the living world is not just an extremely messy example of the same phenomena that can be studied in non-biological contexts. Amazingly, this hope is actually shared by many leading biologists. In one of the most influential papers on cancer research in the past decades. Hanahan and Weinberg argue that 'one day, we imagine that cancer biology and treatment-at present, a patchwork quilt of cell biology, genetics, histopathology, biochemistry, immunology, and pharmacology-will become a science with a conceptual structure and logical coherence that rivals that of chemistry or physics.' We should take up the challenge, not just for cancer, and Physical Biology should help. Figuring out exactly how best to do this is now my responsibility, and I look forward to hearing from you and working with all of you, in order to

  14. Using Physics Principles in the Teaching of Chemistry.

    ERIC Educational Resources Information Center

    Gulden, Warren

    1996-01-01

    Presents three examples that show how students can use traditional physics principles or laws for the purpose of understanding chemistry better. Examples include Coulomb's Law and melting points, the Faraday Constant, and the Rydberg Constant. Presents a list of some other traditional topics in a chemistry course that could be enhanced by the…

  15. Materials: Bringing Relevance to Chemistry and Physics Education

    NASA Astrophysics Data System (ADS)

    Whittingham, M. Stanley

    1997-03-01

    In 1988 Binghamton started to integrate materials throughout the "chemistry" curriculum. A one semester general chemistry course, that is required of physics, engineering and geology majors was first restructured so that the middle one-third of the course emphasized materials, both inorganic and organic (NSF 90-60). It's aim was to involve students in today's science in both lecture and

  16. Energy and Matter: Differences in Discourse in Physical and Biological Sciences Can Be Confusing for Introductory Biology Students

    ERIC Educational Resources Information Center

    Hartley, Laurel M.; Momsen, Jennifer; Maskiewicz, April; D'Avanzo, Charlene

    2012-01-01

    Biology majors often take introductory biology, chemistry, and physics courses during their first two years of college. The various and sometimes conflicting discourse about and explanations of matter and energy in these courses may contribute to confusion and alternative conceptions (those that differ from scientific consensus) in biology…

  17. Gas Plasma Surface Chemistry for Biological Assays.

    PubMed

    Sahagian, Khoren; Larner, Mikki

    2015-01-01

    Biological systems respond to and interact with surfaces. Gas plasma provides a scalable surface treatment method for designing interactive surfaces. There are many commercial examples of plasma-modified products. These include well plates, filtration membranes, dispensing tools, and medical devices. This chapter presents an overview of gas plasma technology and provides a guide to using gas plasma for modifying surfaces for research or product development.

  18. Biological chemistry of hydrogen sulfide and persulfides.

    PubMed

    Cuevasanta, Ernesto; Möller, Matías N; Alvarez, Beatriz

    2017-03-01

    Hydrogen sulfide (H2S) has been traditionally considered to be a toxic molecule for mammals. However, it can be formed endogenously and exert physiological effects with potential health benefits. H2S can partition two-fold in biological membranes and traverse them rapidly, diffusing between compartments. H2S reactivity has similarities to that of thiols, although it is less nucleophilic than thiols and it can form different products. H2S can react with oxidants derived from the partial reduction of oxygen, but direct scavenging is unlikely to explain H2S protective actions. Important effects are exerted on mitochondria including the stimulation or the inhibition of the electron transport chain. Possible mechanisms for unleashing biological consequences are the reactions with metal centers and with thiol oxidation products. The reactions of H2S with disulfides (RSSR) and sulfenic acids (RSOH) lead to the formation of persulfides (RSSH). Persulfides have enhanced nucleophilicity with respect to the corresponding thiol, consistent with the alpha effect. Besides, the inner and outer sulfurs can both act as electrophiles. In this review, we describe the reactions of H2S with oxidized thiol products and the properties of the persulfides formed in the context of the chemical biology of H2S.

  19. The Biology and Chemistry of Brewing: An Interdisciplinary Course

    ERIC Educational Resources Information Center

    Hooker, Paul D.; Deutschman, William A.; Avery, Brian J.

    2014-01-01

    For the past nine years, we have been offering an interdisciplinary course for science majors: The Biology and Chemistry of Brewing. This course is primarily laboratory- and inquiry-based; from a total of 24 h of student/instructor contact time, approximately 6 h are devoted to lecture, and the other 18 h are divided between laboratory exercises,…

  20. Lysozyme Thermal Denaturation and Self-Interaction: Four Integrated Thermodynamic Experiments for the Physical Chemistry Laboratory

    ERIC Educational Resources Information Center

    Schwinefus, Jeffrey J.; Schaefle, Nathaniel J.; Muth, Gregory W.; Miessler, Gary L.; Clark, Christopher A.

    2008-01-01

    As part of an effort to infuse our physical chemistry laboratory with biologically relevant, investigative experiments, we detail four integrated thermodynamic experiments that characterize the denaturation (or unfolding) and self-interaction of hen egg white lysozyme as a function of pH and ionic strength. Students first use Protein Explorer to…

  1. The Application of Physical Organic Chemistry to Biochemical Problems.

    ERIC Educational Resources Information Center

    Westheimer, Frank

    1986-01-01

    Presents the synthesis of the science of enzymology from application of the concepts of physical organic chemistry from a historical perspective. Summarizes enzyme and coenzyme mechanisms elucidated prior to 1963. (JM)

  2. Using Microcomputers in the Physical Chemistry Laboratory: Activation Energy Experiment.

    ERIC Educational Resources Information Center

    Touvelle, Michele; Venugopalan, Mundiyath

    1986-01-01

    Describes a computer program, "Activation Energy," which is designed for use in physical chemistry classes and can be modified for kinetic experiments. Provides suggestions for instruction, sample program listings, and information on the availability of the program package. (ML)

  3. Proceedings of the physics and chemistry of oxide superconductors

    SciTech Connect

    Iye, Y.; Yasuoka, H.

    1992-01-01

    This book contains the proceedings of the physics and chemistry of oxide superconductors. Topics covered include: materials; electronic states; spectroscopy; lattice properties; pressure effects; carrier dynamics; doping effects; spin dynamics; magnetism; strong correlation, and superconducting properties.

  4. Quantum Dots: An Experiment for Physical or Materials Chemistry

    ERIC Educational Resources Information Center

    Winkler, L. D.; Arceo, J. F.; Hughes, W. C.; DeGraff, B. A.; Augustine, B. H.

    2005-01-01

    An experiment is conducted for obtaining quantum dots for physical or materials chemistry. This experiment serves to both reinforce the basic concept of quantum confinement and providing a useful bridge between the molecular and solid-state world.

  5. Contrail: A Module from Physical Chemistry On-Line Project

    ERIC Educational Resources Information Center

    Chen, Franklin; Zielinski, Theresa Julia; Long, George

    2007-01-01

    The impact of contrails on Earth's climate is researched to understand the active area. It is suggested that the process of contrail formation involves combustion, cooling and ice formation, which are good comprehensive learning exercise for physical chemistry students.

  6. Survival Guide for Physical Chemistry (by Michelle Francl)

    NASA Astrophysics Data System (ADS)

    Elrod, Matthew

    2002-09-01

    Overall, I would recommend that instructors of physical chemistry consider Francl's text as a supplementary text for their courses. However, instructors who use a main textbook like Donald McQuarrie and John Simon's Physical Chemistry: A Molecular Approach, which contains “math chapters” to deal with many of the same mathematical issues addressed by Francl, may find that this supplementary text is not complementary enough to justify recommending its purchase to students.

  7. Molecular knots in biology and chemistry

    NASA Astrophysics Data System (ADS)

    Lim, Nicole C. H.; Jackson, Sophie E.

    2015-09-01

    Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.

  8. Applications of physical chemistry to glass technology

    NASA Astrophysics Data System (ADS)

    Stewart, Ogie Gregory

    2001-07-01

    Industrial manufacturing of glass, called float glass, involves a process in which flat pieces of glass are produced by pouring molten glass on a bath of molten tin metal. The glass is then coated with thin film coatings for such applications as solar radiation control and "privacy" glass. In this thesis, principles of physical chemistry are applied to selected aspects of glass production and thin film coatings in an effort to better understand these processes with the hope of improving film and glass quality. The research described here consists of three major studies. Part 1 describes the production of thin films by Atmospheric Pressure Chemical Vapor Deposition (APCVD) and characterization of the films by various analytical techniques. Vanadium oxide films were produced from vanadium (IV) chloride and each of several alcohols to determine the feasibility of this method of deposition and to investigate its use in an electrochromic device. The focus here was to investigate the levels of carbon contamination in the films. It was found that the level of carbon present in the films depend on the type of amine used. Part 2 is an investigation of the flow dynamics that occur during the two thin film deposition processes. APCVD and Powder Spray Pyrolysis (PSP). Information regarding flow dynamics and particle distribution in the region above the films' substrates were obtained and related to film formation and quality. Part 3 is a kinetic study of the gas phase reactions that occur in the vapor region above the glass during float glass production. A kinetic model of the possible reactions was devised and integrated to predict the formation of these impurities with time. An experimental setup to test the model's predictions is also discussed. The research described in this thesis lays the groundwork for several possibilities for future work. Electrochromic films can be produced by APCVD to construct an all-solid-state device. Two dimensional imaging coupled with Laser

  9. PERSPECTIVE: From computational quantum chemistry to computational biology: experiments and computations are (full) partners

    NASA Astrophysics Data System (ADS)

    Ma, Buyong; Nussinov, Ruth

    2004-12-01

    Computations are being integrated into biological research at an increasingly fast pace. This has not only changed the way in which biological information is managed; it has also changed the way in which experiments are planned in order to obtain information from nature. Can experiments and computations be full partners? Computational chemistry has expanded over the years, proceeding from computations of a hydrogen molecule toward the challenging goal of systems biology, which attempts to handle the entire living cell. Applying theories from ab initio quantum mechanics to simplified models, the virtual worlds explored by computations provide replicas of real-world phenomena. At the same time, the virtual worlds can affect our perception of the real world. Computational biology targets a world of complex organization, for which a unified theory is unlikely to exist. A computational biology model, even if it has a clear physical or chemical basis, may not reduce to physics and chemistry. At the molecular level, computational biology and experimental biology have already been partners, mutually benefiting from each other. For the perception to become reality, computation and experiment should be united as full partners in biological research.

  10. Magnetic field effects in chemistry and biology

    NASA Astrophysics Data System (ADS)

    Schulten, Klaus

    Chemical and biological photoprocesses which involve bimolecular reactions between non-zero spin intermediates, e.g. doublet molecules 2A+2B, often produce the intermediate molecular pair in a pure overall spin state, e.g. a singlet state 1(2A+2B). and select for the reaction channels again such spin states, e.g. a triplet state 3(2A+2B). The necessery transition 1(2A+2B)→3(2A+2B) is affected by magnetic interactions (hyperfine, Zeeman, zero field splitting) and can be influenced by magnetic fields. Examples are photoinduced electron transfer processes, e.g. the primary reaction of photosynthesis.

  11. Biological Physics major as a means to stimulate an undergraduate physics program

    NASA Astrophysics Data System (ADS)

    Jaeger, Herbert; Eid, Khalid; Yarrison-Rice, Jan

    2013-03-01

    In an effort to stress the cross-disciplinary nature of modern physics we added a Biological Physics major. Drawing from coursework in physics, biology, chemistry, mathematics, and related disciplines, it combines a broad curriculum with physical and mathematical rigor in preparation for careers in biophysics, medical physics, and biomedical engineering. Biological Physics offers a new path of studies to a large pool of life science students. We hope to grow our physics majors from 70-80 to more than 100 students and boost our graduation rate from the mid-teens to the mid-twenties. The new major brought about a revision of our sophomore curriculum to make room for modern topics without sidelining fundamentals. As a result, we split our 1-semester long Contemporary Physics course (4 cr hrs) into a year-long sequence Contemporary Physics Foundations and Contemporary Physics Frontiers (both 3 cr hrs). Foundations starts with relativity, then focuses on 4 quantum mechanics topics: wells, spin 1/2, oscillators, and hydrogen. Throughout the course applications are woven in whenever the opportunity arises, e.g. magnetism and NMR with spin 1/2. The following semester Frontiers explores scientific principles and technological advances that make quantum science and resulting technologies different from the large scale. Frontiers covers enabling techniques from atomic, molecular, condensed matter, and particle physics, as well as advances in nanotechnology, quantum optics, and biophysics.

  12. Student Use of Energy Concepts from Physics in Chemistry Courses

    ERIC Educational Resources Information Center

    Nagel, Megan L.; Lindsey, Beth A.

    2015-01-01

    This paper describes an interdisciplinary investigation of students' usage of ideas about energy from physics in the context of introductory chemistry. We focus on student understanding of the idea that potential energy is a function of distance between interacting objects, a concept relevant to understanding potential energy in both physical and…

  13. Quantitative biology: where modern biology meets physical sciences

    PubMed Central

    Shekhar, Shashank; Zhu, Lian; Mazutis, Linas; Sgro, Allyson E.; Fai, Thomas G.; Podolski, Marija

    2014-01-01

    Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines. PMID:25368426

  14. Quantitative biology: where modern biology meets physical sciences.

    PubMed

    Shekhar, Shashank; Zhu, Lian; Mazutis, Linas; Sgro, Allyson E; Fai, Thomas G; Podolski, Marija

    2014-11-05

    Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines.

  15. Chemistry and Structural Biology of DNA Damage and Biological Consequences

    PubMed Central

    Stone, Michael P.; Huang, Hai; Brown, Kyle L.; Shanmugam, Ganesh

    2013-01-01

    The formation of adducts by the reaction of chemicals with DNA is a critical step for the initiation of carcinogenesis. The structural analysis of various DNA adducts reveals that conformational and chemical rearrangements and interconversions are a common theme. Conformational changes are modulated both by the nature of adduct and the base sequences neighboring the lesion sites. Equilibria between conformational states may modulate both DNA repair and error-prone replication past these adducts. Likewise, chemical rearrangements of initially formed DNA adducts are also modulated both by the nature of adducts and the base sequences neighboring the lesion sites. In this review, we focus on DNA damage caused by a number of environmental and endogenous agents, and biological consequences. PMID:21922653

  16. Algebraic algorithms for structure determination in biological chemistry

    NASA Astrophysics Data System (ADS)

    Emiris, Ioannis Z.; Fritzilas, Epaminondas D.; Manocha, Dinesh

    Several problems in computational chemistry, structural molecular biology, and biological chemistry can be solved by symbolic-numerical algorithms. We introduce suitable algebraic tools and then survey their usage in concrete applications. In particular, questions on molecular structure can be modeled by systems of polynomial equations, mainly by drawing on techniques from robot kinematics. Resultant-based algorithms, including sparse resultants and their matrix formulae, are described in order to reduce the solving of polynomial systems to numerical linear algebra. As an illustration, we focus on computing all conformations of cyclic molecules and on matching pharmacophores under distance constraints; in both cases, the number of independent degrees of freedom is relatively small. We summarize some existing results as well as sketch some original work. Both lead to complete and accurate solutions for those problems in the sense that our algorithms output all solutions with sufficiently high precision for the needs of biochemical applications.

  17. Seeing the chemistry in biology with neutron crystallography

    PubMed Central

    Langan, Paul; Chen, Julian C.-H.

    2017-01-01

    New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible in neutron structures. Using X-rays allows one to see structure, while neutrons allow one to reveal the chemistry inherent in these macromolecular structures. A number of surprising and sometimes controversial results have emerged from recent neutron structures; because it is difficult to see or predict hydrogen atoms in X-ray structures, when they are seen by neutrons they can be in unexpected locations with important chemical and biological consequences. Here we describe examples of chemistry seen with neutrons for the first time in biological macromolecules over the past few years. PMID:23852376

  18. Chemistry and biology of the caged Garcinia xanthones.

    PubMed

    Chantarasriwong, Oraphin; Batova, Ayse; Chavasiri, Warinthorn; Theodorakis, Emmanuel A

    2010-09-03

    Natural products have been a great source of many small molecule drugs for various diseases. In spite of recent advances in biochemical engineering and fermentation technologies that allow us to explore microorganisms and the marine environment as alternative sources of drugs, more than 70 % of the current small molecule therapeutics derive their structures from plants used in traditional medicine. Natural-product-based drug discovery relies heavily on advances made in the sciences of biology and chemistry. Whereas biology aims to investigate the mode of action of a natural product, chemistry aims to overcome challenges related to its supply, bioactivity, and target selectivity. This review summarizes the explorations of the caged Garcinia xanthones, a family of plant metabolites that possess a unique chemical structure, potent bioactivities, and a promising pharmacology for drug design and development.

  19. Seeing the chemistry in biology with neutron crystallography.

    PubMed

    Langan, Paul; Chen, Julian C-H

    2013-09-07

    New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible with neutrons. Using X-rays allows one to see structure, while neutrons allow one to reveal the chemistry inherent in these macromolecular structures. A number of surprising and sometimes controversial results have emerged; because it is difficult to see or predict hydrogen atoms in X-ray structures, when they are seen by neutrons they can be in unexpected locations with important chemical and biological consequences. Here we describe examples of chemistry seen with neutrons for the first time in biological macromolecules over the past few years.

  20. Chemistry and Biology of the Caged Garcinia Xanthones

    PubMed Central

    Chantarasriwong, Oraphin; Batova, Ayse; Chavasiri, Warinthorn

    2011-01-01

    Natural products have been a great source of many small molecule drugs for various diseases. In spite of recent advances in biochemical engineering and fermentation technologies that allow us to explore microorganisms and the marine environment as alternative sources of drugs, more than 70% of the current small molecule therapeutics derive their structures from plants used in traditional medicine. Natural-product-based drug discovery relies heavily on advances made in the sciences of biology and chemistry. Whereas biology aims to investigate the mode of action of a natural product, chemistry aims to overcome challenges related to its supply, bioactivity, and target selectivity. This review summarizes the explorations of the caged Garcinia xanthones, a family of plant metabolites that possess a unique chemical structure, potent bioactivities, and a promising pharmacology for drug design and development. PMID:20648491

  1. New physics and chemistry in high electrostatic fields

    NASA Astrophysics Data System (ADS)

    Karahka, M. L.; Kreuzer, H. J.

    2016-01-01

    Fields of the order of volts per meter exist along micron-sized tips. They are of the magnitude of fields inside atoms and molecules and can affect their electronic structure. This leads to a continuous periodic table resulting in new field-induced chemistry. We will present a tutorial treatment of this new physics and chemistry explaining such surprising phenomena like covalent bonding of helium to metal surfaces, metallization of semiconductors and insulators, and more.

  2. Protection against radiation (biological, pharmacological, chemical, physical)

    NASA Technical Reports Server (NTRS)

    Saksonov, P. P.

    1975-01-01

    Physical, chemical, and biological protection for astronauts from penetrating radiation on long-term space flights is discussed. The status of pharmacochemical protection, development of protective substances, medical use of protective substances, protection for spacecraft ecologic systems, adaptogens and physical conditioning, bone marrow transplants and local protection are discussed. Combined use of local protection and pharmacochemical substances is also briefly considered.

  3. Physics and Size in Biological Systems.

    ERIC Educational Resources Information Center

    Barnes, George

    1989-01-01

    Described is the subject of biological scaling for physics teachers including examples and in-depth reading. Topics are elements of scaling, terminal velocities, Lilliputian and Brobdingnagian, brain evolution, dolphin echolocation, surface tension, gravity change, food and oxygen, and seeing. Ten references on physics and size, and ten questions…

  4. The future of discovery chemistry: quo vadis? Academic to industrial--the maturation of medicinal chemistry to chemical biology.

    PubMed

    Hoffmann, Torsten; Bishop, Cheryl

    2010-04-01

    At Roche, we set out to think about the future role of medicinal chemistry in drug discovery in a project involving both Roche internal stakeholders and external experts in drug discovery chemistry. To derive a coherent strategy, selected scientists were asked to take extreme positions and to derive two orthogonal strategic options: chemistry as the traditional mainstream science and chemistry as the central entrepreneurial science. We believe today's role of medicinal chemistry in industry has remained too narrow. To provide the innovation that industry requires, medicinal chemistry must play its part and diversify at pace with our increasing understanding of chemical biology and network pharmacology.

  5. Interactive Digital Computing in Undergraduate Physical Chemistry

    ERIC Educational Resources Information Center

    Herber, R. H.; Hazony, Y.

    1974-01-01

    Presents the results of educational experiments aimed at incorporating APL programming techniques in an undergraduate physical-analytical laboratory course. Included are a list of first year experiments and some examples of operations. (CC)

  6. Perspective: Reaches of chemical physics in biology.

    PubMed

    Gruebele, Martin; Thirumalai, D

    2013-09-28

    Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.

  7. The biology and chemistry of the zoanthamine alkaloids.

    PubMed

    Behenna, Douglas C; Stockdill, Jennifer L; Stoltz, Brian M

    2008-01-01

    Marine natural products have long played an important role in natural products chemistry and drug discovery. Mirroring the rich variety and complicated interactions of the marine environment, the substances isolated from sea creatures tend to be incredibly diverse in both molecular structure and biological activity. The natural products isolated from the polyps of marine zoanthids are no exception. The zoanthamine alkaloids, the first of which were isolated over 20 years ago, are of particular interest to the synthetic community because they feature a novel structural framework and exhibit a broad range of biological activities. In this Review, we summarize the major contributions to understanding the zoanthamine natural products with regard to their isolation and structure determination, as well as studies on their biological activity and total synthesis.

  8. Advances in the biology and chemistry of sialic acids.

    PubMed

    Chen, Xi; Varki, Ajit

    2010-02-19

    Sialic acids are a subset of nonulosonic acids, which are nine-carbon alpha-keto aldonic acids. Natural existing sialic acid-containing structures are presented in different sialic acid forms, various sialyl linkages, and on diverse underlying glycans. They play important roles in biological, pathological, and immunological processes. Sialobiology has been a challenging and yet attractive research area. Recent advances in chemical and chemoenzymatic synthesis, as well as large-scale E. coli cell-based production, have provided a large library of sialoside standards and derivatives in amounts sufficient for structure-activity relationship studies. Sialoglycan microarrays provide an efficient platform for quick identification of preferred ligands for sialic acid-binding proteins. Future research on sialic acid will continue to be at the interface of chemistry and biology. Research efforts not only will lead to a better understanding of the biological and pathological importance of sialic acids and their diversity but also could lead to the development of therapeutics.

  9. Ask not what physics can do for biology--ask what biology can do for physics.

    PubMed

    Frauenfelder, Hans

    2014-10-08

    Stan Ulam, the famous mathematician, said once to Hans Frauenfelder: 'Ask not what Physics can do for biology, ask what biology can do for physics'. The interaction between biologists and physicists is a two-way street. Biology reveals the secrets of complex systems, physics provides the physical tools and the theoretical concepts to understand the complexity. The perspective gives a personal view of the path to some of the physical concepts that are relevant for biology and physics (Frauenfelder et al 1999 Rev. Mod. Phys. 71 S419-S442). Schrödinger's book (Schrödinger 1944 What is Life? (Cambridge: Cambridge University Press)), loved by physicists and hated by eminent biologists (Dronamraju 1999 Genetics 153 1071-6), still shows how a great physicist looked at biology well before the first protein structure was known.

  10. Organic chemistry and biology: chemical biology through the eyes of collaboration.

    PubMed

    Hruby, Victor J

    2009-12-18

    From a scientific perspective, efforts to understand biology including what constitutes health and disease has become a chemical problem. However, chemists and biologists "see" the problems of understanding biology from different perspectives, and this has retarded progress in solving the problems especially as they relate to health and disease. This suggests that close collaboration between chemists and biologists is not only necessary but essential for progress in both the biology and chemistry that will provide solutions to the global questions of biology. This perspective has directed my scientific efforts for the past 45 years, and in this overview I provide my perspective of how the applications of synthetic chemistry, structural design, and numerous other chemical principles have intersected in my collaborations with biologists to provide new tools, new science, and new insights that were only made possible and fruitful by these collaborations.

  11. Photoelectroconversion by Semiconductors: A Physical Chemistry Experiment.

    ERIC Educational Resources Information Center

    Fan, Qinbai; And Others

    1995-01-01

    Presents an experiment designed to give students some experience with photochemistry, electrochemistry, and basic theories about semiconductors. Uses a liquid-junction solar cell and illustrates some fundamental physical and chemical principles related to light and electricity interconversion as well as the properties of semiconductors. (JRH)

  12. Physics and chemistry of layered chalcogenide superconductors

    PubMed Central

    Deguchi, Keita; Takano, Yoshihiko; Mizuguchi, Yoshikazu

    2012-01-01

    Structural and physical properties of layered chalcogenide superconductors are summarized. In particular, we review the remarkable properties of the Fe-chalcogenide superconductors, FeSe and FeTe-based materials. Furthermore, we introduce the recently discovered BiS2-based layered superconductors and discuss their prospects. PMID:27877516

  13. Air and water stable ionic liquids in physical chemistry.

    PubMed

    Endres, Frank; Zein El Abedin, Sherif

    2006-05-14

    Ionic liquids are defined today as liquids which solely consist of cations and anions and which by definition must have a melting point of 100 degrees C or below. Originating from electrochemistry in AlCl(3) based liquids an enormous progress was made during the recent 10 years to synthesize ionic liquids that can be handled under ambient conditions, and today about 300 ionic liquids are already commercially available. Whereas the main interest is still focussed on organic and technical chemistry, various aspects of physical chemistry in ionic liquids are discussed now in literature. In this review article we give a short overview on physicochemical aspects of ionic liquids, such as physical properties of ionic liquids, nanoparticles, nanotubes, batteries, spectroscopy, thermodynamics and catalysis of/in ionic liquids. The focus is set on air and water stable ionic liquids as they will presumably dominate various fields of chemistry in future.

  14. Understanding the chemistry and physics of coal structure (A Review)

    PubMed Central

    Levine, Duane G.; Schlosberg, Richard H.; Silbernagel, Bernard G.

    1982-01-01

    This article outlines our current understanding of the structure of coal in terms of both the chemical and physical bonding processes responsible for its structural integrity and the extensive network of pores that permeate the organic material. Information on the microscopic chemistry of coal and its relationship to coal's physical structure and reactivity is an essential component in the successful development of the next generation of coal conversion technologies. Although coal is an extremely complex and heterogeneous material, many of its fundamental properties can be determined by the coordinated efforts of organic and physical chemists, solid state physicists, and chemical engineers. The scientific questions that emerge from these efforts lie at the frontiers of chemistry and physics research.

  15. Miniature spectroscopic instrumentation: Applications to biology and chemistry

    NASA Astrophysics Data System (ADS)

    Bacon, Christina P.; Mattley, Yvette; DeFrece, Ronald

    2004-01-01

    Spectroscopy is a fundamental analytical tool utilized throughout all of the sciences. For chemistry and biology alone, there are thousands of applications. In the past two decades there have been monumental advances in the miniaturization of components used in spectrophotometric systems. The key components include detector arrays, laser diodes, and fiber optics. Currently, there are numerous commercially available miniature spectrometer systems as well as discrete components that are used by researchers in designing their own systems. A comprehensive summary of current instrumentation available for the design and development of miniaturized spectroscopy applications is described, including detectors, wavelength discriminating components, light sources, and sampling assemblies. Recommendations are made for designing spectrometer systems for specific applications. Current literature is reviewed for chemical and biological applications specifically using miniaturized spectrometer systems with the focus being on ultraviolet-visible-near-infrared spectrometers. The applications include laboratory applications, environmental sensing, on-site industrial analyses, botany and ecology applications, and finally clinical and biochemical studies. Additionally, microspectrometers, two-dimensional arrays, and photonics crystals are discussed in regards to their future role in chemistry and biology applications.

  16. Empowering Girls with Chemistry, Exercise and Physical Activity

    ERIC Educational Resources Information Center

    Clapham, Emily D.; Ciccomascolo, Lori E.; Clapham, Andrew J.

    2015-01-01

    Research suggests that a girl's career interests in the areas of science, technology, engineering and mathematics (STEM) declines between grades 6 and 8. Similarly, in middle school, there is a decrease in physical activity among girls. Researchers at the University of Rhode Island (URI) conducted a chemistry-based science camp that took place…

  17. Polymer Principles in the Undergraduate Physical Chemistry Course. Part 2.

    ERIC Educational Resources Information Center

    Journal of Chemical Education, 1985

    1985-01-01

    Part l (SE 538 305) covered application of classical thermodynamics, polymer crystallinity, and phase diagrams to teaching physical chemistry. This part covers statistical thermodynamics, conformation, molecular weights, rubber elasticity and viscoelasticity, and kinetics of polymerization. Eight polymer-oriented, multiple-choice test questions…

  18. The Lebanese Brevet Chemistry and Physics Examinations: An Exploratory Study

    ERIC Educational Resources Information Center

    Vlaardingerbroek, Barend; Jaber, Lama Z.; Rizk, Nadya G.; Bayoud, Jana M.

    2009-01-01

    The high-stakes Lebanese Brevet examinations are undertaken by almost all school students at the end of year 9 and include papers in Chemistry and Physics. This research presents an analysis of the 2007 examinations in these two science subjects using official statistics and response patterns arising from samples of candidate scripts. The…

  19. Radical Recombination Kinetics: An Experiment in Physical Organic Chemistry.

    ERIC Educational Resources Information Center

    Pickering, Miles

    1980-01-01

    Describes a student kinetic experiment involving second order kinetics as well as displaying photochromism using a wide variety of techniques from both physical and organic chemistry. Describes measurement of (1) the rate of the recombination reaction; (2) the extinction coefficient; and (3) the ESR spectrometer signal. (Author/JN)

  20. Simulation of the Physical Chemistry of Gas Chromatography

    NASA Astrophysics Data System (ADS)

    Haigh, John; Lord, J. R.

    2000-11-01

    A menu allows navigation between the sections of Simulation of the Physical Chemistry of Gas Chromatography. Experiments can be stopped and restarted easily. Many definitions and other technical points are available as hypertext. The student is encouraged to look quickly through the whole package, then to carefully work through the text and experiments.

  1. The Freezing Point Depression Law in Physical Chemistry.

    ERIC Educational Resources Information Center

    Franzen, Hugo F.

    1988-01-01

    Suggests a change in physical chemistry courses to use a slightly more complicated but significantly more useful generalization of the simple freezing point depression law. Lists reasons for the change and presents the treatment of solid-liquid equilibria where solid-solution is allowed. Provides a mathematical treatment. (MVL)

  2. An Integrated, Statistical Molecular Approach to the Physical Chemistry Curriculum

    ERIC Educational Resources Information Center

    Cartier, Stephen F.

    2009-01-01

    As an alternative to the "thermodynamics first" or "quantum first" approaches to the physical chemistry curriculum, the statistical definition of entropy and the Boltzmann distribution are introduced in the first days of the course and the entire two-semester curriculum is then developed from these concepts. Once the tools of statistical mechanics…

  3. A Physical Chemistry Experiment in Polymer Crystallization Kinetics

    ERIC Educational Resources Information Center

    Singfield, Kathy L.; Chisholm, Roderick A.; King, Thomas L.

    2012-01-01

    A laboratory experiment currently used in an undergraduate physical chemistry lab to investigate the rates of crystallization of a polymer is described. Specifically, the radial growth rates of typical disc-shaped crystals, called spherulites, growing between microscope glass slides are measured and the data are treated according to polymer…

  4. Bridging the gap between physics and biology.

    PubMed

    Volodyaev, Ilya

    2005-01-01

    The work is devoted to the historical development of physics and biology. Various aspects of their interactions are shown: antagonism, mutual penetration and a lot of bridges, built or being built between them. The gradual "evolution of the world picture" from going away of the "pre-scientific" animated Universe and the appearance of mechanicism and vitalism to the development of systems and field approaches is traced. The last part of the paper is concerned with some present-day works at the joint between physics and biology.

  5. The new biology and computational statistical physics

    NASA Astrophysics Data System (ADS)

    Rintoul, Mark D.

    2002-06-01

    While it has historically been an exploratory, descriptive, and empirical science, in the past 100 years, biology has become more discovery- and mechanism-oriented. There are a number of ways in which this new paradigm is driving much of the current biological research toward statistical physics. This is happening at a molecular level due to the very large nature of biological molecules, such as proteins and nucleic acids. It is also occurring at the cellular level where random processes play an important role in cell function. There are even examples that describe the behavior of large numbers of individual organisms within one or more species. Finally, this trend has been accelerated with the advent of high-throughput experimental techniques that are driving biology towards information science. Analysis and discovery of the information gained from such experiments will rely heavily on techniques that have traditionally been applied in statistical physics. This paper will focus on examples of how statistical physics techniques are being applied and hope to be applied to biological problems, with an emphasis on high-performance computing. We will also speculate on what we feel are the necessary computing requirements to solve many of the outstanding problems in computational biology using the techniques that will be discussed.

  6. 2010 Tetrapyrroles, Chemistry & Biology of Gordon Research Conference

    SciTech Connect

    Angela Wilks

    2010-07-30

    The objective of the Chemistry & Biology of Tetrapyrroles Gordon Conference is to bring together researchers from diverse disciplines that otherwise would not interact. By bringing biologists, chemists, engineers and clinicians with a common interest in tetrapyrroles the conference provides a forum for cross-disciplinary ideas and collaboration. The perspective provided by biologists, chemists, and clinicians working in fields such as newly discovered defects in human porphyrin metabolism, the myriad of strategies for light harvesting in photosynthetic organisms, novel tetrapyrroles that serve as auxiliary chromophores or enzyme cofactors, synthetic strategies in the design of novel tetrapyrrole scaffolds, and tetrapyrrole based cell signaling and regulatory systems, makes this conference unique in the field. Over the years the growing evidence for the role of tetrapyrroles and their reactive intermediates in cell signaling and regulation has been of increasing importance at this conference. The 2010 conference on Chemistry & Biology of Tetrapyrroles will focus on many of these new frontiers as outlined in the preliminary program listed. Speakers will emphasize unpublished results and new findings in the field. The oral sessions will be followed by the highly interactive afternoon poster sessions. The poster sessions provide all conferees with the opportunity to present their latest research and to exchange ideas in a more informal setting. As in the past, this opportunity will continue during the nightly social gathering that takes place in the poster hall following the evening lectures. All conferees are encouraged to submit and present posters. At the conference the best poster in the areas of biology, chemistry and medicine will be selected by a panel of previous conference chairs.

  7. Persulfides: Current Knowledge and Challenges in Chemistry and Chemical Biology

    PubMed Central

    Park, Chung-Min; Weerasinghe, Laksiri; Day, Jacob J.; Fukuto, Jon M.; Xian, Ming

    2015-01-01

    Recent studies conducted in hydrogen sulfide (H2S) signaling have revealed potential importance of persulfides (RSSH) in redox biology. The inherent instability of RSSH makes these species difficult to study and sometimes controversial results are reported. In this review article we summarize known knowledge about both small molecule persulfides and protein persulfides. Their fundamental physical and chemical properties such as preparation/formation and reactivity are discussed. The biological implications of persulfides and their detection methods are also discussed. PMID:25969163

  8. Bridging physics and biology teaching through modeling

    NASA Astrophysics Data System (ADS)

    Hoskinson, Anne-Marie; Couch, Brian A.; Zwickl, Benjamin M.; Hinko, Kathleen A.; Caballero, Marcos D.

    2014-05-01

    As the frontiers of biology become increasingly interdisciplinary, the physics education community has engaged in ongoing efforts to make physics classes more relevant to life science majors. These efforts are complicated by the many apparent differences between these fields, including the types of systems that each studies, the behavior of those systems, the kinds of measurements that each makes, and the role of mathematics in each field. Nonetheless, physics and biology are both sciences that rely on observations and measurements to construct models of the natural world. In this article, we propose that efforts to bridge the teaching of these two disciplines must emphasize shared scientific practices, particularly scientific modeling. We define modeling using language common to both disciplines and highlight how an understanding of the modeling process can help reconcile apparent differences between the teaching of physics and biology. We elaborate on how models can be used for explanatory, predictive, and functional purposes and present common models from each discipline demonstrating key modeling principles. By framing interdisciplinary teaching in the context of modeling, we aim to bridge physics and biology teaching and to equip students with modeling competencies applicable in any scientific discipline.

  9. Biology is more theoretical than physics.

    PubMed

    Gunawardena, Jeremy

    2013-06-01

    The word "theory" is used in at least two senses--to denote a body of widely accepted laws or principles, as in "Darwinian theory" or "quantum theory," and to suggest a speculative hypothesis, often relying on mathematical analysis, that has not been experimentally confirmed. It is often said that there is no place for the second kind of theory in biology and that biology is not theoretical but based on interpretation of data. Here, ideas from a previous essay are expanded upon to suggest, to the contrary, that the second kind of theory has always played a critical role and that biology, therefore, is a good deal more theoretical than physics.

  10. Odour sampling 1: Physical chemistry considerations.

    PubMed

    Hudson, N; Ayoko, G A

    2008-07-01

    The selection of an odour sampling device may influence the composition of the resulting odour sample. Limited comparison of emission rates derived from turbulent and essentially quiescent sampling devices confirms that the emission rates derived from these devices are quite different. There is therefore compelling evidence that current odour sampling practice should have greater regard for fundamental physical and chemical principles, the nature of the odour source and the conditions created by the sampling device. Such consideration may identify the most appropriate situations under which the use of these devices may or may not be correct.

  11. Teaching a Chemistry MOOC with a Virtual Laboratory: Lessons Learned from an Introductory Physical Chemistry Course

    ERIC Educational Resources Information Center

    O'Malley, Patrick J.; Agger, Jonathan R.; Anderson, Michael W.

    2015-01-01

    An analysis is presented of the experience and lessons learned of running a MOOC in introductory physical chemistry. The course was unique in allowing students to conduct experimental measurements using a virtual laboratory constructed using video and simulations. A breakdown of the student background and motivation for taking the course is…

  12. Advanced Physical Chemistry of Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Li, Jun; Pandey, Gaind P.

    2015-04-01

    The past decade has seen a surge of exciting research and applications of carbon nanotubes (CNTs) stimulated by deeper understanding of their fundamental properties and increasing production capability. The intrinsic properties of various CNTs were found to strongly depend on their internal microstructures. This review summarizes the fundamental structure-property relations of seamless tube-like single- and multiwalled CNTs and conically stacked carbon nanofibers, as well as the organized architectures of these CNTs (including randomly stacked thin films, parallel aligned thin films, and vertically aligned arrays). It highlights the recent development of CNTs as key components in selected applications, including nanoelectronics, filtration membranes, transparent conductive electrodes, fuel cells, electrical energy storage devices, and solar cells. Particular emphasis is placed on the link between the basic physical chemical properties of CNTs and the organized CNT architectures with their functions and performance in each application.

  13. Critical-Thinking Grudge Match: Biology vs. Chemistry--Examining Factors That Affect Thinking Skill in Nonmajors Science

    ERIC Educational Resources Information Center

    Quitadamo, Ian J.; Kurtz, Martha J.; Cornell, Caitlyn Nicole; Griffith, Lindsay; Hancock, Julie; Egbert, Brandi

    2011-01-01

    Chemistry students appear to bring significantly higher critical-thinking skill to their nonmajors course than do biology students. Knowing student preconceptions and thinking ability is essential to learning growth and effective teaching. Of the factors investigated, ethnicity and high school physics had the largest impact on critical-thinking…

  14. Coherence of Physics and Chemistry Curricula in Terms of the Electron Concept

    NASA Astrophysics Data System (ADS)

    Elena, Ivanova

    2016-08-01

    One of the major contradictions in subject teaching is the contradiction between the unity of the world and the discrete separated generalized content of natural sciences that study natural phenomena. These are physics, chemistry, biology and more. One can eliminate the conflict if opens the content's interdisciplinary links set by the events that are studied by different disciplines. The corresponding contexts of the phenomenon content arise depending on the discipline, and they are not enough coordinated. Obviously, we need a mechanism that allows establishing interdisciplinary links in the content quickly and without losing the logic of the material and assess their coherence in academic disciplines. This article uses a quantitative method of coherence assessment elaborated by T.N. Gnitetskaya. The definition of the concept of the semantic state introduced by the authors is given in this article. The method is applied to coherence assessment of physics and chemistry textbooks. The coherence of two pairs of chemistry and physics textbooks by different authors in different combinations was calculated. The most cohered pairs of textbooks (chemistry-physics) were identified. One can recommend using the pair of textbooks for eighth grade that we offered that favors the development of holistic understandings of the world around us.

  15. Selected chapters from general chemistry in physics teaching with the help of e - learning

    NASA Astrophysics Data System (ADS)

    Feszterová, Melánia

    2017-01-01

    Education in the field of natural disciplines - Mathematics, Physics, Chemistry, Ecology and Biology takes part in general education at all schools on the territory of Slovakia. Its aim is to reach the state of balanced development of all personal characteristics of pupils, to teach them correctly identify and analyse problems, propose solutions and above all how to solve the problem itself. High quality education can be reached only through the pedagogues who have a good expertise knowledge, practical experience and high level of pedagogical abilities. The teacher as a disseminator of natural-scientific knowledge should be not only well-informed about modern tendencies in the field, but he/she also should actively participate in project tasks This is the reason why students of 1st year of study (bachelor degree) at the Department of Physics of Constantine the Philosopher University in Nitra attend lectures in the frame of subject General Chemistry. In this paper we present and describe an e - learning course called General Chemistry that is freely accessible to students. One of the aims of this course is to attract attention towards the importance of cross-curricular approach which seems to be fundamental in contemporary natural-scientific education (e.g. between Physics and Chemistry). This is why it is so important to implement a set of new topics and tasks that support development of abilities to realise cross-curricular goals into the process of preparation of future teachers of Physics.

  16. The Intersection of Physics and Biology

    SciTech Connect

    Liphardt, Jan

    2010-05-26

    In April 1953, Watson and Crick largely defined the program of 20th century biology: obtaining the blueprint of life encoded in the DNA. Fifty years later, in 2003, the sequencing of the human genome was completed. Like any major scientific breakthrough, the sequencing of the human genome raised many more questions than it answered. I'll brief you on some of the big open problems in cell and developmental biology, and I'll explain why approaches, tools, and ideas from the physical sciences are currently reshaping biological research. Super-resolution light microscopies are revealing the intricate spatial organization of cells, single-molecule methods show how molecular machines function, and new probes are clarifying the role of mechanical forces in cell and tissue function. At the same time, Physics stands to gain beautiful new problems in soft condensed matter, quantum mechanics, and non-equilibrium thermodynamics.

  17. The Intersection of Physics and Biology

    ScienceCinema

    Liphardt, Jan [University of California, Berkeley, California, United States

    2016-07-12

    In April 1953, Watson and Crick largely defined the program of 20th century biology: obtaining the blueprint of life encoded in the DNA. Fifty years later, in 2003, the sequencing of the human genome was completed. Like any major scientific breakthrough, the sequencing of the human genome raised many more questions than it answered. I'll brief you on some of the big open problems in cell and developmental biology, and I'll explain why approaches, tools, and ideas from the physical sciences are currently reshaping biological research. Super-resolution light microscopies are revealing the intricate spatial organization of cells, single-molecule methods show how molecular machines function, and new probes are clarifying the role of mechanical forces in cell and tissue function. At the same time, Physics stands to gain beautiful new problems in soft condensed matter, quantum mechanics, and non-equilibrium thermodynamics.

  18. Radiation physics, biophysics, and radiation biology. Progress report, December 1, 1993--November 30, 1994

    SciTech Connect

    Hall, E.J.; Zaider, M.

    1994-05-01

    Research at the Center for Radiological Research is a blend of physics, chemistry and biology and epitomizes the multidisciplinary approach towards understanding the mechanisms involved in the health problems resulting from human exposure to ionizing radiations. To an increasing extent, the focus of attention is on biochemistry and the application of the techniques of molecular biology to the problems of radiation biology. Research highlights from the past year are briefly described.

  19. Recent Advances in the Chemistry and Biology of Podophyllotoxins.

    PubMed

    Yu, Xiang; Che, Zhiping; Xu, Hui

    2017-04-03

    Podophyllotoxin and its related aryltetralin cyclolignans belong to a family of important products that exhibit various biological properties (e.g., cytotoxic, insecticidal, antifungal, antiviral, anti-inflammatory, neurotoxic, immunosuppressive, antirheumatic, antioxidative, antispasmogenic, and hypolipidemic activities). This Review provides a survey of podophyllotoxin and its analogues isolated from plants. In particular, recent developments in the elegant total chemical synthesis, structural modifications, biosynthesis, and biotransformation of podophyllotoxin and its analogues are summarized. Moreover, a deoxypodophyllotoxin-based chemosensor for selective detection of mercury ion is described. In addition to the most active podophyllotoxin derivatives in each series against human cancer cell lines and insect pests listed in the tables, the structure-activity relationships of podophyllotoxin derivatives as cytotoxic and insecticidal agents are also outlined. Future prospects and further developments in this area are covered at the end of the Review. We believe that this Review will provide necessary information for synthetic, medicinal, and pesticidal chemistry researchers who are interested in the chemistry and biology of podophyllotoxins.

  20. The Chemistry and Biological Activities of Mimosine: A Review.

    PubMed

    Nguyen, Binh Cao Quan; Tawata, Shinkichi

    2016-08-01

    Mimosine [β-[N-(3-hydroxy-4-oxypyridyl)]-α-aminopropionic acid] is a non-protein amino acid found in the members of Mimosoideae family. There are a considerable number of reports available on the chemistry, methods for estimation, biosynthesis, regulation, and degradation of this secondary metabolite. On the other hand, over the past years of active research, mimosine has been found to have various biological activities such as anti-cancer, antiinflammation, anti-fibrosis, anti-influenza, anti-virus, herbicidal and insecticidal activities, and others. Mimosine is a leading compound of interest for use in the development of RAC/CDC42-activated kinase 1 (PAK1)-specific inhibitors for the treatment of various diseases/disorders, because PAK1 is not essential for the growth of normal cells. Interestingly, the new roles of mimosine in malignant glioma treatment, regenerative dentistry, and phytoremediation are being emerged. These identified properties indicate an exciting future for this amino acid. The present review is focused on the chemistry and recognized biological activities of mimosine in an attempt to draw a link between these two characteristics. Copyright © 2016 John Wiley & Sons, Ltd.

  1. Chemistry, biological activity, and uses of formamidine pesticides.

    PubMed Central

    Hollingworth, R M

    1976-01-01

    The formamidines, a relatively new group of acaricide-insecticides, are novel both in their range of biological activities and in their mode of action, which is presently unknown. This paper is a review of the historical development, properties, structures, uses, and chemistry of this group of pesticides, with particular emphasis on chlordimeform (Galecron or Fundal), N'-4-chloro-o-tolyl-N,N-dimethylformamidine, and amitraz, 1,3=di-(2,4-dimethylphenylimino)-2-methyl-2-azapropane. Their biological activity and uses are defined by their toxicity to spider mites, ticks, and certain insects, and they are particularly effective against juvenile and resistant forms of these organisms. A significant, but poorly understood feature of their field effectiveness is their breadth of toxic action which includes direct lethality, excitant-repellant behavioral effects, and chemosterilization. They are generally of low hazard for nontarget species with the significant exception of predaceous mites. Several aspects of the chemistry of these compounds are considered, including structure--activity relations, synthetic pathways, isomerism and configuration, and their chemical and environmental stability. A significant feature of the metabolism and toxicity of these agents is the possible activation of chlordimeform by N-demethylation in vivo. Strong evidence for this has been presented with the cattle tick, but recent results discussed here suggest that in other species, i.e., mice, German cockroaches or black cutworm eggs, N-demethylation is neither a strong activation nor a detoxication reaction. PMID:789070

  2. On the interrelation between the methodologies of chemistry and physics

    NASA Astrophysics Data System (ADS)

    Anan'eva, E. A.; Mesyats, E. A.; Nagovitsyna, O. A.; Sergievskii, V. V.

    2016-02-01

    Aspects of the methodology and language of chemistry and physics are discussed. Chemistry defines the chemical properties of any substance from the results of its interaction with other substances using the logic of relations. Therefore, describing the properties of substances means using sets of different ideas, including ones that are opposite in meaning. Consequently, depending on the nature of reagents with respect to which properties are established, substances show chemical dualism. This dualism was established in chemistry long before the discovery of wave-particle dualism, to understand which N. Bohr proposed the complementarity principle in 1927. The methodology of natural sciences corresponds to the principle of complementarity and the need to use it to understand the world and record the results in the linguistic reality of several languages.

  3. Platensimycin and platencin: Inspirations for chemistry, biology, enzymology, and medicine.

    PubMed

    Rudolf, Jeffrey D; Dong, Liao-Bin; Shen, Ben

    2016-11-16

    Natural products have served as the main source of drugs and drug leads, and natural products produced by microorganisms are one of the most prevalent sources of clinical antibiotics. Their unparalleled structural and chemical diversities provide a basis to investigate fundamental biological processes while providing access to a tremendous amount of chemical space. There is a pressing need for novel antibiotics with new mode of actions to combat the growing challenge of multidrug resistant pathogens. This review begins with the pioneering discovery and biological activities of platensimycin (PTM) and platencin (PTN), two antibacterial natural products isolated from Streptomyces platensis. The elucidation of their unique biochemical mode of action, structure-activity relationships, and pharmacokinetics is presented to highlight key aspects of their biological activities. It then presents an overview of how microbial genomics has impacted the field of PTM and PTN and revealed paradigm-shifting discoveries in terpenoid biosynthesis, fatty acid metabolism, and antibiotic and antidiabetic therapies. It concludes with a discussion covering the future perspectives of PTM and PTN in regard to natural products discovery, bacterial diterpenoid biosynthesis, and the pharmaceutical promise of PTM and PTN as antibiotics and for the treatment of metabolic disorders. PTM and PTN have inspired new discoveries in chemistry, biology, enzymology, and medicine and will undoubtedly continue to do so.

  4. Physics and the origins of molecular biology.

    PubMed

    Holliday, Robin

    2006-08-01

    Bohr, Delbrück and Schrödinger were physicists who had important influences on biology in the second half of the twentieth century. They thought that future studies of the gene might reveal new principles or paradoxes, analogous to the wave/particle paradox of light propagation, or even new physical laws. This stimulated several physicists to enter the field of biology. Delbrück founded the bacteriophage group which provided one of the roots of molecular biology. Another was X-ray crystallography which led to the discovery of DNA structure. The strength and success of molecular biology came from the many interactions between geneticists, physicists, chemists and biochemists. It was also characterized by a powerful combination of theoretical and experimental approaches.

  5. Physical biology of human brain development

    PubMed Central

    Budday, Silvia; Steinmann, Paul; Kuhl, Ellen

    2015-01-01

    Neurodevelopment is a complex, dynamic process that involves a precisely orchestrated sequence of genetic, environmental, biochemical, and physical events. Developmental biology and genetics have shaped our understanding of the molecular and cellular mechanisms during neurodevelopment. Recent studies suggest that physical forces play a central role in translating these cellular mechanisms into the complex surface morphology of the human brain. However, the precise impact of neuronal differentiation, migration, and connection on the physical forces during cortical folding remains unknown. Here we review the cellular mechanisms of neurodevelopment with a view toward surface morphogenesis, pattern selection, and evolution of shape. We revisit cortical folding as the instability problem of constrained differential growth in a multi-layered system. To identify the contributing factors of differential growth, we map out the timeline of neurodevelopment in humans and highlight the cellular events associated with extreme radial and tangential expansion. We demonstrate how computational modeling of differential growth can bridge the scales–from phenomena on the cellular level toward form and function on the organ level–to make quantitative, personalized predictions. Physics-based models can quantify cortical stresses, identify critical folding conditions, rationalize pattern selection, and predict gyral wavelengths and gyrification indices. We illustrate that physical forces can explain cortical malformations as emergent properties of developmental disorders. Combining biology and physics holds promise to advance our understanding of human brain development and enable early diagnostics of cortical malformations with the ultimate goal to improve treatment of neurodevelopmental disorders including epilepsy, autism spectrum disorders, and schizophrenia. PMID:26217183

  6. Physical biology of human brain development.

    PubMed

    Budday, Silvia; Steinmann, Paul; Kuhl, Ellen

    2015-01-01

    Neurodevelopment is a complex, dynamic process that involves a precisely orchestrated sequence of genetic, environmental, biochemical, and physical events. Developmental biology and genetics have shaped our understanding of the molecular and cellular mechanisms during neurodevelopment. Recent studies suggest that physical forces play a central role in translating these cellular mechanisms into the complex surface morphology of the human brain. However, the precise impact of neuronal differentiation, migration, and connection on the physical forces during cortical folding remains unknown. Here we review the cellular mechanisms of neurodevelopment with a view toward surface morphogenesis, pattern selection, and evolution of shape. We revisit cortical folding as the instability problem of constrained differential growth in a multi-layered system. To identify the contributing factors of differential growth, we map out the timeline of neurodevelopment in humans and highlight the cellular events associated with extreme radial and tangential expansion. We demonstrate how computational modeling of differential growth can bridge the scales-from phenomena on the cellular level toward form and function on the organ level-to make quantitative, personalized predictions. Physics-based models can quantify cortical stresses, identify critical folding conditions, rationalize pattern selection, and predict gyral wavelengths and gyrification indices. We illustrate that physical forces can explain cortical malformations as emergent properties of developmental disorders. Combining biology and physics holds promise to advance our understanding of human brain development and enable early diagnostics of cortical malformations with the ultimate goal to improve treatment of neurodevelopmental disorders including epilepsy, autism spectrum disorders, and schizophrenia.

  7. Competency-Based Reforms of the Undergraduate Biology Curriculum: Integrating the Physical and Biological Sciences

    PubMed Central

    Thompson, Katerina V.; Chmielewski, Jean; Gaines, Michael S.; Hrycyna, Christine A.; LaCourse, William R.

    2013-01-01

    The National Experiment in Undergraduate Science Education project funded by the Howard Hughes Medical Institute is a direct response to the Scientific Foundations for Future Physicians report, which urged a shift in premedical student preparation from a narrow list of specific course work to a more flexible curriculum that helps students develop broad scientific competencies. A consortium of four universities is working to create, pilot, and assess modular, competency-based curricular units that require students to use higher-order cognitive skills and reason across traditional disciplinary boundaries. Purdue University; the University of Maryland, Baltimore County; and the University of Miami are each developing modules and case studies that integrate the biological, chemical, physical, and mathematical sciences. The University of Maryland, College Park, is leading the effort to create an introductory physics for life sciences course that is reformed in both content and pedagogy. This course has prerequisites of biology, chemistry, and calculus, allowing students to apply strategies from the physical sciences to solving authentic biological problems. A comprehensive assessment plan is examining students’ conceptual knowledge of physics, their attitudes toward interdisciplinary approaches, and the development of specific scientific competencies. Teaching modules developed during this initial phase will be tested on multiple partner campuses in preparation for eventual broad dissemination. PMID:23737624

  8. Competency-based reforms of the undergraduate biology curriculum: integrating the physical and biological sciences.

    PubMed

    Thompson, Katerina V; Chmielewski, Jean; Gaines, Michael S; Hrycyna, Christine A; LaCourse, William R

    2013-06-01

    The National Experiment in Undergraduate Science Education project funded by the Howard Hughes Medical Institute is a direct response to the Scientific Foundations for Future Physicians report, which urged a shift in premedical student preparation from a narrow list of specific course work to a more flexible curriculum that helps students develop broad scientific competencies. A consortium of four universities is working to create, pilot, and assess modular, competency-based curricular units that require students to use higher-order cognitive skills and reason across traditional disciplinary boundaries. Purdue University; the University of Maryland, Baltimore County; and the University of Miami are each developing modules and case studies that integrate the biological, chemical, physical, and mathematical sciences. The University of Maryland, College Park, is leading the effort to create an introductory physics for life sciences course that is reformed in both content and pedagogy. This course has prerequisites of biology, chemistry, and calculus, allowing students to apply strategies from the physical sciences to solving authentic biological problems. A comprehensive assessment plan is examining students' conceptual knowledge of physics, their attitudes toward interdisciplinary approaches, and the development of specific scientific competencies. Teaching modules developed during this initial phase will be tested on multiple partner campuses in preparation for eventual broad dissemination.

  9. Physical chemistry and membrane properties of two phosphatidylinositol bisphosphate isomers†

    PubMed Central

    Wang, Yu-Hsiu; Radhakrishnan, Ravi; Janmey, Paul A.

    2015-01-01

    The most highly charged phospholipids, polyphosphoinositides, are often involved in signaling pathways that originate at cell-cell and cell-matrix contacts, and different isomers of polyphosphoinositides have distinct biological functions that cannot be explained by separate highly specific protein ligand binding sites [Lemmon, Nature Reviews Molecular and Cell Biology, 2008, 9 99–111]. PtdIns(3,5)P2 is a low abundance phosphoinositide localized to cytoplasmic-facing membrane surfaces, with relatively few known ligands, yet PtdIns(3,5)P2 plays a key role in controlling membrane trafficking events and cellular stress responses that cannot be duplicated by other phosphoinositides [Dove et al., Nature, 1997, 390, 187–192; Michell, FEBS Journal, 2013, 280, 6281–6294]. Here we show that PtdIns(3,5)P2 is structurally distinct from PtdIns(4,5)P2 and other more common phospholipids, with unique physical chemistry. Using multiscale molecular dynamics techniques on the quantum level, single molecule, and in bilayer settings, we found that the negative charge of PtdIns(3,5)P2 is spread over a larger area, compared to PtdIns(4,5)P2, leading to a decreased ability to bind divalent ions. Additionally, our results match well with experimental data characterizing the cluster forming potential of these isomers in the presence of Ca2+ [Wang et al., Journal of the American Chemical Society, 2012, 134, 3387–3395; van den Bogaart et al., Nature, 2011, 479, 552–555]. Our results demonstrate that the different cellular roles of PtdIns(4,5)P2 and PtdIns(3,5)P2 in vivo are not simply determined by their localization by enzymes that produce or degrade them, but also by their molecular size, ability to chelate ions, and the partial dehydration of those ions, which might affect the ability of PtdIns(3,5)P2 and PtdIns(4,5)P2 to form phosphoinositide-rich clusters in vitro and in vivo. PMID:25901568

  10. The physics and chemistry of the Schottky barrier height

    SciTech Connect

    Tung, Raymond T.

    2014-03-15

    The formation of the Schottky barrier height (SBH) is a complex problem because of the dependence of the SBH on the atomic structure of the metal-semiconductor (MS) interface. Existing models of the SBH are too simple to realistically treat the chemistry exhibited at MS interfaces. This article points out, through examination of available experimental and theoretical results, that a comprehensive, quantum-mechanics-based picture of SBH formation can already be constructed, although no simple equations can emerge, which are applicable for all MS interfaces. Important concepts and principles in physics and chemistry that govern the formation of the SBH are described in detail, from which the experimental and theoretical results for individual MS interfaces can be understood. Strategies used and results obtained from recent investigations to systematically modify the SBH are also examined from the perspective of the physical and chemical principles of the MS interface.

  11. Physical Chemistry Research Toward Proton Exchange Membrane Fuel Cell Advancement.

    PubMed

    Swider-Lyons, Karen E; Campbell, Stephen A

    2013-02-07

    Hydrogen fuel cells, the most common type of which are proton exchange membrane fuel cells (PEMFCs), are on a rapid path to commercialization. We credit physical chemistry research in oxygen reduction electrocatalysis and theory with significant breakthroughs, enabling more cost-effective fuel cells. However, most of the physical chemistry has been restricted to studies of platinum and related alloys. More work is needed to better understand electrocatalysts generally in terms of properties and characterization. While the advent of such highly active catalysts will enable smaller, less expensive, and more powerful stacks, they will require better understanding and a complete restructuring of the diffusion media in PEMFCs to facilitate faster transport of the reactants (O2) and products (H2O). Even Ohmic losses between materials become more important at high power. Such lessons from PEMFC research are relevant to other electrochemical conversion systems, including Li-air batteries and flow batteries.

  12. The chemistry and physics of transition metal clusters

    SciTech Connect

    Parks, E.K.; Jellinek, J.; Knickelbein, M.B.; Riley, S.J.

    1994-06-01

    In this program the authors study the fundamental properties of isolated clusters of transition metal atoms. Experimental studies of cluster chemistry include determination of cluster structure, reactivity, and the nature of cluster-adsorbate interactions. Studies of physical properties include measurements of cluster ionization potentials and photoabsorption cross sections. Theoretical studies focus on the structure and dynamics of clusters, including isomers, phases and phase changes, interactions with molecules, and fragmentation process.

  13. Consideration of coastal carbonate chemistry in understanding biological calcification

    NASA Astrophysics Data System (ADS)

    Fassbender, Andrea J.; Sabine, Christopher L.; Feifel, Kirsten M.

    2016-05-01

    Correlations between aragonite saturation state (ΩAr) and calcification have been identified in many laboratory manipulation experiments aiming to assess biological responses to ocean acidification (OA). These relationships have been used with projections of ΩAr under continued OA to evaluate potential impacts on marine calcifiers. Recent work suggests, however, that calcification in some species may be controlled by the ratio of bicarbonate to hydrogen ion, or the substrate-to-inhibitor ratio (SIR), rather than ΩAr. SIR and ΩAr are not always positively correlated in the natural environment, which means that ΩAr can be a poor indicator of the calcifying environment when ΩAr->1. Highly variable carbonate chemistry in the coastal zone challenges our ability to monitor fluctuations in ΩAr, SIR, and the ΩAr-SIR relationship making it difficult to assess biological OA exposures and vulnerability. Careful consideration of natural variability throughout ocean environments is required to accurately determine the influence of OA on biological calcification.

  14. Advances in the Biology and Chemistry of Sialic Acids

    PubMed Central

    Chen, Xi; Varki, Ajit

    2010-01-01

    Sialic acids are a subset of nonulosonic acids, which are nine-carbon alpha-keto aldonic acids. Natural existing sialic acid-containing structures are presented in different sialic acid forms, various sialyl linkages, and on diverse underlying glycans. They play important roles in biological, pathological, and immunological processes. Sialobiology has been a challenging and yet attractive research area. Recent advances in chemical and chemoenzymatic synthesis as well as large-scale E. coli cell-based production have provided a large library of sialoside standards and derivatives in amounts sufficient for structure-activity relationship studies. Sialoglycan microarrays provide an efficient platform for quick identification of preferred ligands for sialic acid-binding proteins. Future research on sialic acid will continue to be at the interface of chemistry and biology. Research efforts will not only lead to a better understanding of the biological and pathological importance of sialic acids and their diversity, but could also lead to the development of therapeutics. PMID:20020717

  15. Physics met biology, and the consequence was...

    PubMed

    McLeish, Tom

    2011-06-01

    We summarise the contributions to the discussion and the links between them. The complex relationship between the physical and biological sciences demonstrates three "axes of tension": the role of simulation, the interplay between levels of explanation, and the generality of "laws". We identify examples of true synergy between approaches that genuinely explore new research territory, and underscore the contemporary value of the type of discussions contained in this volume.

  16. Biology is more theoretical than physics

    PubMed Central

    Gunawardena, Jeremy

    2013-01-01

    The word “theory” is used in at least two senses—to denote a body of widely accepted laws or principles, as in “Darwinian theory” or “quantum theory,” and to suggest a speculative hypothesis, often relying on mathematical analysis, that has not been experimentally confirmed. It is often said that there is no place for the second kind of theory in biology and that biology is not theoretical but based on interpretation of data. Here, ideas from a previous essay are expanded upon to suggest, to the contrary, that the second kind of theory has always played a critical role and that biology, therefore, is a good deal more theoretical than physics. PMID:23765269

  17. Natural product synthesis at the interface of chemistry and biology

    PubMed Central

    2014-01-01

    Nature has evolved to produce unique and diverse natural products that possess high target affinity and specificity. Natural products have been the richest sources for novel modulators of biomolecular function. Since the chemical synthesis of urea by Wöhler, organic chemists have been intrigued by natural products, leading to the evolution of the field of natural product synthesis over the past two centuries. Natural product synthesis has enabled natural products to play an essential role in drug discovery and chemical biology. With the introduction of novel, innovative concepts and strategies for synthetic efficiency, natural product synthesis in the 21st century is well poised to address the challenges and complexities faced by natural product chemistry and will remain essential to progress in biomedical sciences. PMID:25043880

  18. Natural product synthesis at the interface of chemistry and biology.

    PubMed

    Hong, Jiyong

    2014-08-11

    Nature has evolved to produce unique and diverse natural products that possess high target affinity and specificity. Natural products have been the richest sources for novel modulators of biomolecular function. Since the chemical synthesis of urea by Wöhler, organic chemists have been intrigued by natural products, leading to the evolution of the field of natural product synthesis over the past two centuries. Natural product synthesis has enabled natural products to play an essential role in drug discovery and chemical biology. With the introduction of novel, innovative concepts and strategies for synthetic efficiency, natural product synthesis in the 21st century is well poised to address the challenges and complexities faced by natural product chemistry and will remain essential to progress in biomedical sciences.

  19. Androgen receptor modulators: a marriage of chemistry and biology.

    PubMed

    McEwan, Iain J

    2013-06-01

    Androgenic steroids are important for male development in utero and secondary sexual characteristics at puberty. In addition, androgens play a role in non-reproductive tissues, such as bone and muscle in both sexes. The actions of the androgens testosterone and dihydrotestosterone are mediated by a single receptor protein, the androgen receptor. Over the last 60-70 years there has been considerable research interest in the development of inhibitors of androgen receptor for the management of diseases such as prostate cancer. However, more recently, there is also a growing appreciation of the need for selective androgen modulators that would demonstrate tissue-selective agonist or antagonist activity. The chemistry and biology of selective agonists, antagonists and selective androgen receptor modulators will be discussed in this review.

  20. Investigations of physical model of biological tissue

    NASA Astrophysics Data System (ADS)

    Linkov, Kirill G.; Kisselev, Gennady L.; Loschenov, Victor B.

    1996-12-01

    Physical model of a biological tissue for comparison with earlier created mathematical model of a biological tissue and researches of distribution photosensitizer in a depth was created and investigated. Mathematical model is based on granulated representation of optical medium. The model of a biological tissue was created on the basis of enough thin layers of a special material. For fluorescence excitation laser sources with a various wavelength were used. For investigation of scattering and fluorescent signal laser- fiber spectrum-analyzer LESA-5 was applied. Water solution of aluminum phthalocyanine and oil solution of zinc phthalocyanine were used for receiving of fluorescent signal. Created samples have certain absorbing and fluorescent properties. Scattering properties of samples are close to scattering properties of real human skin. By virtue of layered structure the model permits to simulate as a biological tissue without photosensitizer accumulation in it, as tissue with photosensitizer accumulation with certain distribution in a depth. Dependence of fields distribution on a surface was investigated at change of parameters of a model. Essential changes of distribution on a surface depending on the characteristics of model was revealed. The space and angular characteristics was investigated also. The investigations with physical model correspond to predicted results of theoretical model.

  1. Bridging Physics and Biology Using Resistance and Axons

    ERIC Educational Resources Information Center

    Dyer, Joshua M.

    2014-01-01

    When teaching physics, it is often difficult to get biology-oriented students to see the relevance of physics. A complaint often heard is that biology students are required to take physics for the Medical College Admission Test (MCAT) as part of a "weeding out" process, but that they don't feel like they need physics for biology. Despite…

  2. Analytical chemistry at the interface between materials science and biology

    NASA Astrophysics Data System (ADS)

    O'Brien, Janese Christine

    This work describes several research efforts that lie at the new interfaces between analytical chemistry and other disciplines, namely materials science and biology. In the materials science realm, the search for new materials that may have useful or unique chromatographic properties motivated the synthesis and characterization of electrically conductive sol-gels. In the biology realm, the search for new surface fabrication schemes that would permit or even improve the detection of specific biological reactions motivated the design of miniaturized biological arrays. Collectively, this work represents some of analytical chemistry's newest forays into these disciplines. This dissertation is divided into six chapters. Chapter 1 is an introductory chapter that provides background information pertinent to several key aspects of the work contained in this dissertation. Chapter 2 describes the synthesis and characterization of electrically conductive sol-gels derived from the acid-catalyzed hydrolysis of a vanadium alkoxide. Specifically, this chapter describes our attempts to increase the conductivity of vanadium sol-gels by optimizing the acidic and drying conditions used during synthesis. Chapter 3 reports the construction of novel antigenic immunosensing platforms of increased epitope density using Fab'-SH antibody fragments on gold. Here, X-ray photoelectron spectroscopy (XPS), thin-layer cell (TLC) and confocal fluorescence spectroscopies, and scanning force microscopy (SFM) are employed to characterize the fragment-substrate interaction, to quantify epitope density, and to demonstrate fragment viability and specificity. Chapter 4 presents a novel method for creating and interrogating double-stranded DNA (dsDNA) microarrays suitable for screening protein:dsDNA interactions. Using the restriction enzyme ECoR1, we demonstrate the ability of the atomic force microscope (AFM) to detect changes in topography that result from the enzymatic cleavage of dsDNA microarrays

  3. The Physics and Physical Chemistry of Molecular Machines.

    PubMed

    Astumian, R Dean; Mukherjee, Shayantani; Warshel, Arieh

    2016-06-17

    The concept of a "power stroke"-a free-energy releasing conformational change-appears in almost every textbook that deals with the molecular details of muscle, the flagellar rotor, and many other biomolecular machines. Here, it is shown by using the constraints of microscopic reversibility that the power stroke model is incorrect as an explanation of how chemical energy is used by a molecular machine to do mechanical work. Instead, chemically driven molecular machines operating under thermodynamic constraints imposed by the reactant and product concentrations in the bulk function as information ratchets in which the directionality and stopping torque or stopping force are controlled entirely by the gating of the chemical reaction that provides the fuel for the machine. The gating of the chemical free energy occurs through chemical state dependent conformational changes of the molecular machine that, in turn, are capable of generating directional mechanical motions. In strong contrast to this general conclusion for molecular machines driven by catalysis of a chemical reaction, a power stroke may be (and often is) an essential component for a molecular machine driven by external modulation of pH or redox potential or by light. This difference between optical and chemical driving properties arises from the fundamental symmetry difference between the physics of optical processes, governed by the Bose-Einstein relations, and the constraints of microscopic reversibility for thermally activated processes.

  4. Blurring Boundaries among Physics, Chemistry, & Astronomy: The Mosely Centenary

    NASA Astrophysics Data System (ADS)

    Trimble, Virginia

    2013-04-01

    Scientists are territorial animals, not just about our parking spaces & seats in the colloquium room, but also about our scientific territories, from the narrowest thesis topic (``Who's been working on my Nebula and left it covered with dust?'') to the whole of physics, chemistry, or astronomy. Many 19th century astronomers resented spectroscopes invading their observatories; chemists objected to Moseley's use of X-rays outgaming their retorts and test tubes in 1913; and chemists & physicists typically disbelieve astronomers suggesting new science on the basis of astronomical data (3 other combinations are possible). The talk will explore some of these transgressions, successes and failures. Moseley's own contributions included sorting out the rare earths, putting paid to nebulium, coronium, etc, and putting Prout's hypothesis on a firm foundation ready for the structure Cameron and B2FH would eventually erect there. Back in 1935 Gamow asked whether a new discipline should be called nuclear physics or nuclear chemistry (both now exist within APS and ACS), and 30+ years later, chemist L.S. Trimble was still complaining that physicists had grabbed the territory of atomic and nuclear composition away from chemistry. Some historians agree.

  5. Alcohol Pharmacology Education Partnership: Using Chemistry and Biology Concepts to Educate High School Students about Alcohol

    ERIC Educational Resources Information Center

    Godin, Elizabeth A.; Kwiek, Nicole; Sikes, Suzanne S.; Halpin, Myra J.; Weinbaum, Carolyn A.; Burgette, Lane F.; Reiter, Jerome P.; Schwartz-Bloom, Rochelle D.

    2014-01-01

    We developed the Alcohol Pharmacology Education Partnership (APEP), a set of modules designed to integrate a topic of interest (alcohol) with concepts in chemistry and biology for high school students. Chemistry and biology teachers (n = 156) were recruited nationally to field-test APEP in a controlled study. Teachers obtained professional…

  6. PASCAL Data Base File Description and Indexing Rules in Chemistry, Biology and Medicine.

    ERIC Educational Resources Information Center

    Gaillardin, R.; And Others

    This report on the multidisciplinary PASCAL database describes the files and the indexing rules for chemistry, biology, and medicine. PASCAL deals with all aspects of chemistry within two subfiles whose combined yearly growth is about 100,000 references. The Biopascal file, organized in the two subfiles of Plant Science and Biology and Medicine,…

  7. The physical chemistry of Criegee intermediates in the gas phase

    DOE PAGES

    Osborn, David L.; Taatjes, Craig A.

    2015-07-24

    Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular andmore » bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.« less

  8. The physical chemistry of Criegee intermediates in the gas phase

    SciTech Connect

    Osborn, David L.; Taatjes, Craig A.

    2015-07-24

    Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular and bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.

  9. Chemistry, physico-chemistry and applications linked to biological activities of β-glucans.

    PubMed

    Barsanti, Laura; Passarelli, Vincenzo; Evangelista, Valtere; Frassanito, Anna Maria; Gualtieri, Paolo

    2011-03-01

    β-Glucans is the common name given to a group of chemically heterogeneous polysaccharides. They are long- or short-chain polymers of (1-->3)-β-linked glucose moieties which may be branched, with the branching chains linked to the backbone by a (1-->6)-β linkage. β-(1-->3)-Glucans are widely distributed in bacteria, algae, fungi and plants, where they are involved in cell wall structure and other biological function. β-Glucans have been shown to provide a remarkable range of health benefits, and are especially important against the two most common conventional causes of death in industrialized countries, i.e. cardiovascular diseases (where they promote healthy cholesterol and blood glucose levels) and cancer (where they enhance immune system functions). This Highlight provides a comprehensive and up-to-date commentary on β-glucans, their chemistry, physico-chemistry, functional role in immunological responses, and possible applications as therapeutic tools. In addition, we discuss the mechanism behind their health benefits, which are not yet fully understood.

  10. Physical chemistry and membrane properties of two phosphatidylinositol bisphosphate isomers.

    PubMed

    Slochower, David R; Wang, Yu-Hsiu; Radhakrishnan, Ravi; Janmey, Paul A

    2015-05-21

    The most highly charged phospholipids, polyphosphoinositides, are often involved in signaling pathways that originate at cell-cell and cell-matrix contacts, and different isomers of polyphosphoinositides have distinct biological functions that cannot be explained by separate highly specific protein ligand binding sites [Lemmon, Nat. Rev. Mol. Cell Biol., 2008, 9, 99-111]. PtdIns(3,5)P2 is a low abundance phosphoinositide localized to cytoplasmic-facing membrane surfaces, with relatively few known ligands, yet PtdIns(3,5)P2 plays a key role in controlling membrane trafficking events and cellular stress responses that cannot be duplicated by other phosphoinositides [Dove et al., Nature, 1997, 390, 187-192; Michell, FEBS J., 2013, 280, 6281-6294]. Here we show that PtdIns(3,5)P2 is structurally distinct from PtdIns(4,5)P2 and other more common phospholipids, with unique physical chemistry. Using multiscale molecular dynamics techniques on the quantum level, single molecule, and in bilayer settings, we found that the negative charge of PtdIns(3,5)P2 is spread over a larger area, compared to PtdIns(4,5)P2, leading to a decreased ability to bind divalent ions. Additionally, our results match well with experimental data characterizing the cluster forming potential of these isomers in the presence of Ca(2+) [Wang et al., J. Am. Chem. Soc., 2012, 134, 3387-3395; van den Bogaart et al., Nature, 2011, 479, 552-555]. Our results demonstrate that the different cellular roles of PtdIns(4,5)P2 and PtdIns(3,5)P2in vivo are not simply determined by their localization by enzymes that produce or degrade them, but also by their molecular size, ability to chelate ions, and the partial dehydration of those ions, which might affect the ability of PtdIns(3,5)P2 and PtdIns(4,5)P2 to form phosphoinositide-rich clusters in vitro and in vivo.

  11. Modelling biological complexity: a physical scientist's perspective

    PubMed Central

    Coveney, Peter V; Fowler, Philip W

    2005-01-01

    We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the

  12. Modelling biological complexity: a physical scientist's perspective.

    PubMed

    Coveney, Peter V; Fowler, Philip W

    2005-09-22

    We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the

  13. NASA physics and chemistry experiments in-space program

    NASA Technical Reports Server (NTRS)

    Gabris, E. A.

    1981-01-01

    The Physics and Chemistry Experiments Program (PACE) is part of the Office of Aeronautics and Space Technology (OAST) research and technology effort in understanding the fundamental characteristics of physics and chemical phenomena. This program seeks to increase the basic knowledge in these areas by well-planned research efforts which include in-space experiments when the limitations of ground-based activities precludes or restricts the achievement of research goals. Overview study areas are concerned with molecular beam experiments for Space Shuttle, experiments on drops and bubbles in a manned earth-orbiting laboratory, the study of combustion experiments in space, combustion experiments in orbiting spacecraft, gravitation experiments in space, and fluid physics, thermodynamics, and heat-transfer experiments. Procedures for the study program have four phases. An overview study was conducted in the area of materials science.

  14. An Investigation of the Factors Influencing Student Performance in Physical Chemistry.

    ERIC Educational Resources Information Center

    Nicoll, Gayle; Francisco, Joseph S.

    2001-01-01

    Studies students in two physical chemistry classes to determine what factors influenced their performance, what their perceptions were of their own abilities, and what factors they believe influence student performance. Concludes that achievement in a physical chemistry course designed for chemistry fields is significantly related to students'…

  15. Developing Technical Writing Skills in the Physical Chemistry Laboratory: A Progressive Approach Employing Peer Review

    ERIC Educational Resources Information Center

    Gragson, Derek E.; Hagen, John P.

    2010-01-01

    Writing formal "journal-style" lab reports is often one of the requirements chemistry and biochemistry students encounter in the physical chemistry laboratory. Helping students improve their technical writing skills is the primary reason this type of writing is a requirement in the physical chemistry laboratory. Developing these skills is an…

  16. Physics of a random biological process

    NASA Astrophysics Data System (ADS)

    Canessa, E.; Calmetta, A.

    1994-07-01

    We analyze the successive fluctuations of the daytime and nighttime sleep pattern of a newborn baby by using tools of far-from-equilibrium statistical physics. We find that this class of natural random biological process displays a remarkable long-range power-law correlation that extends for, at least, the first six months of life. Such a scaling behavior might help to characterize the underlying dynamics of the (early) growth and development of humans through analyzing the time series generated when asleep.

  17. The Validity of Stirling's Approximation: A Physical Chemistry Project

    NASA Astrophysics Data System (ADS)

    Wallner, A. S.; Brandt, K. A.

    1999-10-01

    Often in physical chemistry courses, the direct proof of Stirling's approximation is omitted owing to the complexity of the mathematics involved. We present an accessible proof of this result that requires only an understanding of first-year calculus. We also present an undergraduate project dealing with the validity of Stirling's approximation. This assignment asks students to study the validity of the formula using mathematical tools such as programmable calculators, commercially available computer software such as Derive, and basic computer programming. Examples of students' solutions are provided.

  18. An Aerosol Physical Chemistry Model for the Upper Troposphere

    NASA Technical Reports Server (NTRS)

    Lin, Jin-Sheng

    2001-01-01

    This report is the final report for the Cooperative Agreement NCC2-1000. The tasks outlined in the various proposals are listed with a brief comment as to the research performed. The publications titles are: The effects of particle size and nitric acid uptake on the homogenous freezing of sulfate aerosols; Parameterization of an aerosol physical chemistry model (APCM) for the NH3/H2SO4/HNO3/H2O system at cold temperatures; and The onset, extent and duration of dehydration in the Southern Hemisphere polar vortex.

  19. Integrative Biological Chemistry Program Includes The Use Of Informatics Tools, GIS And SAS Software Applications

    PubMed Central

    D’Souza, Malcolm J.; Kashmar, Richard J.; Hurst, Kent; Fiedler, Frank; Gross, Catherine E.; Deol, Jasbir K.; Wilson, Alora

    2015-01-01

    Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning courses using instrumentation, data-collection, data-storage, statistical-modeling analysis, visualization, and computational techniques. In this revised curriculum, students begin with a traditional set of biology, chemistry, physics, and mathematics major core-requirements, a geographic information systems (GIS) course, a choice of an instrumental analysis course or a statistical analysis systems (SAS) programming course, and then, students can add major-electives that further add depth and value to their future post-graduate specialty areas. Open-sourced georeferenced census, health and health disparity data were coupled with GIS and SAS tools, in a public health surveillance system project, based on US county zip-codes, to develop use-cases for chronic adult obesity where income, poverty status, health insurance coverage, education, and age were categorical variables. Across the 48 contiguous states, obesity rates are found to be directly proportional to high poverty and inversely proportional to median income and educational achievement. For the State of Delaware, age and educational attainment were found to be limiting obesity risk-factors in its adult population. Furthermore, the 2004–2010 obesity trends showed that for two of the less densely populated Delaware counties; Sussex and Kent, the rates of adult obesity were found to be progressing at much higher proportions when compared to the national average. PMID:26191337

  20. Integrative Biological Chemistry Program Includes The Use Of Informatics Tools, GIS And SAS Software Applications.

    PubMed

    D'Souza, Malcolm J; Kashmar, Richard J; Hurst, Kent; Fiedler, Frank; Gross, Catherine E; Deol, Jasbir K; Wilson, Alora

    Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning courses using instrumentation, data-collection, data-storage, statistical-modeling analysis, visualization, and computational techniques. In this revised curriculum, students begin with a traditional set of biology, chemistry, physics, and mathematics major core-requirements, a geographic information systems (GIS) course, a choice of an instrumental analysis course or a statistical analysis systems (SAS) programming course, and then, students can add major-electives that further add depth and value to their future post-graduate specialty areas. Open-sourced georeferenced census, health and health disparity data were coupled with GIS and SAS tools, in a public health surveillance system project, based on US county zip-codes, to develop use-cases for chronic adult obesity where income, poverty status, health insurance coverage, education, and age were categorical variables. Across the 48 contiguous states, obesity rates are found to be directly proportional to high poverty and inversely proportional to median income and educational achievement. For the State of Delaware, age and educational attainment were found to be limiting obesity risk-factors in its adult population. Furthermore, the 2004-2010 obesity trends showed that for two of the less densely populated Delaware counties; Sussex and Kent, the rates of adult obesity were found to be progressing at much higher proportions when compared to the national average.

  1. Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology

    PubMed Central

    Cook, Daniel L.; Bookstein, Fred L.; Gennari, John H.

    2011-01-01

    As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities—molecules, cells, organs—are well-established, there are no principled ontologies of physical properties—energies, volumes, flow rates—of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB), a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration. PMID:22216106

  2. Physical properties of biological entities: an introduction to the ontology of physics for biology.

    PubMed

    Cook, Daniel L; Bookstein, Fred L; Gennari, John H

    2011-01-01

    As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB), a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration.

  3. The Cytoskeleton: Mechanical, Physical, and Biological Interactions

    NASA Technical Reports Server (NTRS)

    1996-01-01

    This workshop, entitled "The Cytoskeleton: Mechanical, Physical, and Biological Interactions," was sponsored by the Center for Advanced Studies in the Space Life Sciences at the Marine Biological Laboratory. This Center was established through a cooperative agreement between the MBL and the Life Sciences Division of the National Aeronautics and Space Administration. To achieve these goals, the Center sponsors a series of workshops on various topics in the life sciences. Elements of the cytoskeleton have been implicated in the effects of gravity on the growth of plants fungi. An intriguing finding in this regard is the report indicating that an integrin-like protein may be the gravireceptor in the internodal cells of Chara. Involvement of the cytoskeleton in cellular graviperception of the basidiomycete Flammulina velutipes has also been reported. Although the responses of mammalian cells to gravity are not well documented, it has been proposed that integrins can act as mechanochemical transducers in mammalian cells. Little is known about the integrated mechanical and physical properties of cytoplasm, this workshop would be the best place to begin developing interdisciplinary approaches to the effects of mechanical stresses on cells and their most likely responsive cytoplasmic elements- the fibrous proteins comprising the cytoskeleton.

  4. Methylglyoxal in living organisms: chemistry, biochemistry, toxicology and biological implications.

    PubMed

    Kalapos, M P

    1999-11-22

    Despite the growing interest towards methylglyoxal and glyoxalases their real role in metabolic network is still obscure. In the light of developments several reviews have been published in this field mainly dealing with only a narrow segment of this research area. In this article a trial is made to present a comprehensive overview of methylglyoxal research, extending discussion from chemistry to biological implications by reviewing some important characteristics of methylglyoxal metabolism and toxicity in a wide variety of species, and emphasizing the action of methylglyoxal on energy production, free radical generation and cell killing. Special attention is paid to the discussion of alpha-oxoaldehyde production in the environment as a potential risk factor and to the possible role of this a-dicarbonyl in diseases. Concerning the interaction of methylglyoxal with biological macromolecules (DNA, RNA, proteins) an earlier review (Kalapos, Toxicology Letters, 73, 1994, 3-24) means a supplementation to this paper, thus hoping the avoidance of unnecessary bombast. The paper arrives at the conclusion that since the early stage of evolution the function of methylglyoxalase pathway has been related to carbohydrate metabolism, but its significance has been changed over the thousands of years. Namely, at the beginning of evolution methylglyoxalase path was essential for the reductive citric acid cycle as an anaplerotic route, while in the extant metabolism it concerns with the detoxification of methylglyoxal and plays some regulatory role in triose-phosphate household. As there is a tight junction between methylglyoxal and carbohydrate metabolism its pathological role in the events of the development of diabetic complications emerges in a natural manner and further progress is hoped in this field. In contrast, significant advancement cannot be expected in relation to cancer research.

  5. Chemistry, biogenesis, and biological activities of Cinnamomum zeylanicum.

    PubMed

    Jayaprakasha, G K; Rao, L Jagan Mohan

    2011-07-01

    The genus Cinnamomum comprises of several hundreds of species, which are distributed in Asia and Australia. Cinnamomum zeylanicum, the source of cinnamon bark and leaf oils, is an indigenous tree of Sri Lanka, although most oil now comes from cultivated areas. C. zeylanicum is an important spice and aromatic crop having wide applications in flavoring, perfumery, beverages, and medicines. Volatile oils from different parts of cinnamon such as leaves, bark, fruits, root bark, flowers, and buds have been isolated by hydro distillation/steam distillation and supercritical fluid extraction. The chemical compositions of the volatile oils have been identified by GC and GC-MS. More than 80 compounds were identified from different parts of cinnamon. The leaf oil has a major component called eugenol. Cinnamaldehyde and camphor have been reported to be the major components of volatile oils from stem bark and root bark, respectively. Trans-cinnamyl acetate was found to be the major compound in fruits, flowers, and fruit stalks. These volatile oils were found to exhibit antioxidant, antimicrobial, and antidiabetic activities. C. zeylanicum bark and fruits were found to contain proanthocyandins with doubly linked bis-flavan-3-ol units in the molecule. The present review provides a coherent presentation of scattered literature on the chemistry, biogenesis, and biological activities of cinnamon.

  6. Chemistry and Biology of the Pyrrole-Imidazole Alkaloids.

    PubMed

    Lindel, Thomas

    2017-01-01

    More than a decade after our last review on the chemistry of the pyrrole-imidazole alkaloids, it was time to analyze once more the developments in that field. The comprehensive article focusses on the total syntheses of pyrrole-imidazole alkaloids that have appeared since 2005. The classic monomeric pyrrole-imidazole alkaloids have all been synthesized, sometimes primarily to demonstrate the usefulness of a new method, as in the case of the related molecules agelastatin A and cyclooroidin with more than 15 syntheses altogether. The phakellin skeleton has been made more than 10 times, too, with a focus on the target structure itself. Thus, some of the pyrrole-imidazole alkaloids are now available in gram amounts, and the supply problem has been solved. The total synthesis of the dimeric pyrrole-imidazole alkaloids is still mostly in its pioneering phase with two routes to palau'amine and massadine discovered and three routes to the axinellamines and ageliferin. In addition, the review summarizes recent discoveries regarding the biological activity of the pyrrole-imidazole alkaloids. Regarding the biosynthesis of sceptrin, a pathway is proposed that starts from nagelamide I and proceeds via two electrocyclizations and reduction.

  7. Physical biology in cancer. 1. Cellular physics of cancer metastasis.

    PubMed

    Moore, Nicole M; Nagahara, Larry A

    2014-01-15

    One of the major challenges in cancer research today is developing new therapeutic strategies to control metastatic disease, the spread of cancer cells from a primary tumor to seed in a distant site. Advances in diagnosis and treatment options have increased the survival rate for most patients with local tumors; however, less progress has been made in treatment of disseminated disease. According to the SEER Cancer Statistics Review, 1975-2010, in the case of breast and prostate cancers, only one in four patients diagnosed with distant metastatic disease will survive more than five years. Current research efforts largely focus on identifying biological targets, such as specific genes and signaling pathways that drive two key steps of metastasis, invasion from the primary tumor and growth in the secondary site. On the other hand, there are phenotypic traits and dynamics in the metastatic process that are not encoded by single genes or signaling pathways but, rather, a larger system of events and biophysical characteristics. Connecting genomic and pathway investigations with quantitative physical phenotypic characteristics of cells, the physical microenvironment, and the physical spatiotemporal interactions of the metastatic process provides a stronger complementary understanding of the disease.

  8. Stimulated Raman adiabatic passage in physics, chemistry, and beyond

    NASA Astrophysics Data System (ADS)

    Vitanov, Nikolay V.; Rangelov, Andon A.; Shore, Bruce W.; Bergmann, Klaas

    2017-01-01

    The technique of stimulated Raman adiabatic passage (STIRAP), which allows efficient and selective population transfer between quantum states without suffering loss due to spontaneous emission, was introduced in 1990 by Gaubatz et al.. Since then STIRAP has emerged as an enabling methodology with widespread successful applications in many fields of physics, chemistry, and beyond. This article reviews the many applications of STIRAP emphasizing the developments since 2001, the time when the last major review on the topic was written (Vitanov, Fleischhauer et al.). A brief introduction into the theory of STIRAP and the early applications for population transfer within three-level systems is followed by the discussion of several extensions to multilevel systems, including multistate chains and tripod systems. The main emphasis is on the wide range of applications in atomic and molecular physics (including atom optics, cavity quantum electrodynamics, formation of ultracold molecules, etc.), quantum information (including single- and two-qubit gates, entangled-state preparation, etc.), solid-state physics (including processes in doped crystals, nitrogen-vacancy centers, superconducting circuits, semiconductor quantum dots and wells), and even some applications in classical physics (including waveguide optics, polarization optics, frequency conversion, etc.). Promising new prospects for STIRAP are also presented (including processes in optomechanics, precision experiments, detection of parity violation in molecules, spectroscopy of core-nonpenetrating Rydberg states, population transfer with x-ray pulses, etc.).

  9. Biological grand universality and its physical challenge

    NASA Astrophysics Data System (ADS)

    Azbel‧, Mark Ya.

    1999-12-01

    Presented quantitative laws of metabolism, mortality and evolution are valid for animals from bacteria to mammals and demonstrate grand universality in biology. Its microscopic origin may be a physical and mathematical challenge. Natural evolution is accurately reduced to the continuous one, “weak” and “strong” Gould-Eldredge spurts. The discovery of writing, i.e. non-genetic, long range, collective information transfer from generation to generation with human rather than natural selection, leads to post-evolution. Technological post-evolution is exponentially rapid and may lead to the extinction of a civilization. This might resolve the Fermi-Hart paradox: if extra-terrestrial intelligence exists, why it cannot be contacted?

  10. Insights from a Subject Knowledge Enhancement Course for Preparing New Chemistry and Physics Teachers

    ERIC Educational Resources Information Center

    Inglis, Michael; Mallaburn, Andrea; Tynan, Richard; Clays, Ken; Jones, Robert Bryn

    2013-01-01

    A recent Government response to shortages of new physics and chemistry teachers is the extended subject knowledge enhancement (SKE) course. Graduates without a physics or chemistry bachelor degree are prepared by an SKE course to enter a Postgraduate Certificate in Education (PGCE) programme to become science teachers with a physics or chemistry…

  11. Guide for Teaching Chemistry-Physics Combined 1-2, 3-4 (PSSC - CHEMS).

    ERIC Educational Resources Information Center

    Millstone, H. George

    This guide is written for a combined physics-chemistry course taught over a two-year period. The subject matter contains the major ideas in Chemical Education Materials Study (CHEMS) Chemistry and Physical Science Study Committee (PSSC) Physics. The guide includes discussion of text references, laboratory experiments, films, testing and evaluation…

  12. Classical Challenges in the Physical Chemistry of Polymer Networks and the Design of New Materials.

    PubMed

    Wang, Rui; Sing, Michelle K; Avery, Reginald K; Souza, Bruno S; Kim, Minkyu; Olsen, Bradley D

    2016-12-20

    incorporating shear-thinning coiled-coil protein motifs into the midblock of a micelle-forming block copolymer, we are able to responsively adjust the gel toughness through controlling the nanostructure. Finally, we review the development of novel application-oriented materials that emerge from our enhanced understanding of gel physical chemistry, including injectable gel hemostats designed to treat internal wounds and engineered nucleoporin-like polypeptide (NLP) hydrogels that act as biologically selective filters. We believe that the fundamental physical chemistry questions articulated in this Account will provide inspiration to fully understand the design of polymer networks, a group of mysterious yet critically important materials.

  13. Physical chemistry of nucleic acids and their complexes.

    PubMed

    Ghirlando, Rodolfo; Felsenfeld, Gary

    2013-12-01

    Studies of the physical properties of nucleic acids began almost immediately following the discovery of the DNA structure. Early investigations focused on the stability and specificity of multi-strand polynucleotide complexes, then gradually on their interaction with other molecules, particularly proteins. As molecular and structural biology expanded to provide detailed information about biochemical mechanisms, physical studies eventually acquired the additional constraint that they should be relevant to functioning biological systems. We describe work in our laboratory that began with investigations of relatively simple questions about the role of electrostatic interactions in the stabilization of multi-strand nucleic acid structures, and evolved to studies of chromatin structure in vitro and within the nucleus.

  14. Molecular Signposts of the Physics and Chemistry of Planet Formation

    NASA Astrophysics Data System (ADS)

    Cleeves, Lauren Ilsedore

    Observations of molecules in planet-forming circumstellar disks are powerful diagnostic tools, enabling characterization of both gas composition and underlying physical conditions using molecular excitation. My thesis has primarily focused on the role of disk structure and ionization for the chemistry of disks and the corresponding submillimeter emission. Changes in the overall morphology of disks, including inner holes or gaps, significantly alters the stellar irradiation of the disk, which will affect the disk heating, especially at the walls of an inner hole (Chapter 2). I have modeled the 3D chemistry of gapped disks, carved out by planets, including for the first time heating by a luminous protoplanet. The planet sublimates ices beyond expected disk "snow-lines" leading to observable signatures detectable with ALMA (Chapter 3). Regarding ionization, I have studied disk ionization by cosmic rays (Chapter 4), short-lived radionuclides (Chapter 5), and X-rays from the central star (Chapter 6). In Chapter 6, I investigated the molecular dependence on each of these processes and made testable predictions for sensitive submillimeter observations to map out disk ionization, which I applied to the TW Hya disk, finding a substantially lower than interstellar cosmic ray rate (Chapter 7). One of the major implications of this work is related to the formation chemistry of water, which requires ionization to proceed. In the absence of water-formation in the solar nebula protoplanetary disk, this work demonstrates that there must be a substantial inheritance of water from earlier evolutionary stages, pre-dating the Sun's formation (Chapter 8). Together, these projects have also enabled the development of a comprehensive 2D and 3D disk modeling framework, useful for parameter space studies and source-targeted modeling.

  15. Exploration of the central dogma at the interface of chemistry and biology: 2010 Yale Chemical Biology Symposium.

    PubMed

    Zhou, Alice Qinhua

    2010-09-01

    Ever since the term "central dogma" was coined in 1958, researchers have sought to control information flow from nucleic acids to proteins. Talks delivered by Drs. Anna Pyle and Hiroaki Suga at this year's Chemical Biology Symposium at Yale in May 2010 applauded recent advances in this area, at the interface between chemistry and biology.

  16. The universal numbers. From Biology to Physics.

    PubMed

    Marchal, Bruno

    2015-12-01

    I will explain how the mathematicians have discovered the universal numbers, or abstract computer, and I will explain some abstract biology, mainly self-reproduction and embryogenesis. Then I will explain how and why, and in which sense, some of those numbers can dream and why their dreams can glue together and must, when we assume computationalism in cognitive science, generate a phenomenological physics, as part of a larger phenomenological theology (in the sense of the greek theologians). The title should have been "From Biology to Physics, through the Phenomenological Theology of the Universal Numbers", if that was not too long for a title. The theology will consist mainly, like in some (neo)platonist greek-indian-chinese tradition, in the truth about numbers' relative relations, with each others, and with themselves. The main difference between Aristotle and Plato is that Aristotle (especially in its common and modern christian interpretation) makes reality WYSIWYG (What you see is what you get: reality is what we observe, measure, i.e. the natural material physical science) where for Plato and the (rational) mystics, what we see might be only the shadow or the border of something else, which might be non physical (mathematical, arithmetical, theological, …). Since Gödel, we know that Truth, even just the Arithmetical Truth, is vastly bigger than what the machine can rationally justify. Yet, with Church's thesis, and the mechanizability of the diagonalizations involved, machines can apprehend this and can justify their limitations, and get some sense of what might be true beyond what they can prove or justify rationally. Indeed, the incompleteness phenomenon introduces a gap between what is provable by some machine and what is true about that machine, and, as Gödel saw already in 1931, the existence of that gap is accessible to the machine itself, once it is has enough provability abilities. Incompleteness separates truth and provable, and machines can

  17. Applied Biology and Chemistry. Course Materials: Chemistry 111, 112, 113, 114. Seattle Tech Prep Applied Academics Project.

    ERIC Educational Resources Information Center

    South Seattle Community Coll., Washington.

    This publication contains materials for four courses in Applied Biology/Chemistry in the Applied Academics program at South Seattle Community College. It begins with the article, "Community College Applied Academics: The State of the Art?" (George B. Neff), which describes the characteristics, model, courses, and coordination activity…

  18. Determination of Rate Constants for Ouabain Inhibition of Adenosine Triphosphatase: An Undergraduate Biological Chemistry Laboratory Experiment

    ERIC Educational Resources Information Center

    Sall, Eri; And Others

    1978-01-01

    Describes an undergraduate biological chemistry laboratory experiment which provides students with an example of pseudo-first-order kinetics with the cardiac glycoside inhibition of mammalism sodium and potassium transport. (SL)

  19. Ontology of physics for biology: representing physical dependencies as a basis for biological processes

    PubMed Central

    2013-01-01

    Background In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based biosimulation models. We introduced OPB:Physical entity and OPB:Physical property classes that extend available spatiotemporal representations of physical entities and processes to explicitly represent the thermodynamics and dynamics of physiological processes. Our utilitarian, long-term aim is to develop computational tools for creating and querying formalized physiological knowledge for use by multiscale “physiome” projects such as the EU’s Virtual Physiological Human (VPH) and NIH’s Virtual Physiological Rat (VPR). Results Here we describe the OPB:Physical dependency taxonomy of classes that represent of the laws of classical physics that are the “rules” by which physical properties of physical entities change during occurrences of physical processes. For example, the fluid analog of Ohm’s law (as for electric currents) is used to describe how a blood flow rate depends on a blood pressure gradient. Hooke’s law (as in elastic deformations of springs) is used to describe how an increase in vascular volume increases blood pressure. We classify such dependencies according to the flow, transformation, and storage of thermodynamic energy that occurs during processes governed by the dependencies. Conclusions We have developed the OPB and annotation methods to represent the meaning—the biophysical semantics—of the mathematical statements of physiological analysis and the biophysical content of models and datasets. Here we describe and discuss our approach to an ontological representation of physical laws (as dependencies) and properties as encoded for the mathematical analysis of biophysical processes. PMID:24295137

  20. Physics and Chemistry in UV Illuminated Regions: the Horsehead Case

    NASA Astrophysics Data System (ADS)

    Guzman, Viviana V.; Pety, Jérôme; Gratier, Pierre; Goicoechea, Javier; Gerin, Maryvonne; Roueff, Evelyne

    2014-06-01

    Molecular lines are used to trace the structure of the interstellar medium and the physical conditions of the gas in different environments, from protoplanetary disks to high-z galaxies. To fully benefit from the diagnostic power of molecular lines, the formation and destruction paths of the molecules, including the interplay between gas-phase and grain surface chemistry, must be quantitatively understood. Well-defined sets of observations of simple template sources are key to benchmark the theoretical models. In this context the PDR of the Horsehead mane is a particularly interesting case because it has a simple geometry (almost 1D, viewed edge-on) and the density profile across the PDR is well constrained. In this talk, I will summarize our recent results on the ISM physics and chemistry in the Horsehead, from a complete and unbiased line survey at 1, 2 and 3mm performed with the IRAM-30m telescope, where approximately 30 species (plus their isotopologues) are detected with up to 7 atoms. I will show the importance of the interplay between the solid and gas phase chemistry in the formation of (complex) organic molecules, like H_2CO, CH_3OH, and CH_3CN, which reveal that photo-desorption of ices is an efficient mechanism to release molecules into the gas phase. The case of CH_3CN is especially surprising, as it is 40 times more abundant in the warm (Tkin˜60 K) UV-illuminated edge of the nebula, than in the shielded and colder (Tkin˜20 K) inner layers. I will show that complex molecules, such as HCOOH, CH_2CO, CH_3CHO, and CH_3CCH are easily detected in the PDR. I will also discuss new diagnostics of the UV-illuminated gas, like CF^+ (for which we recently resolved its hyperfine structure for the first time), which is observable from the ground, and we propose it can be used as a proxy of C^+. I will finish by reporting the first detection of a new molecule, recently confirmed to be the small hydrocarbon C_3H^+, which shows that photo-erosion of PAHs is needed to

  1. PREFACE: XV International Seminar on Physics and Chemistry of Solids

    NASA Astrophysics Data System (ADS)

    Kotur, Bogdan; Brągiel, Piotr

    2011-03-01

                      Logo     Logo The XV International Seminar on Physics and Chemistry of Solids (ISPCS15) was held from 7-10 June 2009 in Szklarska Poręba. Over eighty participants joined together in this mountain resort, at the foot of Szrenica peak, in the Polish part of the Sudety range. The majority or participants, in accordance with Seminar tradition, were from Ukraine and Poland. The pleasant and warm atmosphere created by the organizers was conducive to fruitful discussions, making new contacts and to joyful gatherings with friends. Even the rainy weather could not change that. Lectures and communications mainly covered the fields of solid state physics and chemistry, and possible applications. This time, however, a new section was introduced - one devoted to modern topics in liquid chemistry. Sometimes such a look over the borders of scientific specialties leads to interesting insights and original research solutions. Some of the papers presented during ISPCS15 are collected in this volume. Their diversity is representative of both the scope and character of this Seminar. The majority of the papers are research reports, but a review article and a paper focussed on problems connected with environmental protection are also included. This Conference has functioned for over a decade due to the permanent support of the rectors of both co-organizing universities: Professor Ivan Vakarchuk from Ivan Franko National University of Lviv and Professor Zygmunt Bąk from Jan Dlugosz University in Częstochowa. It is our pleasure, on behalf of the all participants of the past Seminars, to express our gratitude for this assistance. We would also like to thank all the invited speakers who kindly accepted our invitation, namely Professors Roman Gladyshevskii (Ivan Franko National University, Lviv, Ukraine), Mihaela Gulea (Laboratoire de Chimie Moleculare et Thioorganique, CAEN, France), Osama I Abd El-Salam (National Research

  2. Some physics problems in biological networks

    NASA Astrophysics Data System (ADS)

    Bialek, William

    2007-03-01

    Most of the interesting things that happen in living organisms require interactions among many components, and it is convenient to think of these as a ``network'' of interactions. We use this language at the level of single molecules (the network of interactions among amino acids that determine protein structure), single cells (the network of protein-DNA interactions responsible for the regulation of gene expression) and complex multicellular organisms (the networks of neurons in our brain). In this talk I'll try to look at two very different kinds of theoretical physics problems that arise in thinking about such networks. The first problems are phenomenological: Given what our experimentalists friends can measure, can we generate a global view of network function and dynamics? I'll argue that maximum entropy methods can be useful here, and show how such methods have been used in very recent work on networks of neurons, enzymes, genes and (in disguise) amino acids. In this line of reasoning there are of course interesting connections to statistical mechanics, and we'll see that natural statistical mechanics questions about the underlying models actually teach us something about how the real biological system works, in ways that will be tested through new experiments. In the second half of the talk I'll ask if there are principles from which we might actually be able to predict the structure and dynamics of biological networks. I'll focus on optimization principles, in particular the optimization of information flow in transcriptional regulation. Even setting up these arguments forces us to think critically about our understanding of the signals, specificity and noise in these systems, all current topics of research. Although we don't know if we have the right principles, trying to work out the consequences of such optimization again suggests new experiments.

  3. Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry.

    PubMed

    Bax, Ben; Chung, Chun Wa; Edge, Colin

    2017-02-01

    There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms. This ambiguity is far from rare, since about 25% of drugs have more than one tautomeric form. This paper focuses on the most common, `prototropic', tautomers, which are isomers that readily interconvert by the exchange of an H atom accompanied by the switch of a single and an adjacent double bond. Hydrogen-exchange rates and different protonation states of compounds (e.g. buffers) are also briefly discussed. The difference in heavy (non-H) atom positions between two tautomers can be small, and careful refinement of all possible tautomers may single out the likely bound ligand tautomer. Experimental methods to determine H-atom positions, such as neutron crystallography, are often technically challenging. Therefore, chemical knowledge and computational approaches are frequently used in conjugation with experimental data to deduce the bound tautomer state. Proton movement is a key feature of many enzymatic reactions, so understanding the orchestration of hydrogen/proton motion is of critical importance to biological chemistry. For example, structural studies have suggested that, just as a chemist may use heat, some enzymes use directional movement to protonate specific O atoms on phosphates to catalyse phosphotransferase reactions. To inhibit `wriggly' enzymes that use movement to effect catalysis, it may be advantageous to have inhibitors that can maintain favourable contacts by adopting different tautomers as the enzyme `wriggles'.

  4. Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry

    PubMed Central

    Bax, Ben; Chung, Chun-wa; Edge, Colin

    2017-01-01

    There are more H atoms than any other type of atom in an X-ray crystal structure of a protein–ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are ‘hard to see’. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in ‘riding positions’. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms. This ambiguity is far from rare, since about 25% of drugs have more than one tautomeric form. This paper focuses on the most common, ‘prototropic’, tautomers, which are isomers that readily interconvert by the exchange of an H atom accompanied by the switch of a single and an adjacent double bond. Hydrogen-exchange rates and different protonation states of compounds (e.g. buffers) are also briefly discussed. The difference in heavy (non-H) atom positions between two tautomers can be small, and careful refinement of all possible tautomers may single out the likely bound ligand tautomer. Experimental methods to determine H-atom positions, such as neutron crystallography, are often technically challenging. Therefore, chemical knowledge and computational approaches are frequently used in conjugation with experimental data to deduce the bound tautomer state. Proton movement is a key feature of many enzymatic reactions, so understanding the orchestration of hydrogen/proton motion is of critical importance to biological chemistry. For example, structural studies have suggested that, just as a chemist may use heat, some enzymes use directional movement to protonate specific O atoms on phosphates to catalyse phosphotransferase reactions. To inhibit ‘wriggly’ enzymes that use movement to effect catalysis, it may be advantageous to have inhibitors that can maintain favourable contacts by adopting different tautomers as the enzyme

  5. Rescue Interventions in Biological and Physical Networks

    NASA Astrophysics Data System (ADS)

    Cornelius, Sean

    2011-03-01

    Gene knockout experiments on single cells have established that expression of most genes is not needed for optimal growth. Yet, environmental and genetic perturbations to these organisms are known to be accompanied by the transient activation of a large number of latent metabolic pathways, suggesting that the temporarily activated reactions increase growth in the presence of perturbations. We have tested this hypothesis computationally and found, surprisingly, that the availability of latent pathways tends in fact to inhibit growth after genetic perturbations. This adverse effect indicates that latent pathway activation is derivative of a suboptimal response and that consequently, growth can actually be improved by removing these pathways from the network. In this talk, I will relate this counterintuitive effect to very recent research showing that a loss in network performance inflicted by an external perturbation can be mitigated by the application of additional perturbations. The challenge is to identify such ``rescues'' under constraints that limit the type of perturbations that can be made. I will present an approach to identify such eligible rescues for general networks modeled as dynamical systems, and present computational examples for biological and physical networks.

  6. Complex network problems in physics, computer science and biology

    NASA Astrophysics Data System (ADS)

    Cojocaru, Radu Ionut

    lattice at zero temperature and then we apply this formalism to the K-SAT problem defined in Chapter 1. The phase transition which physicists study often corresponds to a change in the computational complexity of the corresponding computer science problem. Chapter 3 presents phase transitions which are specific to the problems discussed in Chapter 1 and also known results for the K-SAT problem. We discuss the replica method and experimental evidences of replica symmetry breaking. The physics approach to hard problems is based on replica methods which are difficult to understand. In Chapter 4 we develop novel methods for studying hard problems using methods similar to the message passing techniques that were discussed in Chapter 2. Although we concentrated on the symmetric case, cavity methods show promise for generalizing our methods to the un-symmetric case. As has been highlighted by John Hopfield, several key features of biological systems are not shared by physical systems. Although living entities follow the laws of physics and chemistry, the fact that organisms adapt and reproduce introduces an essential ingredient that is missing in the physical sciences. In order to extract information from networks many algorithm have been developed. In Chapter 5 we apply polynomial algorithms like minimum spanning tree in order to study and construct gene regulatory networks from experimental data. As future work we propose the use of algorithms like min-cut/max-flow and Dijkstra for understanding key properties of these networks.

  7. Track structure: time evolution from physics to chemistry.

    PubMed

    Dingfelder, M

    2006-01-01

    This review discusses interaction cross sections of charged particles (electrons, protons, light ions) with atoms and molecules. The focus is on biological relevant targets like liquid water which serves as a substitute of soft tissue in most Monte Carlo codes. The spatial distribution of energy deposition patterns by different radiation qualities and their importance to the time evolution from the physical to the chemical stage or radiation response is discussed. The determination of inelastic interaction cross sections for charged particles in condensed matter is discussed within the relativistic plane-wave Born approximation and semi-empirical models. The dielectric-response-function of liquid water is discussed.

  8. Subject Knowledge Enhancement (SKE) Courses for Creating New Chemistry and Physics Teachers: Do They Work?

    ERIC Educational Resources Information Center

    Tynan, Richard; Mallaburn, Andrea; Jones, Robert Bryn; Clays, Ken

    2014-01-01

    During extended subject knowledge enhancement (SKE) courses, graduates without chemistry or physics bachelor degrees prepared to enter a Postgraduate Certificate in Education (PGCE) programme to become chemistry or physics teachers. Data were gathered from the exit survey returned by Liverpool John Moores University SKE students about to start…

  9. Guided-Inquiry Experiments for Physical Chemistry: The POGIL-PCL Model

    ERIC Educational Resources Information Center

    Hunnicutt, Sally S.; Grushow, Alexander; Whitnell, Robert

    2015-01-01

    The POGIL-PCL project implements the principles of process-oriented, guided-inquiry learning (POGIL) in order to improve student learning in the physical chemistry laboratory (PCL) course. The inquiry-based physical chemistry experiments being developed emphasize modeling of chemical phenomena. In each experiment, students work through at least…

  10. Students' Understanding of Mathematical Expressions in Physical Chemistry Contexts: An Analysis Using Sherin's Symbolic Forms

    ERIC Educational Resources Information Center

    Becker, Nicole; Towns, Marcy

    2012-01-01

    Undergraduate physical chemistry courses require students to be proficient in calculus in order to develop an understanding of thermodynamics concepts. Here we present the findings of a study that examines student understanding of mathematical expressions, including partial derivative expressions, in two undergraduate physical chemistry courses.…

  11. Terra Firma: "Physics First" for Teaching Chemistry to Pre-Service Elementary School Teachers

    ERIC Educational Resources Information Center

    More, Michelle B.

    2007-01-01

    A pre-service elementary school teacher chemistry class that incorporates the physics first idea is described. This class is taught basic physics followed by introductory chemistry and the students' response indicates that both science literacy and science interest increase using this method.

  12. Exploring the Random Phase Approximately for materials chemistry and physics

    SciTech Connect

    Ruzsinsky, Adrienn

    2015-03-23

    This proposal focuses on improved accuracy for the delicate energy differences of interest in materials chemistry with the fully nonlocal random phase approximation (RPA) in a density functional context. Could RPA or RPA-like approaches become standard methods of first-principles electronic-structure calculation for atoms, molecules, solids, surfaces, and nano-structures? Direct RPA includes the full exact exchange energy and a nonlocal correlation energy from the occupied and unoccupied Kohn-Sham orbitals and orbital energies, with an approximate but universal description of long-range van der Waals attraction. RPA also improves upon simple pair-wise interaction potentials or vdW density functional theory. This improvement is essential to capture accurate energy differences in metals and different phases of semiconductors. The applications in this proposal are challenges for the simpler approximations of Kohn-Sham density functional theory, which are part of the current “standard model” for quantum chemistry and condensed matter physics. Within this project we already applied RPA on different structural phase transitions on semiconductors, metals and molecules. Although RPA predicts accurate structural parameters, RPA has proven not equally accurate in all kinds of structural phase transitions. Therefore a correction to RPA can be necessary in many cases. We are currently implementing and testing a nonempirical, spatially nonlocal, frequency-dependent model for the exchange-correlation kernel in the adiabatic-connection fluctuation-dissipation context. This kernel predicts a nearly-exact correlation energy for the electron gas of uniform density. If RPA or RPA-like approaches prove to be reliably accurate, then expected increases in computer power may make them standard in the electronic-structure calculations of the future.

  13. Integrating Computational Chemistry into the Physical Chemistry Laboratory Curriculum: A Wet Lab/Dry Lab Approach

    ERIC Educational Resources Information Center

    Karpen, Mary E.; Henderleiter, Julie; Schaertel, Stephanie A.

    2004-01-01

    The usage of computational chemistry in a pedagogically effective manner in the undergraduate chemistry curriculum is described. The changes instituted for an effective course structure and the assessment of the course efficacy are discussed.

  14. How chemistry supports cell biology: the chemical toolbox at your service.

    PubMed

    Wijdeven, Ruud H; Neefjes, Jacques; Ovaa, Huib

    2014-12-01

    Chemical biology is a young and rapidly developing scientific field. In this field, chemistry is inspired by biology to create various tools to monitor and modulate biochemical and cell biological processes. Chemical contributions such as small-molecule inhibitors and activity-based probes (ABPs) can provide new and unique insights into previously unexplored cellular processes. This review provides an overview of recent breakthroughs in chemical biology that are likely to have a significant impact on cell biology. We also discuss the application of several chemical tools in cell biology research.

  15. BASIC Simulation Programs; Volumes I and II. Biology, Earth Science, Chemistry.

    ERIC Educational Resources Information Center

    Digital Equipment Corp., Maynard, MA.

    Computer programs which teach concepts and processes related to biology, earth science, and chemistry are presented. The seven biology problems deal with aspects of genetics, evolution and natural selection, gametogenesis, enzymes, photosynthesis, and the transport of material across a membrane. Four earth science problems concern climates, the…

  16. Solving Biology's Iron Chemistry Problem with Ferritin Protein Nanocages.

    PubMed

    Theil, Elizabeth C; Tosha, Takehiko; Behera, Rabindra K

    2016-05-17

    cage symmetry (3-fold and 4-fold axes) and amino acid conservation coincide with function, shown by amino acid substitution effects. 3-Fold symmetry axes control Fe(2+) entry (enzyme catalysis of Fe(2+)/O2 oxidoreduction) and Fe(2+) exit (reductive ferritin mineral dissolution); 3-fold symmetry axes influence Fe(2+)exit from dissolved mineral; bacterial ferritins diverge slightly in Fe/O2 reaction mechanisms and intracage paths of iron-oxy complexes. Biosynthesis rates of ferritin protein change with Fe(2+) and O2 concentrations, dependent on DNA-binding, and heme binding protein, Bach 1. Increased cellular O2 indirectly stabilizes ferritin DNA/Bach 1 interactions. Heme, Fe-protoporphyrin IX, decreases ferritin DNA-Bach 1 binding, causing increased ferritin mRNA biosynthesis (transcription). Direct Fe(2+) binding to ferritin mRNA decreases binding of an inhibitory protein, IRP, causing increased ferritin mRNA translation (protein biosynthesis). Newly synthesized ferritin protein consumes Fe(2+) in biomineral, decreasing Fe(2)(+) and creating a regulatory feedback loop. Ferritin without iron is "apoferritin". Iron removal from ferritin, experimentally, uses biological reductants, for example, NADH + FMN, or chemical reductants, for example, thioglycolic acid, with Fe(2+) chelators; physiological mechanism(s) are murky. Clear, however, is the necessity of ferritin for terrestrial life by conferring oxidant protection (plants, animals, and bacteria), virulence (bacteria), and embryonic survival (mammals). Future studies of ferritin structure/function and Fe(2+)/O2 chemistry will lead to new ferritin uses in medicine, nutrition, and nanochemistry.

  17. Seeking the chemical roots of darwinism: bridging between chemistry and biology.

    PubMed

    Pross, Addy

    2009-08-24

    Chemistry and biology are intimately connected sciences yet the chemistry-biology interface remains problematic and central issues regarding the very essence of living systems remain unresolved. In this essay we build on a kinetic theory of replicating systems that encompasses the idea that there are two distinct kinds of stability in nature-thermodynamic stability, associated with "regular" chemical systems, and dynamic kinetic stability, associated with replicating systems. That fundamental distinction is utilized to bridge between chemistry and biology by demonstrating that within the parallel world of replicating systems there is a second law analogue to the second law of thermodynamics, and that Darwinian theory may, through scientific reductionism, be related to that second law analogue. Possible implications of these ideas to the origin of life problem and the relationship between chemical emergence and biological evolution are discussed.

  18. The Interface between Physics and Biology: An Unexplored Territory.

    ERIC Educational Resources Information Center

    Marx, George

    1980-01-01

    Discusses from the physicist's point of view the connection between biology and physics and the usefulness of physical laws for understanding biological processes. Discusses these fields of research in secondary school science: molecular science, regulation, statistics and information, corrosion and evolution, chance and necessity, and…

  19. Psychological Profiles of Physical and Biological Science Choosers.

    ERIC Educational Resources Information Center

    Collings, John; Smithers, Alan

    1983-01-01

    Investigated male/female sixth-formers studying physical and biological science A-level courses, examining cognitive style, convergent/divergent thinking, career plans, and other characteristics. Differences between biology/physics students tend to be of the same kind as those between scientists as a whole compared to nonscientists. (JN)

  20. BOOK REVIEW Handbook of Physics in Medicine and Biology Handbook of Physics in Medicine and Biology

    NASA Astrophysics Data System (ADS)

    Tabakov, Slavik

    2010-11-01

    This is a multi-author handbook (66 authors) aiming to describe various applications of physics to medicine and biology, from anatomy and physiology to medical equipment. This unusual reference book has 44 chapters organized in seven sections: 1. Anatomical physics; 2. Physics of perception; 3. Biomechanics; 4. Electrical physics; 5. Diagnostic physics; 6. Physics of accessory medicine; 7. Physics of bioengineering. Each chapter has separate page numbering, which is inconvenient but understandable with the number of authors. Similarly there is some variation in the emphasis of chapters: for some the emphasis is more technical and for others clinical. Each chapter has a separate list of references. The handbook includes hundreds of diagrams, images and tables, making it a useful tool for both medical physicists/engineers and other medical/biology specialists. The first section (about 40 pages) includes five chapters on physics of the cell membrane; protein signaling; cell biology and biophysics of the cell membrane; cellular thermodynamics; action potential transmission and volume conduction. The physics of these is well explained and illustrated with clear diagrams and formulae, so it could be a suitable reference for physicists/engineers. The chapters on cellular thermodynamics and action potential transmission have a very good balance of technical/clinical content. The second section (about 85 pages) includes six chapters on medical decision making; senses; somatic senses: touch and pain; hearing; vision; electroreception. Again these are well illustrated and a suitable reference for physicists/engineers. The chapter on hearing stands out with good balance and treatment of material, but some other chapters contain less physics and are close to typical physiological explanations. One could query the inclusion of the chapter on medical decision making, which also needs more detail. The third section (about 80 pages) includes eight chapters on biomechanics

  1. DNA-METAFECTENE PRO complexation: a physical chemistry study.

    PubMed

    Alatorre-Meda, Manuel; González-Pérez, Alfredo; Rodríguez, Julio R

    2010-07-21

    Complexes formed between cationic liposomes and DNA (also known as lipoplexes or genosomes) have proven, for years now, to be a suitable option for gene delivery to cells, transfection, however, some aspects regarding the liposome-DNA interaction mechanism and complex stability remain still unclear. This work aims to improve the understanding of the poorly defined mechanisms and structural conformation associated with the interaction of METAFECTENE PRO (MEP), a commercial liposomal transfection reagent, with poly-anion DNA at mass ratios around the mass ratio recommended for transfection (L/D congruent with 700). A physical chemistry characterization was conducted at a pH of 6.5 and at a temperature of 25 degrees C by means of dynamic light scattering (DLS), electrophoretic mobility (zeta-potential), transmission electron microscopy (TEM), and atomic force microscopy (AFM). Five parameters important for transfection were determined for the lipoplexes: (i) the hydrodynamic radius, R(H), (ii) the stability with time, (iii) the mass ratio of at which both moieties start to interact, (L/D)(i), (iv) the overall charge, and (v) the morphology. Results in ensemble point to a "beads on a string" conformation, with the lipoplex formation occurring well below isoneutrality from (L/D)(i) congruent with 600. The lipoplexes were found to be stable within at least seven days presenting an average R(H) of 135 nm.

  2. An Assessment of a Physical Chemistry Online Activity

    NASA Astrophysics Data System (ADS)

    Hamby Towns, Marcy; Kreke, Kelley; Sauder, Deborah; Stout, Roland; Long, George; Zielinski, Theresa Julia

    1998-12-01

    A questionnaire and list server archive were used to investigate the perception of students and faculty who took part in a physical chemistry online project. Students at four universities worked cooperatively in their own classrooms and collaborated as a larger team on the Internet via a list server to determine the best mathematical model to describe the PV behavior of a gas at a specified temperature. The strengths of the project were the interaction among students, the use of Mathcad and modern technology, and the experience of authentic problem-solving. The weaknesses were the problems with the technology, the facilitation of interaction, and the student's ability to ask questions to solve an ill-defined problem. The suggestions for improvements focused on facilitating interuniversity interaction between students, clarifying tasks and goals, and implementation of the online activities. We discuss how our evaluation of the project guided and informed the design of a subsequent online project, and our planning for future projects. In addition, we describe the professional learning community that evolved among faculty who participated in this project.

  3. Identification of the biologically active liquid chemistry induced by a nonthermal atmospheric pressure plasma jet.

    PubMed

    Wende, Kristian; Williams, Paul; Dalluge, Joe; Gaens, Wouter Van; Aboubakr, Hamada; Bischof, John; von Woedtke, Thomas; Goyal, Sagar M; Weltmann, Klaus-Dieter; Bogaerts, Annemie; Masur, Kai; Bruggeman, Peter J

    2015-06-06

    The mechanism of interaction of cold nonequilibrium plasma jets with mammalian cells in physiologic liquid is reported. The major biological active species produced by an argon RF plasma jet responsible for cell viability reduction are analyzed by experimental results obtained through physical, biological, and chemical diagnostics. This is complemented with chemical kinetics modeling of the plasma source to assess the dominant reactive gas phase species. Different plasma chemistries are obtained by changing the feed gas composition of the cold argon based RF plasma jet from argon, humidified argon (0.27%), to argon/oxygen (1%) and argon/air (1%) at constant power. A minimal consensus physiologic liquid was used, providing isotonic and isohydric conditions and nutrients but is devoid of scavengers or serum constituents. While argon and humidified argon plasma led to the creation of hydrogen peroxide dominated action on the mammalian cells, argon-oxygen and argon-air plasma created a very different biological action and was characterized by trace amounts of hydrogen peroxide only. In particular, for the argon-oxygen (1%), the authors observed a strong negative effect on mammalian cell proliferation and metabolism. This effect was distance dependent and showed a half life time of 30 min in a scavenger free physiologic buffer. Neither catalase and mannitol nor superoxide dismutase could rescue the cell proliferation rate. The strong distance dependency of the effect as well as the low water solubility rules out a major role for ozone and singlet oxygen but suggests a dominant role of atomic oxygen. Experimental results suggest that O reacts with chloride, yielding Cl2(-) or ClO(-). These chlorine species have a limited lifetime under physiologic conditions and therefore show a strong time dependent biological activity. The outcomes are compared with an argon MHz plasma jet (kinpen) to assess the differences between these (at least seemingly) similar plasma sources.

  4. Alcohol Pharmacology Education Partnership: Using Chemistry and Biology Concepts To Educate High School Students about Alcohol

    PubMed Central

    2015-01-01

    We developed the Alcohol Pharmacology Education Partnership (APEP), a set of modules designed to integrate a topic of interest (alcohol) with concepts in chemistry and biology for high school students. Chemistry and biology teachers (n = 156) were recruited nationally to field-test APEP in a controlled study. Teachers obtained professional development either at a conference-based workshop (NSTA or NCSTA) or via distance learning to learn how to incorporate the APEP modules into their teaching. They field-tested the modules in their classes during the following year. Teacher knowledge of chemistry and biology concepts increased significantly following professional development, and was maintained for at least a year. Their students (n = 14 014) demonstrated significantly higher scores when assessed for knowledge of both basic and advanced chemistry and biology concepts compared to students not using APEP modules in their classes the previous year. Higher scores were achieved as the number of modules used increased. These findings are consistent with our previous studies, demonstrating higher scores in chemistry and biology after students use modules that integrate topics interesting to them, such as drugs (the Pharmacology Education Partnership). PMID:24803686

  5. Alcohol Pharmacology Education Partnership: Using Chemistry and Biology Concepts To Educate High School Students about Alcohol.

    PubMed

    Godin, Elizabeth A; Kwiek, Nicole; Sikes, Suzanne S; Halpin, Myra J; Weinbaum, Carolyn A; Burgette, Lane F; Reiter, Jerome P; Schwartz-Bloom, Rochelle D

    2014-02-11

    We developed the Alcohol Pharmacology Education Partnership (APEP), a set of modules designed to integrate a topic of interest (alcohol) with concepts in chemistry and biology for high school students. Chemistry and biology teachers (n = 156) were recruited nationally to field-test APEP in a controlled study. Teachers obtained professional development either at a conference-based workshop (NSTA or NCSTA) or via distance learning to learn how to incorporate the APEP modules into their teaching. They field-tested the modules in their classes during the following year. Teacher knowledge of chemistry and biology concepts increased significantly following professional development, and was maintained for at least a year. Their students (n = 14 014) demonstrated significantly higher scores when assessed for knowledge of both basic and advanced chemistry and biology concepts compared to students not using APEP modules in their classes the previous year. Higher scores were achieved as the number of modules used increased. These findings are consistent with our previous studies, demonstrating higher scores in chemistry and biology after students use modules that integrate topics interesting to them, such as drugs (the Pharmacology Education Partnership).

  6. Integrating pharmacology topics in high school biology and chemistry classes improves performance

    NASA Astrophysics Data System (ADS)

    Schwartz-Bloom, Rochelle D.; Halpin, Myra J.

    2003-11-01

    Although numerous programs have been developed for Grade Kindergarten through 12 science education, evaluation has been difficult owing to the inherent problems conducting controlled experiments in the typical classroom. Using a rigorous experimental design, we developed and tested a novel program containing a series of pharmacology modules (e.g., drug abuse) to help high school students learn basic principles in biology and chemistry. High school biology and chemistry teachers were recruited for the study and they attended a 1-week workshop to learn how to integrate pharmacology into their teaching. Working with university pharmacology faculty, they also developed classroom activities. The following year, teachers field-tested the pharmacology modules in their classrooms. Students in classrooms using the pharmacology topics scored significantly higher on a multiple choice test of basic biology and chemistry concepts compared with controls. Very large effect sizes (up to 1.27 standard deviations) were obtained when teachers used as many as four modules. In addition, biology students increased performance on chemistry questions and chemistry students increased performance on biology questions. Substantial gains in achievement may be made when high school students are taught science using topics that are interesting and relevant to their own lives.

  7. An overview of silica in biology: its chemistry and recent technological advances.

    PubMed

    Perry, Carole C

    2009-01-01

    Biomineralisation is widespread in the biological world and occurs in bacteria, single-celled protists, plants, invertebrates and vertebrates. Minerals formed in the biological environment often show unusual physical properties (e.g. strength, degree of hydration) and often have structures that exhibit order on many length scales. Biosilica, found in single cell organisms through to higher plants and primitive animals (sponges), is formed from an environment that is undersaturated with respect to silicon and under conditions of around neutral pH and low temperature, ca. 4-40 degrees C. Formation of the mineral may occur intra- or extra-cellularly, and specific biochemical locations for mineral deposition that include lipids, proteins and carbohydrates are known. In most cases, the formation of the mineral phase is linked to cellular processes, understanding of which could lead to the design of new materials for biomedical, optical and other applications. This Chapter briefly describes the occurrence of silica in biology including known roles for the mineral phase, the chemistry of the material, the associated biomolecules and some recent applications of this knowledge in materials chemistry.The terminology which is used in this and other contributions within this volume is as follows: Si: the chemical symbol for the element and the generic term used when the nature of the specific silicon compound is not known. Si(OH) ( 4 ): orthosilicic acid, the fundamental building block used in the formation of silicas. SiO ( 2 ) x nH ( 2 ) O or SiO ( 2-x ) (OH) ( 2x ) x 2H ( 2 ) O: amorphous, hydrated, polymerised material. Oligomerisation: the formation of dimers and small oligomers from orthosilicic acid by removal of water. For example, 2Si(OH)(4) <--> (HO)(3)Si-O-Si(OH)(3) + H(2)O Polymerisation: the mutual condensation of silicic acid to give molecularly coherent units of increasing size. Organosilicon compound: must contain silicon covalently bonded to carbon within a

  8. Physical and biological mechanisms of nanosecond- and microsecond-pulsed FE-DBD plasma interaction with biological objects

    NASA Astrophysics Data System (ADS)

    Dobrynin, Danil

    2013-09-01

    Mechanisms of plasma interaction with living tissues and cells can be quite complex, owing to the complexity of both the plasma and the tissue. Thus, unification of all the mechanisms under one umbrella might not be possible. Here, analysis of interaction of floating electrode dielectric barrier discharge (FE-DBD) with living tissues and cells is presented and biological and physical mechanisms are discussed. In physical mechanisms, charged species are identified as the major contributors to the desired effect and a mechanism of this interaction is proposed. Biological mechanisms are also addressed and a hypothesis of plasma selectivity and its effects is offered. Spatially uniform nanosecond and sub-nanosecond short-pulsed dielectric barrier discharge plasmas are gaining popularity in biological and medical applications due to their increased uniformity, lower plasma temperature, lower surface power density, and higher concentration of the active species produced. In this presentation we will compare microsecond pulsed plasmas with nanosecond driven systems and their applications in biology and medicine with specific focus on wound healing and tissue regeneration. Transition from negative to positive streamer will be discussed with proposed hypothesis of uniformity mechanisms of positive streamer and the reduced dependence on morphology and surface chemistry of the second electrode (human body) being treated. Uniform plasma offers a more uniform delivery of active species to the tissue/surface being treated thus leading to better control over the biological results.

  9. Ethnopharmacology, Chemistry and Biological Properties of Four Malian Medicinal Plants

    PubMed Central

    Malterud, Karl Egil

    2017-01-01

    The ethnopharmacology, chemistry and pharmacology of four Malian medicinal plants, Biophytum umbraculum, Burkea africana, Lannea velutina and Terminalia macroptera are reviewed. These plants are used by traditional healers against numerous ailments: malaria, gastrointestinal diseases, wounds, sexually transmitted diseases, insect bites and snake bites, etc. The scientific evidence for these uses is, however, limited. From the chemical and pharmacological evidence presented here, it seems possible that the use in traditional medicine of these plants may have a rational basis, although more clinical studies are needed. PMID:28230801

  10. Controls on the physics and chemistry of seafloor hydrothermal circulation

    NASA Astrophysics Data System (ADS)

    Schultz, A.; Elderfield, H.

    Low temperature diffuse hydrothermal circulation is a natural consequence of the cooling of the oceanic lithosphere. Diffuse flow is expected to be ubiquitous, and will be present both within mid-ocean ridge crest axial zones of young age (0-1 Ma), and also on the older ridge crest flanks and limbs. If underlying thermal models are correct, hydrothermal circulation should persist for oceanic lithosphere of age 0-65 Ma, and is present over half the total area of the ocean basins. By using numerical models of hydrothermal circulation in cracked permeable media, we show qualitatively how diffuse flow is an intrinsic feature of high temperature axial (0-1 Ma) hydrothermal systems, and is not restricted to older (more than 1 Ma) lithosphere. This is in agreement with our field observations which suggest that in such high temperature vent fields the greatest part of the heat and volume flux is due to lower temperature diffuse flow, rather than high temperature black smoker venting. By combining direct measurements of the physical properties of diffusely flowing effluent within axial hydrothermal systems with concurrent sampling of the chemical properties of that effluent, and by considering also the chemistry of unmixed black smoker endmember fluids from the same hydrothermal systems, the processes of mineral deposition and dissolution can be studied directly. By referring to the present-day lithology of such areas, it is possible to examine the balance between concurrent mineral deposition and dissolution processes, and the retention rate of specific mineral assemblages integrated over the history of the hydrothermal system. Thus details of the episodicity of hydrothermal venting within the system may be revealed. An example of this method of combining a variety of direct measurements of diffuse and high temperature effluent properties is given from the TAG hydrothermal field, Mid-Atlantic Ridge. Long time series observations of the physical properties of diffuse and

  11. BIO2010 and beyond: What undergraduate physics does the next generation of molecular biology researchers need?

    NASA Astrophysics Data System (ADS)

    Howard, Jonathon

    2004-03-01

    What fundamental skills in mathematics, chemistry, physics, computer science and engineering are required at the undergraduate level to prepare the next generation of biology majors who will become research scientists? To address this question, Bruce Alberts, President of the National Academy of Sciences, established BIO2010, a committee of the National Research Council (USA), chaired by Lubert Stryer. The report of the committee was published in 2003 as BIO2010: Transforming Undergraduate Education for Future Research Biologists (National Academies Press, Washington DC, www.national-academies.com). I will summarize the recommendations of the Physics and Engineering Panel that was chaired by John Hopfield and give my own views of what physics is essential for researchers in cell and molecular biology.

  12. Chemistry meets biology in colitis-associated carcinogenesis.

    PubMed

    Mangerich, A; Dedon, P C; Fox, J G; Tannenbaum, S R; Wogan, G N

    2013-11-01

    The intestine comprises an exceptional venue for a dynamic and complex interplay of numerous chemical and biological processes. Here, multiple chemical and biological systems, including the intestinal tissue itself, its associated immune system, the gut microbiota, xenobiotics, and metabolites meet and interact to form a sophisticated and tightly regulated state of tissue homoeostasis. Disturbance of this homeostasis can cause inflammatory bowel disease (IBD)-a chronic disease of multifactorial etiology that is strongly associated with increased risk for cancer development. This review addresses recent developments in research into chemical and biological mechanisms underlying the etiology of inflammation-induced colon cancer. Beginning with a general overview of reactive chemical species generated during colonic inflammation, the mechanistic interplay between chemical and biological mediators of inflammation, the role of genetic toxicology, and microbial pathogenesis in disease development are discussed. When possible, we systematically compare evidence from studies utilizing human IBD patients with experimental investigations in mice. The comparison reveals that many strong pathological and mechanistic correlates exist between mouse models of colitis-associated cancer, and the clinically relevant situation in humans. We also summarize several emerging issues in the field, such as the carcinogenic potential of novel inflammation-related DNA adducts and genotoxic microbial factors, the systemic dimension of inflammation-induced genotoxicity, and the complex role of genome maintenance mechanisms during these processes. Taken together, current evidence points to the induction of genetic and epigenetic alterations by chemical and biological inflammatory stimuli ultimately leading to cancer formation.

  13. An Investigation into the Effectiveness of Problem-Based Learning in a Physical Chemistry Laboratory Course

    ERIC Educational Resources Information Center

    Gurses, Ahmet; Acikyildiz, Metin; Dogar, Cetin; Sozbilir, Mustafa

    2007-01-01

    The aim of this study was to investigate the effectiveness of a problem-based learning (PBL) approach in a physical chemistry laboratory course. The parameters investigated were students' attitudes towards a chemistry laboratory course, scientific process skills of students and their academic achievement. The design of the study was one group…

  14. Morpho-chemistry and functionality of diseased biological tissues

    NASA Astrophysics Data System (ADS)

    Lange, Marta; Cicchi, Riccardo; Pavone, Francesco

    2014-09-01

    Heart and cardiovascular diseases are one of the most common in the world, in particular - arthrosclerosis. The aim of the research is to distinguish pathological and healthy tissue regions in biological samples, in this case - to distinguish collagen and lipid rich regions within the arterial wall. In the work a specific combination of such methods are used: FLIM and SHG in order to evaluate the biological tissue morphology and functionality, so that this research could give a contribution for creating a new biological tissue imaging standard in the closest future. During the study the most appropriate parameter for fluorescence lifetime decay was chosen in order to evaluate lifetime decay parameters and the isotropy of the arterial wall and deposition, using statistical methods FFT and GLCM. The research gives a contribution or the future investigations for evaluating lipid properties when it can de-attach from the arterial wall and cause clotting in the blood vessel or even a stroke.

  15. Chemistry and biology of self-cleaving ribozymes

    PubMed Central

    Jimenez, Randi M.; Polanco, Julio A.; Lupták, Andrej

    2015-01-01

    Self-cleaving ribozymes were discovered thirty years ago, but their biological distribution and catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a distinct structure with unique active sites accelerating the same transesterification reaction across the families. Biochemical studies show that general acid-base catalysis is the most common mechanism of self-cleavage, but metal ions and metabolites can be employed as cofactors. Ribozymes have been discovered in highly diverse genomic contexts throughout nature, from viroids to vertebrates. Their biological roles include self-scission during rolling-circle replication of RNA genomes, co-transcriptional processing of retrotransposons, and metabolite-dependent gene expression regulation in bacteria. Other examples, including highly conserved mammalian ribozymes, suggest that many new biological roles are yet to be discovered. PMID:26481500

  16. Physics Meets Biology (LBNL Summer Lecture Series)

    ScienceCinema

    Chu, Steve [Director, LBNL

    2016-07-12

    Summer Lecture Series 2006: If scientists could take advantage of the awesomely complex and beautiful functioning of biologys natural molecular machines, their potential for application in many disciplines would be incalculable. Nobel Laureate and Director of the Lawrence Berkeley National Laboratory Steve Chu explores Possible solutions to global warming and its consequences.

  17. Physics Meets Biology (LBNL Summer Lecture Series)

    SciTech Connect

    Chu, Steve

    2006-07-01

    Summer Lecture Series 2006: If scientists could take advantage of the awesomely complex and beautiful functioning of biologys natural molecular machines, their potential for application in many disciplines would be incalculable. Nobel Laureate and Director of the Lawrence Berkeley National Laboratory Steve Chu explores Possible solutions to global warming and its consequences.

  18. Bioorganic Chemistry. A Natural Reunion of the Physical and Life Sciences

    PubMed Central

    Poulter, C. Dale

    2009-01-01

    Organic substances were conceived as those found in living organisms. Although the definition was soon broadened to include all carbon-containing compounds, naturally occurring molecules have always held a special fascination for organic chemists. From these beginnings, molecules from nature were indespensible tools as generations of organic chemists developed new techniques for determining structures, analyzed the mechanisms of reactions, explored the effects conformation and stereochemistry on reactions, and found challenging new targets to synthesize. Only recently have organic chemists harnessed the powerful techniques of organic chemistry to study the functions of organic molecules in their biological hosts, the enzymes that synthesize molecules and the complex processes that occur in a cell. In this Perspective, I present a personal account my entrée into bioorganic chemistry as a physical organic chemist and subsequent work to understand the chemical mechanisms of enzyme-catalyzed reactions, to develop techniques to identify and assign hydrogen bonds in tRNAs through NMR studies with isotopically labeled molecules, and to study how structure determines function in biosynthetic enzymes with proteins obtained by genetic engineering. PMID:19323569

  19. Bioorganic chemistry. A natural reunion of the physical and life sciences.

    PubMed

    Poulter, C Dale

    2009-04-03

    Organic substances were conceived as those found in living organisms. Although the definition was soon broadened to include all carbon-containing compounds, naturally occurring molecules have always held a special fascination for organic chemists. From these beginnings, molecules from nature were indespensible tools as generations of organic chemists developed new techniques for determining structures, analyzed the mechanisms of reactions, explored the effects conformation and stereochemistry on reactions, and found challenging new targets to synthesize. Only recently have organic chemists harnessed the powerful techniques of organic chemistry to study the functions of organic molecules in their biological hosts, the enzymes that synthesize molecules and the complex processes that occur in a cell. In this Perspective, I present a personal account of my entree into bioorganic chemistry as a physical organic chemist and subsequent work to understand the chemical mechanisms of enzyme-catalyzed reactions, to develop techniques to identify and assign hydrogen bonds in tRNAs through NMR studies with isotopically labeled molecules, and to study how structure determines function in biosynthetic enzymes with proteins obtained by genetic engineering.

  20. Elucidating the coordination chemistry and mechanism of biological nitrogen fixation.

    PubMed

    Dance, Ian

    2007-08-03

    How does the enzyme nitrogenase reduce the inert molecule N2 to NH3 under ambient conditions that are so different from the energy-expensive conditions of the best industrial practices? This review focuses on recent theoretical investigations of the catalytic site, the iron-molybdenum cofactor FeMo-co, and the way in which it is hydrogenated by protons and electrons and then binds N2. Density functional calculations provide reaction profiles and activation energies for possible mechanistic steps. This establishes a conceptual framework and the principles for the coordination chemistry of FeMo-co that are essential to the chemical mechanism of catalysis. The model advanced herein explains relevant experimental data.

  1. The Kinetics and Thermodynamics of the Phenol from Cumene Process: A Physical Chemistry Experiment.

    ERIC Educational Resources Information Center

    Chen, Edward C. M.; Sjoberg, Stephen L.

    1980-01-01

    Presents a physical chemistry experiment demonstrating the differences between thermodynamics and kinetics. The experiment used the formation of phenol and acetone from cumene hydroperoxide, also providing an example of an industrially significant process. (CS)

  2. Radiological and Environmental Research Division annual report, October 1979-September 1980: fundamental molecular physics and chemistry

    SciTech Connect

    Inokuti, Mitio; Dehmer, P. M.; Pratt, S. T.; Poliakoff, E. D.; Dehmer, J. L.; Stockbauer, Roger; Dill, Dan; Parr, A. C.; Jackson, K. H.; Zare, R. N.; Person, J. C.; Nicole, P. P.; Fowler, D. E.; Codling, K.; West, J. B.; Ederer, D. L.; Cole, B. E.; Loomba, D.; Wallace, Scott; Swanson, J. R.; Poliakoff, E. D.; Spence, David; Chupka, W. A.; Stevens, C. M.; Shyn, W. T.; Sharp, W. E.; Kim, Y. K.; Eggarter, E.; Baer, T.; Hanson, J. D.; Shimamura, Isao; Dillon, Michael A.

    1981-09-01

    Research is reported on the physics and chemistry of atoms, ions, and molecules, especially their interactions with external agents such as photons and electrons. Individual items from the report were prepared separately for the data base. (GHT)

  3. Physical Therapists

    MedlinePlus

    ... specific educational prerequisites, such as classes in anatomy, physiology, biology, chemistry, and physics. Some programs admit college ... therapist programs often include courses in biomechanics, anatomy, physiology, neuroscience, and pharmacology. Physical therapist students also complete ...

  4. Photo-Triggered Click Chemistry for Biological Applications

    PubMed Central

    Herner, András; Lin, Qing

    2016-01-01

    In the last decade and a half, numerous bioorthogonal reactions have been developed with a goal to study biological processes in their native environment, i.e., in living cells and animals. Among them, the photo-triggered reactions offer several unique advantages including operational simplicity with the use of light rather than toxic metal catalysts and ligands, and exceptional spatiotemporal control through the application of an appropriate light source with pre-selected wavelength, light intensity and exposure time. While the photoinduced reactions have been studied extensively in materials research, e.g., on macromolecular surface, the adaptation of these reactions for chemical biology applications is still in its infancy. In this chapter, we review the recent efforts in the discovery and optimization the photo-triggered bioorthogonal reactions, with a focus on those that have shown broad utility in biological systems. We discuss in each cases the chemical and mechanistic background, the kinetics of the reactions and the biological applicability together with the limiting factors. PMID:27397964

  5. Chemistry and Biology Laboratories. Design--Construction--Equipment.

    ERIC Educational Resources Information Center

    Schramm, Werner

    Guidelines for planning, building, and equipping the biological and chemical laboratory are revealed, along with construction methods for the modernization or building of new academic or industrial type laboratories. Building equipment, services, utilities, and materials data are given with rules concerning the dimensions and services of…

  6. Simple Laser Scattering Experiment for Biology-Oriented Physics Labs.

    ERIC Educational Resources Information Center

    Orwig, L.; Schrank, G.

    1979-01-01

    Describes a physics exercise designed for biology and premed majors. The activity is a low intensity laser light scattering laboratory exercise to determine the diameter of micron-sized latex spheres (simulated microbes) in water suspension. (GA)

  7. TOWARD EFFICIENT RIPARIAN RESTORATION: INTEGRATING ECONOMIC, PHYSICAL, AND BIOLOGICAL MODELS

    EPA Science Inventory

    This paper integrates economic, biological, and physical models to determine the efficient combination and spatial allocation of conservation efforts for water quality protection and salmonid habitat enhancement in the Grande Ronde basin, Oregon. The integrated modeling system co...

  8. Quantitative Measurement of Magnetic Hyperfine Parameters and the Physical Organic Chemistry of Supramolecular Systems

    NASA Astrophysics Data System (ADS)

    Bender, Christopher J.

    The physical principles that underlie organic reactions were established by a systematic study of chemical reaction dynamics that employed correlated measurements of reaction rates and a physical parameter that could be related of the electronic properties of the molecules in question (Hammett, 1970). Today, molecular science emphasizes the concept of molecular device, which connotes a supramolecular structure (the term "supramolecule" loosely means a molecule that has multiple functionalities associated with it; for example, an enzyme might be regarded as a supramolecule in the sense that it features a supported metal catalyst and a receptor site that recognizes a specific substrate upon which the catalyst acts) that acts in some specific fashion. A molecular device may be biological (e.g., enzymes, contractile proteins; cf. Tanford & Reynolds, 2001), or it may be produced by synthetic means (e.g., molecular wires, switches, machines, etc.; cf. Sauvage, 2001; Balzani et al., 2003). Current synthetic chemistry provides the technical means that enable one to create and modify molecular devices so that structure may elicit some specific function, and so physical organic chemists are interested in reactions that involve engineered and structurally complex systems such as supported catalysts, protein active sites, or nanostructures (cf. amilton, 1996; Tidwell et al., 1997).

  9. Radiation physics, biophysics, and radiation biology

    SciTech Connect

    Hall, E.J.

    1992-05-01

    The following research programs from the Center for Radiological Research of Columbia University are described: Design and development of a new wall-less ultra miniature proportional counter for nanodosimetry; some recent measurements of ionization distributions for heavy ions at nanometer site sizes with a wall-less proportional counter; a calculation of exciton energies in periodic systems with helical symmetry: application to a hydrogen fluoride chain; electron energy-loss function in polynucleotide and the question of plasmon excitation; a non-parametric, microdosimetric-based approach to the evaluation of the biological effects of low doses of ionizing radiation; high-LET radiation risk assessment at medium doses; high-LET radiobiological effects: increased lesion severity or increased lesion proximity; photoneutrons generated by high energy medical linacs; the biological effectiveness of neutrons; implications for radiation protection; molecular characterization of oncogenes induced by neutrons; and the inverse dose-rate effect for oncogenic transformation by charged particles is LET dependent.

  10. A Study to Maximize the Learning Experience in the Physical Chemistry Laboratory

    DTIC Science & Technology

    1979-01-01

    designed to teach physical chemistry concepts in a laboratory setting, a portion of which was designed to teach thcse concepts exclusive of the L lecture...validation of a set of curriculum materials designed to teach certain physical chemistry concepts with little or no reinforcement from a lecture setting...8217 understanding of the discipline being studied. Anderson says not only is there a need for new perspectives for teaching science, but It is especially

  11. Physical aspects of biological activity and cancer

    NASA Astrophysics Data System (ADS)

    Pokorný, Jiří

    2012-03-01

    Mitochondria are organelles at the boundary between chemical-genetic and physical processes in living cells. Mitochondria supply energy and provide conditions for physical mechanisms. Protons transferred across the inner mitochondrial membrane diffuse into cytosol and form a zone of a strong static electric field changing water into quasi-elastic medium that loses viscosity damping properties. Mitochondria and microtubules form a unique cooperating system in the cell. Microtubules are electrical polar structures that make possible non-linear transformation of random excitations into coherent oscillations and generation of coherent electrodynamic field. Mitochondria supply energy, may condition non-linear properties and low damping of oscillations. Electrodynamic activity might have essential significance for material transport, organization, intra- and inter-cellular interactions, and information transfer. Physical processes in cancer cell are disturbed due to suppression of oxidative metabolism in mitochodria (Warburg effect). Water ordering level in the cell is decreased, excitation of microtubule electric polar oscilations diminished, damping increased, and non-linear energy transformation shifted towards the linear region. Power and coherence of the generated electrodynamic field are reduced. Electromagnetic activity of healthy and cancer cells may display essential differences. Local invasion and metastastatic growth may strongly depend on disturbed electrodynamic activity. Nanotechnological measurements may disclose yet unknown properties and parameters of electrodynamic oscillations and other physical processes in healthy and cancer cells.

  12. A random walk in physical biology

    NASA Astrophysics Data System (ADS)

    Peterson, Eric Lee

    Biology as a scientific discipline is becoming evermore quantitative as tools become available to probe living systems on every scale from the macro to the micro and now even to the nanoscale. In quantitative biology the challenge is to understand the living world in an in vivo context, where it is often difficult for simple theoretical models to connect with the full richness and complexity of the observed data. Computational models and simulations offer a way to bridge the gap between simple theoretical models and real biological systems; towards that aspiration are presented in this thesis three case studies in applying computational models that may give insight into native biological structures.The first is concerned with soluble proteins; proteins, like DNA, are linear polymers written in a twenty-letter "language" of amino acids. Despite the astronomical number of possible proteins sequences, a great amount of similarity is observed among the folded structures of globular proteins. One useful way of discovering similar sequences is to align their sequences, as done e.g. by the popular BLAST program. By clustering together amino acids and reducing the alphabet that proteins are written in to fewer than twenty letters, we find that pairwise sequence alignments are actually more sensitive to proteins with similar structures.The second case study is concerned with the measurement of forces applied to a membrane. We demonstrate a general method for extracting the forces applied to a fluid lipid bilayer of arbitrary shape and show that the subpiconewton forces applied by optical tweezers to vesicles can be accurately measured in this way.In the third and final case study we examine the forces between proteins in a lipid bilayer membrane. Due to the bending of the membrane surrounding them, such proteins feel mutually attractive forces which can help them to self-organize and act in concert. These finding are relevant at the areal densities estimated for membrane

  13. Biological inorganic chemistry at the beginning of the 21st century.

    PubMed

    Gray, Harry B

    2003-04-01

    Advances in bioinorganic chemistry since the 1970s have been driven by three factors: rapid determination of high-resolution structures of proteins and other biomolecules, utilization of powerful spectroscopic tools for studies of both structures and dynamics, and the widespread use of macromolecular engineering to create new biologically relevant structures. Today, very large molecules can be manipulated at will, with the result that certain proteins and nucleic acids themselves have become versatile model systems for elucidating biological function.

  14. Click Chemistry Mediated Functionalization of Vertical Nanowires for Biological Applications.

    PubMed

    Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica; Buch-Månson, Nina; Bovet, Nicolas; Nygård, Jesper; Martinez, Karen L; Meldal, Morten

    2016-01-11

    Semiconductor nanowires (NWs) are gaining significant importance in various biological applications, such as biosensing and drug delivery. Efficient and controlled immobilization of biomolecules on the NW surface is crucial for many of these applications. Here, we present for the first time the use of the Cu(I) -catalyzed alkyne-azide cycloaddition and its strain-promoted variant for the covalent functionalization of vertical NWs with peptides and proteins. The potential of the approach was demonstrated in two complementary applications of measuring enzyme activity and protein binding, which is of general interest for biological studies. The attachment of a peptide substrate provided NW arrays for the detection of protease activity. In addition, green fluorescent protein was immobilized in a site-specific manner and recognized by antibody binding to demonstrate the proof-of-concept for the use of covalently modified NWs for diagnostic purposes using minute amounts of material.

  15. Bridging Physics and Biology Using Resistance and Axons

    NASA Astrophysics Data System (ADS)

    Dyer, Joshua M.

    2014-11-01

    When teaching physics, it is often difficult to get biology-oriented students to see the relevance of physics.1 A complaint often heard is that biology students are required to take physics for the Medical College Admission Test (MCAT) as part of a "weeding out" process, but that they don't feel like they need physics for biology. Despite this impression held by students, there have been calls for better physics education for future physicians and life scientists.2,3 Research is being performed to improve physics classes and labs by linking topics in biology and physics.4,5 Described here is a laboratory experiment covering the topics of resistance of materials and circuits/Kirchhoff's laws in a biology context with their direct application to neurons, axons, and electrical impulse transmission within animals. This experiment will also demonstrate the mechanism believed to cause multiple sclerosis. The apparatus was designed with low-cost and readily available materials in mind.

  16. Design, Development, and Psychometric Analysis of a General, Organic, and Biological Chemistry Topic Inventory Based on the Identified Main Chemistry Topics Relevant to Nursing Clinical Practice

    ERIC Educational Resources Information Center

    Brown, Corina E.

    2013-01-01

    This two-stage study focused on the undergraduate nursing course that covers topics in general, organic, and biological (GOB) chemistry. In the first stage, the central objective was to identify the main concepts of GOB chemistry relevant to the clinical practice of nursing. The collection of data was based on open-ended interviews of both nursing…

  17. Suitable Class Experiments in Biochemistry for High-school Chemistry and Biology Courses.

    ERIC Educational Resources Information Center

    Myers, A.

    1987-01-01

    Illustrates the scope of experimental investigations for biochemistry education in high school biology and chemistry courses. Gives a brief overview of biochemistry experiments with proteins, enzymes, carbohydrates, lipids, nucleic acids, vitamins, metabolism, electron transport, and photosynthesis including materials, procedures, and outcomes.…

  18. Biodiesel and Integrated STEM: Vertical Alignment of High School Biology/Biochemistry and Chemistry

    ERIC Educational Resources Information Center

    Burrows, Andrea C.; Breiner, Jonathan M.; Keiner, Jennifer; Behm, Chris

    2014-01-01

    This article explores the vertical alignment of two high school classes, biology and chemistry, around the core concept of biodiesel fuel production. High school teachers and university faculty members investigated biodiesel as it relates to societal impact through a National Science Foundation Research Experience for Teachers. Using an action…

  19. Water. Shopware[R] Applied Biology/Chemistry. [CD-ROM].

    ERIC Educational Resources Information Center

    2000

    This CD-ROM is part of a multimedia software and video collection for high school and vocational schools. Applied Biology/Chemistry is one of many series providing resources for science education. There are six individual titles in this series which include: (1) Natural Resources; (2) Air and Other Gases; (3) Nutrition; (4) Continuity of Life; (5)…

  20. Using Biocatalysis to Integrate Organic Chemistry into a Molecular Biology Laboratory Course

    ERIC Educational Resources Information Center

    Beers, Mande; Archer, Crystal; Feske, Brent D.; Mateer, Scott C.

    2012-01-01

    Current cutting-edge biomedical investigation requires that the researcher have an operational understanding of several diverse disciplines. Biocatalysis is a field of science that operates at the crossroads of organic chemistry, biochemistry, microbiology, and molecular biology, and provides an excellent model for interdisciplinary research. We…

  1. Biosynthetic inorganic chemistry.

    PubMed

    Lu, Yi

    2006-08-25

    Inorganic chemistry and biology can benefit greatly from each other. Although synthetic and physical inorganic chemistry have been greatly successful in clarifying the role of metal ions in biological systems, the time may now be right to utilize biological systems to advance coordination chemistry. One such example is the use of small, stable, easy-to-make, and well-characterized proteins as ligands to synthesize novel inorganic compounds. This biosynthetic inorganic chemistry is possible thanks to a number of developments in biology. This review summarizes the progress in the synthesis of close models of complex metalloproteins, followed by a description of recent advances in using the approach for making novel compounds that are unprecedented in either inorganic chemistry or biology. The focus is mainly on synthetic "tricks" learned from biology, as well as novel structures and insights obtained. The advantages and disadvantages of this biosynthetic approach are discussed.

  2. Piquing Student Interest with Pharmacology: An Interdisciplinary Program Helps High School Students Learn Biology and Chemistry Principles

    ERIC Educational Resources Information Center

    Halpin, Myra J.; Hoeffler, Leanne; Schwartz-Bloom, Rochelle D.

    2005-01-01

    To help students learn science concepts, Pharmacology Education Partnership (PEP)--a science education program that incorporates relevant topics related to drugs and drug abuse into standard biology and chemistry curricula was developed. The interdisciplinary PEP curriculum provides six modules to teach biology and chemistry principles within the…

  3. Robotics and Biology: Lets get Physical

    NASA Astrophysics Data System (ADS)

    Choset, Howie

    Our research group investigates the core fundamentals of locomotion as it exists in biology and as it applies to locomoting robotic systems. Initially, our work advanced techniques found in geometric mechanics to design cyclic controllers, often called gaits, for snake robots, highly articulated mechanisms that can thread through tightly packed spaces to access locations people cannot. We had considerable success in designing snake robot gaits, but found our systems stymied in terrains characterized by sandy substrates. Sandy terrains and other granular media pose a challenge to snake robots because it is unclear how the mechanism interacts with environment: we cannot simply assume the robot is on hard-ground nor in a fluid. Simulating granular interactions can prove to be computationally intractable for real-time use on the robots. Therefore, we developed experimental tools that allowed us to sieve out models of the locomoting systems operating on granular media. We were then able to bring these models into harmony with the elegant formulation of our geometric mechanics approach. This allowed us to derive adaptive controllers for our snake robots in sandy terrains, and enabled us to gain deeper insight into of how biological systems move over similar terrains as well.

  4. ROSics: chemistry and proteomics of cysteine modifications in redox biology.

    PubMed

    Kim, Hee-Jung; Ha, Sura; Lee, Hee Yoon; Lee, Kong-Joo

    2015-01-01

    Post-translational modifications (PTMs) occurring in proteins determine their functions and regulations. Proteomic tools are available to identify PTMs and have proved invaluable to expanding the inventory of these tools of nature that hold the keys to biological processes. Cysteine (Cys), the least abundant (1-2%) of amino acid residues, are unique in that they play key roles in maintaining stability of protein structure, participating in active sites of enzymes, regulating protein function and binding to metals, among others. Cys residues are major targets of reactive oxygen species (ROS), which are important mediators and modulators of various biological processes. It is therefore necessary to identify the Cys-containing ROS target proteins, as well as the sites and species of their PTMs. Cutting edge proteomic tools which have helped identify the PTMs at reactive Cys residues, have also revealed that Cys residues are modified in numerous ways. These modifications include formation of disulfide, thiosulfinate and thiosulfonate, oxidation to sulfenic, sulfinic, sulfonic acids and thiosulfonic acid, transformation to dehydroalanine (DHA) and serine, palmitoylation and farnesylation, formation of chemical adducts with glutathione, 4-hydroxynonenal and 15-deoxy PGJ2, and various other chemicals. We present here, a review of relevant ROS biology, possible chemical reactions of Cys residues and details of the proteomic strategies employed for rapid, efficient and sensitive identification of diverse and novel PTMs involving reactive Cys residues of redox-sensitive proteins. We propose a new name, "ROSics," for the science which describes the principles of mode of action of ROS at molecular levels.

  5. Biological and Physical Thresholds in Biogeomorphologically Self-organizing Systems.

    NASA Astrophysics Data System (ADS)

    Herman, P.; Bouma, T. J.; Van de Koppel, J.; Borsje, B.; van Belzen, J.; Balke, T.

    2012-12-01

    Many coastal and estuarine landscapes are formed as a consequence of biological-physical interactions. We review examples that we recently studied: coastal vegetations, microphytobenthos-stabilized mudflats, macrofauna-dominated sediments, sand wave formation influenced by animals. In these diverse ecosystems, self-organisation of the coupled landscape results from the existence of positive feedback loops between the physical and biological components. We focus on the question where, in space and/or in time, such feedback systems develop and what determines their persistence and their ability to shape the landscape. We hypothesize that an equilibrium of forces between physical and biological factors is necessary for a feedback loop to develop. This implies a scale match and a commensurate strength of the different factors. There are many examples of systems that are physically too dynamic for the development of biological populations that affect the landscape. We also show an example where biological influence, in the form of strong grazing pressure on microphytobenthos, disrupts a self-organized system on a mudflat. Thus, we define thresholds in parameter space which constrain the development of strongly interacting biogeomorphological systems. The hypothesis of commensurate physical and biological forces as a condition for the development of biogeomorphological systems has important consequences for the establishment and recruitment of such systems. Biological interactions and biological effects on the physical system develop in time with the recruitment and maturation of the biological system. Fully developed systems can therefore be in balance with stronger physical forces than immature, early recruiting phases. This represents a successional threshold that is difficult to overcome. We stress the importance of stochastic variability in physical conditions at a diversity of scales as a prerequisite for phase transitions from physically dominated to

  6. Ask not what physics can do for biology—ask what biology can do for physics

    NASA Astrophysics Data System (ADS)

    Frauenfelder, Hans

    2014-10-01

    Stan Ulam, the famous mathematician, said once to Hans Frauenfelder: ‘Ask not what Physics can do for biology, ask what biology can do for physics’. The interaction between biologists and physicists is a two-way street. Biology reveals the secrets of complex systems, physics provides the physical tools and the theoretical concepts to understand the complexity. The perspective gives a personal view of the path to some of the physical concepts that are relevant for biology and physics (Frauenfelder et al 1999 Rev. Mod. Phys. 71 S419-S442). Schrödinger’s book (Schrödinger 1944 What is Life? (Cambridge: Cambridge University Press)), loved by physicists and hated by eminent biologists (Dronamraju 1999 Genetics 153 1071-6), still shows how a great physicist looked at biology well before the first protein structure was known.

  7. From epoxomicin to carfilzomib: chemistry, biology, and medical outcomes.

    PubMed

    Kim, Kyung Bo; Crews, Craig M

    2013-05-01

    The initial enthusiasm following the discovery of a pharmacologically active natural product is often fleeting due to the poor prospects for its ultimate clinical application. Despite this, the ever-changing landscape of modern biology has a constant need for molecular probes that can aid in our understanding of biological processes. After its initial discovery by Bristol-Myers Squibb as a microbial anti-tumor natural product, epoxomicin was deemed unfit for development due to its peptide structure and potentially labile epoxyketone pharmacophore. Despite its drawbacks, epoxomicin's pharmacophore was found to provide unprecedented selectivity for the proteasome. Epoxomicin also served as a scaffold for the generation of a synthetic tetrapeptide epoxyketone with improved activity, YU-101, which became the parent lead compound of carfilzomib (Kyprolis™), the recently approved therapeutic agent for multiple myeloma. In this era of rational drug design and high-throughput screening, the prospects for turning an active natural product into an approved therapy are often slim. However, by understanding the journey that began with the discovery of epoxomicin and ended with the successful use of carfilzomib in the clinic, we may find new insights into the keys for success in natural product-based drug discovery.

  8. From Epoxomicin to Carfilzomib: Chemistry, Biology, and Medical Outcomes

    PubMed Central

    Kim, Kyung Bo; Crews, Craig M.

    2013-01-01

    The initial enthusiasm following the discovery of a pharmacologically active natural product is often fleeting due to the poor prospects for its ultimate clinical application. Despite this, the ever-changing landscape of modern biology has a constant need for molecular probes that can aid in our understanding of biological processes. After its initial discovery by Bristol-Myers Squibb as a microbial anti-tumor natural product, epoxomicin was deemed unfit for development due to its peptide structure and potentially labile epoxyketone pharmacophore. Despite its drawbacks, epoxomicin’s pharmacophore was found to provide unprecedented selectivity for the proteasome. Epoxomicin also served as a scaffold for the generation of a synthetic tetrapeptide epoxyketone with improved activity, YU-101, which became the parent lead compound of carfilzomib (Kyprolis™), the recently approved therapeutic agent for multiple myeloma. In this era of rational drug design and high-throughput screening, the prospects for turning an active natural product into an approved therapy are often slim. However, by understanding the journey that began with the discovery of epoxomicin and ended with the successful use of carfilzomib in the clinic, we may find new insights into the keys for success in natural product-based drug discovery. PMID:23575525

  9. Nuclear Physics in a biological context

    NASA Astrophysics Data System (ADS)

    Discher, Dennis

    2012-02-01

    A solid tissue can be soft like fat or brain, stiff like striated muscle and heart, or rigid like bone -- and of course every cell has a nucleus that contributes in some way small or large to tissue mechanics. Indeed, nuclei generally exhibit rheology and plasticity that reflects both the chromatin and the nuclear envelope proteins called lamins, all of which change in differentiation. Profiling of tissue nuclei shows that the nuclear intermediate filament protein Lamin-A/C varies over 30-fold between adult tissues and scales strongly with micro-elasticity of tissue, while other nuclear envelope components such as Lamin-B exhibit small variations. Lamin-A/C has been implicated in aging syndromes that affect muscle and fat but not brain, and we find nuclei in brain-derived cells are indeed dominated by Lamin-B and are much softer than nuclei derived from muscle cells with predominantly Lamin-A/C. In vitro, matrix elasticity can affect expression of nuclear envelope components in adult stem cells, and major changes in Lamin-A/C are indeed shown to direct lineage with lower levels favoring soft tissue and higher levels promoting rigid tissue lineage. Further molecular studies provide evidence that the nucleus transduces physical stress. References: (1) J.D. Pajerowski, K.N. Dahl, F.L. Zhong, P.J. Sammak, and D.E. Discher. Physical plasticity of the nucleus in stem cell differentiation. PNAS 104: 15619-15624 (2007). (2) A. Buxboim, I. Ivanova, and D.E. Discher. Matrix Elasticity, Cytoskeletal Forces, and Physics of the Nucleus: how deeply do cells `feel' outside and in? Journal of Cell Science 123: 297-308 (2010).

  10. Brownian ratchets in physics and biology

    NASA Astrophysics Data System (ADS)

    Bier, Martin

    1997-06-01

    Thirty years ago Feynman et al. presented a paradox in the Lectures on Physics: an imagined device could let Brownian motion do work by allowing it in one direction and blocking it in the opposite direction. In the chapter Feynman et al. eventually show that such ratcheting can only be achieved if there is, in compliance with the basic conservation laws, some energy input from an external source. Now that technology is going into ever smaller dimensions, ratcheting Brownian motion seems to be a real possibility in nanotechnological applications. Furthermore, Brownian motion plays an essential role in the action of motor proteins (individual molecules that convert chemical energy into motion).

  11. The contribution of statistical physics to evolutionary biology.

    PubMed

    de Vladar, Harold P; Barton, Nicholas H

    2011-08-01

    Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time.

  12. Cyclopamine and hedgehog signaling: chemistry, biology, medical perspectives.

    PubMed

    Heretsch, Philipp; Tzagkaroulaki, Lito; Giannis, Athanassios

    2010-05-03

    When Odysseus left the devastated city of Troy after ten years of siege he could not foresee the perils he still had to face. The encounter with the cyclops, a giant with only one eye placed in the middle of its forehead, was doubtlessly one of the creepiest and most dangerous of his adventures. In the end, Odysseus could only escape with the help of a sheep. Whether Homers cyclops was inspired by the observation of terribly malformed neonates remains speculative. However, when sheep herders in Idaho in the middle of the 20th century faced an increasing number of cyclops-like sheep in their herds, a unique cascade of chemical, biological, and medicinal discoveries was initiated. This Minireview tells this story and shows its impact on modern biomedical research.

  13. Biological regulation of atmospheric chemistry en route to planetary oxygenation.

    PubMed

    Izon, Gareth; Zerkle, Aubrey L; Williford, Kenneth H; Farquhar, James; Poulton, Simon W; Claire, Mark W

    2017-03-28

    Emerging evidence suggests that atmospheric oxygen may have varied before rising irreversibly ∼2.4 billion years ago, during the Great Oxidation Event (GOE). Significantly, however, pre-GOE atmospheric aberrations toward more reducing conditions-featuring a methane-derived organic-haze-have recently been suggested, yet their occurrence, causes, and significance remain underexplored. To examine the role of haze formation in Earth's history, we targeted an episode of inferred haze development. Our redox-controlled (Fe-speciation) carbon- and sulfur-isotope record reveals sustained systematic stratigraphic covariance, precluding nonatmospheric explanations. Photochemical models corroborate this inference, showing Δ(36)S/Δ(33)S ratios are sensitive to the presence of haze. Exploiting existing age constraints, we estimate that organic haze developed rapidly, stabilizing within ∼0.3 ± 0.1 million years (Myr), and persisted for upward of ∼1.4 ± 0.4 Myr. Given these temporal constraints, and the elevated atmospheric CO2 concentrations in the Archean, the sustained methane fluxes necessary for haze formation can only be reconciled with a biological source. Correlative δ(13)COrg and total organic carbon measurements support the interpretation that atmospheric haze was a transient response of the biosphere to increased nutrient availability, with methane fluxes controlled by the relative availability of organic carbon and sulfate. Elevated atmospheric methane concentrations during haze episodes would have expedited planetary hydrogen loss, with a single episode of haze development providing up to 2.6-18 × 10(18) moles of O2 equivalents to the Earth system. Our findings suggest the Neoarchean likely represented a unique state of the Earth system where haze development played a pivotal role in planetary oxidation, hastening the contingent biological innovations that followed.

  14. The chemistry and biological activity of heterocycle-fused quinolinone derivatives: A review.

    PubMed

    Shiro, Tomoya; Fukaya, Takayuki; Tobe, Masanori

    2015-06-05

    Among all heterocycles, the heterocycle-fused quinolinone scaffold is one of the privileged structures in drug discovery as heterocycle-fused quinolinone derivatives exhibit various biological activities allowing them to act as anti-inflammatory, anticancer, antidiabetic, and antipsychotic agents. This wide spectrum of biological activity has attracted a great deal of attention in the field of medicinal chemistry. In this review, we provide a comprehensive description of the biological and pharmacological properties of various heterocycle-fused quinolinone scaffolds and discuss the synthetic methods of some of their derivatives.

  15. Physical activity and biological maturation: a systematic review

    PubMed Central

    Bacil, Eliane Denise Araújo; Mazzardo, Oldemar; Rech, Cassiano Ricardo; Legnani, Rosimeide Francisco dos Santos; de Campos, Wagner

    2015-01-01

    OBJECTIVE: To analyze the association between physical activity (PA) and biological maturation in children and adolescents. DATA SOURCE: We performed a systematic review in April 2013 in the electronic databases of PubMed/MEDLINE, SportDiscus, Web of Science and LILACS without time restrictions. A total of 628 potentially relevant articles were identified and 10 met the inclusion criteria for this review: cross-sectional or longitudinal studies, published in Portuguese, English or Spanish, with schoolchildren aged 9-15 years old of both genders. DATA SYNTHESIS: Despite the heterogeneity of the studies, there was an inverse association between PA and biological maturation. PA decreases with increased biological and chronological age in both genders. Boys tend to be more physically active than girls; however, when controlling for biological age, the gender differences disappear. The association between PA and timing of maturation varies between the genders. Variation in the timing of biological maturation affects the tracking of PA in early adolescent girls. This review suggests that mediators (BMI, depression, low self-esteem, and concerns about body weight) can explain the association between PA and biological maturation. CONCLUSIONS: There is an association between PA and biological maturation. PA decreases with increasing biological age with no differences between genders. As for the timing of biological maturation, this association varies between genders. PMID:25583624

  16. PSL Chemical Biology Symposia First 2016 Edition: When Chemistry and Biology Share the Language of Discovery.

    PubMed

    Gautier, Arnaud; Rodriguez, Raphaël

    2017-03-30

    Chemical biology, the science of understanding biological processes at the molecular level, has grown exponentially with the development of chemical strategies to manipulate and quantify biology with unprecedented precision. Recent advances presented at the Université Paris Sciences et Lettres symposium are discussed.

  17. Recent developments and applications of clickable photoprobes in medicinal chemistry and chemical biology.

    PubMed

    Lapinsky, David J; Johnson, Douglas S

    2015-01-01

    Photoaffinity labeling is a well-known biochemical technique that has grown significantly since the turn of the century, principally due to its combination with bioorthogonal/click chemistry reactions. This review highlights new developments and applications of clickable photoprobes in medicinal chemistry and chemical biology. In particular, recent examples of clickable photoprobes for target identification, activity- or affinity-based protein profiling (ABPP or AfBPP), characterization of sterol- or lipid-protein interactions and characterization of ligand-binding sites are presented.

  18. Toward university modeling instruction--biology: adapting curricular frameworks from physics to biology.

    PubMed

    Manthey, Seth; Brewe, Eric

    2013-06-01

    University Modeling Instruction (UMI) is an approach to curriculum and pedagogy that focuses instruction on engaging students in building, validating, and deploying scientific models. Modeling Instruction has been successfully implemented in both high school and university physics courses. Studies within the physics education research (PER) community have identified UMI's positive impacts on learning gains, equity, attitudinal shifts, and self-efficacy. While the success of this pedagogical approach has been recognized within the physics community, the use of models and modeling practices is still being developed for biology. Drawing from the existing research on UMI in physics, we describe the theoretical foundations of UMI and how UMI can be adapted to include an emphasis on models and modeling for undergraduate introductory biology courses. In particular, we discuss our ongoing work to develop a framework for the first semester of a two-semester introductory biology course sequence by identifying the essential basic models for an introductory biology course sequence.

  19. Toward University Modeling Instruction—Biology: Adapting Curricular Frameworks from Physics to Biology

    PubMed Central

    Manthey, Seth; Brewe, Eric

    2013-01-01

    University Modeling Instruction (UMI) is an approach to curriculum and pedagogy that focuses instruction on engaging students in building, validating, and deploying scientific models. Modeling Instruction has been successfully implemented in both high school and university physics courses. Studies within the physics education research (PER) community have identified UMI's positive impacts on learning gains, equity, attitudinal shifts, and self-efficacy. While the success of this pedagogical approach has been recognized within the physics community, the use of models and modeling practices is still being developed for biology. Drawing from the existing research on UMI in physics, we describe the theoretical foundations of UMI and how UMI can be adapted to include an emphasis on models and modeling for undergraduate introductory biology courses. In particular, we discuss our ongoing work to develop a framework for the first semester of a two-semester introductory biology course sequence by identifying the essential basic models for an introductory biology course sequence. PMID:23737628

  20. Physical Chemistry: A Molecular Approach (by Donald A. McQuarrie and John D. Simon)

    NASA Astrophysics Data System (ADS)

    Kovac, Jeffrey D.

    1998-05-01

    University Science Books: Sausalito, CA, 1997. xxiii + 1270 pp. Figs and tables. 10.28 x 7.27 x 2.34 in. ISBN 0-935702-99-7. $80.00. This book will not appeal to traditionalists. Those willing to take a fresh look at the subject, however, will find this well-executed text an attractive alternative. Most undergraduate physical chemistry textbooks begin with thermodynamics, then proceed to quantum chemistry and finally to statistical thermodynamics and kinetics. This structure derives from the classic textbooks such as Physical Chemistry by Alberty and Silbey, which traces its origin to the Outline of Theoretical Chemistry written by Herbert Getman in 1913 when thermodynamics was the core of physical chemistry and quantum mechanics was in its infancy. Occasional authors have tried to deviate from this orthodoxy. I learned my undergraduate physical chemistry from the solid textbook written in 1964 by a University of Washington team: Eggers, Gregory, Halsey, and Rabinovitch. That text opens with quantum mechanics, as does the elegant and sophisticated book by Berry, Rice, and Ross. None of these books has been very successful, however, partly because they challenge tradition in a pedagogically conservative profession.

  1. Chemistry and Biological Activities of Flavonoids: An Overview

    PubMed Central

    Kumar, Shashank; Pandey, Abhay K.

    2013-01-01

    There has been increasing interest in the research on flavonoids from plant sources because of their versatile health benefits reported in various epidemiological studies. Since flavonoids are directly associated with human dietary ingredients and health, there is need to evaluate structure and function relationship. The bioavailability, metabolism, and biological activity of flavonoids depend upon the configuration, total number of hydroxyl groups, and substitution of functional groups about their nuclear structure. Fruits and vegetables are the main dietary sources of flavonoids for humans, along with tea and wine. Most recent researches have focused on the health aspects of flavonoids for humans. Many flavonoids are shown to have antioxidative activity, free radical scavenging capacity, coronary heart disease prevention, hepatoprotective, anti-inflammatory, and anticancer activities, while some flavonoids exhibit potential antiviral activities. In plant systems, flavonoids help in combating oxidative stress and act as growth regulators. For pharmaceutical purposes cost-effective bulk production of different types of flavonoids has been made possible with the help of microbial biotechnology. This review highlights the structural features of flavonoids, their beneficial roles in human health, and significance in plants as well as their microbial production. PMID:24470791

  2. Chemistry and biological activities of flavonoids: an overview.

    PubMed

    Kumar, Shashank; Pandey, Abhay K

    2013-01-01

    There has been increasing interest in the research on flavonoids from plant sources because of their versatile health benefits reported in various epidemiological studies. Since flavonoids are directly associated with human dietary ingredients and health, there is need to evaluate structure and function relationship. The bioavailability, metabolism, and biological activity of flavonoids depend upon the configuration, total number of hydroxyl groups, and substitution of functional groups about their nuclear structure. Fruits and vegetables are the main dietary sources of flavonoids for humans, along with tea and wine. Most recent researches have focused on the health aspects of flavonoids for humans. Many flavonoids are shown to have antioxidative activity, free radical scavenging capacity, coronary heart disease prevention, hepatoprotective, anti-inflammatory, and anticancer activities, while some flavonoids exhibit potential antiviral activities. In plant systems, flavonoids help in combating oxidative stress and act as growth regulators. For pharmaceutical purposes cost-effective bulk production of different types of flavonoids has been made possible with the help of microbial biotechnology. This review highlights the structural features of flavonoids, their beneficial roles in human health, and significance in plants as well as their microbial production.

  3. An Aerosol Physical Chemistry Model for the Upper Troposphere

    NASA Technical Reports Server (NTRS)

    Lin, Jin-Sheng

    2001-01-01

    This report is the final report for the Cooperative Agreement NCC2-1000. The tasks outlined in the various proposals are: (1) Development of an aerosol chemistry model; (2) Utilization of satellite measurements of trace gases along with analysis of temperatures and dynamic conditions to understand ice cloud formation, dehydration and sedimentation in the winter polar regions; (3) Comparison of the HALOE and SAGE II time dependencies of the Pinatubo aerosol decay. The publications are attached.

  4. Fractal landscapes in physics and biology

    NASA Astrophysics Data System (ADS)

    Eugene Stanley, H.

    1992-07-01

    This article is based upon the Thirtieth Saha Memorial Lecture (delivered on 4 January 1992) and the Fourth Bose Memorial Lecture (delivered on 5 January 1992). I felt deeply touched to have been so honored by invitations to deliver these lectures, especially in view of the list of illustrious predecessors who have held this honor. At the outset I wish to acknowledge that almost all of my work is connected in one way or another to random walks, a topic about which I learned most from the classic 1943 review of the great Indian physicist S. Chandrasekar. I also wish to acknowledge my personal debt to the great culture and music of India, and to the many Indian scholars who have taught me their unique insights into the mysteries of physics. In particular, I wish to dedicate this work to the late Bengali genius Satyajit Ray, whose recent passing has left the world immeasurably poorer. It was my dream while in Calcutta to have the opportunity of meeting this hero of mine, but his ill health at that time prevented our meeting.

  5. Mental Rolodexing: Senior Chemistry Majors' Understanding of Chemical and Physical Properties

    ERIC Educational Resources Information Center

    DeFever, Ryan S.; Bruce, Heather; Bhattacharyya, Gautam

    2015-01-01

    Using a constructivist framework, eight senior chemistry majors were interviewed twice to determine: (i) structural inferences they are able to make from chemical and physical properties; and (ii) their ability to apply their inferences and understandings of these chemical and physical properties to solve tasks on the reactivity of organic…

  6. Technical liaison with the Institute of Physical Chemistry (Russian Academy of Science)

    SciTech Connect

    Delegard, C.

    1996-10-01

    DOE has engaged the Institute of Physical Chemistry of the Russian Academy of Science (IPC/RAS) to conduct studies of the fundamental and applied chemistry of the transuranium elements (TRU, primarily neptunium, plutonium, and americium) and technetium in alkaline media. This work is supported by DOE because the radioactive wastes stored in underground tanks at DOE sites (Hanford, Savannah River, and Oak Ridge) contain TRU and technetium, are alkaline, and the chemistries of TRU and technetium are not well developed in this system. Previous studies at the IPC/RAS centered on the fundamental chemistry and on coprecipitation. In FY 1996, the work will focus more on the applied chemistry of TR and technetium in alkaline media and work will continue on the coprecipitation task.

  7. Sarcopenia as the Biological Substrate of Physical Frailty.

    PubMed

    Landi, Francesco; Calvani, Riccardo; Cesari, Matteo; Tosato, Matteo; Martone, Anna Maria; Bernabei, Roberto; Onder, Graziano; Marzetti, Emanuele

    2015-08-01

    Physical function decreases with aging, which may result in adverse outcomes (eg, disability, loss of independence, institutionalization, death). Physical function impairment is a common trait of frailty and sarcopenia. These two conditions, albeit highly common, have not yet received a unique operational definition, which has impeded their implementation in standard practice. Here, we introduce a conceptual model in which sarcopenia is proposed as the biological substrate and the pathway whereby the consequences of physical frailty develop. This conceptualization may open new venues for the design of interventions against physical frailty and promote the translation of findings to the clinical arena.

  8. Understanding recognition and self-assembly in biology using the chemist's toolbox. Insight into medicinal chemistry.

    PubMed

    Quirolo, Z B; Benedini, L A; Sequeira, M A; Herrera, M G; Veuthey, T V; Dodero, V I

    2014-01-01

    Medicinal chemistry is intimately connected with basic science such as organic synthesis, chemical biology and biophysical chemistry among other disciplines. The reason of such connections is due to the power of organic synthesis to provide designed molecules; chemical biology to give tools to discover biological and/or pathological pathways and biophysical chemistry which provides the techniques to characterize and the theoretical background to understand molecular behaviour. The present review provides some selective examples of these research areas. Initially, template dsDNA organic synthesis and the spatio-temporal control of transcription are presenting following by the supramolecular entities used in drug delivery, such as liposomes and liquid crystal among others. Finally, peptides and protein self-assembly is connected with biomaterials and as an important event in the balance between health and disease. The final aim of the present review is to show the power of chemical tools not only for the synthesis of new molecules but also to improve our understanding of recognition and self-assembly in the biological context.

  9. Liaison activities with the Institute of Physical Chemistry, Russian Academy of Sciences: FY 1997

    SciTech Connect

    Delegard, C.H.; Elovich, R.J.

    1997-09-01

    The Institute of Physical Chemistry of the Russian Academy of Sciences is conducting a program of fundamental and applied research into the chemistry of the actinides and technetium in alkaline media such as are present in the Hanford Site underground waste storage tanks. This work is being coordinated and the results disseminated through a technical liaison maintained at the Pacific Northwest National Laboratory. The technical liaison is performing laboratory studies on plutonium chemistry in alkaline media. The activities at the Institute of Physical Chemistry and through the liaison are pursued to improve understanding of the chemical behavior of key long-lived radioactive elements under current operating and proposed tank waste processing conditions. Both activities are supported by the Efficient Separations and Processing Crosscutting Program under the Office of Science and Technology of the U.S. Department of Energy.

  10. Fundamental molecular physics and chemistry. Radiological and Environmental Research Division annual report, October 1981-December 1982. Pt. 1

    SciTech Connect

    Not Available

    1983-12-01

    This document is the twelfth Annual Report of our Fundamental Molecular Physics and Chemistry Program. Scientifically, the work of the program deals with aspects of the physics and chemistry of molecules related to their interactions with photons, electrons, and other external agents. We chose these areas of study in view of our matic goals; that is to say, we chose them so that the eventual outcome of our work meets some of the needs of the US Department of Energy (DOE) and of other government agencies that support our research. First, we endeavor to determine theoretically and experimentally cross sections for electron and photon interactions with molecules, because those cross sections are indispensable for detailed microscopic analyses of the earliest processes of radiation action on any molecular substance, including biological materials. Those analyses in turn provide a sound basis for radiology and radiation dosimetry. Second, we study the spectroscopy of certain molecules and of small clusters of molecules because this topic is fundamental to the full understanding of atmospheric-pollutant chemistry.

  11. Recent Advances in the Chemistry and Biology of Naturally Occurring Antibiotics

    PubMed Central

    Chen, Jason S.; Edmonds, David J.; Estrada, Anthony A.

    2009-01-01

    Lead-in Ever since the world-shaping discovery of penicillin, nature’s molecular diversity has been extensively screened for new medications and lead compounds in drug discovery. The search for anti-infective agents intended to combat infectious diseases has been of particular interest and has enjoyed a high degree of success. Indeed, the history of antibiotics is marked with impressive discoveries and drug development stories, the overwhelming majority of which have their origins in nature. Chemistry, and in particular chemical synthesis, has played a major role in bringing naturally occurring antibiotics and their derivatives to the clinic, and no doubt these disciplines will continue to be key enabling technologies for future developments in the field. In this review article, we highlight a number of recent discoveries and advances in the chemistry, biology, and medicine of naturally occurring antibiotics, with particular emphasis on the total synthesis, analog design, and biological evaluation of molecules with novel mechanisms of action. PMID:19130444

  12. Associations between selected demographic, biological, school environmental and physical education based correlates, and adolescent physical activity.

    PubMed

    Hilland, Toni A; Ridgers, Nicola D; Stratton, Gareth; Fairclough, Stuart J

    2011-02-01

    The study investigated associations between selected physical activity correlates among 299 adolescents (90 boys, age 12-14 years) from 3 English schools. Physical activity was assessed by self-report and accelerometry. Correlates represented biological, predisposing, and demographic factors as described in the Youth Physical Activity Promotion Model. Boys engaged in more self-reported (p < .01) and accelerometer assessed physical activity than girls (p = .02). Positive associations between sex (male), BMI, Perceived PE Ability, Perceived PE Worth, number of enrolled students, and physical activity outcomes were evident (p < .05). School-based physical activity promotion should emphasize sex-specific enhancement of students' perceived PE competence and enjoyment.

  13. Design, synthesis, and biological evaluation of novel histone deacetylase 1 inhibitors through click chemistry.

    PubMed

    Sun, Qiao; Yao, Yiwu; Liu, Chunping; Li, Hua; Yao, Hequan; Xue, Xiaowen; Liu, Jinsong; Tu, Zhengchao; Jiang, Sheng

    2013-06-01

    We report the design, synthesis, and biological evaluation of a new series of HDAC1 inhibitors using click chemistry. Compound 17 bearing a phenyl ring at meta-position was identified to show much better selectivity for HDAC1 over HDAC7 than SAHA. The compond 17 also showed better in vitro anticancer activities against several cancer cell lines than that of SAHA. This work could serve as a foundation for further exploration of selective HDAC inhibitors using the compound 17 molecular scaffold.

  14. Complex molecules in galactic dust cores: Biologically interesting molecules and dust chemistry

    NASA Astrophysics Data System (ADS)

    Liu, Shen-Yuan

    2000-06-01

    The astronomical study of molecules has been an essential research field since the development of radio astronomy. Presently nearly 120 molecules have been identified in interstellar and circumstellar environments. The complexity of molecular species, and particularly organic molecules, that can be synthesized in the interstellar medium (ISM) leads to one interesting and important subfield in interstellar molecular studies, namely, the search and study for molecules of possible biological interest. Observationally, complex and most saturated molecules are observed exclusively toward compact hot, dense regions, often called ``hot cores'', in molecular clouds. To account for the observed amount of saturated organic molecules, interstellar dust particles play an important role. It has often been suggested that solid state reactions on grain surfaces provide an efficient way to synthesis saturated organic molecules. The objective of this study is to obtain observational data on biologically interesting molecules and to study important complex interstellar molecules. Since hot molecular cores are inherently compact, interferometric observations are therefore an ideal approach to study these sources. All our observations were all made with the Berkeley-Illinois-Maryland-Association (BIMA) Array. We conducted the first survey of formic acid (HCOOH) with an interferometric array, and identified at least three sources. HCOOH is found with column densities above 1015 cm-2 in these sources. The correlation between HCOOH and HCOOCH3 emission implies a surface chemistry origin of HCOOH. Details of the results are given in Chapter 2. Meanwhile, we continued to search for molecules of biological interest, namely urea, acetic acid, and glycine. In Chapter 3, the results of column density limits set by our observations are discussed. We have also investigated properties of individual hot molecular cores. It is very important to obtain the physical and chemical properties of these

  15. Diversity of Secondary Metabolites from Marine Bacillus Species: Chemistry and Biological Activity

    PubMed Central

    Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Islam, Mohammad Tofazzal

    2013-01-01

    Marine Bacillus species produce versatile secondary metabolites including lipopeptides, polypeptides, macrolactones, fatty acids, polyketides, and isocoumarins. These structurally diverse compounds exhibit a wide range of biological activities, such as antimicrobial, anticancer, and antialgal activities. Some marine Bacillus strains can detoxify heavy metals through reduction processes and have the ability to produce carotenoids. The present article reviews the chemistry and biological activities of secondary metabolites from marine isolates. Side by side, the potential for application of these novel natural products from marine Bacillus strains as drugs, pesticides, carotenoids, and tools for the bioremediation of heavy metal toxicity are also discussed. PMID:23941823

  16. Inorganic sulfur-nitrogen compounds: from gunpowder chemistry to the forefront of biological signaling.

    PubMed

    Cortese-Krott, Miriam M; Butler, Anthony R; Woollins, J Derek; Feelisch, Martin

    2016-04-14

    The reactions between inorganic sulfur and nitrogen-bearing compounds to form S-N containing species have a long history and, besides assuming importance in industrial synthetic processes, are of relevance to microbial metabolism; waste water treatment; aquatic, soil and atmospheric chemistry; and combustion processes. The recent discovery that hydrogen sulfide and nitric oxide exert often similar, sometimes mutually dependent effects in a variety of biological systems, and that the chemical interaction of these two species leads to formation of S-N compounds brought this chemistry to the attention of physiologists, biochemists and physicians. We here provide a perspective about the potential role of S-N compounds in biological signaling and briefly review their chemical properties and bioactivities in the context of the chronology of their discovery. Studies of the biological role of NO revealed why its chemistry is ideally suited for the tasks Nature has chosen for it; realising how the distinctive properties of sulfur can enrich this bioactivity does much to revive 'die Freude am experimentellen Spiel' of the pioneers in this field.

  17. Adenine Synthesis in a Model Prebiotic Reaction: Connecting Origin of Life Chemistry with Biology.

    PubMed

    Anumukonda, Lakshmi N; Young, Avery; Lynn, David G; Buckley, Ragan; Warrayat, Amena; Graves, Christina L; Bean, Heather D; Hud, Nicholas V

    2011-12-01

    Many high school laboratory experiments demonstrate concepts related to biological evolution, but few exist that allow students to investigate life's chemical origins. This series of laboratory experiments has been developed to allow students to explore and appreciate the deep connection that exists between prebiotic chemistry, chemical evolution, and contemporary biological systems. In the first experiment of the series, students synthesize adenine, one of the purine nucleobases of DNA and RNA, from plausibly prebiotic precursor molecules. Students compare their product to authentic standards using thin-layer chromatography. The second and third experiments of the series allow students to extract DNA from a familiar organism, the strawberry, and hydrolyze it, releasing adenine, which they can then compare to the previously chemically-synthesized adenine. A fourth, optional experiment is included where the technique of thin-layer chromatography is introduced and chromatographic skills are developed for use in the other three experiments that comprise this series. Concepts relating to organic and analytical chemistry, as well as biochemistry and DNA structure, are incorporated throughout, allowing this series of laboratory experiments to be easily inserted into existing laboratory courses and to reinforce concepts already included in any high school chemistry or biology curriculum.

  18. Adenine Synthesis in a Model Prebiotic Reaction: Connecting Origin of Life Chemistry with Biology

    PubMed Central

    2011-01-01

    Many high school laboratory experiments demonstrate concepts related to biological evolution, but few exist that allow students to investigate life’s chemical origins. This series of laboratory experiments has been developed to allow students to explore and appreciate the deep connection that exists between prebiotic chemistry, chemical evolution, and contemporary biological systems. In the first experiment of the series, students synthesize adenine, one of the purine nucleobases of DNA and RNA, from plausibly prebiotic precursor molecules. Students compare their product to authentic standards using thin-layer chromatography. The second and third experiments of the series allow students to extract DNA from a familiar organism, the strawberry, and hydrolyze it, releasing adenine, which they can then compare to the previously chemically-synthesized adenine. A fourth, optional experiment is included where the technique of thin-layer chromatography is introduced and chromatographic skills are developed for use in the other three experiments that comprise this series. Concepts relating to organic and analytical chemistry, as well as biochemistry and DNA structure, are incorporated throughout, allowing this series of laboratory experiments to be easily inserted into existing laboratory courses and to reinforce concepts already included in any high school chemistry or biology curriculum. PMID:22075932

  19. Synthetic biology and biomimetic chemistry as converging technologies fostering a new generation of smart biosensors.

    PubMed

    Scognamiglio, Viviana; Antonacci, Amina; Lambreva, Maya D; Litescu, Simona C; Rea, Giuseppina

    2015-12-15

    Biosensors are powerful tunable systems able to switch between an ON/OFF status in response to an external stimulus. This extraordinary property could be engineered by adopting synthetic biology or biomimetic chemistry to obtain tailor-made biosensors having the desired requirements of robustness, sensitivity and detection range. Recent advances in both disciplines, in fact, allow to re-design the configuration of the sensing elements - either by modifying toggle switches and gene networks, or by producing synthetic entities mimicking key properties of natural molecules. The present review considered the role of synthetic biology in sustaining biosensor technology, reporting examples from the literature and reflecting on the features that make it a useful tool for designing and constructing engineered biological systems for sensing application. Besides, a section dedicated to bioinspired synthetic molecules as powerful tools to enhance biosensor potential is reported, and treated as an extension of the concept of biomimetic chemistry, where organic synthesis is used to generate artificial molecules that mimic natural molecules. Thus, the design of synthetic molecules, such as aptamers, biomimetics, molecular imprinting polymers, peptide nucleic acids, and ribozymes were encompassed as "products" of biomimetic chemistry.

  20. Introducing chemical biology applications to introductory organic chemistry students using series of weekly assignments.

    PubMed

    Kanin, Maralee R; Pontrello, Jason K

    2016-01-01

    Calls to bring interdisciplinary content and examples into introductory science courses have increased, yet strategies that involve course restructuring often suffer from the need for a significant faculty commitment to motivate change. Minimizing the need for dramatic course reorganization, the structure, reactivity, and chemical biology applications of classes of biological monomers and polymers have been integrated into introductory organic chemistry courses through three series of semester-long weekly assignments that explored (a) Carbohydrates and Oligosaccharides, (b) Amino Acids, Peptides, and Proteins, and (c) Nucleosides, Nucleotides, and Nucleic Acids. Comparisons of unannounced pre- and post tests revealed improved understanding of a reaction introduced in the assignments, and course examinations evaluated cumulative assignment topics. Course surveys revealed that demonstrating biologically relevant applications consistently throughout the semesters enhanced student interest in the connection between basic organic chemistry content and its application to new and unfamiliar bio-related examples. Covering basic material related to these classes of molecules outside of the classroom opened lecture time to allow the instructor to further build on information developed through the weekly assignments, teaching advanced topics and applications typically not covered in an introductory organic chemistry lecture course. Assignments were implemented as homework, either with or without accompanying discussion, in both laboratory and lecture organic courses within the context of the existing course structures.

  1. Potential biological chemistry of hydrogen sulfide (H2S) with the nitrogen oxides.

    PubMed

    Bruce King, S

    2013-02-01

    Hydrogen sulfide, an important gaseous signaling agent generated in numerous biological tissues, influences many physiological processes. This biological profile seems reminiscent of nitric oxide, another important endogenously synthesized gaseous signaling molecule. Hydrogen sulfide reacts with nitric oxide or oxidized forms of nitric oxide and nitric oxide donors in vitro to form species that display distinct biology compared to both hydrogen sulfide and NO. The products of these interesting reactions may include small-molecule S-nitrosothiols or nitroxyl, the one-electron-reduced form of nitric oxide. In addition, thionitrous acid or thionitrite, compounds structurally analogous to nitrous acid and nitrite, may constitute a portion of the reaction products. Both the chemistry and the biology of thionitrous acid and thionitrite, compared to nitric oxide or hydrogen sulfide, remain poorly defined. General mechanisms for the formation of S-nitrosothiols, nitroxyl, and thionitrous acid based upon the ability of hydrogen sulfide to act as a nucleophile and a reducing agent with reactive nitric oxide-based intermediates are proposed. Hydrogen sulfide reactivity seems extensive and could have an impact on numerous areas of redox-controlled biology and chemistry, warranting more work in this exciting and developing area.

  2. PREFACE: Physics and biology of neurodegenerative diseases Physics and biology of neurodegenerative diseases

    NASA Astrophysics Data System (ADS)

    Pastore, Annalisa

    2012-06-01

    , about 15 years after the original reports, it is clear that amyloids are special structures that occur in nature under several different guises, some good, some evil [3]. The number of diseases associated with misfolding and fibrillogenesis has steadily increased. Examples of fairly common pathologies associated with fibre formation include Alzheimer's disease (currently one of the major threats for human health in our increasingly aging world), Parkinson's disease and several rare, but not less severe, pathologies. On the other hand, it is also clear that amyloid formation is a convenient mechanism for storing peptides and/or proteins in a compact and resistant way. The number of organisms/tissues in which amyloid deposits are found is thus increasing. It is also not too far-fetched to expect that the mechanical properties of amyloids could be used in biotechnology to design new materials. Because of the importance of this topic in so many scientific fields, we have dedicated this special issue of Journal of Physics: Condensed Matter to the topic of protein aggregation and disease. In the following pages we have collected two reviews and five articles that explore new and interesting developments in the field. References [1] Olby R 1994 The Path of the Double Helix: The Discovery of DNA (New York: Dover) [2] Dobson C M 2004 Principles of protein folding, misfolding and aggregation Semin. Cell Dev. Biol. 15 3-16 [3] Hammer N D, Wang X, McGuffie B A, Chapman M R 2008 Amyloids: friend or foe? J. Alzheimers Dis. 13 407-19 Physics and biology of neurodegenerative diseases contents Protein aggregation and misfolding: good or evil?Annalisa Pastore and Pierandrea Temussi Alzheimer's disease: biological aspects, therapeutic perspectives and diagnostic toolsM Di Carlo, D Giacomazza and P L San Biagio Entrapment of Aβ1-40 peptide in unstructured aggregatesC Corsale, R Carrotta, M R Mangione, S Vilasi, A Provenzano, G Cavallaro, D Bulone and P L San Biagio Elemental micro

  3. Linking Physics, Chemistry, and Math for Sustained Reform in Teacher Education

    NASA Astrophysics Data System (ADS)

    Kirchhoff, Mary; Lewis, W. James; Vokos, Stamatis; Plisch, Monica

    2012-02-01

    Physics, chemistry and math consistently rank as the highest need disciplines for qualified teachers. There are many common challenges faced by teacher educators in these disciplines, as well as some key differences. The panel will discuss these similarities and differences, and explore possible links between disciplinary efforts to promote sustained reform. The discussion will build on the work of the Task Force on Teacher Education in Physics, the ACS effort to launch the Chemistry Teacher Education Coalition, and the Conference Board of Mathematical Sciences report on the Mathematical Education of Teachers.

  4. Solid-State NMR Spectroscopy for the Physical Chemistry Laboratory

    ERIC Educational Resources Information Center

    Kinnun, Jacob J.; Leftin, Avigdor; Brown, Michael F.

    2013-01-01

    Solid-state nuclear magnetic resonance (NMR) spectroscopy finds growing application to inorganic and organic materials, biological samples, polymers, proteins, and cellular membranes. However, this technique is often neither included in laboratory curricula nor typically covered in undergraduate courses. On the other hand, spectroscopy and…

  5. Physical Chemistry to the Rescue: Differentiating Nicotinic and Cholinergic Agonists

    ERIC Educational Resources Information Center

    King, Angela G.

    2005-01-01

    Researches suggest that two agonists can bind to the same binding site of an important transmembrane protein and elicit a biological response through strikingly different binding interactions. Evidence is provided which suggests two possible types of nicotinic acetylcholine receptor agonist binding like acetlycholine (cholinergic) or like nicotine…

  6. Milkweed Seed Dispersal: A Means for Integrating Biology and Physics.

    ERIC Educational Resources Information Center

    Bisbee, Gregory D.; Kaiser, Cheryl A.

    1997-01-01

    Describes an activity that integrates biology and physics concepts by experimenting with the seed dispersal of common milkweed or similar wind-dispersed seeds. Student teams collect seeds and measure several parameters, review principles of trajectory motion, perform experiments, and graph data. Students examine the ideas of…

  7. Working together at the interface of physics and biology

    NASA Astrophysics Data System (ADS)

    Bassler, Bonnie L.; Wingreen, Ned S.

    2014-10-01

    Good communication, whether it is between quorum-sensing bacteria or the different scientists studying those critters, is the key to a successful interdisciplinary collaboration, Bonnie Bassler and Ned Wingreen provide a personal perspective on working at the interface between the physical and biological sciences.

  8. Physics for Medicine and Biology: Determining Body Fat Content

    NASA Astrophysics Data System (ADS)

    Aaron, Ronald; Altman, Albert

    2011-04-01

    Hydrostatic weighing is a technique for determining body fat content that is based on Archimedes principle and varied applications of the ideal gas law. We use this procedure as an example of the types of physics material which should be presented in an introductory course for students that are interested in careers in biology and medicine.

  9. When physics and biology meet: the nanoscale case.

    PubMed

    Bueno, Otávio

    2011-06-01

    As an illustration of the complexities involved in connecting physics and molecular biology at the nanoscale, in this paper I discuss two case studies from nanoscience. The first examines the use of a biological structure (DNA) to build nanostructures in a controlled way. The second discusses the attempt to build a single molecular wire, and then decide whether such a wire is indeed conducting. After presenting the central features of each case study, I examine the role played in them by microscopic imaging, the different styles of reasoning involved, and the various theoretical, methodological, and axiological differences. I conclude by arguing that, except for the probe microscopes that are used, there is very little in common between the two cases. At the nanoscale, physics and molecular biology seem to meet in a non-unified way.

  10. From physics to biology by extending criticality and symmetry breakings.

    PubMed

    Longo, G; Montévil, M

    2011-08-01

    Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not "just" processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions.

  11. Extended physics as a theoretical framework for systems biology?

    PubMed

    Miquel, Paul-Antoine

    2011-08-01

    In this essay we examine whether a theoretical and conceptual framework for systems biology could be built from the Bailly and Longo (2008, 2009) proposal. These authors aim to understand life as a coherent critical structure, and propose to develop an extended physical approach of evolution, as a diffusion of biomass in a space of complexity. Their attempt leads to a simple mathematical reconstruction of Gould's assumption (1989) concerning the bacterial world as a "left wall of least complexity" that we will examine. Extended physical systems are characterized by their constructive properties. Time is acting and new properties emerge by their history that can open the list of their initial properties. This conceptual and theoretical framework is nothing more than a philosophical assumption, but as such it provides a new and exciting approach concerning the evolution of life, and the transition between physics and biology.

  12. Influence of Biological Macromolecules and Aquatic Chemistries on the Inhibition of Nitrifying Bacteria by Silver Nanoparticles

    NASA Astrophysics Data System (ADS)

    Radniecki, T. S.; Anderson, J. W.; Schneider, M. C.; Stankus, D. P.; Nason, J. A.; Semprini, L.

    2010-12-01

    The use of silver nanoparticles (Ag-NP) as a broad spectrum biocide in a wide range of consumer goods has grown exponentially since 2006 (1), which may result in an increased release of Ag-NP into wastewater streams and ultimately the receiving bodies of water. Ammonia oxidizing bacteria (AOB) play a critical role in the global nitrogen cycle through the oxidation of ammonia (NH3) to nitrite (NO2-) and are widely considered to be the most sensitive microbial fauna in the environment being readily inhibited by contaminants, including Ag-NP (2). This research used physiological techniques in combination with physical/chemical assays to characterize the inhibition of Nitrosomonas europaea, the model AOB, by silver ions (Ag+), 3-5 nm Ag-NP, 20 nm Ag-NP and 80 nm Ag-NP under a variety of aqueous chemistries. In addition, the stability of Ag-NP suspensions was examined under a variety of aqueous chemistries including in the presences of divalent cations, chloride anions, natural organic matter (NOM), proteins (BSA) and lipopolysaccharides (alginate). Using the stable Ag-NP/test media suspensions, N. europaea was found to be extremely sensitive to Ag+, 3-5 nm Ag-NP, 20 nm Ag-NP and 80 nm Ag-NP with concentrations of 0.1, 0.12, 0.5 and 1.5 ppm, respectively, resulting in a 50% decrease in nitrification rates. The inhibition was correlated with the amount of Ag+ released into solution. It is suspected that the inhibition observed from Ag-NP exposure is caused by the liberated Ag+. The aquatic chemistry of the test media was found to have a profound influence on the stability of Ag-NP suspensions. The presence of Ag ligands (e.g. EDTA and Cl-) reduced toxicity of Ag-NP through the formation of Ag-ligand complexes with the liberated Ag+. The presence of divalent cations (e.g. Ca2+ or Mg2+) resulted in the rapid aggregation of Ag-NP leading to a decrease in Ag+ liberation and thus a decrease in N. europaea inhibition. The presence of 5 ppm NOM resulted in a highly stable Ag

  13. A Study of Faculty Approaches to Teaching Undergraduate Physical Chemistry Courses

    NASA Astrophysics Data System (ADS)

    Mack, Michael Ryan

    Chemistry education researchers have not adequately studied teaching and learning experiences at all levels in the undergraduate chemistry curriculum leaving gaps in discipline-based STEM education communities understanding about how the upper- division curricula works (National Research Council, 2012b; Towns, 2013). This study explored faculty approaches to teaching in upper-division physical chemistry course settings using an interview-based methodology. Two conceptualizations of approaches to teaching emerged from a phenomenographic analysis of interview transcripts: (1) faculty beliefs about the purposes for teaching physical chemistry and (2) their conceptions of their role as an instructor in these course settings. Faculty who reported beliefs predominantly centered on helping students develop conceptual knowledge and problem-solving skills in physical chemistry often worked with didactic models of teaching, which emphasized the transfer of expert knowledge to students. When faculty expressed beliefs that were more inclusive of conceptual, epistemic, and social learning goals in science education they often described more student-centered models of teaching and learning, which put more responsibilities on them to facilitate students' interactive engagement with the material and peers during regularly scheduled class time. Knowledge of faculty thinking, as evinced in a rich description of their accounts of their experience, provides researchers and professional developers with useful information about the potential opportunities or barriers that exist for helping faculty align their beliefs and goals for teaching with research-based instructional strategies.

  14. Radiation physics and chemistry of biomolecules. Recent developments

    NASA Astrophysics Data System (ADS)

    Spotheim-Maurizot, Melanie

    2016-11-01

    A chapter of the book ;Radiation chemistry. From basics to application in materials and life sciences (EDP Science, Paris, France, 2008); was devoted to the state-of-the-art in the research on ionizing radiation (IR) effects on biomolecules. An update, eight years later, seemed pertinent enough to the editors of this journal who accepted to dedicate a Special Issue to the latest developments in this area of high interest for cancer radiotherapy, nuclear workers' radioprotection and food radiosterilisation. We sincerely thank them and the authors who accepted to present reviews of their most recent work. Obviously, only a small part of the research in the fascinating domain of molecular radiobiology can be covered here. Some articles are presenting the contribution of biophysical models and computational techniques to the understanding of IR effects on molecules such as DNA and proteins, or on larger systems such as chromatin, chromosomes and even cells (Nikjoo et al., Štěpán & Davídková, Ballarini & Carante, and Nikitaki et al.). In these papers, as well as in many others, several qualities of IR are compared in order to explain the observed differences of effects. The damages induced by the low energy electrons and new techniques involved in their study are discussed in great detail (Sanche and Fromm & Boulanouar). The chemistry behind the IR induced damages (single or clustered), studied in many laboratories around the world is presented in several papers (Cadet & Wagner, Sevilla et al., Chatgilialoglu et al., and Greenberg). One of them addresses a very useful comparison between the effects of IR and UV exposure on DNA (Ravanat & Douki). The majority of the papers in this Special Issue is dealing with DNA and this reflects the real situation: damages of DNA are more studied than those of other biomolecules. This is due to the role of DNA as main support of hereditary information. Nevertheless, more and more studies are outlining the influence of epigenetic

  15. Computers in Undergraduate Education: Mathematics, Physics, Statistics, and Chemistry.

    ERIC Educational Resources Information Center

    Lockard, J. David

    This is the report of a conference which was initiated by the National Science Foundation's Office of Computing Activities and which explored and summarized current thinking about the role of the computer for undergraduate curricula in the physical and mathematical sciences. The conference focused on deciding which goals of the existing…

  16. Enthalpy of Vaporization by Gas Chromatography: A Physical Chemistry Experiment

    ERIC Educational Resources Information Center

    Ellison, Herbert R.

    2005-01-01

    An experiment is conducted to measure the enthalpy of vaporization of volatile compounds like methylene chloride, carbon tetrachloride, and others by using gas chromatography. This physical property was measured using a very tiny quantity of sample revealing that it is possible to measure the enthalpies of two or more compounds at the same time.

  17. A Course on the Physics and Chemistry of Pollution

    ERIC Educational Resources Information Center

    Hodges, Laurent

    1971-01-01

    Describes a course on environmental pollution which stresses physical and chemical principles. Course presents a unified discussion of air and water pollution and solid waste with special treatment of pesticides, thermal pollution, radioactivity, and electric power generation. Uses historical and current statistics extensively to set pollution…

  18. Physical activity and cancer prevention: etiologic evidence and biological mechanisms.

    PubMed

    Friedenreich, Christine M; Orenstein, Marla R

    2002-11-01

    Scientific evidence is accumulating on physical activity as a means for the primary prevention of cancer. Nearly 170 observational epidemiologic studies of physical activity and cancer risk at a number of specific cancer sites have been conducted. The evidence for decreased risk with increased physical activity is classified as convincing for breast and colon cancers, probable for prostate cancer, possible for lung and endometrial cancers and insufficient for cancers at all other sites. Despite the large number of studies conducted on physical activity and cancer, most have been hampered by incomplete assessment of physical activity and a lack of full examination of effect modification and confounding. Several plausible hypothesized biological mechanisms exist for the association between physical activity and cancer, including changes in endogenous sexual and metabolic hormone levels and growth factors, decreased obesity and central adiposity and possibly changes in immune function. Weight control may play a particularly important role because links between excess weight and increased cancer risk have been established for several sites, and central adiposity has been particularly implicated in promoting metabolic conditions amenable to carcinogenesis. Based on existing evidence, some public health organizations have issued physical activity guidelines for cancer prevention, generally recommending at least 30 min of moderate-to-vigorous intensity physical activity on > or =5 d/wk. Although most research has focused on the efficacy of physical activity in cancer prevention, evidence is increasing that exercise also influences other aspects of the cancer experience, including cancer detection, coping, rehabilitation and survival after diagnosis.

  19. Combining research in physical chemistry and chemical education: Part A. The femtosecond molecular dynamics of small gas-phase anion clusters. Part B. Surveying student beliefs about chemistry and the development of physical chemistry learning tutorials

    NASA Astrophysics Data System (ADS)

    Barbera, Jack

    2007-12-01

    This dissertation combines work in the areas of experimental physical chemistry and chemical education. In the area of physical chemistry, femtosecond pump-probe spectroscopy is used to interrogate the time-dependence for energy redistribution, solvent reorientation, and dissociation dynamics in small gas-phase anion clusters. The chemical education research addressed in this manuscript include the development and validation of a survey to measure students' beliefs about chemistry and the learning of chemistry and the development and testing of learning tutorials for use in undergraduate physical chemistry courses in thermodynamics and kinetics. In the first part of this dissertation, the Cu(CD3OD) dynamics are investigated using a combination of femtosecond pump-probe experiments and ab initio calculations. Dissociation of this complex into Cu and CD3OD occurs on two distinct time scales: 3 and 30 ps, which arise, respectively, from the coupling of intermolecular solvent rotations and excited methyl rotor rotation into the Cu-O dissociation component upon electron photodetachment of the precursor anion. In the second part of this dissertation, the time-resolved recombination of photodissociated IBr-(CO2)n (n = 5 - 10) cluster anions is investigated. Upon excitation to the A' 2pi 1/2 state of the chromophore, the bare anion results in I- and Br products, upon solvation with CO2, the IBr- chromophore regains near-IR absorption after recombination and vibrational relaxation on the ground electronic state. The recombination times vary with the number of solvent molecules from 12 ps for n = 5 to 900 ps for n = 10. Extensive electronic structure and non-adiabatic molecular dynamic simulations provide a framework to understand this behavior. In the third part of this dissertation, the modification and validation of the Colorado Learning Attitudes about Science Survey (CLASS) for use in chemistry is presented in detail. The CLASS survey is designed to measure student

  20. Biologic: Gene circuits and feedback in an introductory physics sequence for biology and premedical students

    NASA Astrophysics Data System (ADS)

    Cahn, S. B.; Mochrie, S. G. J.

    2014-05-01

    We describe an educational module on feedback and gene circuits that constitute the final topic in a new year-long introductory physics sequence aimed at biology and premedical students at Yale University. The overall goals of this sequence are threefold. First to demonstrate the application of physics and mathematics in the life sciences. Second to introduce biological science majors to mathematical and physical tools, principles, and experiences. Third to seed an enduring appreciation of quantitative approaches in biology and medicine. Here, we present a module on feedback and gene circuits that focuses on a genetic toggle switch and a repressilator. The genetic toggle switch consists of two genes, each of whose protein products represses the other's expression, while the repressilator consists of three genes, each of whose protein products represses the next gene's expression. Analytic, numerical, and electronic treatments of the genetic toggle switch show bistability. A similar treatment of the repressilator reveals sustained oscillations.

  1. Surface chemistry and physics of deuterium retention in lithiated graphite

    SciTech Connect

    Taylor, C. N.; Krstic, Predrag S; Allain, J. P.; Heim, B.; Skinner, C. H.; Kugel, H.

    2011-01-01

    Lithium wall conditioning in TFTR, CDX-U, T-11M, TJ-II and NSTX is found to yield enhanced plasma performance manifest, in part, through improved deuterium particle control. X-ray photoelectron spectroscopy (XPS) experiments examine the affect of D irradiation on lithiated graphite and show that the surface chemistry of lithiated graphite after D ion bombardment (500 eV/amu) is fundamentally different from that of non-Li conditioned graphite. Instead of simple LiD bonding seen in pure liquid Li, graphite introduces additional complexities. XPS spectra show that Li-O-D (533.0 {+-} 0.6 eV) and Li-C-D (291.4 {+-} 0.6 eV) bonds, for a nominal Li dose of 2 {micro}m, become 'saturated' with D at fluences between 3.8 and 5.2 x 10{sup 17} cm{sup -2}. Atomistic modeling indicate that Li-O-D-C interactions may be a result of multibody effects as opposed to molecular bonding.

  2. The effects of urbanization on the biological, physical, and chemical characteristics of coastal New England streams

    USGS Publications Warehouse

    Coles, James F.; Cuffney, Thomas F.; McMahon, Gerard; Beaulieu, Karen M.

    2004-01-01

    During August 2000, responses of biological communities (invertebrates, fish, and algae), physical habitat, and water chemistry to urban intensity were compared among 30 streams within 80 miles of Boston, Massachusetts. Sites chosen for sampling represented a gradient of the intensity of urban development (urban intensity) among drainage basins that had minimal natural variability. In this study, spatial differences were used as surrogates for temporal changes to represent the effects of urbanization over time. The degree of urban intensity for each drainage basin was characterized with a standardized urban index (0-100, lowest to highest) derived from land cover, infrastructure, and socioeconomic variables. Multivariate and multimetric analyses were used to compare urban index values with biological, physical, and chemical data to determine how the data indicated responses to urbanization. Multivariate ordinations were derived for the invertebrate-, fish-, and algae-community data by use of correspondence analysis, and ordinations were derived for the chemical and physical data by use of principal-component analysis. Site scores from each of the ordinations were plotted in relation to the urban index to test for a response. In all cases, the primary axis scores showed the strongest response to the urban index, indicating that urbanization was a primary factor affecting the data ordination. For the multimetric analyses, each of the biological data sets was used to calculate a series of community metrics. For the sets of chemical and physical data, the individual variables and various combinations of individual variables were used as measured and derived metrics, respectively. Metrics that were generally most responsive to the urban index for each data set included: EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa for invertebrates; cyprinid taxa for fish; diatom taxa for algae; bicarbonate, conductivity, and nitrogen for chemistry; and water depth and temperature

  3. The effects of urbanization on the biological, physical, and chemical characteristics of coastal New England streams

    USGS Publications Warehouse

    Coles, J.F.; Cuffney, T.F.; McMahon, G.; Beaulieu, K.M.

    2004-01-01

    During August 2000, responses of biological communities (invertebrates, fish, and algae), physical habitat, and water chemistry to urban intensity were compared among 30 streams within 80 miles of Boston, Massachusetts. Sites chosen for sampling represented a gradient of the intensity of urban development (urban intensity) among drainage basins that had minimal natural variability. In this study, spatial differences were used as surrogates for temporal changes to represent the effects of urbanization over time. The degree of urban intensity for each drainage basin was characterized with a standardized urban index (0?100, lowest to highest) derived from land cover, infrastructure, and socioeconomic variables. Multivariate and multimetric analyses were used to compare urban index values with biological, physical, and chemical data to determine how the data indicated responses to urbanization. Multivariate ordinations were derived for the invertebrate-, fish-, and algaecommunity data by use of correspondence analysis, and ordinations were derived for the chemical and physical data by use of principal-component analysis. Site scores from each of the ordinations were plotted in relation to the urban index to test for a response. In all cases, the primary axis scores showed the strongest response to the urban index, indicating that urbanization was a primary factor affecting the data ordination. For the multimetric analyses, each of the biological data sets was used to calculate a series of community metrics. For the sets of chemical and physical data, the individual variables and various combinations of individual variables were used as measured and derived metrics, respectively. Metrics that were generally most responsive to the urban index for each data set included: EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa for invertebrates; cyprinid taxa for fish; diatom taxa for algae; bicarbonate, conductivity, and nitrogen for chemistry; and water depth and temperature

  4. Variational Principles and Methods in Theoretical Physics and Chemistry

    NASA Astrophysics Data System (ADS)

    Nesbet, Robert K.

    2005-07-01

    Preface; Part I. Classical Mathematics and Physics: 1. History of variational theory; 2. Classical mechanics; 3. Applied mathematics; Part II. Bound States in Quantum Mechanics: 4. Time-independent quantum mechanics; 5. Independent-electron models; 6. Time-dependent theory and linear response; Part III. Continuum States and Scattering Theory: 7. Multiple scattering theory for molecules and solids; 8. Variational methods for continuum states; 9. Electron-impact rovibrational excitation of molecules; Part IV. Field Theories: 10. Relativistic Lagrangian theories.

  5. Biomorphodynamics: Physical-biological feedbacks that shape landscapes

    USGS Publications Warehouse

    Murray, A.B.; Knaapen, M.A.F.; Tal, M.; Kirwan, M.L.

    2008-01-01

    Plants and animals affect morphological evolution in many environments. The term "ecogeomorphology" describes studies that address such effects. In this opinion article we use the term "biomorphodynamics" to characterize a subset of ecogeomorphologic studies: those that investigate not only the effects of organisms on physical processes and morphology but also how the biological processes depend on morphology and physical forcing. The two-way coupling precipitates feedbacks, leading to interesting modes of behavior, much like the coupling between flow/sediment transport and morphology leads to rich morphodynamic behaviors. Select examples illustrate how even the basic aspects of some systems cannot be understood without considering biomorphodynamic coupling. Prominent examples include the dynamic interactions between vegetation and flow/sediment transport that can determine river channel patterns and the multifaceted biomorphodynamic feedbacks shaping tidal marshes and channel networks. These examples suggest that the effects of morphology and physical processes on biology tend to operate over the timescale of the evolution of the morphological pattern. Thus, in field studies, which represent a snapshot in the pattern evolution, these effects are often not as obvious as the effects of biology on physical processes. However, numerical modeling indicates that the influences on biology from physical processes can play a key role in shaping landscapes and that even local and temporary vegetation disturbances can steer large-scale, long-term landscape evolution. The prevalence of biomorphodynamic research is burgeoning in recent years, driven by societal need and a confluence of complex systems-inspired modeling approaches in ecology and geomorphology. To make fundamental progress in understanding the dynamics of many landscapes, our community needs to increasingly learn to look for two-way, biomorphodynamic feedbacks and to collect new types of data to support the

  6. Biomorphodynamics: Physical-biological feedbacks that shape landscapes

    NASA Astrophysics Data System (ADS)

    Murray, A. B.; Knaapen, M. A. F.; Tal, M.; Kirwan, M. L.

    2008-11-01

    Plants and animals affect morphological evolution in many environments. The term "ecogeomorphology" describes studies that address such effects. In this opinion article we use the term "biomorphodynamics" to characterize a subset of ecogeomorphologic studies: those that investigate not only the effects of organisms on physical processes and morphology but also how the biological processes depend on morphology and physical forcing. The two-way coupling precipitates feedbacks, leading to interesting modes of behavior, much like the coupling between flow/sediment transport and morphology leads to rich morphodynamic behaviors. Select examples illustrate how even the basic aspects of some systems cannot be understood without considering biomorphodynamic coupling. Prominent examples include the dynamic interactions between vegetation and flow/sediment transport that can determine river channel patterns and the multifaceted biomorphodynamic feedbacks shaping tidal marshes and channel networks. These examples suggest that the effects of morphology and physical processes on biology tend to operate over the timescale of the evolution of the morphological pattern. Thus, in field studies, which represent a snapshot in the pattern evolution, these effects are often not as obvious as the effects of biology on physical processes. However, numerical modeling indicates that the influences on biology from physical processes can play a key role in shaping landscapes and that even local and temporary vegetation disturbances can steer large-scale, long-term landscape evolution. The prevalence of biomorphodynamic research is burgeoning in recent years, driven by societal need and a confluence of complex systems-inspired modeling approaches in ecology and geomorphology. To make fundamental progress in understanding the dynamics of many landscapes, our community needs to increasingly learn to look for two-way, biomorphodynamic feedbacks and to collect new types of data to support the

  7. Nitrogen-Containing Constituents of Black Cohosh: Chemistry, Structure Elucidation, and Biological Activities

    PubMed Central

    Lankin, David C.; Cisowska, Tamara; Chen, Shao-Nong; Pauli, Guido F.; van Breemen, Richard B.

    2016-01-01

    The roots/rhizomes of black cohosh (Actaea racemosa L. syn. Cimicifuga racemosa [L]. Nutt., Ranunculaceae) have been used traditionally by Native Americans to treat colds, rheumatism, and a variety of conditions related to women’s health. In recent years black cohosh preparations have become popular dietary supplements among women seeking alternative treatments for menopausal complaints. The popularity of the plant has led to extensive phytochemical and biological investigations, including several clinical trials. Most of the phytochemical and biological research has focused on two abundant classes of compounds: the triterpene glycosides and phenolic acids. A third group of phytoconstituents that has received far less attention consists of the alkaloids and related compounds that contain nitrogen. This chapter summarizes the current state of knowledge of the chemistry and biological activities associated with this group of constituents and provides some perspective on their significance for future research on this interesting plant. PMID:27795590

  8. Some Aspects of Rubberlike Elasticity Useful in Teaching Basic Concepts in Physical Chemistry.

    ERIC Educational Resources Information Center

    Mark, J. E.

    2002-01-01

    Explains the benefits of including polymer topics in both graduate and undergraduate physical chemistry courses. Provides examples of how to use rubberlike elasticity to demonstrate some of the general and thermodynamic concepts including equations of state, Carnot cycles and mechanochemistry, gel collapse, energy storage and hysteresis, and…

  9. Retention of Differential and Integral Calculus: A Case Study of a University Student in Physical Chemistry

    ERIC Educational Resources Information Center

    Jukic Matic, Ljerka; Dahl, Bettina

    2014-01-01

    This paper reports a study on retention of differential and integral calculus concepts of a second-year student of physical chemistry at a Danish university. The focus was on what knowledge the student retained 14 months after the course and on what effect beliefs about mathematics had on the retention. We argue that if a student can quickly…

  10. A Stopped-Flow Kinetics Experiment for the Physical Chemistry Laboratory Using Noncorrosive Reagents

    ERIC Educational Resources Information Center

    Prigodich, Richard V.

    2014-01-01

    Stopped-flow kinetics techniques are important to the study of rapid chemical and biochemical reactions. Incorporation of a stopped-flow kinetics experiment into the physical chemistry laboratory curriculum would therefore be an instructive addition. However, the usual reactions studied in such exercises employ a corrosive reagent that can over…

  11. X-Ray Diffraction of Intermetallic Compounds: A Physical Chemistry Laboratory Experiment

    ERIC Educational Resources Information Center

    Varberg, Thomas D.; Skakuj, Kacper

    2015-01-01

    Here we describe an experiment for the undergraduate physical chemistry laboratory in which students synthesize the intermetallic compounds AlNi and AlNi3 and study them by X-ray diffractometry. The compounds are synthesized in a simple one-step reaction occurring in the solid state. Powder X-ray diffractograms are recorded for the two compounds…

  12. Thermodynamic Exploration of Eosin-Lysozyme Binding: A Physical Chemistry and Biochemistry Laboratory Experiment

    ERIC Educational Resources Information Center

    Huisman, Andrew J.; Hartsell, Lydia R.; Krueger, Brent P.; Pikaart, Michael J.

    2010-01-01

    We developed a modular pair of experiments for use in the undergraduate physical chemistry and biochemistry laboratories. Both experiments examine the thermodynamics of the binding of a small molecule, eosin Y, to the protein lysozyme. The assay for binding is the quenching of lysozyme fluorescence by eosin through resonant energy transfer. In…

  13. 3D Printed Potential and Free Energy Surfaces for Teaching Fundamental Concepts in Physical Chemistry

    ERIC Educational Resources Information Center

    Kaliakin, Danil S.; Zaari, Ryan R.; Varganov, Sergey A.

    2015-01-01

    Teaching fundamental physical chemistry concepts such as the potential energy surface, transition state, and reaction path is a challenging task. The traditionally used oversimplified 2D representation of potential and free energy surfaces makes this task even more difficult and often confuses students. We show how this 2D representation can be…

  14. Measurement of the Compressibility Factor of Gases: A Physical Chemistry Laboratory Experiment

    ERIC Educational Resources Information Center

    Varberg, Thomas D.; Bendelsmith, Andrew J.; Kuwata, Keith T.

    2011-01-01

    In this article, we describe an experiment for the undergraduate physical chemistry laboratory in which students measure the compressibility factor of two gases, helium and carbon dioxide, as a function of pressure at constant temperature. The experimental apparatus is relatively inexpensive to construct and is described and diagrammed in detail.…

  15. For the Love of Learning Science: Connecting Learning Orientation and Career Productivity in Physics and Chemistry

    ERIC Educational Resources Information Center

    Hazari, Zahra; Potvin, Geoff; Tai, Robert H.; Almarode, John

    2010-01-01

    An individual's motivational orientation serves as a drive to action and can influence their career success. This study examines how goal orientation toward the pursuit of a graduate degree in physics and chemistry influences later success outcomes of practicing physicists and chemists. Two main categories of goal orientation are examined in this…

  16. Investigating Intermolecular Interactions via Scanning Tunneling Microscopy: An Experiment for the Physical Chemistry Laboratory

    ERIC Educational Resources Information Center

    Pullman, David; Peterson, Karen I.

    2004-01-01

    A scanning tunneling microscope (STM) project designed as a module for the undergraduate physical chemistry laboratory is described. The effects of van der Waals interactions on the condensed-phase structure are examined by the analysis of the pattern of the monolayer structures.

  17. The Nature of Students' Chemical Reasoning Employed in Scientific Argumentation in Physical Chemistry

    ERIC Educational Resources Information Center

    Moon, A.; Stanford, C.; Cole, R.; Towns, M.

    2016-01-01

    Recent science education reform efforts have emphasized scientific practices in addition to scientific knowledge. Less work has been done at the tertiary level to consider students' engagement in scientific practices. In this work, we consider physical chemistry students' engagement in argumentation and construction of causal explanations.…

  18. A Practical and Convenient Diffusion Apparatus: An Undergraduate Physical Chemistry Experiment.

    ERIC Educational Resources Information Center

    Clifford, Ben; Ochiai, E. I.

    1980-01-01

    Described is a diffusion apparatus to be used in an undergraduate physical chemistry laboratory experiment to determine the diffusion coefficients of aqueous solutions of sucrose and potassium dichromate. Included is the principle of the method, apparatus design and description, and experimental procedure. (Author/DS)

  19. EPR Studies of Spin-Spin Exchange Processes: A Physical Chemistry Experiment.

    ERIC Educational Resources Information Center

    Eastman, Michael P.

    1982-01-01

    Theoretical background, experimental procedures, and analysis of experimental results are provided for an undergraduate physical chemistry experiment on electron paramagnetic resonance (EPR) linewidths. Source of line broadening observed in a spin-spin exchange process between radicals formed in aqueous solutions of potassium peroxylamine…

  20. A Writing and Ethics Component for a Quantum Mechanics, Physical Chemistry Course

    ERIC Educational Resources Information Center

    Reilly, John T.; Strickland, Michael

    2010-01-01

    A writing-across-the-curriculum and ethics component is presented for a second-semester, physical chemistry course. The activity involves introducing ethical issues pertinent to scientists. Students are asked to read additional material, participate in discussions, and write essays and a paper on an ethical issue. The writing and discussion…

  1. Addition of a Project-Based Component to a Conventional Expository Physical Chemistry Laboratory

    ERIC Educational Resources Information Center

    Tsaparlis, Georgios; Gorezi, Marianna

    2007-01-01

    Students should enjoy their laboratory classes and for this purpose a project-based activity is added to a conventional physical chemistry laboratory. Students were given project work instead of conventional experiment and then they had to make progress in the project according to instructions and then carry out experiments related to the project.

  2. A Game-Based Approach to an Entire Physical Chemistry Course

    ERIC Educational Resources Information Center

    Daubenfeld, Thorsten; Zenker, Dietmar

    2015-01-01

    We designed, implemented, and evaluated a game-based learning approach to increase student motivation and achievement for an undergraduate physical chemistry course. By focusing only on the most important game aspects, the implementation was realized with a production ratio of 1:8 (study load in hours divided by production effort in hours).…

  3. The James Webb Space Telescope: Inspiration and Context for Physics and Chemistry Teaching

    ERIC Educational Resources Information Center

    Hillier, Dan; Johnston, Tania; Davies, John

    2012-01-01

    This article describes the design, delivery, evaluation and impact of a CPD course for physics and chemistry teachers. A key aim of the course was to use the context of the James Webb Space Telescope project to inspire teachers and lead to enriched teaching of STEM subjects. (Contains 1 box and 3 figures.)

  4. Teaching about Ethics through Socioscientific Issues in Physics and Chemistry: Teacher Candidates' Beliefs

    ERIC Educational Resources Information Center

    Barrett, Sarah Elizabeth; Nieswandt, Martina

    2010-01-01

    The purpose of this qualitative study was to identify and explain the origins of physics and chemistry teacher candidates' beliefs about teaching about ethics through socioscientific issues (SSI). This study utilized a series of in-depth interviews, while the participants (n = 12) were enrolled in a 9-month teacher education program at an urban…

  5. Faculty Beliefs about the Purposes for Teaching Undergraduate Physical Chemistry Courses

    ERIC Educational Resources Information Center

    Mack, Michael R.; Towns, Marcy H.

    2016-01-01

    We report the results of a phenomenographic analysis of faculty beliefs about the purposes for teaching upper-division physical chemistry courses in the undergraduate curriculum. A purposeful sampling strategy was used to recruit a diverse group of faculty for interviews. Collectively, the participating faculty regularly teach or have taught…

  6. An Attenuated Total Reflectance Sensor for Copper: An Experiment for Analytical or Physical Chemistry

    ERIC Educational Resources Information Center

    Shtoyko, Tanya; Zudans, Imants; Seliskar, Carl J.; Heineman, William R.; Richardson, John N.

    2004-01-01

    A sensor experiment which can be applied to advanced undergraduate laboratory course in physical or analytical chemistry is described along with certain concepts like the demonstration of chemical sensing, preparation of thin films on a substrate, microtitration, optical determination of complex ion stoichiometry and isosbestic point. It is seen…

  7. Integrating a Single Tablet PC in Chemistry, Engineering, and Physics Courses

    ERIC Educational Resources Information Center

    Rogers, James W.; Cox, James R.

    2008-01-01

    A tablet PC is a versatile computer that combines the computing power of a notebook with the pen functionality of a PDA (Cox and Rogers 2005b). The authors adopted tablet PC technology in order to improve the process and product of the lecture format in their chemistry, engineering, and physics courses. In this high-tech model, a single tablet PC…

  8. Linear Dichroism of Cyanine Dyes in Stretched Polyvinyl Alcohol Films: A Physical Chemistry Laboratory Experiment.

    ERIC Educational Resources Information Center

    Natarajan, L. V.; And Others

    1983-01-01

    Provides background information, procedures, and results of an undergraduate physical chemistry experiment on the polarization of absorption spectra of cyanine dyes in stretched polyvinyl alcohol films. The experiment gives a simple demonstration of the concept of linear dichromism and the validity of the TEM method used in the analyses. (JN)

  9. Advanced Experiments in Nuclear Science, Volume I: Advanced Nuclear Physics and Chemistry Experiments.

    ERIC Educational Resources Information Center

    Duggan, Jerome L.; And Others

    The experiments in this manual represent state-of-the-art techniques which should be within the budgetary constraints of a college physics or chemistry department. There are fourteen experiments divided into five modules. The modules are on X-ray fluorescence, charged particle detection, neutron activation analysis, X-ray attenuation, and…

  10. Computational Modeling of the Optical Rotation of Amino Acids: An "in Silico" Experiment for Physical Chemistry

    ERIC Educational Resources Information Center

    Simpson, Scott; Autschbach, Jochen; Zurek, Eva

    2013-01-01

    A computational experiment that investigates the optical activity of the amino acid valine has been developed for an upper-level undergraduate physical chemistry laboratory course. Hybrid density functional theory calculations were carried out for valine to confirm the rule that adding a strong acid to a solution of an amino acid in the l…

  11. Framing a Program Designed to Train New Chemistry/Physics Teachers for California Outlying Regions

    ERIC Educational Resources Information Center

    Bodily, Gerald P., Jr.

    2010-01-01

    The purpose of this study was to develop guidelines for a new high school chemistry and physics teacher training program. Eleven participants were interviewed who attended daylong workshops, every other Saturday, for 10 months. The instructors used Modeling Instruction pedagogy and curriculum. All the instructors had high school teaching…

  12. Oxygen supersaturation in the ocean: biological versus physical contributions.

    PubMed

    Craig, H; Hayward, T

    1987-01-09

    A method based on measurements of dissolved molecular nitrogen, molecular oxygen, and argon can distingish biological from physical contributions to oxygen supersaturation in the ocean. The derived values of biological O(2) production can be used as a check on estimates of total organic productivity measured by instantaneous rates of carbon-14 assimilation. Application to the shallow summer O(2) maxima in the North Pacific gyres shows that about 72% of the O(2) supersaturation maximum at 28 degrees N and about 86% of the maximum at 40 degrees N are due to net photosynthetic production.

  13. Synthesis of silver nanoparticles: chemical, physical and biological methods

    PubMed Central

    Iravani, S.; Korbekandi, H.; Mirmohammadi, S.V.; Zolfaghari, B.

    2014-01-01

    Silver nanoparticles (NPs) have been the subjects of researchers because of their unique properties (e.g., size and shape depending optical, antimicrobial, and electrical properties). A variety of preparation techniques have been reported for the synthesis of silver NPs; notable examples include, laser ablation, gamma irradiation, electron irradiation, chemical reduction, photochemical methods, microwave processing, and biological synthetic methods. This review presents an overview of silver nanoparticle preparation by physical, chemical, and biological synthesis. The aim of this review article is, therefore, to reflect on the current state and future prospects, especially the potentials and limitations of the above mentioned techniques for industries. PMID:26339255

  14. The Relationship Between Responses to Science Concepts on a Semantic Differential Instrument and Achievement in Freshman Physics and Chemistry.

    ERIC Educational Resources Information Center

    Rothman, Arthur Israel

    Students taking freshman physics and freshman chemistry at The State University of New York at Buffalo (SUNYAB) were administered a science-related semantic differential instrument. This same test was administered to physics and chemistry graduate students from SUNYAB and the University of Rochester. A scoring procedure was developed which…

  15. Electrostatic correlations at the Stern layer: Physics or chemistry?

    NASA Astrophysics Data System (ADS)

    Travesset, A.; Vangaveti, S.

    2009-11-01

    We introduce a minimal free energy describing the interaction of charged groups and counterions including both classical electrostatic and specific interactions. The predictions of the model are compared against the standard model for describing ions next to charged interfaces, consisting of Poisson-Boltzmann theory with additional constants describing ion binding, which are specific to the counterion and the interfacial charge ("chemical binding"). It is shown that the "chemical" model can be appropriately described by an underlying "physical" model over several decades in concentration, but the extracted binding constants are not uniquely defined, as they differ depending on the particular observable quantity being studied. It is also shown that electrostatic correlations for divalent (or higher valence) ions enhance the surface charge by increasing deprotonation, an effect not properly accounted within chemical models. The charged phospholipid phosphatidylserine is analyzed as a concrete example with good agreement with experimental results. We conclude with a detailed discussion on the limitations of chemical or physical models for describing the rich phenomenology of charged interfaces in aqueous media and its relevance to different systems with a particular emphasis on phospholipids.

  16. Interface chemistry between complex oxides and semiconductors: where chemistry and physics meet

    NASA Astrophysics Data System (ADS)

    Marchiori, Chiara

    2010-03-01

    Even though heavily based on semiconductors, microelectronics CMOS technology would not exist without the integration of thin oxide films which enable the exploitation of the semiconductor properties. Indeed, working principle of the metal-oxide-semiconductor field-effect transistor, the main building block of such a technology, is the modulation of charges at the oxide/semiconductor interface. The quality of this interface is of fundamental importance for device performance. For over four decades, SiO2 was the gate dielectric of choice and device scaling meant improving performance while lowering production costs. However, as scaling is approaching fundamental limits, direct tunneling across the dielectric becomes unacceptable. At this point, the integration of more complex and higher dielectric constant oxides - ``high-K dielectrics''- with Si or even more complex semiconductors (Ge, III-V) is the key enabler of performance gain. I will review critical issues related to the oxide/semiconductor interfaces, starting with SiO2/Si. Then, I will discuss how the level of complexity increases with the introduction of high-K dielectrics and other semiconductors in the stack. Among the issues to be addressed to fabricate high-performance devices, I will discuss the role played by: 1) interfacial chemistry and thermodynamical stability, 2) band alignment and surface band bending, 3) presence of defects at the interface and in the oxide bulk, 4) evolution of the gate stack properties upon post-deposition treatments. The impact of these parameters on electrical performance of devices will be discussed in detail. Finally, epitaxial oxide on Si will be explored as a promising approach for ultimate EOT scaling and the parameters governing the epitaxial growth of complex crystalline oxides on Si will be addressed. I will show that the development performed in this area might enable the integration of epitaxial oxides for monolithic integration, paving the way to technological

  17. Analysing hierarchy in the organization of biological and physical systems.

    PubMed

    Jagers op Akkerhuis, Gerard A J M

    2008-02-01

    A structured approach is discussed for analysing hierarchy in the organization of biological and physical systems. The need for a structured approach follows from the observation that many hierarchies in the literature apply conflicting hierarchy rules and include ill-defined systems. As an alternative, we suggest a framework that is based on the following analytical steps: determination of the succession stage of the universe, identification of a specific system as part of the universe, specification of external influences on a system's creation and analysis of a system's internal organization. At the end, the paper discusses practical implications of the proposed method for the analysis of system organization and hierarchy in biology, ecology and physics.

  18. Interconnection of reactive oxygen species chemistry across the interfaces of atmospheric, environmental, and biological processes.

    PubMed

    Anglada, Josep M; Martins-Costa, Marilia; Francisco, Joseph S; Ruiz-López, Manuel F

    2015-03-17

    Oxidation reactions are ubiquitous and play key roles in the chemistry of the atmosphere, in water treatment processes, and in aerobic organisms. Ozone (O3), hydrogen peroxide (H2O2), hydrogen polyoxides (H2Ox, x > 2), associated hydroxyl and hydroperoxyl radicals (HOx = OH and HO2), and superoxide and ozonide anions (O2(-) and O3(-), respectively) are the primary oxidants in these systems. They are commonly classified as reactive oxygen species (ROS). Atmospheric chemistry is driven by a complex system of chain reactions of species, including nitrogen oxides, hydroxyl and hydroperoxide radicals, alkoxy and peroxy radicals, and ozone. HOx radicals contribute to keeping air clean, but in polluted areas, the ozone concentration increases and creates a negative impact on plants and animals. Indeed, ozone concentration is used to assess air quality worldwide. Clouds have a direct effect on the chemical composition of the atmosphere. On one hand, cloud droplets absorb many trace atmospheric gases, which can be scavenged by rain and fog. On the other hand, ionic species can form in this medium, which makes the chemistry of the atmosphere richer and more complex. Furthermore, recent studies have suggested that air-cloud interfaces might have a significant impact on the overall chemistry of the troposphere. Despite the large differences in molecular composition, concentration, and thermodynamic conditions among atmospheric, environmental, and biological systems, the underlying chemistry involving ROS has many similarities. In this Account, we examine ROS and discuss the chemical characteristics common to all of these systems. In water treatment, ROS are key components of an important subset of advanced oxidation processes. Ozonation, peroxone chemistry, and Fenton reactions play important roles in generating sufficient amounts of hydroxyl radicals to purify wastewater. Biochemical processes within living organisms also involve ROS. These species can come from pollutants in

  19. Heterogeneous processes at the intersection of chemistry and biology: A computational approach

    SciTech Connect

    Kuo, I W; Mundy, C J

    2008-02-11

    Heterogeneous processes hold the key to understanding many problems in biology and atmospheric science. In particular, recent experiments have shown that heterogeneous chemistry at the surface of sea-salt aerosols plays a large role in important atmospheric processes with far reaching implications towards understanding of the fate and transport of aerosolized chemical weapons (i.e. organophosphates such as sarin and VX). Unfortunately, the precise mechanistic details of the simplest surface enhanced chemical reactions remain unknown. Understanding heterogeneous processes also has implications in the biological sciences. Traditionally, it is accepted that enzymes catalyze reactions by stabilizing the transition state, thereby lowering the free energy barrier. However, recent findings have shown that a multitude of phenomena likely contribute to the efficiency of enzymes, such as coupled protein motion, quantum mechanical tunneling, or strong electrostatic binding. The objective of this project was to develop and validate a single computational framework based on first principles simulations using tera-scale computational resources to answer fundamental scientific questions about heterogeneous chemical processes relevant to atmospheric chemistry and biological sciences.

  20. Evaluating the effectiveness of integrating food science lessons in high school Biology curriculum in comparison to high school Chemistry curriculum

    NASA Astrophysics Data System (ADS)

    Ivey, Lauren Elizabeth

    Historically, high school chemistry has been the predominate venue for introducing food science curriculum to students. The purpose of this research was to determine if high school students in a biology class without a chemistry background could comprehend eight basic food science principles equally as well as students in a chemistry class that were taught the same principles. This study assessed baseline knowledge of high school students, determined the effect of food science-based lessons on baseline knowledge and level of understanding, and determined the effect of food science-based lessons on students' awareness of and interest in food science. Baseline knowledge and awareness of food science was low. Food science-based instruction resulted in higher post-test scores. Results indicated no differences between biology and chemistry and supported the idea of further incorporating a food science curriculum into high school biology.

  1. The Mediating Role of Physical Self-Concept on Relations between Biological Maturity Status and Physical Activity in Adolescent Females

    ERIC Educational Resources Information Center

    Cumming, Sean P.; Standage, Martyn; Loney, Tom; Gammon, Catherine; Neville, Helen; Sherar, Lauren B.; Malina, Robert M.

    2011-01-01

    The current study examined the mediating role of physical self-concept on relations between biological maturity status and self-reported physical activity in adolescent British females. Biological maturity status, physical self-concept and physical activity were assessed in 407 female British year 7-9 pupils (M age = 13.2 years, SD = 1.0).…

  2. Emergence of life: Physical chemistry changes the paradigm.

    PubMed

    Spitzer, Jan; Pielak, Gary J; Poolman, Bert

    2015-06-10

    Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental concepts, including the question of 'what is life?'. To re-energize the research and define a new experimental paradigm, we advance four premises to better understand the physicochemical complexities of life's emergence: (1) Chemical and Darwinian (biological) evolutions are distinct, but become continuous with the appearance of heredity. (2) Earth's chemical evolution is driven by energies of cycling (diurnal) disequilibria and by energies of hydrothermal vents. (3) Earth's overall chemical complexity must be high at the origin of life for a subset of (complex) chemicals to phase separate and evolve into living states. (4) Macromolecular crowding in aqueous electrolytes under confined conditions enables evolution of molecular recognition and cellular self-organization. We discuss these premises in relation to current 'constructive' (non-evolutionary) paradigm of origins research - the process of complexification of chemical matter 'from the simple to the complex'. This paradigm artificially avoids planetary chemical complexity and the natural tendency of molecular compositions toward maximum disorder embodied in the second law of thermodynamics. Our four premises suggest an empirical program of experiments involving complex chemical compositions under cycling gradients of temperature, water activity and electromagnetic radiation.

  3. Optimizing Introductory Physics for the Life Sciences: Placing Physics in Biological Context

    NASA Astrophysics Data System (ADS)

    Crouch, Catherine

    2014-03-01

    Physics is a critical foundation for today's life sciences and medicine. However, the physics content and ways of thinking identified by life scientists as most important for their fields are often not taught, or underemphasized, in traditional introductory physics courses. Furthermore, such courses rarely give students practice using physics to understand living systems in a substantial way. Consequently, students are unlikely to recognize the value of physics to their chosen fields, or to develop facility in applying physics to biological systems. At Swarthmore, as at several other institutions engaged in reforming this course, we have reorganized the introductory course for life science students around touchstone biological examples, in which fundamental physics contributes significantly to understanding biological phenomena or research techniques, in order to make explicit the value of physics to the life sciences. We have also focused on the physics topics and approaches most relevant to biology while seeking to develop rigorous qualitative reasoning and quantitative problem solving skills, using established pedagogical best practices. Each unit is motivated by and culminates with students analyzing one or more touchstone examples. For example, in the second semester we emphasize electric potential and potential difference more than electric field, and start from students' typically superficial understanding of the cell membrane potential and of electrical interactions in biochemistry to help them develop a more sophisticated understanding of electric forces, field, and potential, including in the salt water environment of life. Other second semester touchstones include optics of vision and microscopes, circuit models for neural signaling, and magnetotactic bacteria. When possible, we have adapted existing research-based curricular materials to support these examples. This talk will describe the design and development process for this course, give examples of

  4. Deciphering the physics and chemistry of perovskites with transmission electron microscopy.

    PubMed

    Polking, Mark J

    2016-03-28

    Perovskite oxides exhibit rich structural complexity and a broad range of functional properties, including ferroelectricity, ferromagnetism, and superconductivity. The development of aberration correction for the transmission electron microscope and concurrent progress in electron spectroscopy, electron holography, and other techniques has fueled rapid progress in the understanding of the physics and chemistry of these materials. New techniques based on the transmission electron microscope are first surveyed, and the applications of these techniques for the study of the structure, chemistry, electrostatics, and dynamics of perovskite oxides are then explored in detail, with a particular focus on ferroelectric materials.

  5. Deciphering the physics and chemistry of perovskites with transmission electron microscopy

    NASA Astrophysics Data System (ADS)

    Polking, Mark J.

    2016-03-01

    Perovskite oxides exhibit rich structural complexity and a broad range of functional properties, including ferroelectricity, ferromagnetism, and superconductivity. The development of aberration correction for the transmission electron microscope and concurrent progress in electron spectroscopy, electron holography, and other techniques has fueled rapid progress in the understanding of the physics and chemistry of these materials. New techniques based on the transmission electron microscope are first surveyed, and the applications of these techniques for the study of the structure, chemistry, electrostatics, and dynamics of perovskite oxides are then explored in detail, with a particular focus on ferroelectric materials.

  6. Lithography of Polymer Nanostructures on Glass for Teaching Polymer Chemistry and Physics.

    PubMed

    Sahar-Halbany, Adi; Vance, Jennifer M; Drain, Charles Michael

    2011-05-01

    As nanolithography becomes increasingly important in technology and daily life, a variety of inexpensive and creative methods toward communicating the concepts underpinning these processes in the classroom are necessary. An experiment is described that uses simple CD-Rs, C-clamps, an oven, and a freezer to provide concrete examples and insights into the chemistry and principles of nanolithography. The experiment also has flexibility, making it suitable for a range of classroom levels from high school to more advanced labs in college. Because CD-Rs are composed of grooves of polycarbonate, the experiment provides a basis for discussions and exploration into the chemistry and physics of polymers on the nanoscale.

  7. The Oil Drop Experiment: Do Physical Chemistry Textbooks Refer to its Controversial Nature?

    NASA Astrophysics Data System (ADS)

    Niaz, Mansoor; Rodríguez, María A.

    Most general chemistry textbooks consider the oil drop experiment as a classic experiment, characterized by its simplicity and precise results. A review of the history and philosophy of science literature shows that the experiment is difficult to perform (even today!) and generated a considerable amount of controversy. Acceptance of the quantization of the elementary electrical charge was preceded by a bitter dispute between R.A. Millikan and F. Ehrenhaft, that lasted for many years (1910-1925). The objective of this study was to investigate whether physical chemistry textbooks refer to the controversial nature of the experiment. Based on six criteria developed previously, 28 physical chemistry textbooks were evaluated. Analysis of the texts using six identified criteria demonstrated that the textbooks neither referred to the controversial nature of the experiment nor recognized the difficulty of the experimental procedure. Only a few texts even attempted to include any discussion of the history or philosophy of the experiment. The instructor of a physical chemistry course could include aspects of the Millikan-Ehrenhaft controversy to motivate classroom discussion and help facilitate an understanding of the role that controversy has in scientific progress.

  8. A review on biological sources, chemistry and pharmacological activities of pinostrobin.

    PubMed

    Patel, Neeraj K; Jaiswal, Gaurav; Bhutani, Kamlesh K

    2016-09-01

    Pinostrobin, a dietary bioflavonoid discovered more than 6 decades ago in the heart-wood of pine (Pinus strobus), has depicted many pharmacological activities including anti-viral, anti-oxidant, anti-leukaemic, anti-inflammatory and anti-aromatase activities. It is an inhibitor of sodium channel and Ca(2+) signalling pathways and also inhibits intestinal smooth muscle contractions. In spite of the fact that pinostrobin has an application as functional foods, till-to-date no comprehensive review on pinostrobin has been carried out. Hence, the present review deals with the biological sources, chemistry and pharmacological activities of pinostrobin.

  9. The chemistry-biology-medicine continuum and the drug discovery and development process in academia.

    PubMed

    Nicolaou, K C

    2014-09-18

    Admirable as it is, the drug discovery and development process is continuously undergoing changes and adjustments in search of further improvements in efficiency, productivity, and profitability. Recent trends in academic-industrial partnerships promise to provide new opportunities for advancements of this process through transdisciplinary collaborations along the entire spectrum of activities involved in this complex process. This perspective discusses ways to promote the emerging academic paradigm of the chemistry-biology-medicine continuum as a means to advance the drug discovery and development process.

  10. Ethnic Differences in Physical Fitness, Blood Pressure and Blood Chemistry in Women (AGES 20-63)

    NASA Technical Reports Server (NTRS)

    Ayers, G. W.; Wier, L. T.; Jackson, A. S.; Stuteville, J. E.; Keptra, Sean (Technical Monitor)

    1999-01-01

    This study examined the role of ethnicity on the aerobic fitness, blood pressure, and selected blood chemistry values of women. One hundred twenty-four females (mean age 41.37 +/- 9.0) were medically Examined at the NASA/Johnson Space Center occupational health clinic. Ethnic groups consisted of 23 Black (B), 18 Hispanic (H) and 83 Non-minority (NM). Each woman had a maximum Bruce treadmill stress test (RER greater than or = 1.1) and a negative ECG. Indirect calorimetry, skinfolds, self-report physical activity (NASA activity scale), seated blood pressure, and blood chemistry panel determined VO2max, percent fat, level of physical activity, blood pressure and blood chemistry values. ANOVA revealed that the groups did not differ (p greater than 0.05) in age, VO2 max, weight, percent fat, level of physical activity, total cholesterol, or HDL-C. However, significant differences (p greater than 0.05) were noted in BMI, diastolic blood pressure, and blood chemistries. BMI was 3.17 higher in H than in NM; resting diastolic pressures were 5.69 and 8.05 mmHg. lower in NM and H than in B; triglycerides were 48.07 and 37.21 mg/dl higher in H than in B and NM; hemoglobin was .814 gm/dl higher in NM than B; fasting blood sugar was 15.41 mg/dl higher in H than NM; The results of this study showed that ethnic groups differed in blood pressure and blood chemistry values but not aerobic fitness or physical activity. There was an ethnic difference in BMI but not percent fat.

  11. [From physics to biology: the intrinsic dynamics of the cosmos].

    PubMed

    González de Posada, Francisco

    2003-01-01

    The History of Universe is described in an extremely summarized manner through the use of graphics, from Big bang until today. This is done according to the most recent standard models of Cosmology and Physics of elementary particles; in other words, according to those fields in Physics of a presupposed universal reference. The History of Life is immersed in this universal physical context, in a frame where our knowledge from Geology and Biology can be only terrestrial. The underlying ideas we try to arise are: 1) the transition from a relatively elementary structure to a posterior and a relatively more complex one requires some very special "environmental" conditions; and 2) the new structure can not be described only through its materic constituents, because in cosmic dynamicity new structures and new relationships (of intrinsic respectivity) arise, together with new laws (of extrinsic respectivity). Consequently and as an objective, physical knowledge (for example, elementary particles or atoms) alone in no way can explain biological reality (for example, cell or man).

  12. Förster Resonance Energy Transfer and Conformational Stability of Proteins: An Advanced Biophysical Module for Physical Chemistry Students.

    PubMed

    Sanchez, Katheryn M; Schlamadinger, Diana E; Gable, Jonathan E; Kim, Judy E

    2008-09-01

    Protein folding is an exploding area of research in biophysics and physical chemistry. Here, we describe the integration of several techniques, including absorption spectroscopy, fluorescence spectroscopy, and Förster resonance energy transfer (FRET) measurements, to probe important topics in protein folding. Cytochrome c is used as a model protein; comparison of conformational stabilities ( ΔGH2O∘) measured via two chemical denaturants, urea and guanidinium hydrochloride, illustrate important concepts in protein folding and intermolecular interactions. In addition, the determination of intraprotein distances based upon the FRET pair Trp-59 and the heme group for unfolded states of cytochrome c highlights the evolution of the protein structure under unfolding conditions. Analysis and discussion of these results provide opportunities to gain in-depth understanding of models for protein folding while enhancing students' skills with optical techniques. Collectively, the combination of optical spectroscopy, rigorous quantitative analysis, and a focus on biophysics illustrates the significance of fundamental research at the growing intersection of chemistry, biology, and physics.

  13. Förster Resonance Energy Transfer and Conformational Stability of Proteins: An Advanced Biophysical Module for Physical Chemistry Students

    PubMed Central

    Sanchez, Katheryn M.; Schlamadinger, Diana E.; Gable, Jonathan E.; Kim, Judy E.

    2009-01-01

    Protein folding is an exploding area of research in biophysics and physical chemistry. Here, we describe the integration of several techniques, including absorption spectroscopy, fluorescence spectroscopy, and Förster resonance energy transfer (FRET) measurements, to probe important topics in protein folding. Cytochrome c is used as a model protein; comparison of conformational stabilities ( ΔGH2O∘) measured via two chemical denaturants, urea and guanidinium hydrochloride, illustrate important concepts in protein folding and intermolecular interactions. In addition, the determination of intraprotein distances based upon the FRET pair Trp-59 and the heme group for unfolded states of cytochrome c highlights the evolution of the protein structure under unfolding conditions. Analysis and discussion of these results provide opportunities to gain in-depth understanding of models for protein folding while enhancing students’ skills with optical techniques. Collectively, the combination of optical spectroscopy, rigorous quantitative analysis, and a focus on biophysics illustrates the significance of fundamental research at the growing intersection of chemistry, biology, and physics. PMID:19756254

  14. A study of the physics and chemistry of TMC-1

    NASA Technical Reports Server (NTRS)

    Pratap, P.; Dickens, J. E.; Snell, R. L.; Miralles, M. P.; Bergin, E. A.; Irvine, W. M.; Schloerb, F. P.

    1997-01-01

    We present a comprehensive study of the physical and chemical conditions along the TMC-1 ridge. Temperatures were estimated from observations of CH3CCH, NH3, and CO. Densities were obtained from a multitransition study of HC3N. The values of the density and temperature allow column densities for 13 molecular species to be estimated from statistical equilibrium calculations, using observations of rarer isotopomers where possible, to minimize opacity effects. The most striking abundance variations relative to HCO+ along the ridge were seen for HC3N, CH3CCH, and SO, while smaller variations were seen in CS, C2H, and HCN. On the other hand, the NH3, HNC, and N2H+ abundances relative to HCO+ were determined to be constant, indicating that the so-called NH3 peak in TMC-1 is probably a peak in the ammonia column density rather than a relative abundance peak. In contrast, the well-studied cyanopolyyne peak is most likely due to an enhancement in the abundance of long-chain carbon species. Comparisons of the derived abundances to the results of time-dependent chemical models show good overall agreement for chemical timescales around 10(5) yr. We find that the observed abundance gradients can be explained either by a small variation in the chemical timescale from 1.2 x 10(5) to 1.8 x 10(5) yr or by a factor of 2 change in the density along the ridge. Alternatively, a variation in the C/O ratio from 0.4 to 0.5 along the ridge produces an abundance gradient similar to that observed.

  15. Amplification without instability: applying fluid dynamical insights in chemistry and biology

    NASA Astrophysics Data System (ADS)

    McCoy, Jonathan H.

    2013-11-01

    While amplification of small perturbations often arises from instability, transient amplification is possible locally even in asymptotically stable systems. That is, knowledge of a system's stability properties can mislead one's intuition for its transient behaviors. This insight, which has an interesting history in fluid dynamics, has more recently been rediscovered in ecology. Surprisingly, many nonlinear fluid dynamical and ecological systems share linear features associated with transient amplification of noise. This paper aims to establish that these features are widespread in many other disciplines concerned with noisy systems, especially chemistry, cell biology and molecular biology. Here, using classic nonlinear systems and the graphical language of network science, we explore how the noise amplification problem can be reframed in terms of activatory and inhibitory interactions between dynamical variables. The interaction patterns considered here are found in a great variety of systems, ranging from autocatalytic reactions and activator-inhibitor systems to influential models of nerve conduction, glycolysis, cell signaling and circadian rhythms.

  16. [Research progress and trend analysis of biology and chemistry of Taxus medicinal resources].

    PubMed

    Hao, Da-Cheng; Xiao, Pei-Gen; Peng, Yong; Liu, Ming; Huo, Li

    2012-07-01

    Taxus is the source plant of anti-cancer drug paclitaxel and its biosynthetic precursor, analogs and derivatives, which has been studying for decades. There are many endemic Taxus species in China, which have been studied in the field of multiple disciplines. Based on the recent studies of the researchers, this review comments on the study of Taxus biology and chemistry. The bibliometric method is used to quantify the global scientific production of Taxus-related research, and identify patterns and tendencies of Taxus-related articles. Gaps are present in knowledge about the genomics, epigenomics, transcriptomics, proteomics, metabolomics and bioinformatics of Taxus and their endophytic fungi. Systems biology and various omics technologies will play an increasingly important role in the coming decades.

  17. Microdroplets in microfluidics: an evolving platform for discoveries in chemistry and biology.

    PubMed

    Theberge, Ashleigh B; Courtois, Fabienne; Schaerli, Yolanda; Fischlechner, Martin; Abell, Chris; Hollfelder, Florian; Huck, Wilhelm T S

    2010-08-09

    Microdroplets in microfluidics offer a great number of opportunities in chemical and biological research. They provide a compartment in which species or reactions can be isolated, they are monodisperse and therefore suitable for quantitative studies, they offer the possibility to work with extremely small volumes, single cells, or single molecules, and are suitable for high-throughput experiments. The aim of this Review is to show the importance of these features in enabling new experiments in biology and chemistry. The recent advances in device fabrication are highlighted as are the remaining technological challenges. Examples are presented to show how compartmentalization, monodispersity, single-molecule sensitivity, and high throughput have been exploited in experiments that would have been extremely difficult outside the microfluidics platform.

  18. Integration of Science on Biological and Physical Processes to Understand Ecological Diversity of Stream Fishes

    NASA Astrophysics Data System (ADS)

    Rieman, B.; Dunham, J.

    2002-12-01

    tools in biology such as molecular genetics and otolith chemistry promise new advances, but the integration with research on the physical processes structuring stream environments will be key as well.

  19. Degradation of polystyrene and selected analogues by biological Fenton chemistry approaches: Opportunities and limitations.

    PubMed

    Krueger, Martin C; Seiwert, Bettina; Prager, Andrea; Zhang, Shangwei; Abel, Bernd; Harms, Hauke; Schlosser, Dietmar

    2017-04-01

    Conventional synthetic polymers typically are highly resistant to microbial degradation, which is beneficial for their intended purpose but highly detrimental when such polymers get lost into the environment. Polystyrene is one of the most widespread of such polymers, but knowledge about its biological degradability is scarce. In this study, we investigated the ability of the polymer-degrading brown-rot fungus Gloeophyllum trabeum to attack polystyrene via Fenton chemistry driven by the redox-cycling of quinones. Indications of superficial oxidation were observed, but the overall effects on the polymer were weak. To assess factors constraining biodegradation of polystyrene, the small water-soluble model compounds ethylbenzene and isopropylbenzene (cumene) were also subjected to biodegradation by G. trabeum. Likewise, ethylbenzene sulfonate, cumene sulfonate and the dimer 1,3-diphenylbutane sulfonate were used as model compounds for comparison with polystyrene sulfonate, which G. trabeum can substantially depolymerise. All model compounds but cumene were degraded by G. trabeum and yielded a large variety of oxidised metabolites, suggesting that both the very poor bioavailability of polystyrene and its inert basic structure play important roles constraining biodegradability via biologically driven Fenton chemistry.

  20. Bio-Physics Manifesto -- for the Future of Physics and Biology

    NASA Astrophysics Data System (ADS)

    Oono, Y.

    2008-04-01

    The Newtonian revolution taught us how to dissect phenomena into contingencies (e.g., initial conditions) and fundamental laws (e.g., equations of motion). Since then, `fundamental physics' has been pursuing purer and leaner fundamental laws. Consequently, to explain real phenomena a lot of auxiliary conditions become required. Isn't it now the time to start studying `auxiliary conditions' seriously? The study of biological systems has a possibility of shedding light on this neglected side of phenomena in physics, because we organisms were constructed by our parents who supplied indispensable auxiliary conditions; we never self-organize. Thus, studying the systems lacking self-organizing capability (such as complex systems) may indicate new directions to physics and biology (biophysics). There have been attempts to construct a `general theoretical framework' of biology, but most of them never seriously looked at the actual biological world. Every serious natural science must start with establishing a phenomenological framework. Therefore, this must be the main part of bio-physics. However, this article is addressed mainly to theoretical physicists and discusses only certain theoretical aspects (with real illustrative examples).

  1. Developing and Evaluating an Eighth Grade Curriculum Unit That Links Foundational Chemistry to Biological Growth: Using Student Measures to Evaluate the Promise of the Intervention

    ERIC Educational Resources Information Center

    Herrmann-Abell, Cari F.; Flanagan, Jean C.; Roseman, Jo Ellen

    2013-01-01

    Students often have trouble understanding key biology ideas, in part because they lack an understanding of foundational chemistry ideas. AAAS [American Association for the Advancement of Science] is collaborating with BSCS [Biological Sciences Curriculum Study] in the development of a curriculum unit that connects core chemistry and biology ideas…

  2. Research at the interface of physics and biology: bridging the two fields.

    PubMed

    Shukla, Kamal

    2014-10-08

    I firmly believe that interaction between physics and biology is not only natural, but inevitable. Kamal Shukla provides a personal perspective on working at the interface between the physical and biological sciences.

  3. Research at the interface of physics and biology: bridging the two fields

    NASA Astrophysics Data System (ADS)

    Shukla, Kamal

    2014-10-01

    I firmly believe that interaction between physics and biology is not only natural, but inevitable. Kamal Shukla provides a personal perspective on working at the interface between the physical and biological sciences.

  4. Using biocatalysis to integrate organic chemistry into a molecular biology laboratory course.

    PubMed

    Beers, Mande; Archer, Crystal; Feske, Brent D; Mateer, Scott C

    2012-01-01

    Current cutting-edge biomedical investigation requires that the researcher have an operational understanding of several diverse disciplines. Biocatalysis is a field of science that operates at the crossroads of organic chemistry, biochemistry, microbiology, and molecular biology, and provides an excellent model for interdisciplinary research. We have developed an inquiry-based module that uses the mutagenesis of the yeast reductase, YDL124w, to study the bioorganic synthesis of the taxol side-chain, a pharmacologically important molecule. Using related structures, students identify regions they think will affect enzyme stereoselective, design and generate site-specific mutants, and then characterize the effect of these changes on enzyme activity. This laboratory activity gives our students experience, working in a scientific discipline outside of biology and exposes them to techniques and equipment they do not normally work with in a molecular biology course. These inter-disciplinary experiences not only show the relevance of other sciences to biology, but also give our students the ability to communicate more effectively with scientists outside their discipline.

  5. Expanded Choices for Vibration-Rotation Spectroscopy in the Physical Chemistry Teaching Laboratory

    NASA Astrophysics Data System (ADS)

    Schmitz, Joel R.; Dolson, David A.

    2015-06-01

    Many third-year physical chemistry laboratory students in the US analyze the vibration-rotation spectrum of HCl in support of lecture concepts in quantum theory and molecular spectroscopy. Contemporary students in physical chemistry teaching laboratories increasingly have access to FTIR spectrometers with 1/8th wn resolution, which allows for expanded choices of molecules for vibration-rotation spectroscopy. Here we present the case for choosing HBr/DBr for such a study, where the 1/8th wn resolution enables the bromine isotopic lines to be resolved. Vibration-rotation lines from the fundamental and first-overtone bands of four hydrogen bromide isotopomers are combined in a global analysis to determine molecular spectroscopic constants. Sample production, spectral appearance, analysis and results will be presented for various resolutions commonly available in teaching laboratories.

  6. An integrated physical and biological model for anaerobic lagoons.

    PubMed

    Wu, Binxin; Chen, Zhenbin

    2011-04-01

    A computational fluid dynamics (CFD) model that integrates physical and biological processes for anaerobic lagoons is presented. In the model development, turbulence is represented using a transition k-ω model, heat conduction and solar radiation are included in the thermal model, biological oxygen demand (BOD) reduction is characterized by first-order kinetics, and methane yield rate is expressed as a linear function of temperature. A test of the model applicability is conducted in a covered lagoon digester operated under tropical climate conditions. The commercial CFD software, ANSYS-Fluent, is employed to solve the integrated model. The simulation procedures include solving fluid flow and heat transfer, predicting local resident time based on the converged flow fields, and calculating the BOD reduction and methane production. The simulated results show that monthly methane production varies insignificantly, but the time to achieve a 99% BOD reduction in January is much longer than that in July.

  7. Biological and Physical Space Research Laboratory 2002 Science Review

    NASA Technical Reports Server (NTRS)

    Curreri, P. A. (Editor); Robinson, M. B. (Editor); Murphy, K. L. (Editor)

    2003-01-01

    With the International Space Station Program approaching core complete, our NASA Headquarters sponsor, the new Code U Enterprise, Biological and Physical Research, is shifting its research emphasis from purely fundamental microgravity and biological sciences to strategic research aimed at enabling human missions beyond Earth orbit. Although we anticipate supporting microgravity research on the ISS for some time to come, our laboratory has been vigorously engaged in developing these new strategic research areas.This Technical Memorandum documents the internal science research at our laboratory as presented in a review to Dr. Ann Whitaker, MSFC Science Director, in July 2002. These presentations have been revised and updated as appropriate for this report. It provides a snapshot of the internal science capability of our laboratory as an aid to other NASA organizations and the external scientific community.

  8. Physical, chemical, and biological properties of wonder kelp--Laminaria.

    PubMed

    Kim, Se-Kwon; Bhatnagar, Ira

    2011-01-01

    Laminaria is a kelp that finds its place in the brown algae family. It has been an area of study for past many years, and its wonderful biological properties have always attracted medical professionals and researchers to explore more and more from this wonder kelp. The constituents of Laminaria include iodine, potassium, magnesium, calcium and iron. Iodine compounds, TEA-hydroiodide in particular, are great lipolytic agents as they stimulate lipase activity. Laminarins on the other hand are used as a tumor angiogenic blocker. This genus of the kelps is also rich in algin, a high molecular weight polysaccharide that forms viscous colloidal solutions or gels in water leading to the use of kelp derivatives as bulk laxatives. It has great applications in cosmeceutical science, as well as some antibacterial properties have also been assigned to Laminaria. A deeper insight into the physical, biological, and chemical properties of this wonder kelp would lead to further exploitation of Laminaria for medicinal and cosmeceutical purpose.

  9. Influence of different natural physical fields on biological processes

    NASA Astrophysics Data System (ADS)

    Mashinsky, A. L.

    2001-01-01

    In space flight conditions gravity, magnetic, and electrical fields as well as ionizing radiation change both in size, and in direction. This causes disruptions in the conduct of some physical processes, chemical reactions, and metabolism in living organisms. In these conditions organisms of different phylogenetic level change their metabolic reactions undergo changes such as disturbances in ionic exchange both in lower and in higher plants, changes in cell morphology for example, gyrosity in Proteus ( Proteus vulgaris), spatial disorientation in coleoptiles of Wheat ( Triticum aestivum) and Pea ( Pisum sativum) seedlings, mutational changes in Crepis ( Crepis capillaris) and Arabidopsis ( Arabidopsis thaliana) seedling. It has been found that even in the absence of gravity, gravireceptors determining spatial orientation in higher plants under terrestrial conditions are formed in the course of ontogenesis. Under weightlessness this system does not function and spatial orientation is determined by the light flux gradient or by the action of some other factors. Peculiarities of the formation of the gravireceptor apparatus in higher plants, amphibians, fish, and birds under space flight conditions have been observed. It has been found that the system in which responses were accompanied by phase transition have proven to be gravity-sensitive under microgravity conditions. Such reactions include also the process of photosynthesis which is the main energy production process in plants. In view of the established effects of microgravity and different natural physical fields on biological processes, it has been shown that these processes change due to the absence of initially rigid determination. The established biological effect of physical fields influence on biological processes in organisms is the starting point for elucidating the role of gravity and evolutionary development of various organisms on Earth.

  10. Influence of different natural physical fields on biological processes.

    PubMed

    Mashinsky, A L

    2001-01-01

    In space flight conditions gravity, magnetic, and electrical fields as well as ionizing radiation change both in size, and in direction. This causes disruptions in the conduct of some physical processes, chemical reactions, and metabolism in living organisms. In these conditions organisms of different phylogenetic level change their metabolic reactions undergo changes such as disturbances in ionic exchange both in lower and in higher plants, changes in cell morphology for example, gyrosity in Proteus (Proteus vulgaris), spatial disorientation in coleoptiles of Wheat (Triticum aestivum) and Pea (Pisum sativum) seedlings, mutational changes in Crepis (Crepis capillaris) and Arabidopsis (Arabidopsis thaliana) seedling. It has been found that even in the absence of gravity, gravireceptors determining spatial orientation in higher plants under terrestrial conditions are formed in the course of ontogenesis. Under weightlessness this system does not function and spatial orientation is determined by the light flux gradient or by the action of some other factors. Peculiarities of the formation of the gravireceptor apparatus in higher plants, amphibians, fish, and birds under space flight conditions have been observed. It has been found that the system in which responses were accompanied by phase transition have proven to be gravity-sensitive under microgravity conditions. Such reactions include also the process of photosynthesis which is the main energy production process in plants. In view of the established effects of microgravity and different natural physical fields on biological processes, it has been shown that these processes change due to the absence of initially rigid determination. The established biological effect of physical fields influence on biological processes in organisms is the starting point for elucidating the role of gravity and evolutionary development of various organisms on Earth.

  11. Unexplained overexposures on physical dosimetry reported by biological dosimetry.

    PubMed

    Montoro, A; Almonacid, M; Villaescusa, J I; Verdu, G

    2009-01-01

    The Medical Service of the Radiation Protection Service from the University Hospital La Fe (Valencia, Spain), carries out medical examinations of the workers occupationally exposed to ionising radiation. The Biological Dosimetry Laboratory is developing its activity since 2001. Up to now, the activities have been focused in performing biological dosimetry studies of Interventionists workers from La Fe Hospital. Recently, the Laboratory has been authorized by the Health Authority in the Valencian Community. Unexplained overexposures of workers and patients are also studied. Workers suspected of being overexposed to ionising radiation were referred for investigation by cytogenetic analysis. Two of these were from Hospitals of the Valencian Community and one belonged to an uranium mine from Portugal. Hospital workers had a physical dose by thermoluminiscence dosimeters (TLD) that exceeded the established limit. The worker of the uranium mine received a dose from a lost source of Cesium 137 with an activity of 170 mCi. All three cases showed normal values after the hematological analysis. Finally, the aim of this study consist to determine whether the dose showed by the dosimeter is reliable or not. In the case of workers that wore dosimeter, it is concluded that the doses measured by dosimeter are not corresponding to real doses. Hospital worker with a physical dose of 2.6 Sv and 0.269 Sv had an estimated absorbed dose by biological dosimetry of 0.076 Gy (0-0.165 Gy) and 0 Gy (0-0.089 Gy), respectively. In case of the mine worker an estimated absorbed dose of 0.073 Gy (0-0.159 Gy) was obtained by biological dosimetry. In all cases we used the odds ratio to present the results due to a very low frequency of observed aberrations [1].

  12. Physical bases for a triad of biological similarity theories.

    PubMed

    Gunther, B; Morgado, E

    1986-01-01

    The dimensional analysis of physics, based on the MLT-system (M = mass, L = length, T = time), can be applied to the living world, from mycoplasmas (10(-13) g) to the blue whales (10(8) g). Body mass (M), or body weight (W), are utilized as convenient reference systems, since they represent the integrated masses of all elementary particles--at the atomic level--which conform an organism. A triad of biological similarities (mechanical, biological, transport) have been previously described. Each similarity was based on two postulates, of which the first was common to all three, i.e., the constancy of body density; whereas the second postulates were specific for each of the three theories. In this study a physical foundation for these second postulates, based on three universal constants of nature, is presented, these are: 1) the acceleration of gravity (g = LT-2); 2) the velocity of light (c = LT-1); and 3) the mass-specific quantum (h/m = L2T-1). The realm of each of these biological similarities is the following: 1) the gravitational or mechanical similarity (where g = constant), deals mainly with the relationship between a whole organism and its environment, particularly with locomotion. The acceleration of gravity (g) is also one of the determining factors of the "potential" energy (E = m.g.H), where m is the mass, and H is the height above the reference level; 2) the electrodynamic similarity (formerly biological similarity), (c = constant), is able to quantitatively define the internal organization of an organism from both a morphological and a physiological point of view.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. The Physical-Organic Chemistry of Surfaces, and Its Relevance to Molecular Recognition

    DTIC Science & Technology

    1989-11-01

    THE PHYSICAL-ORGANiC CHEMISTRY OF SURFACES , 0AND ITS RELEVANCE TO MOLECULAR RECOGNITION L N George M. Whitesides and Hans Biebuyck Department of...DEFENSE ADVANCED RESEARCH PROJECTS AGENCY 1400 Wilson Boulevard Arlington VA 22209 DEPARTMENT OF THE NAVY Offic- of Naval Research , Code 1130P 800...Advanced Research Projects Agency or the U.S. Government. LDIST-R-UTI ,j STAApprovcd for pu8bU Y9 1e; 9 Dibu fonl Unlimited SECURITY CLASSIFICATION OF THIS

  14. Biological and Physical Principles in Self-Organization of Brain

    NASA Astrophysics Data System (ADS)

    Kröger, H.

    2007-04-01

    Complexity is a widespread phenomenon in nature. The brain is a foremost example of complexity. We address the question: How does such complexity emerge in brain? Which are the biological, chemical or physical principles at work which organize the formation of complixity? In particular we address the topics (i) adaptive learning, (ii) neuron cell death and pruning of synaptic connection afterbirth, (iii) small world and scale free architecture of neural connectivity, (iv) feature maps and the Kohonen model, (v) self-organized criticality and 1/f frequency scaling.

  15. Health: The No-Man's-Land Between Physics and Biology.

    PubMed

    Mansfield, Peter J

    2015-10-01

    Health as a positive attribute is poorly understood because understanding requires concepts from physics, of which physicians and other life scientists have a very poor grasp. This paper reviews the physics that bears on biology, in particular complex quaternions and scalar fields, relates these to the morphogenetic fields proposed by biologists, and defines health as an attribute of living action within these fields. The distinction of quality, as juxtaposed with quantity, proves essential. Its basic properties are set out, but a science and mathematics of quality are awaited. The implications of this model are discussed, particularly as proper health enhancement could set a natural limit to demand for, and therefore the cost of, medical services.

  16. How G.N. Lewis reset the terms of the dialogue between chemistry and physics.

    PubMed

    Bogaard, Paul A

    2003-05-01

    While quantum physics provided a mathematical framework for understanding the valency of chemical elements, to make use of these mathematical equations required approximations based on chemical experience. To better understand how this establishes limits to the presumption that chemistry can be derived from physics, this paper starts with the warnings in Coulson's widely read text, Valence, as to why there are pitfalls in the interpretation of what "valence" accomplishes. He directs some of these concerns back to Pauling's earlier text, The Nature of the Chemical Bond. Both Coulson and Pauling are aware that quantum theory's ability to approximate the energetic stability of chemical systems is of use to chemistry only if it can be correlated with the molecular structure that results from chemical bonding. While this may now be routinely expected, it was a struggle to see that this was the challenge chemistry posed to physics-and this achievement they both attribute to G.N. Lewis. Until the more mature forms of quantum mechanics arose in the 1920s, Lewis was skeptical that the dynamic models of the atom posed by Bohr could meet this challenge. How Lewis formulates this challenge initially in 1916 and then in his longer work, Valence and the Structure of Atoms and Molecules, will be examined.

  17. From high dilutions to digital biology: the physical nature of the biological signal.

    PubMed

    Thomas, Yolène

    2015-10-01

    The memory of water was a radical idea that arose in the laboratory of Jacques Benveniste in the late 1980s. Twenty-five years have passed and yet the often angry debate on its merits continues despite the increasing number of scientists who have reported confirmation of the basic results. One working hypothesis was that molecules can communicate with each other, exchanging information without being in physical contact and that at least some biological functions can be mimicked by certain energetic modes characteristics of a given molecule. These considerations informed exploratory research which led to the speculation that biological signaling might be transmissible by electromagnetic means. Around 1991, the transfer of specific molecular signals to sensitive biological systems was achieved using an amplifier and electromagnetic coils. In 1995, a more sophisticated procedure was established to record, digitize and replay these signals using a multimedia computer. From a physical and chemical perspective, these experiments pose a riddle, since it is not clear what mechanism can sustain such 'water memory' of the exposure to molecular signals. From a biological perspective, the puzzle is what nature of imprinted effect (water structure) can impact biological function. A parallel can be drawn between this debate on the memory of water, which presumes that the action of molecules is mediated by an electromagnetic phenomenon, and the often acrimonious debate on the transmission of nerve influxes via synaptic transfer of specific molecules, neurotransmitters. The latter debate began in 1921 with the first experiments by Loewi and was still active in 1949, 28 years later. A strong reluctance to accept research that questions basic aspects of long-accepted biochemical paradigms is to be expected. In this paper we will provide a brief summary of experiments relating to the memory of water: the earlier work on high dilutions (HD) and then the experiments, which followed and

  18. K1-95-HW, cruise report 1995: preliminary results. Phase III: sediment chemistry and biological sampling survey

    USGS Publications Warehouse

    Torresan, M.E.; Hampton, M.A.; Barber, J.H.; Wong, F.L.

    1995-01-01

    Mamala Bay, off the south shore of the island of Oahu, has been used as a repository of dredged material primarily from Pearl and Honolulu Harbors for over a century. The U.S. Geological Survey, U.S. Army Corps of Engineers, and the U.S. Environmental Protection Agency are conducting an integrated study on the distribution and character of dredged materials as well as the effects of dredged material on the marine environment. A three phase study is providing information to evaluate the effects on seafloor substrate and the benthic fauna. The studies include geophysical profiling and imaging, bottom photography, sampling, chemical and physical analyses of sediment, and evaluations of the benthic population, population density, and adverse impacts to the benthic fauna. Phase 1, conducted in 1993, inventoried the seafloor via remote sensing. Sidescan sonar and subbottom profilers characterized the seafloor in and around the disposal sites, and the resulting products reveal the character and extent of the dredged material. These data were used to plan Phase 2 in 1994, a sampling program that employed subbottom profilers, video and still photography, and seafloor sampling to ground truth the sonar mosaic and identify the seafloor substrates responsible for the various acoustic signatures on the sonar images and subbottom profiles. Box coring provided the samples necessary to distinguish dredged material from native sediment, and for the chemical analyses used to determine contaminant concentrations. Phase 3 studies conducted in June of 1995 consisted of box core sampling for chemical and biological analyses. Specific studies include: infaunal taxonomy and population density, bioassay/bioaccumulation, sediment chemistry, and post-disposal resuspension and transport. The 1995 survey, conducted June 14 through 17, resulted in the collection of 39 box cores from 20 different stations. Multiple box cores were composited at 7 different locations occupied in 1994, to provide

  19. Physics of transport and traffic phenomena in biology: from molecular motors and cells to organisms

    NASA Astrophysics Data System (ADS)

    Chowdhury, Debashish; Schadschneider, Andreas; Nishinari, Katsuhiro

    2005-12-01

    Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukaryotic cells, sometimes encounter traffic jam that manifests as a disease of the organism. Similarly, traffic jam of collagenase MMP-1, which moves on the collagen fibrils of the extracellular matrix of vertebrates, has also been observed in recent experiments. Novel efforts have been made to utilize some uni-cellular organisms as “micro-transporters”. Traffic-like movements of social insects like ants and termites on trails are, perhaps, more familiar in our everyday life. Experimental, theoretical and computational investigations in the last few years have led to a deeper understanding of the generic or common physical principles involved in these phenomena. In this review we critically examine the current status of our understanding, expose the limitations of the existing methods, mention open challenging questions and speculate on the possible future directions of research in this interdisciplinary area where physics meets not only chemistry and biology but also (nano-)technology.

  20. A Need to Reassess Physical-Organic Curricula: A Course Enhancement Using Readily Available Quantum Chemistry Programs.

    ERIC Educational Resources Information Center

    Lipkowitz, Kenny B.

    1982-01-01

    Describes a graduate-level course in physical-organic chemistry in which students learn to solve problems using computer programs available through the Quantum Chemistry Program Exchange. Includes condensed syllabus and time line showing where various computational programs are introduced. (Author/JN)

  1. Physical and biological characterization of a seawater ultraviolet radiation sterilizer

    NASA Astrophysics Data System (ADS)

    Torrentera, Laura; Uribe, Roberto M.; Rodríguez, Romana R.; Carrillo, Ricardo E.

    1994-03-01

    The physical and biological characterization of a seawater ultraviolet (UV) sterilizer is described. The physical characterization was performed using radiochromic dye films by evaluating the uniformity of the radiant exposure along each lamp, the effect of the radiation from one lamp on the array of adjacent lamps, and by measuring the UV radiation absorption of seawater with respect to distilled water. The biological characterization was performed by measuring the amount of reduction of bacteria in stored seawater after different filtration and UV treatments. Among the filtration methods tested, differential filtration (5, 3 and 0.45 μm filters connected in series) caused the highest bacterial reduction factor of 60%. UV radiant exposures of 212, 424, 636 and 848 J m -2 yielded bacteria reduction factors of 99.86, 99.969, 99.997 and 100%, respectively, for populations of Vibrio and Pseudomonas bacteria present in stored seawater. It is concluded that the system is useful for water disinfection when 1, 2 or 3 lamps are on; when 4 lamps are used the treated water becomes sterile.

  2. Coupled model of physical and biological processes affecting maize pollination

    NASA Astrophysics Data System (ADS)

    Arritt, R.; Westgate, M.; Riese, J.; Falk, M.; Takle, E.

    2003-04-01

    Controversy over the use of genetically modified (GM) crops has led to increased interest in evaluating and controlling the potential for inadvertent outcrossing in open-pollinated crops such as maize. In response to this problem we have developed a Lagrangian model of pollen dispersion as a component of a coupled end-to-end (anther to ear) physical-biological model of maize pollination. The Lagrangian method is adopted because of its generality and flexibility: first, the method readily accommodates flow fields of arbitrary complexity; second, each element of the material being transported can be identified by its source, time of release, or other properties of interest. The latter allows pollen viability to be estimated as a function of such factors as travel time, temperature, and relative humidity, so that the physical effects of airflow and turbulence on pollen dispersion can be considered together with the biological aspects of pollen release and viability. Predicted dispersion of pollen compares well both to observations and to results from a simpler Gaussian plume model. Ability of the Lagrangian model to handle complex air flows is demonstrated by application to pollen dispersion in the vicinity of an agricultural shelter belt. We also show results indicating that pollen viability can be quantified by an "aging function" that accounts for temperature, humidity, and time of exposure.

  3. Attributing physical and biological impacts to anthropogenic climate change.

    PubMed

    Rosenzweig, Cynthia; Karoly, David; Vicarelli, Marta; Neofotis, Peter; Wu, Qigang; Casassa, Gino; Menzel, Annette; Root, Terry L; Estrella, Nicole; Seguin, Bernard; Tryjanowski, Piotr; Liu, Chunzhen; Rawlins, Samuel; Imeson, Anton

    2008-05-15

    Significant changes in physical and biological systems are occurring on all continents and in most oceans, with a concentration of available data in Europe and North America. Most of these changes are in the direction expected with warming temperature. Here we show that these changes in natural systems since at least 1970 are occurring in regions of observed temperature increases, and that these temperature increases at continental scales cannot be explained by natural climate variations alone. Given the conclusions from the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report that most of the observed increase in global average temperatures since the mid-twentieth century is very likely to be due to the observed increase in anthropogenic greenhouse gas concentrations, and furthermore that it is likely that there has been significant anthropogenic warming over the past 50 years averaged over each continent except Antarctica, we conclude that anthropogenic climate change is having a significant impact on physical and biological systems globally and in some continents.

  4. Framing a program designed to train new chemistry/physics teachers for California outlying regions

    NASA Astrophysics Data System (ADS)

    Bodily, Gerald P., Jr.

    The purpose of this study was to develop guidelines for a new high school chemistry and physics teacher training program. Eleven participants were interviewed who attended daylong workshops, every other Saturday, for 10 months. The instructors used Modeling Instruction pedagogy and curriculum. All the instructors had high school teaching experience, but only one possessed a doctorate degree. The interview questions focused on four themes: motivation, epistemology, meta-cognition, and self-regulation; and the resulting transcripts were analyzed using a methodology called Interpretive Phenomenological Analysis. The cases expressed a strong preference for the program's instruction program over learning subject matter knowledge in university classrooms. The data indicated that the cases, as a group, were disciplined scholars seeking a deep understanding of the subject matter knowledge needed to teach high school chemistry and physics. Based on these results a new approach to training teachers was proposed, an approach that offers novel answers to the questions of how and who to train as science teachers. The how part of the training involves using a program called Modeling Instruction. Modeling instruction is currently used to upgrade experienced science teachers and, in the new approach, replaces the training traditionally administered by professional scientists in university science departments. The who aspect proposes that the participants be college graduates, selected not for university science training, but for their high school math and science background. It is further proposed that only 10 months of daily, face-to-face instruction is required to move the learner to a deep understanding of subject matter knowledge required to teach high school chemistry and physics. Two outcomes are sought by employing this new training paradigm, outcomes that have been unachievable by current educational practices. First, it is hoped that new chemistry and physics teachers can

  5. How biological vision succeeds in the physical world.

    PubMed

    Purves, Dale; Monson, Brian B; Sundararajan, Janani; Wojtach, William T

    2014-04-01

    Biological visual systems cannot measure the properties that define the physical world. Nonetheless, visually guided behaviors of humans and other animals are routinely successful. The purpose of this article is to consider how this feat is accomplished. Most concepts of vision propose, explicitly or implicitly, that visual behavior depends on recovering the sources of stimulus features either directly or by a process of statistical inference. Here we argue that, given the inability of the visual system to access the properties of the world, these conceptual frameworks cannot account for the behavioral success of biological vision. The alternative we present is that the visual system links the frequency of occurrence of biologically determined stimuli to useful perceptual and behavioral responses without recovering real-world properties. The evidence for this interpretation of vision is that the frequency of occurrence of stimulus patterns predicts many basic aspects of what we actually see. This strategy provides a different way of conceiving the relationship between objective reality and subjective experience, and offers a way to understand the operating principles of visual circuitry without invoking feature detection, representation, or probabilistic inference.

  6. How biological vision succeeds in the physical world

    PubMed Central

    Purves, Dale; Monson, Brian B.; Sundararajan, Janani; Wojtach, William T.

    2014-01-01

    Biological visual systems cannot measure the properties that define the physical world. Nonetheless, visually guided behaviors of humans and other animals are routinely successful. The purpose of this article is to consider how this feat is accomplished. Most concepts of vision propose, explicitly or implicitly, that visual behavior depends on recovering the sources of stimulus features either directly or by a process of statistical inference. Here we argue that, given the inability of the visual system to access the properties of the world, these conceptual frameworks cannot account for the behavioral success of biological vision. The alternative we present is that the visual system links the frequency of occurrence of biologically determined stimuli to useful perceptual and behavioral responses without recovering real-world properties. The evidence for this interpretation of vision is that the frequency of occurrence of stimulus patterns predicts many basic aspects of what we actually see. This strategy provides a different way of conceiving the relationship between objective reality and subjective experience, and offers a way to understand the operating principles of visual circuitry without invoking feature detection, representation, or probabilistic inference. PMID:24639506

  7. The Colorado Plateau: cultural, biological, and physical research

    USGS Publications Warehouse

    Cole, Kenneth L.; van Riper, Charles

    2004-01-01

    Stretching from the four corners of Arizona, New Mexico, Colorado, and Utah, the Colorado Plateau is a natural laboratory for a wide range of studies. This volume presents 23 original articles drawn from more than 100 research projects presented at the Sixth Biennial Conference of Research on the Colorado Plateau. This scientific gathering revolved around research, inventory, and monitoring of lands in the region. The book's contents cover management techniques for cultural, biological, and physical resources, representing collaborative efforts among federal, university, and private sector scientists and land managers. Chapters on cultural concerns cover benchmarks of modern southwestern anthropological knowledge, models of past human activity and impact of modern visitation at newly established national monuments, challenges in implementing the 1964 Wilderness Act, and opportunities for increased federal research on Native American lands. The section on biological resources comprises sixteen chapters, with coverage that ranges from mammalian biogeography to responses of elk at the urban-wildland interface. Additional biological studies include the effects of fire and grazing on vegetation; research on bald eagles at Grand Canyon and tracking wild turkeys using radio collars; and management of palentological resources. Two final chapters on physical resources consider a proposed rerouting of the Rio de Flag River in urban Flagstaff, Arizona, and an examination of past climate patterns over the Plateau, using stream flow records and tree ring data. In light of similarities in habitat and climate across the Colorado Plateau, techniques useful to particular management units have been found to be applicable in many locations. This volume highlights an abundance of research that will prove useful for all of those working in the region, as well as for others seeking comparative studies that integrate research into land management actions.

  8. More Chemistry with Light! More Light in Chemistry!

    PubMed

    Bach, Thorsten

    2015-09-21

    "…︁ Why is chemistry overlooked when talking about light? Is the photon a physical particle per se? Are all important light-induced processes biological? Maybe the role of light for chemistry and the role of chemistry for light may be far less important than a few eccentric scientists would like to believe. From the perspective of a synthetically oriented photochemist, however, the facts are different …︁" Read more in the Editorial by Thorsten Bach.

  9. 30 CFR 550.216 - What biological, physical, and socioeconomic information must accompany the EP?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 2 2012-07-01 2012-07-01 false What biological, physical, and socioeconomic... and Information Contents of Exploration Plans (ep) § 550.216 What biological, physical, and.... (b) Physical environment reports. Site-specific meteorological, physical oceanographic,...

  10. 30 CFR 550.216 - What biological, physical, and socioeconomic information must accompany the EP?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 2 2014-07-01 2014-07-01 false What biological, physical, and socioeconomic... and Information Contents of Exploration Plans (ep) § 550.216 What biological, physical, and.... (b) Physical environment reports. Site-specific meteorological, physical oceanographic,...

  11. 30 CFR 550.216 - What biological, physical, and socioeconomic information must accompany the EP?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 2 2013-07-01 2013-07-01 false What biological, physical, and socioeconomic... and Information Contents of Exploration Plans (ep) § 550.216 What biological, physical, and.... (b) Physical environment reports. Site-specific meteorological, physical oceanographic,...

  12. Biological vs. Physical Mixing Effects on Benthic Food Web Dynamics

    PubMed Central

    Braeckman, Ulrike; Provoost, Pieter; Moens, Tom; Soetaert, Karline; Middelburg, Jack J.; Vincx, Magda; Vanaverbeke, Jan

    2011-01-01

    Biological particle mixing (bioturbation) and solute transfer (bio-irrigation) contribute extensively to ecosystem functioning in sediments where physical mixing is low. Macrobenthos transports oxygen and organic matter deeper into the sediment, thereby likely providing favourable niches to lower trophic levels (i.e., smaller benthic animals such as meiofauna and bacteria) and thus stimulating mineralisation. Whether this biological transport facilitates fresh organic matter assimilation by the metazoan lower part of the food web through niche establishment (i.e., ecosystem engineering) or rather deprives them from food sources, is so far unclear. We investigated the effects of the ecosystem engineers Lanice conchilega (bio-irrigator) and Abra alba (bioturbator) compared to abiotic physical mixing events on survival and food uptake of nematodes after a simulated phytoplankton bloom. The 13C labelled diatom Skeletonema costatum was added to 4 treatments: (1) microcosms containing the bioturbator, (2) microcosms containing the bio-irrigator, (3) control microcosms and (4) microcosms with abiotic manual surface mixing. Nematode survival and subsurface peaks in nematode density profiles were most pronounced in the bio-irrigator treatment. However, nematode specific uptake (Δδ13C) of the added diatoms was highest in the physical mixing treatment, where macrobenthos was absent and the diatom 13C was homogenised. Overall, nematodes fed preferentially on bulk sedimentary organic material rather than the added diatoms. The total C budget (µg C m−2), which included TO13C remaining in the sediment, respiration, nematode and macrobenthic uptake, highlighted the limited assimilation by the metazoan benthos and the major role of bacterial respiration. In summary, bioturbation and especially bio-irrigation facilitated the lower trophic levels mainly over the long-term through niche establishment. Since the freshly added diatoms represented only a limited food source for

  13. Measurement of the Order Parameter in a Room Temperature Liquid Crystal: An Experiment for the Physical Chemistry Laboratory.

    ERIC Educational Resources Information Center

    DuPre, Donald B.; Chapoy, L. Lawrence

    1979-01-01

    Presented here is a laboratory experiment for a course in physical chemistry. Students are requested to directly measure the degree of orientational order in a liquid crystal at room temperature. A minimum amount of equipment is necessary. (Author/SA)

  14. A Transition from a Traditional to a Project-Like Physical Chemistry Laboratory via a Heterogeneous Catalysis Study.

    ERIC Educational Resources Information Center

    Goldwasser, M. R.; Leal, O.

    1979-01-01

    Outlines an approach for instruction in a physical chemistry laboratory which combines traditional and project-like experiments. An outline of laboratory experiments and examples of project-like experiments are included. (BT)

  15. The pharmaceutical biochemistry group: where pharmaceutical chemistry meets biology and drug delivery.

    PubMed

    Kalia, Yogeshvar N; Perozzo, Remo; Scapozza, Leonardo

    2012-01-01

    Successful drug discovery and development of new therapeutics is a long, expensive multidisciplinary process needing innovation and the integration of smart cutting edge science and technology to overcome the challenges in taking a drug from the bench to the bedside. The research activities of the Pharmaceutical Biochemistry group span the drug discovery and development process, providing an interface that brings together pharmaceutical chemistry, biochemistry, structural biology, computational chemistry and biopharmaceutics. Formulation and drug delivery are brought into play at an earlier stage when facing the perennial challenge of transforming a potent molecule in vitro into a therapeutic agent in vivo. Concomitantly, drug delivery results can be understood at a molecular level. This broad range of interdisciplinary research activities and competences enables us to address key challenges in modern drug discovery and development, provides a powerful collaborative platform for other universities and the pharmaceutical industry and an excellent training platform for pharmacists and pharmaceutical scientists who will later be involved in drug discovery and development.

  16. Blurring the Boundaries Among Astronomy, Physics, and Chemistry: The Moseley Centenary

    NASA Astrophysics Data System (ADS)

    Trimble, Virginia L.

    2013-01-01

    Scientists, like other human beings, are territorial animals, not just about our parking spaces and seats in the colloquium room, but also about our scientific territories, from the narrowest thesis topic ("Who's been working on my Nebula and left it covered with dust?") to the whole of physics, or chemistry, or astronomy. Many 19th century astronomers resented spectroscopes invading their observatories; chemists objected to Moseley's use of X-ray outgaming their retorts and test tubes in 1913; and chemists and physicists typically disbelieve astronomers suggesting new science on the basis of astronomical data (three other combinations are also possible). The talk will explore some of these transgressions, both a few spectacular successes and rather more awkward failures. Moseley's own contributions included sorting out the rare earths, putting paid to nebulium and coronium as elements between H and He, many years before improved understanding of atomic structure led to correct identifications of the ionization states and transitions actually responsible for the lines credited to them, and putting Prout's hypothesis on a firm foundation ready for the structure Cameron and B2FH would eventually erect there. Back in 1935, Gamow asked whether a new discipline should be called nuclear physics or nuclear chemistry (both now exist, within APS and ACS respectively), and 30+ years later, chemist L.S. Trimble was still complaining that the physicists had grabbed away the territory of atomic and nuclear composition, which should have been part of chemistry!

  17. Physics, biology and the origin of life: the physicians' view.

    PubMed

    Goodman, Geoffrey; Gershwin, M Eric

    2011-12-01

    Physicians have a great interest in discussions of life and its origin, including life's persistence through successive cycles of self-replication under extreme climatic and man-made trials and tribulations. We review here the fundamental processes that, contrary to human intuition, life may be seen heuristically as an ab initio, fundamental process at the interface between the complementary forces of gravitation and quantum mechanics. Analogies can predict applications of quantum mechanics to human physiology in addition to that already being applied, in particular to aspects of brain activity and pathology. This potential will also extend eventually to, for example, autoimmunity, genetic selection and aging. We present these thoughts in perspective against a background of changes in some physical fundamentals of science, from the earlier times of the natural philosophers of medicine to the technological medical gurus of today. Despite the enormous advances in medical science, including integration of technological changes that have led to the newer clinical applications of magnetic resonance imaging and PET scans and of computerized drug design, there is an intellectual vacuum as to how the physics of matter became translated to the biology of life. The essence and future of medicine continue to lie in cautious, systematic and ethically bound practice and scientific research based on fundamental physical laws accepted as true until proven false.

  18. ``Physical Concepts in Cell Biology,'' an upper level interdisciplinary course in cell biophysics/mathematical biology

    NASA Astrophysics Data System (ADS)

    Vavylonis, Dimitrios

    2009-03-01

    I will describe my experience in developing an interdisciplinary biophysics course addressed to students at the upper undergraduate and graduate level, in collaboration with colleagues in physics and biology. The students had a background in physics, biology and engineering, and for many the course was their first exposure to interdisciplinary topics. The course did not depend on a formal knowledge of equilibrium statistical mechanics. Instead, the approach was based on dynamics. I used diffusion as a universal ``long time'' law to illustrate scaling concepts. The importance of statistics and proper counting of states/paths was introduced by calculating the maximum accuracy with which bacteria can measure the concentration of diffuse chemicals. The use of quantitative concepts and methods was introduced through specific biological examples, focusing on model organisms and extremes at the cell level. Examples included microtubule dynamic instability, the search and capture model, molecular motor cooperativity in muscle cells, mitotic spindle oscillations in C. elegans, polymerization forces and propulsion of pathogenic bacteria, Brownian ratchets, bacterial cell division and MinD oscillations.

  19. Selected Physical, Chemical, and Biological Data for 30 Urbanizing Streams in the North Carolina Piedmont Ecoregion, 2002-2003

    USGS Publications Warehouse

    Giddings, E.M.; Moorman, Michelle; Cuffney, Thomas F.; McMahon, Gerard; Harned, Douglas A.

    2007-01-01

    This report provides summarized physical, chemical, and biological data collected during a study of the effects of urbanization on stream ecosystems as part of the U.S. Geological Survey's National Water-Quality Assessment study. The purpose of this study was to examine differences in biological, chemical, and physical characteristics of streams across a gradient of urban intensity. Thirty sites were selected along an urbanization gradient that represents conditions in the North Carolina Piedmont ecoregion, including the cities of Raleigh, Durham, Cary, Greensboro, Winston-Salem, High Point, Asheboro, and Oxford. Data collected included streamflow variability, stream temperature, instream chemistry, instream aquatic habitat, and collections of the algal, macroinvertebrate, and fish communities. In addition, ancillary data describing land use, socioeconomic conditions, and urban infrastructure were compiled for each basin using a geographic information system analysis. All data were processed and summarized for analytical use and are presented in downloadable data tables, along with the methods of data collection and processing.

  20. [Chemical, physical and biological risks in law enforcement].

    PubMed

    Magrini, Andrea; Grana, Mario; Vicentini, Laura

    2014-01-01

    Chemical, physical and biological risks among public safety and security forces. Law enforcement personnel, involved in routine tasks and in emergency situations, are exposed to numerous and several occupational hazards (chemical, physical and biological) whith likely health and security consequences. These risks are particularly high when the organization and preparation are inadequate, there is a lacking or insufficient coordination, information, education and communication and safety and personal protective equipment are inadequate or insufficient. Despite the objective difficulties, caused by the actual special needs related to the service performed or the organizational peculiarities, the risk identification and assessment is essential for worker health and safety of personnel, as provided for by Legislative Decree no. 81/2008. Chemical risks include airborne pollutants due to vehicular traffic (carbon monoxide, ultrafine particles, benzene, polycyclic aromatic hydrocarbons, aldehydes, nitrogen and sulfur oxides, lead), toxic gases generated by combustion process following fires (aromatic hydrocarbons, PAHs, dioxins and furans, biphenyls, formaldehyde, metals and cyanides), substances emitted in case of chemical accidents (solvents, pesticides, toxic gases, caustics), drugs (methylamphetamine), riot control agents and self-defence spray, lead at firing ranges, and several materials and reagents used in forensic laboratory. The physical hazards are often caused by activities that induce biomechanical overload aid the onset of musculoskeletal disorders, the use of visual display terminals and work environments that may expose to heat stress and discomfort, high and low pressure, noise, vibrations, ionizing and non-ionizing radiation. The main biological risks are blood-borne diseases (viral hepatitis, AIDS), airborne diseases (eg, tuberculosis, meningitis, SARS, anthrax), MRSA, and vector-borne diseases. Many of these risk factors are unavoidable or are not

  1. Lithography of Polymer Nanostructures on Glass for Teaching Polymer Chemistry and Physics

    PubMed Central

    Sahar-Halbany, Adi; Vance, Jennifer M.; Drain, Charles Michael

    2011-01-01

    As nanolithography becomes increasingly important in technology and daily life, a variety of inexpensive and creative methods toward communicating the concepts underpinning these processes in the classroom are necessary. An experiment is described that uses simple CD-Rs, C-clamps, an oven, and a freezer to provide concrete examples and insights into the chemistry and principles of nanolithography. The experiment also has flexibility, making it suitable for a range of classroom levels from high school to more advanced labs in college. Because CD-Rs are composed of grooves of polycarbonate, the experiment provides a basis for discussions and exploration into the chemistry and physics of polymers on the nanoscale. PMID:21686088

  2. [Commentary on the Nobel Prize that has been granted in Medicine-Physiology, Chemistry and Physics to noteable investigators].

    PubMed

    Zárate, Arturo; Apolinar, Leticia Manuel; Saucedo, Renata; Basurto, Lourdes

    2015-01-01

    The Nobel Prize was established by Alfred Nobel in 1901 to award people who have made outstanding achievements in physics, chemistry and medicine. So far, from 852 laureates, 45 have been female. Marie Curie was the first woman to receive the Nobel Prize in 1903 for physics and eight years later also for chemistry It is remarkable that her daughter Irene and her husband also received the Nobel Prize for chemistry in 1935. Other two married couples, Cori and Moser, have also been awarded the Nobel Prize. The present commentary attempts to show the female participation in the progress of scientific activities.

  3. Biological and physical conditions of macroinvertebrates in reference lowland streams

    NASA Astrophysics Data System (ADS)

    de Brouwer, Jan; Eekhout, Joris; Verdonschot, Piet

    2016-04-01

    Channelisation measures taken halfway the 20th century have had destructive consequences for the diversity of the ecology in the majority of the lowland streams in countries such as the Netherlands. Currently, stream restoration measures are being implemented in these degraded lowland streams, where design principles are often based on outdated relationships between biological and physical conditions. Little is known about the reference conditions in these streams. Therefore, the aim of this research is to quantify the relationships between biological and physical conditions of macroinvertebrates in reference lowland streams. The research was conducted in four near-natural lowland streams in Central Poland. Field data were obtained during a field campaign in 2011. The following data were obtained in a 50-m reach in each of the four streams: macroinvertebrate sampling, spatial habitat patterns, bathymetry, and flow-velocity. Furthermore, water level, light sensitivity and temperature sensors were installed to obtain the temporal dynamic of these streams. Macroinvertebrates were sampled in 9 different habitat types, i.e. sand, gravel, fine organic matter, stones, branches, leaves, silt, vegetation, and wood. Macroinvertebrates were determined to the highest taxonomic level possible. Data from the bathymetrical surveys were interpolated on a grid and bathymetrical metrics were determined. Flow velocity measurements were related to habitats and flow velocity metrics were determined. Analysis of the data shows that flow conditions vary among the different habitat, with a gradient from hard substrates towards soft substrates. Furthermore, the data show that stream as a unit best explains species composition, but also specific habitat conditions, such as substrate type and flow velocity, correlate with species composition. More specific, the data shows a strong effect of wood on species composition. These findings may have implications for stream restoration design, which

  4. Space Radiation and Manned Mission: Interface Between Physics and Biology

    NASA Astrophysics Data System (ADS)

    Hei, Tom

    2012-07-01

    The natural radiation environment in space consists of a mixed field of high energy protons, heavy ions, electrons and alpha particles. Interplanetary travel to the International Space Station and any planned establishment of satellite colonies on other solar system implies radiation exposure to the crew and is a major concern to space agencies. With shielding, the radiation exposure level in manned space missions is likely to be chronic, low dose irradiation. Traditionally, our knowledge of biological effects of cosmic radiation in deep space is almost exclusively derived from ground-based accelerator experiments with heavy ions in animal or in vitro models. Radiobiological effects of low doses of ionizing radiation are subjected to modulations by various parameters including bystander effects, adaptive response, genomic instability and genetic susceptibility of the exposed individuals. Radiation dosimetry and modeling will provide conformational input in areas where data are difficult to acquire experimentally. However, modeling is only as good as the quality of input data. This lecture will discuss the interdependent nature of physics and biology in assessing the radiobiological response to space radiation.

  5. Estuary-ocean connectivity: fast physics, slow biology.

    PubMed

    Raimonet, Mélanie; Cloern, James E

    2016-11-01

    Estuaries are connected to both land and ocean so their physical, chemical, and biological dynamics are influenced by climate patterns over watersheds and ocean basins. We explored climate-driven oceanic variability as a source of estuarine variability by comparing monthly time series of temperature and chlorophyll-a inside San Francisco Bay with those in adjacent shelf waters of the California Current System (CCS) that are strongly responsive to wind-driven upwelling. Monthly temperature fluctuations inside and outside the Bay were synchronous, but their correlations weakened with distance from the ocean. These results illustrate how variability of coastal water temperature (and associated properties such as nitrate and oxygen) propagates into estuaries through fast water exchanges that dissipate along the estuary. Unexpectedly, there was no correlation between monthly chlorophyll-a variability inside and outside the Bay. However, at the annual scale Bay chlorophyll-a was significantly correlated with the Spring Transition Index (STI) that sets biological production supporting fish recruitment in the CCS. Wind forcing of the CCS shifted in the late 1990s when the STI advanced 40 days. This shift was followed, with lags of 1-3 years, by 3- to 19-fold increased abundances of five ocean-produced demersal fish and crustaceans and 2.5-fold increase of summer chlorophyll-a in the Bay. These changes reflect a slow biological process of estuary-ocean connectivity operating through the immigration of fish and crustaceans that prey on bivalves, reduce their grazing pressure, and allow phytoplankton biomass to build. We identified clear signals of climate-mediated oceanic variability in this estuary and discovered that the response patterns vary with the process of connectivity and the timescale of ocean variability. This result has important implications for managing nutrient inputs to estuaries connected to upwelling systems, and for assessing their responses to changing

  6. Estuary–ocean connectivity: fast physics, slow biology

    USGS Publications Warehouse

    Raimonet, Mélanie; Cloern, James E.

    2016-01-01

    Estuaries are connected to both land and ocean so their physical, chemical, and biological dynamics are influenced by climate patterns over watersheds and ocean basins. We explored climate-driven oceanic variability as a source of estuarine variability by comparing monthly time series of temperature and chlorophyll-a inside San Francisco Bay with those in adjacent shelf waters of the California Current System (CCS) that are strongly responsive to wind-driven upwelling. Monthly temperature fluctuations inside and outside the Bay were synchronous, but their correlations weakened with distance from the ocean. These results illustrate how variability of coastal water temperature (and associated properties such as nitrate and oxygen) propagates into estuaries through fast water exchanges that dissipate along the estuary. Unexpectedly, there was no correlation between monthly chlorophyll-a variability inside and outside the Bay. However, at the annual scale Bay chlorophyll-a was significantly correlated with the Spring Transition Index (STI) that sets biological production supporting fish recruitment in the CCS. Wind forcing of the CCS shifted in the late 1990s when the STI advanced 40 days. This shift was followed, with lags of 1–3 years, by 3- to 19-fold increased abundances of five ocean-produced demersal fish and crustaceans and 2.5-fold increase of summer chlorophyll-a in the Bay. These changes reflect a slow biological process of estuary–ocean connectivity operating through the immigration of fish and crustaceans that prey on bivalves, reduce their grazing pressure, and allow phytoplankton biomass to build. We identified clear signals of climate-mediated oceanic variability in this estuary and discovered that the response patterns vary with the process of connectivity and the timescale of ocean variability. This result has important implications for managing nutrient inputs to estuaries connected to upwelling systems, and for assessing their responses to

  7. Chemistry and biology of Tc-99m renal function radiopharmaceuticals. Final report, May 1, 1982-January 15, 1983

    SciTech Connect

    Not Available

    1983-01-01

    Progress is reported on research conducted during the period May 1, 1982 to January 15, 1983. The chemistry and biology of two possible renal function radiopharmaceuticals, Tc-99m N, N'-bis (mercaptoacetyl)-2,3-diamino-propanoate (Tc-99m CO/sub 2/DADS, 1(X=OH)) and the Tc-99m complex of penicillamine. (ACR)

  8. What are Contaminants of Emerging Concern (CECs) ?Examples of Biological and Chemistry Approaches to their Detection, Exposure and Effects?

    EPA Science Inventory

    This presentation will overview what Contaminants of Emerging Concern (CECs) are, provide some examples of various CECs and some of the biological and chemistry approaches to assess their exposure and effects to aquatic life. The term CECs has been used since the 1990s to identif...

  9. Two Methods of Determining Total Phenolic Content of Foods and Juices in a General, Organic, and Biological (GOB) Chemistry Lab

    ERIC Educational Resources Information Center

    Shaver, Lee Alan; Leung, Sam H.; Puderbaugh, Amy; Angel, Stephen A.

    2011-01-01

    The determination of total phenolics in foods and fruit juices was used successfully as a laboratory experiment in our undergraduate general, organic, and biological (GOB) chemistry course. Two different colorimetric methods were used over three years and comparative student results indicate that a ferrous ammonium sulfate (FAS) indicator…

  10. Water as Life, Death, and Power: Building an Integrated Interdisciplinary Course Combining Perspectives from Anthropology, Biology, and Chemistry

    ERIC Educational Resources Information Center

    Willermet, Cathy; Mueller, Anja; Juris, Stephen J.; Drake, Eron; Upadhaya, Samik; Chhetri, Pratik

    2013-01-01

    In response to a request from a campus student organization, faculty from three fields came together to develop and teach an integrated interdisciplinary course on water issues and social activism. This course, "Water as Life, Death, and Power", brought together topics from the fields of anthropology, biology and chemistry to explore…

  11. Real-time Image Analysis of Living Cellular-Biology Measurements of Intelligent Chemistry

    SciTech Connect

    Solinsky, James C.; Budge, Scott E.; Majors, Paul D.; Rex, Bruce B.

    2003-08-01

    This paper reports on the Pacific Northwest National Laboratory (PNNL) DOE Initiative in Image Science and Technology (ISAT) research, which is developing algorithms and software tool sets for remote sensing and biological applications. In particular, the PNNL ISAT work is applying these research results to the automated analysis of real-time cellular biology imagery to assist the biologist in determining the correct data collection region for the current state of a conglomerate of living cells in three-dimensional motion. The real-time computation of the typical 120 MB/sec multi-spectral data sets is executed in a Field Programmable Gate Array (FPGA) technology, which has very high processing rates due to large-scale parallelism. The outcome of this artificial vision work will allow the biologist to work with imagery as a creditable set of dye-tagged chemistry measurements in formats for individual cell tracking through regional feature extraction, and animation visualization through individual object isolation/characterization of the microscopy imagery.

  12. Mentha suaveolens Ehrh. (Lamiaceae) Essential Oil and Its Main Constituent Piperitenone Oxide: Biological Activities and Chemistry.

    PubMed

    Božović, Mijat; Pirolli, Adele; Ragno, Rino

    2015-05-13

    Since herbal medicines play an important role in the treatment of a wide range of diseases, there is a growing need for their quality control and standardization. Mentha suaveolens Ehrh. (MS) is an aromatic herb with fruit and a spearmint flavor, used in the Mediterranean areas as a traditional medicine. It has an extensive range of biological activities, including cytotoxic, antimicrobial, antioxidant, anti-inflammatory, hypotensive and insecticidal properties, among others. This study aims to review the scientific findings and research reported to date on MS that prove many of the remarkable various biological actions, effects and some uses of this species as a source of bioactive natural compounds. On the other hand, piperitenone oxide (PO), the major chemical constituent of the carvone pathway MS essential oil, has been reported to exhibit numerous bioactivities in cells and animals. Thus, this integrated overview also surveys and interprets the present knowledge of chemistry and analysis of this oxygenated monoterpene, as well as its beneficial bioactivities. Areas for future research are suggested.

  13. Calamintha nepeta (L.) Savi and its Main Essential Oil Constituent Pulegone: Biological Activities and Chemistry.

    PubMed

    Božović, Mijat; Ragno, Rino

    2017-02-14

    Medicinal plants play an important role in the treatment of a wide range of diseases, even if their chemical constituents are not always completely recognized. Observations on their use and efficacy significantly contribute to the disclosure of their therapeutic properties. Calamintha nepeta (L.) Savi is an aromatic herb with a mint-oregano flavor, used in the Mediterranean areas as a traditional medicine. It has an extensive range of biological activities, including antimicrobial, antioxidant and anti-inflammatory, as well as anti-ulcer and insecticidal properties. This study aims to review the scientific findings and research reported to date on Calamintha nepeta (L.) Savi that prove many of the remarkable various biological actions, effects and some uses of this species as a source of bioactive natural compounds. On the other hand, pulegone, the major chemical constituent of Calamintha nepeta (L.) Savi essential oil, has been reported to exhibit numerous bioactivities in cells and animals. Thus, this integrated overview also surveys and interprets the present knowledge of chemistry and analysis of this oxygenated monoterpene, as well as its beneficial bioactivities. Areas for future research are suggested.

  14. Hydrogen Sulfide (H2S) Releasing Agents: Chemistry and Biological Applications

    PubMed Central

    Zhao, Yu; Biggs, Tyler D.

    2014-01-01

    Hydrogen sulfide (H2S) is a newly recognized signaling molecule with very potent cytoprotective actions. The fields of H2S physiology and pharmacology have been rapidly growing in recent years, but a number of fundamental issues must be addressed to advance our understanding of the biology and clinical potential of H2S in the future. Hydrogen sulfide releasing agents (also known as H2S donors) have been widely used in the field. These compounds are not only useful research tools, but also potential therapeutic agents. It is therefore important to study the chemistry and pharmacology of exogenous H2S and to be aware of the limitations associated with the choice of donors used to generate H2S in vitro and in vivo. In this review we summarized the developments and limitations of current available donors including H2S gas, sulfide salts, garlic-derived sulfur compounds, Lawesson’s reagent/analogs, 1,2-dithiole-3-thiones, thiol-activated donors, photo-caged donors, and thioamino acids. Some biological applications of these donors were also discussed. PMID:25019301

  15. How Did the Tree of Knowledge Get Its Blossom? The Rise of Physical and Theoretical Chemistry, with an Eye on Berlin and Leipzig.

    PubMed

    Friedrich, Bretislav

    2016-04-25

    "Physical chemistry is not just a branch on but the blossom of the tree of knowledge," declared Ostwald, a most vocal advocate of his field, conceived as the basis for all of chemistry. This Essay describes the historical development of physical and theoretical chemistry with a focus on Berlin and Leipzig, its foremost centers in Germany.

  16. The Logical and Psychological Structure of Physical Chemistry and Its Relevance to Graduate Students' Opinions about the Difficulties of the Major Areas of the Subject

    ERIC Educational Resources Information Center

    Tsaparlis, Georgios

    2016-01-01

    In a previous publication, Jensen's scheme for the logical structure of chemistry was employed to identify a logical structure for physical chemistry, which was further used as a tool for analyzing the organization of twenty physical chemistry textbooks. In addition, science education research was considered for the study of the psychological…

  17. The evolution of pedagogical content knowledge in chemistry and physics prospective secondary teachers

    NASA Astrophysics Data System (ADS)

    Veal, William Richard

    1997-09-01

    The purpose of this study was to describe the evolution of pedagogical content knowledge in prospective secondary chemistry and physics teachers. A new paradigmatic framework was developed to guide the research. Craft knowledge and pedagogical content knowledge were compared and combined forming a new perspective from which to view secondary chemistry and physics teachers' "learning to teach." A second purpose of this study was to develop philosophically-derived, domain-specific, pedagogical content knowledge taxonomies. Four taxonomies were developed in all; two general and two domain-specific. The general taxonomies describe types of pedagogical content knowledge and attributes of pedagogical content knowledge. The two domain-specific taxonomies describe topics common to both physics and chemistry and outline domain-specific laboratories for the differentiation between heat and temperature. A methodological theoretical framework, synthesized from radical and social constructivism, was developed to guide the researcher in data collection, analysis, and interpretation. The researcher used four cases, two prospective chemistry teachers and two prospective physics teachers, and followed their development through the science curriculum class and student teaching field experience of their teacher preparation program. Content-specific, situational vignettes were created as a tool to monitor the participants' development of pedagogical content knowledge. The vignettes were administered using a modified microgenetic method. The modified microgenetic procedure involved the repeated administration of a task (vignette) over a period of time to monitor cognitive change. Data were collected through several methods: participant responses to the vignettes, field notes taken during the science curriculum class and student teaching field experience, interviews, artifact collection, and journals. Data were analyzed using qualitative content analysis. The results of this study

  18. 2014 International Conference on Science & Engineering in Mathematics, Chemistry and Physics (ScieTech 2014)

    NASA Astrophysics Data System (ADS)

    2014-04-01

    2014 International Conference on Science & Engineering in Mathematics, Chemistry and Physics (ScieTech 2014), was held at the Media Hotel, Jakarta, Indonesia, on 13-14 January 2014. The ScieTech 2014 conference is aimed to bring together researchers, engineers and scientists in the domain of interest from around the world. ScieTech 2014 is placed on promoting interaction between the theoretical, experimental, and applied communities, so that a high level exchange is achieved in new and emerging areas within Mathematics, Chemistry and Physics. We would like to express our sincere gratitude to all in the Technical Program Committee who have reviewed the papers and developed a very interesting Conference Program as well as the invited and plenary speakers. This year, we received 187 papers and after rigorous review, 50 papers were accepted. The participants come from 16 countries. There are 5 (Five) Paralell Sessions and Four Keynote Speakers. It is an honour to present this volume of Journal of Physics: Conference Series (JPCS) and we deeply thank the authors for their enthusiastic and high-grade contributions. Finally, we would like to thank the conference chairmen, the members of the steering committee, the organizing committee, the organizing secretariat and the financial support from the conference sponsors that allowed the success of ScieTech 2014. The Editors of the Scietech 2014 Proceedings: Dr. Ford Lumban Gaol Dr. Benfano Soewito Dr. P.N. Gajjar

  19. Processes that Drove the Transition from Chemistry to Biology: Concepts and Evidence

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew

    2012-01-01

    Two properties are particularly germane to the transition from chemistry to biology. One is the emergence of complex molecules (polymers) capable of performing non-trivial functions, such as catalysis, energy transduction or transport across cell walls. The other is the ability of several functions to work in concert to provide reproductive advantage to systems hosting these functions. Biological systems exhibit these properties at remarkable levels of efficiency and accuracy in a way that appears effortless. However, dissection of these properties reveals great complexities that are involved. This opens a question: how a simple, ancestral system could have acquired the required properties? Other questions follow. What are the chances that a functional polymer emerges at random? What is the minimum structural complexity of a polymer to carry out a function at a reasonable level of efficiency? Can we identify concrete, protobiologically plausible mechanisms that yield advantageous coupling between different functions? These and similar questions are at the core of the main topic of this session: how soulless chemistry became life? Clearly, we do not have complete answers to any of these questions. However, in recent years a number of new and sometimes unexpected clues have been brought to light. Of particular interest are proteins because they are the main functional polymers in contemporary cells. The emergence of protein functions is a puzzle. It is widely accepted that a well ]defined, compact structure (fold) is a prerequisite for function. It is equally widely accepted that compact folds are rare among random amino acid polymers. Then, how did protein functionality start? According to one hypothesis well folded were preceded by their poorly folded, yet still functional ancestors. Only recently, however, experimental evidence supporting this hypothesis has been presented. In particular, a small enzyme capable of ligating two RNA fragments with the rate of 106

  20. Circulatory bubble dynamics: from physical to biological aspects.

    PubMed

    Papadopoulou, Virginie; Tang, Meng-Xing; Balestra, Costantino; Eckersley, Robert J; Karapantsios, Thodoris D

    2014-04-01

    Bubbles can form in the body during or after decompression from pressure exposures such as those undergone by scuba divers, astronauts, caisson and tunnel workers. Bubble growth and detachment physics then becomes significant in predicting and controlling the probability of these bubbles causing mechanical problems by blocking vessels, displacing tissues, or inducing an inflammatory cascade if they persist for too long in the body before being dissolved. By contrast to decompression induced bubbles whose site of initial formation and exact composition are debated, there are other instances of bubbles in the bloodstream which are well-defined. Gas emboli unwillingly introduced during surgical procedures and ultrasound microbubbles injected for use as contrast or drug delivery agents are therefore also discussed. After presenting the different ways that bubbles can end up in the human bloodstream, the general mathematical formalism related to the physics of bubble growth and detachment from decompression is reviewed. Bubble behavior in the bloodstream is then discussed, including bubble dissolution in blood, bubble rheology and biological interactions for the different cases of bubble and blood composition considered.