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Sample records for biology quantum chemistry

  1. Quantum chemistry

    CERN Document Server

    Lowe, John P

    1993-01-01

    Praised for its appealing writing style and clear pedagogy, Lowe's Quantum Chemistry is now available in its Second Edition as a text for senior undergraduate- and graduate-level chemistry students. The book assumes little mathematical or physical sophistication and emphasizes an understanding of the techniques and results of quantum chemistry, thus enabling students to comprehend much of the current chemical literature in which quantum chemical methods or concepts are used as tools. The book begins with a six-chapter introduction of standard one-dimensional systems, the hydrogen atom,

  2. Advances in quantum chemistry

    CERN Document Server

    Sabin, John R

    2013-01-01

    Advances in Quantum Chemistry presents surveys of current topics in this rapidly developing field that has emerged at the cross section of the historically established areas of mathematics, physics, chemistry, and biology. It features detailed reviews written by leading international researchers. This volume focuses on the theory of heavy ion physics in medicine.Advances in Quantum Chemistry presents surveys of current topics in this rapidly developing field that has emerged at the cross section of the historically established areas of mathematics, physics, chemistry, and biology. It features

  3. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi

    2009-06-01

    Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

  4. Principles of quantum chemistry

    CERN Document Server

    George, David V

    2013-01-01

    Principles of Quantum Chemistry focuses on the application of quantum mechanics in physical models and experiments of chemical systems.This book describes chemical bonding and its two specific problems - bonding in complexes and in conjugated organic molecules. The very basic theory of spectroscopy is also considered. Other topics include the early development of quantum theory; particle-in-a-box; general formulation of the theory of quantum mechanics; and treatment of angular momentum in quantum mechanics. The examples of solutions of Schroedinger equations; approximation methods in quantum c

  5. Quantum mechanics in chemistry

    CERN Document Server

    Schatz, George C

    2002-01-01

    Intended for graduate and advanced undergraduate students, this text explores quantum mechanical techniques from the viewpoint of chemistry and materials science. Dynamics, symmetry, and formalism are emphasized. An initial review of basic concepts from introductory quantum mechanics is followed by chapters examining symmetry, rotations, and angular momentum addition. Chapter 4 introduces the basic formalism of time-dependent quantum mechanics, emphasizing time-dependent perturbation theory and Fermi's golden rule. Chapter 5 sees this formalism applied to the interaction of radiation and matt

  6. Computational quantum chemistry website

    International Nuclear Information System (INIS)

    1997-01-01

    This report contains the contents of a web page related to research on the development of quantum chemistry methods for computational thermochemistry and the application of quantum chemistry methods to problems in material chemistry and chemical sciences. Research programs highlighted include: Gaussian-2 theory; Density functional theory; Molecular sieve materials; Diamond thin-film growth from buckyball precursors; Electronic structure calculations on lithium polymer electrolytes; Long-distance electronic coupling in donor/acceptor molecules; and Computational studies of NOx reactions in radioactive waste storage

  7. Quantum chemistry an introduction

    CERN Document Server

    Kauzmann, Walter

    2013-01-01

    Quantum Chemistry: An Introduction provides information pertinent to the fundamental aspects of quantum mechanics. This book presents the theory of partial differentiation equations by using the classical theory of vibrations as a means of developing physical insight into this essential branch of mathematics.Organized into five parts encompassing 16 chapters, this book begins with an overview of how quantum mechanical deductions are made. This text then describes the achievements and limitations of the application of quantum mechanics to chemical problems. Other chapters provide a brief survey

  8. Chemistry and Biology

    Science.gov (United States)

    Wigston, David L.

    1970-01-01

    Discusses the relationship between chemisty and biology in the science curriculum. Points out the differences in perception of the disciplines, which the physical scientists favoring reductionism. Suggests that biology departments offer a special course for chemistry students, just as the chemistry departments have done for biology students.…

  9. Introductory quantum chemistry

    International Nuclear Information System (INIS)

    Chandra, A.K.

    1974-01-01

    This book on quantum chemistry is primarily intended for university students at the senior undergraduate level. It serves as an aid to the basic understanding of the important concepts of quantum mechanics introduced in the field of chemistry. Various chapters of the book are devoted to the following : (i) Waves and quanta, (ii) Operator concept in quantum chemistry, (iii) Wave mechanics of some simple systems, (iv) Perturbation theory, (v) Many-electron atoms and angular momenta (vi) Molecular orbital theory and its application to the electronic structure of diatomic molecules, (vii) Chemical bonding in polyatomic molecules and (viii) Chemical applications of Hellmann-Feynman theorem. At the end of each chapter, a set of problems is given and the answers to these problems are given at the end of the book. (A.K.)

  10. Quantum Effects in Biological Systems

    CERN Document Server

    2016-01-01

    Since the last decade the study of quantum mechanical phenomena in biological systems has become a vibrant field of research. Initially sparked by evidence of quantum effects in energy transport that is instrumental for photosynthesis, quantum biology asks the question of how methods and models from quantum theory can help us to understand fundamental mechanisms in living organisms. This approach entails a paradigm change challenging the related disciplines: The successful framework of quantum theory is taken out of its low-temperature, microscopic regimes and applied to hot and dense macroscopic environments, thereby extending the toolbox of biology and biochemistry at the same time. The Quantum Effects in Biological Systems conference is a platform for researchers from biology, chemistry and physics to present and discuss the latest developments in the field of quantum biology. After meetings in Lisbon (2009), Harvard (2010), Ulm (2011), Berkeley (2012), Vienna (2013), Singapore (2014) and Florence (2015),...

  11. Fundamentals of quantum chemistry

    CERN Document Server

    House, J E

    2004-01-01

    An introduction to the principles of quantum mechanics needed in physical chemistry. Mathematical tools are presented and developed as needed and only basic calculus, chemistry, and physics is assumed. Applications include atomic and molecular structure, spectroscopy, alpha decay, tunneling, and superconductivity. New edition includes sections on perturbation theory, orbital symmetry of diatomic molecules, the Huckel MO method and Woodward/Hoffman rules as well as a new chapter on SCF and Hartree-Fock methods. * This revised text clearly presents basic q

  12. Quantum biological information theory

    CERN Document Server

    Djordjevic, Ivan B

    2016-01-01

    This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

  13. Handbook of relativistic quantum chemistry

    International Nuclear Information System (INIS)

    Liu, Wenjian

    2017-01-01

    This handbook focuses on the foundations of relativistic quantum mechanics and addresses a number of fundamental issues never covered before in a book. For instance: How can many-body theory be combined with quantum electrodynamics? How can quantum electrodynamics be interfaced with relativistic quantum chemistry? What is the most appropriate relativistic many-electron Hamiltonian? How can we achieve relativistic explicit correlation? How can we formulate relativistic properties? - just to name a few. Since relativistic quantum chemistry is an integral component of computational chemistry, this handbook also supplements the ''Handbook of Computational Chemistry''. Generally speaking, it aims to establish the 'big picture' of relativistic molecular quantum mechanics as the union of quantum electrodynamics and relativistic quantum chemistry. Accordingly, it provides an accessible introduction for readers new to the field, presents advanced methodologies for experts, and discusses possible future perspectives, helping readers understand when/how to apply/develop the methodologies.

  14. Handbook of relativistic quantum chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Wenjian (ed.) [Peking Univ., Beijing (China). Center for Computational Science and Engineering

    2017-03-01

    This handbook focuses on the foundations of relativistic quantum mechanics and addresses a number of fundamental issues never covered before in a book. For instance: How can many-body theory be combined with quantum electrodynamics? How can quantum electrodynamics be interfaced with relativistic quantum chemistry? What is the most appropriate relativistic many-electron Hamiltonian? How can we achieve relativistic explicit correlation? How can we formulate relativistic properties? - just to name a few. Since relativistic quantum chemistry is an integral component of computational chemistry, this handbook also supplements the ''Handbook of Computational Chemistry''. Generally speaking, it aims to establish the 'big picture' of relativistic molecular quantum mechanics as the union of quantum electrodynamics and relativistic quantum chemistry. Accordingly, it provides an accessible introduction for readers new to the field, presents advanced methodologies for experts, and discusses possible future perspectives, helping readers understand when/how to apply/develop the methodologies.

  15. Quantum chemistry on a superconducting quantum processor

    Energy Technology Data Exchange (ETDEWEB)

    Kaicher, Michael P.; Wilhelm, Frank K. [Theoretical Physics, Saarland University, 66123 Saarbruecken (Germany); Love, Peter J. [Department of Physics and Astronomy, Tufts University, Medford, MA 02155 (United States)

    2016-07-01

    Quantum chemistry is the most promising civilian application for quantum processors to date. We study its adaptation to superconducting (sc) quantum systems, computing the ground state energy of LiH through a variational hybrid quantum classical algorithm. We demonstrate how interactions native to sc qubits further reduce the amount of quantum resources needed, pushing sc architectures as a near-term candidate for simulations of more complex atoms/molecules.

  16. Theoretical chemistry periodicities in chemistry and biology

    CERN Document Server

    Eyring, Henry

    1978-01-01

    Theoretical Chemistry: Periodicities in Chemistry and Biology, Volume 4 covers the aspects of theoretical chemistry. The book discusses the stably rotating patterns of reaction and diffusion; the chemistry of inorganic systems exhibiting nonmonotonic behavior; and population cycles. The text also describes the mathematical modeling of excitable media in neurobiology and chemistry; oscillating enzyme reactions; and oscillatory properties and excitability of the heart cell membrane. Selected topics from the theory of physico-chemical instabilities are also encompassed. Chemists, mechanical engin

  17. Elementary quantum chemistry

    CERN Document Server

    Pilar, Frank L

    2003-01-01

    Useful introductory course and reference covers origins of quantum theory, Schrödinger wave equation, quantum mechanics of simple systems, electron spin, quantum states of atoms, Hartree-Fock self-consistent field method, more. 1990 edition.

  18. Quantum Nanobiology and Biophysical Chemistry

    DEFF Research Database (Denmark)

    2013-01-01

    An introduction was provided in the first issue by way of an Editorial to this special two issue volume of Current Physical Chemistry – “Quantum Nanobiology and Biophysical Chemistry” [1]. The Guest Editors would like to thank all the authors and referees who have contributed to this second issue....... Wu et al. use density functional theory to explore the use of Ni/Fe bimetallic nanotechnology in the bioremediation of decabromo-diphenyl esters. Araújo-Chaves et al. explore the binding and reactivity of Mn(III) porphyrins in the membrane mimetic setting of model liposomal systems. Claussen et al....... demonstrate extremely low detection performance of acyl-homoserine lactone in a biologically relevant system using surface enhanced Raman spectroscopy. Sugihara and Bondar evaluate the influence of methyl-groups and the protein environment on retinal geometries in rhodopsin and bacteriorhodopsin, two...

  19. Relativistic quantum chemistry on quantum computers

    DEFF Research Database (Denmark)

    Veis, L.; Visnak, J.; Fleig, T.

    2012-01-01

    The past few years have witnessed a remarkable interest in the application of quantum computing for solving problems in quantum chemistry more efficiently than classical computers allow. Very recently, proof-of-principle experimental realizations have been reported. However, so far only...... the nonrelativistic regime (i.e., the Schrodinger equation) has been explored, while it is well known that relativistic effects can be very important in chemistry. We present a quantum algorithm for relativistic computations of molecular energies. We show how to efficiently solve the eigenproblem of the Dirac......-Coulomb Hamiltonian on a quantum computer and demonstrate the functionality of the proposed procedure by numerical simulations of computations of the spin-orbit splitting in the SbH molecule. Finally, we propose quantum circuits with three qubits and nine or ten controlled-NOT (CNOT) gates, which implement a proof...

  20. Remedial mathematics for quantum chemistry

    NARCIS (Netherlands)

    Koopman, L.; Brouwer, N.; Heck, A.; Buma, W.J.

    2008-01-01

    Proper mathematical skills are important for every science course and mathematics-intensive chemistry courses rely on a sound mathematical pre-knowledge. In the first-year quantum chemistry course at this university, it was noticed that many students lack basic mathematical knowledge. To tackle the

  1. Introducing Relativity into Quantum Chemistry

    Science.gov (United States)

    Li, Wai-Kee; Blinder, S. M.

    2011-01-01

    It is not often realized by chemists that the special theory of relativity is behind several aspects of quantum chemistry. The Schrdinger equation itself is based on relations between space-time and energy-momentum four vectors. Electron spin is, of course, the most obvious manifestation of relativity. The chemistry of some heavy elements is…

  2. Handbook of computational quantum chemistry

    CERN Document Server

    Cook, David B

    2005-01-01

    Quantum chemistry forms the basis of molecular modeling, a tool widely used to obtain important chemical information and visual images of molecular systems. Recent advances in computing have resulted in considerable developments in molecular modeling, and these developments have led to significant achievements in the design and synthesis of drugs and catalysts. This comprehensive text provides upper-level undergraduates and graduate students with an introduction to the implementation of quantum ideas in molecular modeling, exploring practical applications alongside theoretical explanations.Wri

  3. Quantum physics meets biology.

    Science.gov (United States)

    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. Interface of Chemistry and Biology

    OpenAIRE

    I. Kira Astakhova

    2013-01-01

    Many exciting research studies in Science today lie at the interface between various disciplines. The interface between Chemistry and Biology is particularly rich, since it closely reflects Nature and the origins of Life. Multiple research groups in the Chemistry Departments around the world have made substantial efforts to interweave ideas from Chemistry and Biology to solve important questions related to material science and healthcare, just to name a few. International Journal of Bioorgani...

  5. Combining supramolecular chemistry with biology

    NARCIS (Netherlands)

    Uhlenheuer, D.A.; Petkau - Milroy, K.; Brunsveld, L.

    2010-01-01

    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

  6. Quantum Dynamics in Biological Systems

    Science.gov (United States)

    Shim, Sangwoo

    In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

  7. Quantum chemistry and scientific calculus

    International Nuclear Information System (INIS)

    Gervais, H.P.

    1988-01-01

    The 1988 progress report of the Polytechnic School research team, concerning the quantum chemistry and the scientific calculus. The research program involves the following topics: the transition metals - carbon monoxide systems, which are a suitable model for the chemisorption phenomena; the introduction of the vibronic perturbations in the magnetic screen constants; the gauge invariance method (used in the calculation of the magnetic perturbations), extended to the case of the static or dynamic electrical polarizabilities. The published papers, the congress communications and the thesis are listed [fr

  8. Computing protein infrared spectroscopy with quantum chemistry.

    Science.gov (United States)

    Besley, Nicholas A

    2007-12-15

    Quantum chemistry is a field of science that has undergone unprecedented advances in the last 50 years. From the pioneering work of Boys in the 1950s, quantum chemistry has evolved from being regarded as a specialized and esoteric discipline to a widely used tool that underpins much of the current research in chemistry today. This achievement was recognized with the award of the 1998 Nobel Prize in Chemistry to John Pople and Walter Kohn. As the new millennium unfolds, quantum chemistry stands at the forefront of an exciting new era. Quantitative calculations on systems of the magnitude of proteins are becoming a realistic possibility, an achievement that would have been unimaginable to the early pioneers of quantum chemistry. In this article we will describe ongoing work towards this goal, focusing on the calculation of protein infrared amide bands directly with quantum chemical methods.

  9. Exploiting Locality in Quantum Computation for Quantum Chemistry.

    Science.gov (United States)

    McClean, Jarrod R; Babbush, Ryan; Love, Peter J; Aspuru-Guzik, Alán

    2014-12-18

    Accurate prediction of chemical and material properties from first-principles quantum chemistry is a challenging task on traditional computers. Recent developments in quantum computation offer a route toward highly accurate solutions with polynomial cost; however, this solution still carries a large overhead. In this Perspective, we aim to bring together known results about the locality of physical interactions from quantum chemistry with ideas from quantum computation. We show that the utilization of spatial locality combined with the Bravyi-Kitaev transformation offers an improvement in the scaling of known quantum algorithms for quantum chemistry and provides numerical examples to help illustrate this point. We combine these developments to improve the outlook for the future of quantum chemistry on quantum computers.

  10. Second quantized approach to quantum chemistry

    International Nuclear Information System (INIS)

    Surjan, P.R.

    1989-01-01

    The subject of this book is the application of the second quantized approach to quantum chemistry. Second quantization is an alternative tool for dealing with many-electron theory. The vast majority of quantum chemical problems are more easily treated using second quantization as a language. This book offers a simple and pedagogical presentation of the theory and some applications. The reader is not supposed to be trained in higher mathematics, though familiarity with elementary quantum mechanics and quantum chemistry is assumed. Besides the basic formalism and standard illustrative applications, some recent topics of quantum chemistry are reviewed in some detail. This book bridges the gap between sophisticated quantum theory and practical quantum chemistry. (orig.)

  11. Quantum chemistry literature data base

    International Nuclear Information System (INIS)

    Ohno, Kimio; Morokuma, Keiji

    1982-01-01

    Ab initio computations of atomic and molecular electronic structure now appear in so many journals that it is very difficult for interested scientistics to locate proper and comprehensive references. This book is designed to help them and contains more than 2500 references to the literature published in the years 1978-1980. These have been gathered from nineteen well-known international core journals by quantum chemists themselves and the result is a thorough bibliography. Each entry is a full reference consisting of the following items: (1) authors, (2) journal name, volume, page and year, (3) compounds, (4) methods of calculation, (5) basis sets, (6) calculated properties, and (7) comments. For easy access to the references, the reader can consult the compound and author indexes. A short article on the reliability of ab initio calculations is included as an appendix; this gives a rough idea about the accuracy of the calculated results reported. As the book has been complied using the resources of a computer data base of quantum chemistry literature, it is particularly up to date and the authors will be able to provide supplements regularly. This bibliography will be an asset to large departments of chemistry and all university libraries. (orig.)

  12. From wave mechanics to quantum chemistry

    International Nuclear Information System (INIS)

    Daudel, R.

    1996-01-01

    The origin of wave mechanics, which is now called quantum mechanics, is evoked. The main stages of the birth of quantum chemistry are related as resulting from the application of quantum mechanics to the study of molecular properties and chemical reactions. (author). 14 refs

  13. A Quantum Chemistry Concept Inventory for Physical Chemistry Classes

    Science.gov (United States)

    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,…

  14. Quantum chemistry simulation on quantum computers: theories and experiments.

    Science.gov (United States)

    Lu, Dawei; Xu, Boruo; Xu, Nanyang; Li, Zhaokai; Chen, Hongwei; Peng, Xinhua; Xu, Ruixue; Du, Jiangfeng

    2012-07-14

    It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.

  15. Density functional theory in quantum chemistry

    CERN Document Server

    Tsuneda, Takao

    2014-01-01

    This book examines density functional theory based on the foundation of quantum chemistry. Unconventional in approach, it reviews basic concepts, then describes the physical meanings of state-of-the-art exchange-correlation functionals and their corrections.

  16. Quantum Mechanics predicts evolutionary biology.

    Science.gov (United States)

    Torday, J S

    2018-07-01

    Nowhere are the shortcomings of conventional descriptive biology more evident than in the literature on Quantum Biology. In the on-going effort to apply Quantum Mechanics to evolutionary biology, merging Quantum Mechanics with the fundamentals of evolution as the First Principles of Physiology-namely negentropy, chemiosmosis and homeostasis-offers an authentic opportunity to understand how and why physics constitutes the basic principles of biology. Negentropy and chemiosmosis confer determinism on the unicell, whereas homeostasis constitutes Free Will because it offers a probabilistic range of physiologic set points. Similarly, on this basis several principles of Quantum Mechanics also apply directly to biology. The Pauli Exclusion Principle is both deterministic and probabilistic, whereas non-localization and the Heisenberg Uncertainty Principle are both probabilistic, providing the long-sought after ontologic and causal continuum from physics to biology and evolution as the holistic integration recognized as consciousness for the first time. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Simulating chemistry using quantum computers.

    Science.gov (United States)

    Kassal, Ivan; Whitfield, James D; Perdomo-Ortiz, Alejandro; Yung, Man-Hong; Aspuru-Guzik, Alán

    2011-01-01

    The difficulty of simulating quantum systems, well known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on conventional computers, by mapping the quantum system to another, more controllable one. In this review, we discuss to what extent the ideas in quantum computation, now a well-established field, have been applied to chemical problems. We describe algorithms that achieve significant advantages for the electronic-structure problem, the simulation of chemical dynamics, protein folding, and other tasks. Although theory is still ahead of experiment, we outline recent advances that have led to the first chemical calculations on small quantum information processors.

  18. Towards quantum chemistry on a quantum computer.

    Science.gov (United States)

    Lanyon, B P; Whitfield, J D; Gillett, G G; Goggin, M E; Almeida, M P; Kassal, I; Biamonte, J D; Mohseni, M; Powell, B J; Barbieri, M; Aspuru-Guzik, A; White, A G

    2010-02-01

    Exact first-principles calculations of molecular properties are currently intractable because their computational cost grows exponentially with both the number of atoms and basis set size. A solution is to move to a radically different model of computing by building a quantum computer, which is a device that uses quantum systems themselves to store and process data. Here we report the application of the latest photonic quantum computer technology to calculate properties of the smallest molecular system: the hydrogen molecule in a minimal basis. We calculate the complete energy spectrum to 20 bits of precision and discuss how the technique can be expanded to solve large-scale chemical problems that lie beyond the reach of modern supercomputers. These results represent an early practical step toward a powerful tool with a broad range of quantum-chemical applications.

  19. Relativistic quantum chemistry on quantum computers

    Czech Academy of Sciences Publication Activity Database

    Veis, Libor; Višňák, Jakub; Fleig, T.; Knecht, S.; Saue, T.; Visscher, L.; Pittner, Jiří

    2012-01-01

    Roč. 85, č. 3 (2012), 030304 ISSN 1050-2947 R&D Projects: GA ČR GA203/08/0626 Institutional support: RVO:61388955 Keywords : simulation * algorithm * computation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.042, year: 2012

  20. Molecular biology: Self-sustaining chemistry

    Directory of Open Access Journals (Sweden)

    Wrede Paul

    2007-10-01

    Full Text Available Abstract Molecular biology is an established interdisciplinary field within biology that deals fundamentally with the function of any nucleic acid in the cellular context. The molecular biology section in Chemistry Central Journal focusses on the genetically determined chemistry and biochemistry occuring in the cell. How can thousands of chemical reactions interact smoothly to maintain the life of cells, even in a variable environment? How is this self-sustaining system achieved? These are questions that should be answered in the light of molecular biology and evolution, but with the application of biophysical, physico-chemical, analytical and preparative technologies. As the Section Editor for the molecular biology section in Chemistry Central Journal, I hope to receive manuscripts that present new approaches aimed at better answering and shedding light upon these fascinating questions related to the chemistry of livings cells.

  1. Quantum Monte Carlo tunneling from quantum chemistry to quantum annealing

    Science.gov (United States)

    Mazzola, Guglielmo; Smelyanskiy, Vadim N.; Troyer, Matthias

    2017-10-01

    Quantum tunneling is ubiquitous across different fields, from quantum chemical reactions and magnetic materials to quantum simulators and quantum computers. While simulating the real-time quantum dynamics of tunneling is infeasible for high-dimensional systems, quantum tunneling also shows up in quantum Monte Carlo (QMC) simulations, which aim to simulate quantum statistics with resources growing only polynomially with the system size. Here we extend the recent results obtained for quantum spin models [Phys. Rev. Lett. 117, 180402 (2016), 10.1103/PhysRevLett.117.180402], and we study continuous-variable models for proton transfer reactions. We demonstrate that QMC simulations efficiently recover the scaling of ground-state tunneling rates due to the existence of an instanton path, which always connects the reactant state with the product. We discuss the implications of our results in the context of quantum chemical reactions and quantum annealing, where quantum tunneling is expected to be a valuable resource for solving combinatorial optimization problems.

  2. Are Biology and Chemistry Out of Order?

    Science.gov (United States)

    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)

  3. Biomolecular Sciences: uniting Biology and Chemistry

    NARCIS (Netherlands)

    Vrieling, Engel

    2017-01-01

    Biomolecular Sciences: uniting Biology and Chemistry www.rug.nl/research/gbb The scientific discoveries in biomolecular sciences have benefitted enormously from technological innovations. At the Groningen Biomolecular Science and Biotechnology Institute (GBB) we now sequence a genome in days,

  4. Quantum chemistry in environmental pesticide risk assessment.

    Science.gov (United States)

    Villaverde, Juan J; López-Goti, Carmen; Alcamí, Manuel; Lamsabhi, Al Mokhtar; Alonso-Prados, José L; Sandín-España, Pilar

    2017-11-01

    The scientific community and regulatory bodies worldwide, currently promote the development of non-experimental tests that produce reliable data for pesticide risk assessment. The use of standard quantum chemistry methods could allow the development of tools to perform a first screening of compounds to be considered for the experimental studies, improving the risk assessment. This fact results in a better distribution of resources and in better planning, allowing a more exhaustive study of the pesticides and their metabolic products. The current paper explores the potential of quantum chemistry in modelling toxicity and environmental behaviour of pesticides and their by-products by using electronic descriptors obtained computationally. Quantum chemistry has potential to estimate the physico-chemical properties of pesticides, including certain chemical reaction mechanisms and their degradation pathways, allowing modelling of the environmental behaviour of both pesticides and their by-products. In this sense, theoretical methods can contribute to performing a more focused risk assessment of pesticides used in the market, and may lead to higher quality and safer agricultural products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  5. Faster quantum chemistry simulation on fault-tolerant quantum computers

    International Nuclear Information System (INIS)

    Cody Jones, N; McMahon, Peter L; Yamamoto, Yoshihisa; Whitfield, James D; Yung, Man-Hong; Aspuru-Guzik, Alán; Van Meter, Rodney

    2012-01-01

    Quantum computers can in principle simulate quantum physics exponentially faster than their classical counterparts, but some technical hurdles remain. We propose methods which substantially improve the performance of a particular form of simulation, ab initio quantum chemistry, on fault-tolerant quantum computers; these methods generalize readily to other quantum simulation problems. Quantum teleportation plays a key role in these improvements and is used extensively as a computing resource. To improve execution time, we examine techniques for constructing arbitrary gates which perform substantially faster than circuits based on the conventional Solovay–Kitaev algorithm (Dawson and Nielsen 2006 Quantum Inform. Comput. 6 81). For a given approximation error ϵ, arbitrary single-qubit gates can be produced fault-tolerantly and using a restricted set of gates in time which is O(log ϵ) or O(log log ϵ); with sufficient parallel preparation of ancillas, constant average depth is possible using a method we call programmable ancilla rotations. Moreover, we construct and analyze efficient implementations of first- and second-quantized simulation algorithms using the fault-tolerant arbitrary gates and other techniques, such as implementing various subroutines in constant time. A specific example we analyze is the ground-state energy calculation for lithium hydride. (paper)

  6. Chemistry and biology by new multiple choice

    International Nuclear Information System (INIS)

    Seo, Hyeong Seok; Kim, Seong Hwan

    2003-02-01

    This book is divided into two parts, the first part is about chemistry, which deals with science of material, atom structure and periodic law, chemical combination and power between molecule, state of material and solution, chemical reaction and an organic compound. The second part give description of biology with molecule and cell, energy in cells and chemical synthesis, molecular biology and heredity, function on animal, function on plant and evolution and ecology. This book has explanation of chemistry and biology with new multiple choice.

  7. Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulations.

    Science.gov (United States)

    Boggio-Pasqua, Martial; Burmeister, Carl F; Robb, Michael A; Groenhof, Gerrit

    2012-06-14

    Organisms have evolved a wide variety of mechanisms to utilize and respond to light. In many cases, the biological response is mediated by structural changes that follow photon absorption in a protein complex. The initial step in such cases is normally the photoisomerization of a highly conjugated prosthetic group. To understand better the factors controlling the isomerization, we perform atomistic molecular dynamics simulations. In this perspective article we briefly review the key theoretical concepts of photochemical reactions and present a practical simulation scheme for simulating photochemical reactions in biomolecular systems. In our scheme, a multi-configurational quantum mechanical description is used to model the electronic rearrangement for those parts of the system that are involved in the photon absorption. For the remainder, typically consisting of the apo-protein and the solvent, a simple force field model is used. The interactions in the systems are thus computed within a hybrid quantum/classical framework. Forces are calculated on-the-fly, and a diabatic surface hopping procedure is used to model the excited-state decay. To demonstrate how this method is used we review our studies on photoactivation of the photoactive yellow protein, a bacterial photoreceptor. We will show what information can be obtained from the simulations, and, by comparing to recent experimental findings, what the limitations of our simulations are.

  8. Per-Olov Löwdin - father of quantum chemistry

    Science.gov (United States)

    Brändas, Erkki J.

    2017-09-01

    During 2016, we celebrate the 100th anniversary of the birth of Per-Olov Löwdin. He was appointed to the first Lehrstuhl in quantum chemistry at Uppsala University in 1960. Löwdin introduced quantum chemistry as a field in its own right by formulating its goals, establishing fundamental concepts, like the correlation energy, the method of configuration interaction, reduced density matrices, natural spin orbitals, charge and bond order matrices, symmetric orthogonalisation, and generalised self-consistent fields. His exposition of partitioning technique and perturbation theory, wave and reaction operators and associated non-linear summation techniques, introduced mathematical rigour and deductive order in the interpretative organisation of the new field. He brought the first computer to Uppsala University and pioneered the initiation of 'electronic brains' and anticipated their significance for quantum chemistry. Perhaps his single most influential contribution to the field was his education of two generations of future faculty in quantum chemistry through Summer Schools in the Scandinavian Mountains, Winter Institutes at Sanibel Island in the Gulf of Mexico. Per-Olov Löwdin founded the book series Advances in Quantum Chemistry and the International Journal of Quantum Chemistry. The evolution of quantum chemistry is appraised, starting from a collection of cross-disciplinary applications of quantum mechanics to the technologically advanced and predominant field of today, virtually used in all branches of chemistry. The scientific work of Per-Olov Löwdin has been crucial for the development of this new important province of science.

  9. Alternative algebraic approaches in quantum chemistry

    International Nuclear Information System (INIS)

    Mezey, Paul G.

    2015-01-01

    Various algebraic approaches of quantum chemistry all follow a common principle: the fundamental properties and interrelations providing the most essential features of a quantum chemical representation of a molecule or a chemical process, such as a reaction, can always be described by algebraic methods. Whereas such algebraic methods often provide precise, even numerical answers, nevertheless their main role is to give a framework that can be elaborated and converted into computational methods by involving alternative mathematical techniques, subject to the constraints and directions provided by algebra. In general, algebra describes sets of interrelations, often phrased in terms of algebraic operations, without much concern with the actual entities exhibiting these interrelations. However, in many instances, the very realizations of two, seemingly unrelated algebraic structures by actual quantum chemical entities or properties play additional roles, and unexpected connections between different algebraic structures are often giving new insight. Here we shall be concerned with two alternative algebraic structures: the fundamental group of reaction mechanisms, based on the energy-dependent topology of potential energy surfaces, and the interrelations among point symmetry groups for various distorted nuclear arrangements of molecules. These two, distinct algebraic structures provide interesting interrelations, which can be exploited in actual studies of molecular conformational and reaction processes. Two relevant theorems will be discussed

  10. Alternative algebraic approaches in quantum chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Mezey, Paul G., E-mail: paul.mezey@gmail.com [Canada Research Chair in Scientific Modeling and Simulation, Department of Chemistry and Department of Physics and Physical Oceanography, Memorial University of Newfoundland, 283 Prince Philip Drive, St. John' s, NL A1B 3X7 (Canada)

    2015-01-22

    Various algebraic approaches of quantum chemistry all follow a common principle: the fundamental properties and interrelations providing the most essential features of a quantum chemical representation of a molecule or a chemical process, such as a reaction, can always be described by algebraic methods. Whereas such algebraic methods often provide precise, even numerical answers, nevertheless their main role is to give a framework that can be elaborated and converted into computational methods by involving alternative mathematical techniques, subject to the constraints and directions provided by algebra. In general, algebra describes sets of interrelations, often phrased in terms of algebraic operations, without much concern with the actual entities exhibiting these interrelations. However, in many instances, the very realizations of two, seemingly unrelated algebraic structures by actual quantum chemical entities or properties play additional roles, and unexpected connections between different algebraic structures are often giving new insight. Here we shall be concerned with two alternative algebraic structures: the fundamental group of reaction mechanisms, based on the energy-dependent topology of potential energy surfaces, and the interrelations among point symmetry groups for various distorted nuclear arrangements of molecules. These two, distinct algebraic structures provide interesting interrelations, which can be exploited in actual studies of molecular conformational and reaction processes. Two relevant theorems will be discussed.

  11. Disciplines, models, and computers: the path to computational quantum chemistry.

    Science.gov (United States)

    Lenhard, Johannes

    2014-12-01

    Many disciplines and scientific fields have undergone a computational turn in the past several decades. This paper analyzes this sort of turn by investigating the case of computational quantum chemistry. The main claim is that the transformation from quantum to computational quantum chemistry involved changes in three dimensions. First, on the side of instrumentation, small computers and a networked infrastructure took over the lead from centralized mainframe architecture. Second, a new conception of computational modeling became feasible and assumed a crucial role. And third, the field of computa- tional quantum chemistry became organized in a market-like fashion and this market is much bigger than the number of quantum theory experts. These claims will be substantiated by an investigation of the so-called density functional theory (DFT), the arguably pivotal theory in the turn to computational quantum chemistry around 1990.

  12. Ab initio quantum chemistry for combustion

    International Nuclear Information System (INIS)

    Page, M.; Lengsfield, B.H.

    1991-01-01

    Advances in theoretical and computational methods, coupled with the rapid development of powerful and inexpensive computers, fuel the current rapid development in computational quantum chemistry (QC). Nowhere is this more evident than in the areas of QC most relevant to combustion: the description of bond breaking and rate phenomena. although the development of faster computers with larger memories has had a major impact on the scope of problems that can be addressed with QC, the development of new theoretical techniques and capabilities is responsible for adding new dimensions in QC and has paved the way for the unification of QC electronic structure calculations with statistical and dynamical models of chemical reactions. These advances will be stressed in this chapter. This paper describes past accomplishments selectively to set the stage for discussion of ideas or techniques that we believe will have significant impact on combustion research. Thus, the focus of the chapter is as much on the future as it is on the past

  13. Quantum chemistry-assisted synthesis route development

    International Nuclear Information System (INIS)

    Hori, Kenji; Sumimoto, Michinori; Murafuji, Toshihiro

    2015-01-01

    We have been investigating “quantum chemistry-assisted synthesis route development” using in silico screenings and applied the method to several targets. Another example was conducted to develop synthesis routes for a urea derivative, namely 1-(4-(trifluoromethyl)-2-oxo-2H-chromen-7-yl)urea. While five synthesis routes were examined, only three routes passed the second in silico screening. Among them, the reaction of 7-amino-4-(trifluoromethyl)-2H-chromen-2-one and O-methyl carbamate with BF 3 as an additive was ranked as the first choice for synthetic work. We were able to experimentally obtain the target compound even though its yield was as low as 21 %. The theoretical result was thus consistent with that observed. The summary of transition state data base (TSDB) is also provided. TSDB is the key to reducing time of in silico screenings

  14. Consciousness, biology and quantum hypotheses.

    Science.gov (United States)

    Baars, Bernard J; Edelman, David B

    2012-09-01

    Natural phenomena are reducible to quantum events in principle, but quantum mechanics does not always provide the best level of analysis. The many-body problem, chaotic avalanches, materials properties, biological organisms, and weather systems are better addressed at higher levels. Animals are highly organized, goal-directed, adaptive, selectionist, information-preserving, functionally redundant, multicellular, quasi-autonomous, highly mobile, reproducing, dissipative systems that conserve many fundamental features over remarkably long periods of time at the species level. Animal brains consist of massive, layered networks of specialized signaling cells with 10,000 communication points per cell, and interacting up to 1000 Hz. Neurons begin to divide and differentiate very early in gestation, and continue to develop until middle age. Waking brains operate far from thermodynamic equilibrium under delicate homeostatic control, making them extremely sensitive to a range of physical and chemical stimuli, highly adaptive, and able to produce a remarkable range of goal-relevant actions. Consciousness is "a difference that makes a difference" at the level of massive neuronal interactions in the most parallel-interactive anatomical structure of the mammalian brain, the cortico-thalamic (C-T) system. Other brain structures are not established to result in direct conscious experiences, at least in humans. However, indirect extra-cortical influences on the C-T system are pervasive. Learning, brain plasticity and major life adaptations may require conscious cognition. While brains evolved over hundreds of millions of years, and individual brains grow over months, years and decades, conscious events appear to have a duty cycle of ∼100 ms, fading after a few seconds. They can of course be refreshed by inner rehearsal, re-visualization, or attending to recurrent stimulus sources. These very distinctive brain events are needed when animals seek out and cope with new

  15. Consciousness, biology and quantum hypotheses

    Science.gov (United States)

    Baars, Bernard J.; Edelman, David B.

    2012-09-01

    Natural phenomena are reducible to quantum events in principle, but quantum mechanics does not always provide the best level of analysis. The many-body problem, chaotic avalanches, materials properties, biological organisms, and weather systems are better addressed at higher levels. Animals are highly organized, goal-directed, adaptive, selectionist, information-preserving, functionally redundant, multicellular, quasi-autonomous, highly mobile, reproducing, dissipative systems that conserve many fundamental features over remarkably long periods of time at the species level. Animal brains consist of massive, layered networks of specialized signaling cells with 10,000 communication points per cell, and interacting up to 1000 Hz. Neurons begin to divide and differentiate very early in gestation, and continue to develop until middle age. Waking brains operate far from thermodynamic equilibrium under delicate homeostatic control, making them extremely sensitive to a range of physical and chemical stimuli, highly adaptive, and able to produce a remarkable range of goal-relevant actions. Consciousness is “a difference that makes a difference” at the level of massive neuronal interactions in the most parallel-interactive anatomical structure of the mammalian brain, the cortico-thalamic (C-T) system. Other brain structures are not established to result in direct conscious experiences, at least in humans. However, indirect extra-cortical influences on the C-T system are pervasive. Learning, brain plasticity and major life adaptations may require conscious cognition. While brains evolved over hundreds of millions of years, and individual brains grow over months, years and decades, conscious events appear to have a duty cycle of ∼100 ms, fading after a few seconds. They can of course be refreshed by inner rehearsal, re-visualization, or attending to recurrent stimulus sources. These very distinctive brain events are needed when animals seek out and cope with new

  16. Charge Migration in DNA Perspectives from Physics, Chemistry, and Biology

    CERN Document Server

    Chakraborty, Tapash

    2007-01-01

    Charge migration through DNA has been the focus of considerable interest in recent years. A deeper understanding of the nature of charge transfer and transport along the double helix is important in fields as diverse as physics, chemistry and nanotechnology. It has also important implications in biology, in particular in DNA damage and repair. This book presents contributions from an international team of researchers active in this field. It contains a wide range of topics that includes the mathematical background of the quantum processes involved, the role of charge transfer in DNA radiation damage, a new approach to DNA sequencing, DNA photonics, and many others. This book should be of value to researchers in condensed matter physics, chemical physics, physical chemistry, and nanoscale sciences.

  17. From transistor to trapped-ion computers for quantum chemistry.

    Science.gov (United States)

    Yung, M-H; Casanova, J; Mezzacapo, A; McClean, J; Lamata, L; Aspuru-Guzik, A; Solano, E

    2014-01-07

    Over the last few decades, quantum chemistry has progressed through the development of computational methods based on modern digital computers. However, these methods can hardly fulfill the exponentially-growing resource requirements when applied to large quantum systems. As pointed out by Feynman, this restriction is intrinsic to all computational models based on classical physics. Recently, the rapid advancement of trapped-ion technologies has opened new possibilities for quantum control and quantum simulations. Here, we present an efficient toolkit that exploits both the internal and motional degrees of freedom of trapped ions for solving problems in quantum chemistry, including molecular electronic structure, molecular dynamics, and vibronic coupling. We focus on applications that go beyond the capacity of classical computers, but may be realizable on state-of-the-art trapped-ion systems. These results allow us to envision a new paradigm of quantum chemistry that shifts from the current transistor to a near-future trapped-ion-based technology.

  18. Virtually going green: The role of quantum computational chemistry in reducing pollution and toxicity in chemistry

    Science.gov (United States)

    Stevens, Jonathan

    2017-07-01

    Continuing advances in computational chemistry has permitted quantum mechanical calculation to assist in research in green chemistry and to contribute to the greening of chemical practice. Presented here are recent examples illustrating the contribution of computational quantum chemistry to green chemistry, including the possibility of using computation as a green alternative to experiments, but also illustrating contributions to greener catalysis and the search for greener solvents. Examples of applications of computation to ambitious projects for green synthetic chemistry using carbon dioxide are also presented.

  19. Quantum mechanical simulation methods for studying biological systems

    International Nuclear Information System (INIS)

    Bicout, D.; Field, M.

    1996-01-01

    Most known biological mechanisms can be explained using fundamental laws of physics and chemistry and a full understanding of biological processes requires a multidisciplinary approach in which all the tools of biology, chemistry and physics are employed. An area of research becoming increasingly important is the theoretical study of biological macromolecules where numerical experimentation plays a double role of establishing a link between theoretical models and predictions and allowing a quantitative comparison between experiments and models. This workshop brought researchers working on different aspects of the development and application of quantum mechanical simulation together, assessed the state-of-the-art in the field and highlighted directions for future research. Fourteen lectures (theoretical courses and specialized seminars) deal with following themes: 1) quantum mechanical calculations of large systems, 2) ab initio molecular dynamics where the calculation of the wavefunction and hence the energy and forces on the atoms for a system at a single nuclear configuration are combined with classical molecular dynamics algorithms in order to perform simulations which use a quantum mechanical potential energy surface, 3) quantum dynamical simulations, electron and proton transfer processes in proteins and in solutions and finally, 4) free seminars that helped to enlarge the scope of the workshop. (N.T.)

  20. The case for biological quantum computer elements

    Science.gov (United States)

    Baer, Wolfgang; Pizzi, Rita

    2009-05-01

    An extension to vonNeumann's analysis of quantum theory suggests self-measurement is a fundamental process of Nature. By mapping the quantum computer to the brain architecture we will argue that the cognitive experience results from a measurement of a quantum memory maintained by biological entities. The insight provided by this mapping suggests quantum effects are not restricted to small atomic and nuclear phenomena but are an integral part of our own cognitive experience and further that the architecture of a quantum computer system parallels that of a conscious brain. We will then review the suggestions for biological quantum elements in basic neural structures and address the de-coherence objection by arguing for a self- measurement event model of Nature. We will argue that to first order approximation the universe is composed of isolated self-measurement events which guaranties coherence. Controlled de-coherence is treated as the input/output interactions between quantum elements of a quantum computer and the quantum memory maintained by biological entities cognizant of the quantum calculation results. Lastly we will present stem-cell based neuron experiments conducted by one of us with the aim of demonstrating the occurrence of quantum effects in living neural networks and discuss future research projects intended to reach this objective.

  1. Genus Pouteria: chemistry and biological activity

    Directory of Open Access Journals (Sweden)

    Cíntia A. M. Silva

    Full Text Available The genus Pouteria belongs to the family Sapotaceae and can be widely found around the World. These plants have been used as building material, as food, because the eatable fruits, as well as remedies in folk medicine. Some biological activities have been reported to species of this genus such as antioxidant, anti-inflammatory, antibacterial and antifungal. However, the real potential of this genus as source of new drugs or phytomedicines remains unknown. Therefore, a review of the so far known chemical composition and biological activities of this genus is presented to stimulate new studies about the species already reported moreover that species have no reference about chemistry or biological activities could be found until now.

  2. Practical approaches to biological inorganic chemistry

    CERN Document Server

    Louro, Ricardo O

    2012-01-01

    The book reviews the use of spectroscopic and related methods to investigate the complex structures and mechanisms of biological inorganic systems that contain metals. Each chapter presents an overview of the technique including relevant theory, clearly explains what it is and how it works and then presents how the technique is actually used to evaluate biological structures. Practical examples and problems are included to illustrate each technique and to aid understanding. Designed for students and researchers who want to learn both the basics, and more advanced aspects of bioinorganic chemistry. It includes many colour illustrations enable easier visualization of molecular mechanisms and structures. It provides worked examples and problems that are included to illustrate and test the reader's understanding of each technique. It is written by a multi-author team who use and teach the most important techniques used today to analyse complex biological structures.

  3. Solutions to selected exercise problems in quantum chemistry and spectroscopy

    DEFF Research Database (Denmark)

    Spanget-Larsen, Jens

    2016-01-01

    Suggested solutions to a number of problems from the collection "Exercise Problems in Quantum Chemistry and Spectroscopy", previously published on ResearchGate (DOI: 10.13140/RG.2.1.4024.8162).......Suggested solutions to a number of problems from the collection "Exercise Problems in Quantum Chemistry and Spectroscopy", previously published on ResearchGate (DOI: 10.13140/RG.2.1.4024.8162)....

  4. Russian science readings (chemistry, physics, biology)

    CERN Document Server

    Light, L

    1949-01-01

    Some years' experience in teaching Russian to working scientists who had already acquired the rudiments of the grammar convinced me of the need for a reader of the present type that would smooth the path of those wishing to study Russian scientific literature in the original. Although the subject matter comprises what I have described for convenience as chemistry, physics and biology, it could be read with equal profit by those engaged in any branch of pure or applied science. All the passages are taken from school textbooks, and acknowledgements are due to the authors of the works listed at the foot of the contents page.

  5. Chemistry and biology of insect bioluminescence

    International Nuclear Information System (INIS)

    Colepicolo Neto, P.; Bechara, E.J.H.

    1984-01-01

    Basic aspects on the Chemistry and Biology of bioluminescence are reviewed, with emphasis on insects. Data from the investigation of Lampyridae (fireflies) are collected from literature. With regard to Elateridae (click beetles) and Phengodidae (rail road worms), the least explored families of luminescent insects, new data are presented on the following aspects: (i) 'in vivo' emission spectra, (ii) chemical nature of the luciferin, (iii) conection between bioluminescence and 'oxygen toxicity' as a result of molecular oxygen storage and (iv) the role of light emission by larvae and pupae. (Author) [pt

  6. Radiation chemistry in development and research of radiation biology

    International Nuclear Information System (INIS)

    Min Rui

    2010-01-01

    During the establishment and development of radiation biology, radiation chemistry acts like bridge which units the spatial and temporal insight coming from radiation physics with radiation biology. The theory, model, and methodology of radiation chemistry play an important role in promoting research and development of radiation biology. Following research development of radiation biology effects towards systems radiation biology the illustration and exploration both diversity of biological responses and complex process of biological effect occurring remain to need the theory, model, and methodology come from radiation chemistry. (authors)

  7. Human development VIII: a theory of "deep" quantum chemistry and cell consciousness: quantum chemistry controls genes and biochemistry to give cells and higher organisms consciousness and complex behavior.

    Science.gov (United States)

    Ventegodt, Søren; Hermansen, Tyge Dahl; Flensborg-Madsen, Trine; Nielsen, Maj Lyck; Merrick, Joav

    2006-11-14

    Deep quantum chemistry is a theory of deeply structured quantum fields carrying the biological information of the cell, making it able to remember, intend, represent the inner and outer world for comparison, understand what it "sees", and make choices on its structure, form, behavior and division. We suggest that deep quantum chemistry gives the cell consciousness and all the qualities and abilities related to consciousness. We use geometric symbolism, which is a pre-mathematical and philosophical approach to problems that cannot yet be handled mathematically. Using Occam's razor we have started with the simplest model that works; we presume this to be a many-dimensional, spiral fractal. We suggest that all the electrons of the large biological molecules' orbitals make one huge "cell-orbital", which is structured according to the spiral fractal nature of quantum fields. Consciousness of single cells, multi cellular structures as e.g. organs, multi-cellular organisms and multi-individual colonies (like ants) and human societies can thus be explained by deep quantum chemistry. When biochemical activity is strictly controlled by the quantum-mechanical super-orbital of the cell, this orbital can deliver energetic quanta as biological information, distributed through many fractal levels of the cell to guide form and behavior of an individual single or a multi-cellular organism. The top level of information is the consciousness of the cell or organism, which controls all the biochemical processes. By this speculative work inspired by Penrose and Hameroff we hope to inspire other researchers to formulate more strict and mathematically correct hypothesis on the complex and coherence nature of matter, life and consciousness.

  8. From quantum measurement to biology via retrocausality.

    Science.gov (United States)

    Matsuno, Koichiro

    2017-12-01

    A reaction cycle in general or a metabolic cycle in particular owes its evolutionary emergence to the covering reaction environment acting as a measurement apparatus of a natural origin. The quantum measurement of the environmental origin underlying the molecular processes observed in the biological realm is operative cohesively between the measuring and the measured. The measuring part comes to pull in a quantum as an indivisible lump available from an arbitrary material body to be measured. The inevitable difference between the impinging quantum upon the receiving end on the part of the environment and the actual quantum pulled into the receiving end comes to effectively be nullified through the retrocausative propagation of the corresponding wave function proceeding backwards in time. The retrocausal regulation applied to the interface between the measuring and the measured is to function as the organizational agency supporting biology, and is sought in the act for the present in the immediate future within the realm of quantum phenomena. Molecular dynamics in biology owes both the evolutionary buildup and maintenance of its organization to the retrocausal operation of the unitary transformation applied to quantum phenomena proceeding backwards in time. Quantum measurement provides the cohesive agency that is pivotal for implementing the retrocausal regulation. In particular, the physical origin of Darwinian natural selection can be seen in the retrocausal regulation applied to the unitary transformation of a quantum origin. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Biocompatible Quantum Dots for Biological Applications

    Science.gov (United States)

    Rosenthal, Sandra J.; Chang, Jerry C.; Kovtun, Oleg; McBride, James R.; Tomlinson, Ian D.

    2011-01-01

    Semiconductor quantum dots are quickly becoming a critical diagnostic tool for discerning cellular function at the molecular level. Their high brightness, long-lasting, sizetunable, and narrow luminescence set them apart from conventional fluorescence dyes. Quantum dots are being developed for a variety of biologically oriented applications, including fluorescent assays for drug discovery, disease detection, single protein tracking, and intracellular reporting. This review introduces the science behind quantum dots and describes how they are made biologically compatible. Several applications are also included, illustrating strategies toward target specificity, and are followed by a discussion on the limitations of quantum dot approaches. The article is concluded with a look at the future direction of quantum dots. PMID:21276935

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

    Science.gov (United States)

    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.

  12. Nonlinear Oscillations in Biology and Chemistry

    CERN Document Server

    1986-01-01

    This volume contains the proceedings of a meeting entitled 'Nonlinear Oscillations in Biology and Chemistry', which was held at the University of Utah May 9-11,1985. The papers fall into four major categories: (i) those that deal with biological problems, particularly problems arising in cell biology, (ii) those that deal with chemical systems, (iii) those that treat problems which arise in neurophysiology, and (iv), those whose primary emphasis is on more general models and the mathematical techniques involved in their analysis. Except for the paper by Auchmuty, all are based on talks given at the meeting. The diversity of papers gives some indication of the scope of the meeting, but the printed word conveys neither the degree of interaction between the participants nor the intellectual sparks generated by that interaction. The meeting was made possible by the financial support of the Department of Mathe­ matics of the University of Utah. I am indebted to Ms. Toni Bunker of the Department of Mathematics for...

  13. Quantum biological gravitational wave detectors

    International Nuclear Information System (INIS)

    Kopvillem, U.Kh.

    1985-01-01

    A possibility of producing biological detectors of gravitational waves is considered. High sensitivity of biological systems to outer effects can be ensured by existence of molecule subgroups in Dicke states. Existence of clusters in Dicke state-giant electric dipoles (GED) is supposed in the Froehlich theory. Comparison of biological and physical detectors shows that GED systems have unique properties for detection of gravitational waves if the reception range is narrow

  14. Quantum mechanics a comprehensive text for chemistry

    CERN Document Server

    Arora, Kishor

    2010-01-01

    This book contains 14 chapters. The text includes the inadequacy of classical mechanics and covers basic and fundamental concepts of quantum mechanics including concepts of transitional, vibration rotation and electronic energies, introduction to concepts of angular momenta, approximatemethods and their application concepts related to electron spin, symmetery concepts and quantum mechanics and ultimately the book features the theories of chemical bonding and use of softwares in quantum mechanics. the text of the book is presented in a lucid manner with ample examples and illustrations wherever

  15. Principles of conjugating quantum dots to proteins via carbodiimide chemistry

    International Nuclear Information System (INIS)

    Song Fayi; Chan, Warren C W

    2011-01-01

    The covalent coupling of nanomaterials to bio-recognition molecules is a critical intermediate step in using nanomaterials for biology and medicine. Here we investigate the carbodiimide-mediated conjugation of fluorescent quantum dots to different proteins (e.g., immunoglobulin G, bovine serum albumin, and horseradish peroxidase). To enable these studies, we developed a simple method to isolate quantum dot bioconjugates from unconjugated quantum dots. The results show that the reactant concentrations and protein type will impact the overall number of proteins conjugated onto the surfaces of the quantum dots, homogeneity of the protein–quantum dot conjugate population, quantum efficiency, binding avidity, and enzymatic kinetics. We propose general principles that should be followed for the successful coupling of proteins to quantum dots.

  16. Quantum information and computation for chemistry

    CERN Document Server

    Kais, Sabre; Rice, Stuart A

    2014-01-01

    Examines the intersection of quantum information and chemical physics The Advances in Chemical Physics series is dedicated to reviewing new and emerging topics as well as the latest developments in traditional areas of study in the field of chemical physics. Each volume features detailed comprehensive analyses coupled with individual points of view that integrate the many disciplines of science that are needed for a full understanding of chemical physics. This volume of the series explores the latest research findings, applications, and new research paths from the quantum information science

  17. Quantum Chemistry; A concise introduction for students of physics, chemistry, biochemistry and materials science

    Science.gov (United States)

    Thakkar, Ajit J.

    2017-09-01

    This book provides non-specialists with a basic understanding of the underlying concepts of quantum chemistry. It is both a text for second- or third-year undergraduates and a reference for researchers who need a quick introduction or refresher. All chemists and many biochemists, materials scientists, engineers, and physicists routinely use spectroscopic measurements and electronic structure computations in their work. The emphasis of Quantum Chemistry on explaining ideas rather than enumerating facts or presenting procedural details makes this an excellent foundation text/reference.

  18. Medicinal plants from Mali: Chemistry and biology.

    Science.gov (United States)

    Wangensteen, Helle; Diallo, Drissa; Paulsen, Berit Smestad

    2015-12-24

    Mali is one of the countries in West Africa where the health system rely the most on traditional medicine. The healers are mainly using medicinal plants for their treatments. The studies performed being the basis for this review is of importance as they will contribute to sustaining the traditional knowledge. They contribute to evaluate and improve locally produced herbal remedies, and the review gives also an overview of the plant preparations that will have the most potential to be evaluated for new Improved Traditional Medicines. The aim of this review is to give an overview of the studies performed related to medicinal plants from Mali in the period 1995-2015. These studies include ethnopharmacology, chemistry and biological studies of the plants that were chosen based on our interviews with the healers in different regions of Mali, and contribute to sustainable knowledge on the medicinal plants. The Department of Traditional Medicine, Bamako, Mali, is responsible for registering the knowledge of the traditional healers on their use of medicinal plants and also identifying compounds in the plants responsible for the bioactivities claimed. The studies reported aimed at getting information from the healers on the use of medicinal plants, and study the biology and chemistry of selected plants for the purpose of verifying the traditional use of the plants. These studies should form the basis for necessary knowledge for the development of registered Improved Traditional Medicines in Mali. The healers were the ethnopharmacological informants. Questions asked initially were related to wound healing. This was because the immune system is involved when wounds are healed, and additionally the immune system is involved in the majority of the illnesses common in Mali. Based on the results of the interviews the plant material for studies was selected. Studies were performed on the plant parts the healers were using when treating their patients. Conventional chromatographic

  19. Optimizing qubit resources for quantum chemistry simulations in second quantization on a quantum computer

    International Nuclear Information System (INIS)

    Moll, Nikolaj; Fuhrer, Andreas; Staar, Peter; Tavernelli, Ivano

    2016-01-01

    Quantum chemistry simulations on a quantum computer suffer from the overhead needed for encoding the Fermionic problem in a system of qubits. By exploiting the block diagonality of a Fermionic Hamiltonian, we show that the number of required qubits can be reduced while the number of terms in the Hamiltonian will increase. All operations for this reduction can be performed in operator space. The scheme is conceived as a pre-computational step that would be performed prior to the actual quantum simulation. We apply this scheme to reduce the number of qubits necessary to simulate both the Hamiltonian of the two-site Fermi–Hubbard model and the hydrogen molecule. Both quantum systems can then be simulated with a two-qubit quantum computer. Despite the increase in the number of Hamiltonian terms, the scheme still remains a useful tool to reduce the dimensionality of specific quantum systems for quantum simulators with a limited number of resources. (paper)

  20. Electron Transfer in Chemistry and Biology - The Primary Events in ...

    Indian Academy of Sciences (India)

    transfers, occurs in a cascade in many biological processes, including photosynthesis. ... the model reactions of photosynthetic ... biological relevance. GENERAL I ARTICLE of electrons, respectively. This has entirely changed the earlier framework of interpreting reactions in chemistry and biology. This shift in emphasis ...

  1. Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

    Science.gov (United States)

    Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

    2014-03-11

    While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

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

    Science.gov (United States)

    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

  3. AINSE conference on radiation biology and chemistry. Conference handbook

    International Nuclear Information System (INIS)

    1994-01-01

    The conference handbook contains 60 oral and poster presentations dealing with recent advances in radiation chemistry applied to biological studies, radiopharmaceuticals, radiosensitizers as well as to solid state chemical physics

  4. AINSE conference on radiation biology and chemistry. Conference handbook

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    The conference handbook contains 60 oral and poster presentations dealing with recent advances in radiation chemistry applied to biological studies, radiopharmaceuticals, radiosensitizers as well as to solid state chemical physics.

  5. Scents and sensibility: how biology perceives chemistry

    Directory of Open Access Journals (Sweden)

    Stuart Firestein

    2014-07-01

    odor can be detected by several receptors and any given receptor can bind any of several presumably related odors. In our analogy, the keys fit very loosely to differing degrees into many locks. Chemists are particularly interested in those parts of a molecule that are likely to participate in various sorts of reactions and synthetic manipulations. These would include such things as the functional group (aldehyde, acid, ester, etc. or if there are double bonds or charge carrying atoms. However, what is relevant to the synthetic chemist may not be important to the biological system, and in particular to the odor receptor protein. Thus we should begin by taking a biological approach to odor chemistry. For example the definition of an odorant cannot be made chemically – many chemical compounds that appear nearly identical to a known odorant may have a different smell or none at all. The only definition of an odorant is that it binds to an odor receptor to give rise to a biological response. Precisely what parts of a chemical compound influence that binding is one of the most challenging questions in biology. The actual perception of an odorant depends on the particular combination of receptors that are activated. In a complex mixture of tens to hundreds of different odor molecules this can quickly become a very complicated matrix of activated receptors with an astronomical number of combinations. An open question is whether evolution has perhaps found a simplified way of performing this apparently incalculable task. One possible solution would be the existence of a few dozen common chemical structures that would serve as primary features from which all other odors are constructed. This would be similar to the way the visual system can perceive thousands of hues of light by combining only three (blue, green and red primary “colors” or wavelengths. Although the idea of primaries in olfaction has been discussed for several decades it was largely abandoned after the

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

    Science.gov (United States)

    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.

  7. Quantum Chemistry of Solids LCAO Treatment of Crystals and Nanostructures

    CERN Document Server

    Evarestov, Robert A

    2012-01-01

    Quantum Chemistry of Solids delivers a comprehensive account of the main features and possibilities of LCAO methods for the first principles calculations of electronic structure of periodic systems. The first part describes the basic theory underlying the LCAO methods  applied to periodic systems and the use of Hartree-Fock(HF), Density Function theory(DFT) and hybrid Hamiltonians. The translation and site symmetry consideration is included to establish connection between k-space solid –state physics and real-space quantum chemistry. The inclusion of electron correlation effects for periodic systems is considered on the basis of localized crystalline orbitals. The possibilities of LCAO methods for chemical bonding analysis in periodic systems are discussed. The second part deals with the applications of LCAO methods  for calculations of bulk crystal properties, including magnetic ordering and crystal structure optimization.  In the second edition two new chapters are added in the application part II of t...

  8. Quantum Chemistry via Walks in Determinant Space

    Energy Technology Data Exchange (ETDEWEB)

    Umrigar, Cyrus J. [Cornell Univ., Ithaca, NY (United States)

    2016-01-05

    There are many chemical questions of practical interest to the DOE that could be answered if there were an electronic structure method that provided consistently accurate results for all systems at an affordable computational cost. The coupled cluster method with single, double and perturbative triple excitations (CCSD(T)) is the most frequently used high-order method, but it has known deficiencies, e.g., in the description of stretched bonds. The full configuration interaction (FCI) method is the most robust method for treating electronic correlations, but it is little used because its computational cost scales exponentially in the size of the system. The largest calculation that has been done to date employed 10 billion determinants. In this regard, there was a major advance in 2010. The Alavi group at Cambridge University developed a stochastic approach to FCI --- combining it with ideas from quantum Monte Carlo (QMC) --- called FCIQMC, that allows one to go to a far larger number of determinants in certain circumstances. The computational cost is exponential in the system and basis size but with a much reduced exponent compared to conventional FCI. In this project Umrigar's group made several major improvements to the FCIQMC method that increased its efficiency by many orders of magnitude. In addition this project resulted in a cross-fertilization of ideas between the FCIQMC method, the older phaseless auxilliary-field quantum Monte Carlo (AFQMC) method developed by Zhang and Krakauer (two of the PI's of this project), and symmetry-restored wavefunctions developed by Scuseria (also a PI of this project).

  9. Radiation chemistry of biologically compatible polymers

    International Nuclear Information System (INIS)

    Hill, D.J. T.; Pomery, P.J.; Saadat, G.; Whittaker, A.K.

    1996-01-01

    Full text: Poly (2-hydroxy ethyl methacrylate) [PHEMA] and poly (2-ethoxy ethyl methacrylate) [PEEMA] are of biomedical and industrial interest due to their biocompatibility with living tissue. In this paper the effect of high energy radiation on these polymers is reported. PHEMA and PEEMA have similar molecular structures to poly (methyl methacrylate)[PMMA], and the γ irradiation of this polymer is well understood. Hence the radiation chemistry of PMMA is used as model system for the the analysis of the radiation chemistry of these polymers. The mechanism of the radiation induced chemistry of the polymers has been investigated using a range of techniques including electron spin resonance spectroscopy (ESR) to establish free radical pathways, GC to identify small molecule volatile products, NMR to identify small molecule radiation products and Gel Permeation Chromatography (GPC) to determine molecular weight changes. Whilst much of the major part of the radiation chemistry can be attributed to similar reactions which can be observed in PMMA, there are a number of new radicals which are present as a result of the influence of the side chain interactions which reduces the mobility of the polymer chain

  10. Quantum mechanics formalism for biological evolution

    International Nuclear Information System (INIS)

    Bianconi, Ginestra; Rahmede, Christoph

    2012-01-01

    Highlights: ► Biological evolution is an off-equilibrium process described by path integrals over phylogenies. ► The phylogenies are sums of linear lineages for asexual populations. ► For sexual populations, each lineage is a tree and the path integral is given by a sum over these trees. ► Quantum statistics describe the stationary state of biological populations in simple cases. - Abstract: We study the evolution of sexual and asexual populations in fitness landscapes compatible with epistatic interactions. We find intriguing relations between the mathematics of biological evolution and quantum mechanics formalism. We give the general structure of the evolution of sexual and asexual populations which is in general an off-equilibrium process that can be expressed by path integrals over phylogenies. These phylogenies are the sum of linear lineages for asexual populations. For sexual populations, instead, each lineage is a tree of branching ratio two and the path integral describing the evolving population is given by a sum over these trees. Finally we show that the Bose–Einstein and the Fermi–Dirac distributions describe the stationary state of biological populations in simple cases.

  11. NWChem: Quantum Chemistry Simulations at Scale

    Energy Technology Data Exchange (ETDEWEB)

    Apra, Edoardo; Kowalski, Karol; Hammond, Jeff R.; Klemm, Michael

    2015-01-17

    Methods based on quantum mechanics equations have been developed since the 1930's with the purpose of accurately studying the electronic structure of molecules. However, it is only during the last two decades that intense development of new computational algorithms has opened the possibility of performing accurate simulations of challenging molecular processes with high-order many-body methods. A wealth of evidence indicates that the proper inclusion of instantaneous interactions between electrons (or the so-called electron correlation effects) is indispensable for the accurate characterization of chemical reactivity, molecular properties, and interactions of light with matter. The availability of reliable methods for benchmarking of medium-size molecular systems provides also a unique chance to propagate high-level accuracy across spatial scales through the multiscale methodologies. Some of these methods have potential to utilize computational resources in an effi*cient way since they are characterized by high numerical complexity and appropriate level of data granularity, which can be effi*ciently distributed over multi-processor architectures. The broad spectrum of coupled cluster (CC) methods falls into this class of methodologies. Several recent CC implementations clearly demonstrated the scalability of CC formalisms on architectures composed of hundreds thousand computational cores. In this context NWChem provides a collection of Tensor Contraction Engine (TCE) generated parallel implementations of various coupled cluster methods capable of taking advantage of many thousand of cores on leadership class parallel architectures.

  12. Quantum selfish gene (biological evolution in terms of quantum mechanics)

    OpenAIRE

    Ozhigov, Yuri I.

    2013-01-01

    I propose to treat the biological evolution of genoms by means of quantum mechanical tools. We start with the concept of meta- gene, which specifies the "selfish gene" of R.Dawkins. Meta- gene encodes the abstract living unity, which can live relatively independently of the others, and can contain a few real creatures. Each population of living creatures we treat as the wave function on meta- genes, which module squared is the total number of creatures with the given meta-gene, and the phase ...

  13. Synthetic biology, inspired by synthetic chemistry.

    Science.gov (United States)

    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. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

    O' Brien, Janese C. [Iowa State Univ., Ames, IA (United States)

    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.

  15. Spiers Memorial Lecture. Quantum chemistry: the first seventy years.

    Science.gov (United States)

    McWeeny, Roy

    2007-01-01

    Present-day theoretical chemistry is rooted in Quantum Mechanics. The aim of the opening lecture is to trace the evolution of Quantum Chemistry from the Heitler-London paper of 1927 up to the end of the last century, emphasizing concepts rather than calculations. The importance of symmetry concepts became evident in the early years: one thinks of the necessary anti-symmetry of the wave function under electron permutations, the Pauli principle, the aufbau scheme, and the classification of spectroscopic states. But for chemists perhaps the key concept is embodied in the Hellmann-Feynman theorem, which provides a pictorial interpretation of chemical bonding in terms of classical electrostatic forces exerted on the nuclei by the electron distribution. Much of the lecture is concerned with various electron distribution functions--the electron density, the current density, the spin density, and other 'property densities'--and with their use in interpreting both molecular structure and molecular properties. Other topics touched upon include Response theory and propagators; Chemical groups in molecules and the group function approach; Atoms in molecules and Bader's theory; Electron correlation and the 'pair function'. Finally, some long-standing controversies, in particular the EPR paradox, are re-examined in the context of molecular dissociation. By admitting the concept of symmetry breaking, along with the use of the von Neumann-Dirac statistical ensemble, orthodox quantum mechanics can lead to a convincing picture of the dissociation mechanism.

  16. Organic chemistry and biology of the interstellar medium

    Science.gov (United States)

    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.

  17. Notions of radiation chemistry in biological systems

    International Nuclear Information System (INIS)

    Mastro, N.L. del.

    1989-10-01

    The present paper examines some aspects of the direct and indirect biological radiation effects: pair formation, free radicals, superoxide ion, hydrogen peroxide, hydroxyl radical, oxygen singlet together with the endogen radioprotector mechanisms of organisms and the ways in which an improved radioresistance of biochemical systems can be achieved. (author) [pt

  18. Application of Quantum Dots in Biological Imaging

    Directory of Open Access Journals (Sweden)

    Shan Jin

    2011-01-01

    Full Text Available Quantum dots (QDs are a group of semiconducting nanomaterials with unique optical and electronic properties. They have distinct advantages over traditional fluorescent organic dyes in chemical and biological studies in terms of tunable emission spectra, signal brightness, photostability, and so forth. Currently, the major type of QDs is the heavy metal-containing II-IV, IV-VI, or III-V QDs. Silicon QDs and conjugated polymer dots have also been developed in order to lower the potential toxicity of the fluorescent probes for biological applications. Aqueous solubility is the common problem for all types of QDs when they are employed in the biological researches, such as in vitro and in vivo imaging. To circumvent this problem, ligand exchange and polymer coating are proven to be effective, besides synthesizing QDs in aqueous solutions directly. However, toxicity is another big concern especially for in vivo studies. Ligand protection and core/shell structure can partly solve this problem. With the rapid development of QDs research, new elements and new morphologies have been introduced to this area to fabricate more safe and efficient QDs for biological applications.

  19. Relativistic quantum chemistry the fundamental theory of molecular science

    CERN Document Server

    Reiher, Markus

    2014-01-01

    Einstein proposed his theory of special relativity in 1905. For a long time it was believed that this theory has no significant impact on chemistry. This view changed in the 1970s when it was realized that (nonrelativistic) Schrödinger quantum mechanics yields results on molecular properties that depart significantly from experimental results. Especially when heavy elements are involved, these quantitative deviations can be so large that qualitative chemical reasoning and understanding is affected. For this to grasp the appropriate many-electron theory has rapidly evolved. Nowadays relativist

  20. Development of massively parallel quantum chemistry program SMASH

    Energy Technology Data Exchange (ETDEWEB)

    Ishimura, Kazuya [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science 38 Nishigo-Naka, Myodaiji, Okazaki, Aichi 444-8585 (Japan)

    2015-12-31

    A massively parallel program for quantum chemistry calculations SMASH was released under the Apache License 2.0 in September 2014. The SMASH program is written in the Fortran90/95 language with MPI and OpenMP standards for parallelization. Frequently used routines, such as one- and two-electron integral calculations, are modularized to make program developments simple. The speed-up of the B3LYP energy calculation for (C{sub 150}H{sub 30}){sub 2} with the cc-pVDZ basis set (4500 basis functions) was 50,499 on 98,304 cores of the K computer.

  1. Development of massively parallel quantum chemistry program SMASH

    International Nuclear Information System (INIS)

    Ishimura, Kazuya

    2015-01-01

    A massively parallel program for quantum chemistry calculations SMASH was released under the Apache License 2.0 in September 2014. The SMASH program is written in the Fortran90/95 language with MPI and OpenMP standards for parallelization. Frequently used routines, such as one- and two-electron integral calculations, are modularized to make program developments simple. The speed-up of the B3LYP energy calculation for (C 150 H 30 ) 2 with the cc-pVDZ basis set (4500 basis functions) was 50,499 on 98,304 cores of the K computer

  2. Marine natural flavonoids: chemistry and biological activities.

    Science.gov (United States)

    Martins, Beatriz T; Correia da Silva, Marta; Pinto, Madalena; Cidade, Honorina; Kijjoa, Anake

    2018-05-04

    As more than 70% of the world's surface is covered by oceans, marine organisms offer a rich and unlimited resource of structurally diverse bioactive compounds. These organisms have developed unique properties and bioactive compounds that are, in majority of them, unparalleled by their terrestrial counterparts due to the different surrounding ecological systems. Marine flavonoids have been extensively studied in the last decades due to a growing interest concerning their promising biological/pharmacological activities. The most common classes of marine flavonoids are flavones and flavonols, which are mostly isolated from marine plants. Although most of flavonoids are hydroxylated and methoxylated, some marine flavonoids possess an unusual substitution pattern, not commonly found in terrestrial organisms, namely the presence of sulphate, chlorine, and amino groups. This review presents, for the first time in a systematic way, the structure, natural occurrence, and biological activities of marine flavonoids.

  3. Molecular knots in biology and chemistry

    International Nuclear Information System (INIS)

    Lim, Nicole C H; Jackson, Sophie E

    2015-01-01

    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. (paper)

  4. Cold molecules: Progress in quantum engineering of chemistry and quantum matter

    Science.gov (United States)

    Bohn, John L.; Rey, Ana Maria; Ye, Jun

    2017-09-01

    Cooling atoms to ultralow temperatures has produced a wealth of opportunities in fundamental physics, precision metrology, and quantum science. The more recent application of sophisticated cooling techniques to molecules, which has been more challenging to implement owing to the complexity of molecular structures, has now opened the door to the longstanding goal of precisely controlling molecular internal and external degrees of freedom and the resulting interaction processes. This line of research can leverage fundamental insights into how molecules interact and evolve to enable the control of reaction chemistry and the design and realization of a range of advanced quantum materials.

  5. Electron Transfer in Chemistry and Biology – The Primary Events

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 12. Electron Transfer in Chemistry and Biology – The Primary Events in Photosynthesis. V Krishnan. General Article Volume 2 Issue 12 December 1997 pp 77-86. Fulltext. Click here to view fulltext PDF. Permanent link:

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

    Science.gov (United States)

    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,…

  7. Synergy between medicinal chemistry and biological research.

    Science.gov (United States)

    Moncada, Salvador; Coaker, Hannah

    2014-09-01

    Salvador Moncada studied medicine at the University of El Salvador (El Salvador) before coming to the UK in 1971 to work on a PhD with Professor John Vane at the Institute of Basic Medical Sciences, Royal College of Surgeons (UK). After a short period of research at the University of Honduras (Honduras), he joined the Wellcome Research Laboratories (UK) where he became Head of the Department of Prostaglandin Research and later, Director of Research. He returned to academic life in 1996 as founder and director of the Wolfson Institute for Biomedical Research at University College London (UK). Moncada played a role in the discovery of the mechanism of action of aspirin-like drugs and later led the teams which discover prostacyclin and identified nitric oxide as a biological mediator. In his role as a Director of Research of the Wellcome Laboratories, he oversaw the discovery and development of medicines for epilepsy, migraine, malaria and cancer. Currently, he is working on the regulation of cell proliferation as Director of the Institute of Cancer Sciences at the University of Manchester (UK). Moncada has won numerous awards from the international scientific community and in 2010, he received a knighthood from Her Majesty Queen Elizabeth II for his services to science.

  8. Areas of research in radiation chemistry fundamental to radiation biology

    International Nuclear Information System (INIS)

    Powers, E.L.

    1980-01-01

    Among all the environmental hazards to which man is exposed, ionizing radiation is the most thoroughly investigated and the most responsibly monitored and controlled. Nevertheless, because of the importance of radiation in modern society from both the hazard as well as the utilitarian standpoints, much more information concerning the biological effects induced and their modification and reversal is required. Together with radiation physics, an understanding of radiation chemistry is necessary for full appreciation of biological effects of high and low energy radiations, and for the development of prophylactic, therapeutic and potentiating methods and techniques in biological organisms. The necessity of understanding the chemistry of any system, biological or not, that is to be manipulated and controlled, is so obvious as to make trivial a statement to that effect. If any natural phenomenon is to be put to our use, surely the elements of it must be studied and appreciated fully. In the preliminary statements of the various panels of this general group, the need for additional information on the basic radiation chemistry concerned in radiation-induced biological effects pervades throughout

  9. Expression of results in quantum chemistry physical chemistry division commission on physicochemical symbols, terminology and units

    CERN Document Server

    Whiffen, D H

    2013-01-01

    Expression of Results in Quantum Chemistry recommends the appropriate insertion of physical constants in the output information of a theoretical paper in order to make the numerical end results of theoretical work easily transformed to SI units by the reader. The acceptance of this recommendation would circumvent the need for a set of atomic units each with its own symbol and name. It is the traditional use of the phrase """"atomic units"""" in this area which has obscured the real problem. The four SI dimensions of length, mass, time, and current require four physical constants to be permitte

  10. PREFACE: Quantum dots as probes in biology

    Science.gov (United States)

    Cieplak, Marek

    2013-05-01

    The recent availability of nanostructured materials has resulted in an explosion of research focused on their unique optical, thermal, mechanical and magnetic properties. Optical imagining, magnetic enhancement of contrast and drug delivery capabilities make the nanoparticles of special interest in biomedical applications. These materials have been involved in the development of theranostics—a new field of medicine that is focused on personalized tests and treatment. It is likely that multimodal nanomaterials will be responsible for future diagnostic advances in medicine. Quantum dots (QD) are nanoparticles which exhibit luminescence either through the formation of three-dimensional excitons or excitations of the impurities. The excitonic luminescence can be tuned by changing the size (the smaller the size, the higher the frequency). QDs are usually made of semiconducting materials. Unlike fluorescent proteins and organic dyes, QDs resist photobleaching, allow for multi-wavelength excitations and have narrow emission spectra. The techniques to make QDs are cheap and surface modifications and functionalizations can be implemented. Importantly, QDs could be synthesized to exhibit useful optomagnetic properties and, upon functionalization with an appropriate biomolecule, directed towards a pre-selected target for diagnostic imaging and photodynamic therapy. This special issue on Quantum dots in Biology is focused on recent research in this area. It starts with a topical review by Sreenivasan et al on various physical mechanisms that lead to the QD luminescence and on using wavelength shifts for an improvement in imaging. The next paper by Szczepaniak et al discusses nanohybrids involving QDs made of CdSe coated by ZnS and combined covalently with a photosynthetic enzyme. These nanohybrids are shown to maintain the enzymatic activity, however the enzyme properties depend on the size of a QD. They are proposed as tools to study photosynthesis in isolated

  11. Joining Forces: The Chemical Biology-Medicinal Chemistry Continuum.

    Science.gov (United States)

    Plowright, Alleyn T; Ottmann, Christian; Arkin, Michelle; Auberson, Yves P; Timmerman, Henk; Waldmann, Herbert

    2017-09-21

    The scientific advances being made across all disciplines are creating ever-increasing opportunities to enhance our knowledge of biological systems and how they relate to human disease. One of the central driving forces in discovering new medicines is medicinal chemistry, where the design and synthesis of novel compounds has led to multiple drugs. Chemical biology, sitting at the interface of many disciplines, has now emerged as a major contributor to the understanding of biological systems and is becoming an integral part of drug discovery. Bringing chemistry and biology much closer and blurring the boundaries between disciplines is creating new opportunities to probe and understand biology; both disciplines play key roles and need to join forces and work together effectively to synergize their impact. The power of chemical biology will then reach its full potential and drive innovation, leading to the discovery of transformative medicines to treat patients. Advances in cancer biology and drug discovery highlight this potential. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Human Development VIII: A Theory of “Deep” Quantum Chemistry and Cell Consciousness: Quantum Chemistry Controls Genes and Biochemistry to Give Cells and Higher Organisms Consciousness and Complex Behavior

    Directory of Open Access Journals (Sweden)

    Søren Ventegodt

    2006-01-01

    Full Text Available Deep quantum chemistry is a theory of deeply structured quantum fields carrying the biological information of the cell, making it able to remember, intend, represent the inner and outer world for comparison, understand what it “sees”, and make choices on its structure, form, behavior and division. We suggest that deep quantum chemistry gives the cell consciousness and all the qualities and abilities related to consciousness. We use geometric symbolism, which is a pre-mathematical and philosophical approach to problems that cannot yet be handled mathematically. Using Occam’s razor we have started with the simplest model that works; we presume this to be a many-dimensional, spiral fractal. We suggest that all the electrons of the large biological molecules’ orbitals make one huge “cell-orbital”, which is structured according to the spiral fractal nature of quantum fields. Consciousness of single cells, multi cellular structures as e.g. organs, multi-cellular organisms and multi-individual colonies (like ants and human societies can thus be explained by deep quantum chemistry. When biochemical activity is strictly controlled by the quantum-mechanical super-orbital of the cell, this orbital can deliver energetic quanta as biological information, distributed through many fractal levels of the cell to guide form and behavior of an individual single or a multi-cellular organism. The top level of information is the consciousness of the cell or organism, which controls all the biochemical processes. By this speculative work inspired by Penrose and Hameroff we hope to inspire other researchers to formulate more strict and mathematically correct hypothesis on the complex and coherence nature of matter, life and consciousness.

  13. Stochasticity in processes fundamentals and applications to chemistry and biology

    CERN Document Server

    Schuster, Peter

    2016-01-01

    This book has developed over the past fifteen years from a modern course on stochastic chemical kinetics for graduate students in physics, chemistry and biology. The first part presents a systematic collection of the mathematical background material needed to understand probability, statistics, and stochastic processes as a prerequisite for the increasingly challenging practical applications in chemistry and the life sciences examined in the second part. Recent advances in the development of new techniques and in the resolution of conventional experiments at nano-scales have been tremendous: today molecular spectroscopy can provide insights into processes down to scales at which current theories at the interface of physics, chemistry and the life sciences cannot be successful without a firm grasp of randomness and its sources. Routinely measured data is now sufficiently accurate to allow the direct recording of fluctuations. As a result, the sampling of data and the modeling of relevant processes are doomed t...

  14. Chemistry and Biology of the Caged Garcinia Xanthones

    Science.gov (United States)

    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

  15. Quantum Information Biology: From Information Interpretation of Quantum Mechanics to Applications in Molecular Biology and Cognitive Psychology

    Science.gov (United States)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    2015-10-01

    We discuss foundational issues of quantum information biology (QIB)—one of the most successful applications of the quantum formalism outside of physics. QIB provides a multi-scale model of information processing in bio-systems: from proteins and cells to cognitive and social systems. This theory has to be sharply distinguished from "traditional quantum biophysics". The latter is about quantum bio-physical processes, e.g., in cells or brains. QIB models the dynamics of information states of bio-systems. We argue that the information interpretation of quantum mechanics (its various forms were elaborated by Zeilinger and Brukner, Fuchs and Mermin, and D' Ariano) is the most natural interpretation of QIB. Biologically QIB is based on two principles: (a) adaptivity; (b) openness (bio-systems are fundamentally open). These principles are mathematically represented in the framework of a novel formalism— quantum adaptive dynamics which, in particular, contains the standard theory of open quantum systems.

  16. The unitary-group formulation of quantum chemistry

    International Nuclear Information System (INIS)

    Campbell, L.L.

    1990-01-01

    The major part of this dissertation establishes group theoretical techniques that are applicable to the quantum-mechanical many-body atomic and molecular problems. Several matrix element evaluation methods for many-body states are developed. The generator commutation method using generator states is presented for the first time as a complete algorithm, and a computer implementation of the method is developed. A major result of this work is the development of a new method of calculation called the freeon tensor product (FTP) method. This method is much simpler and for many purposes superior to the GUGA procedure (graphical unitary group approach), widely used in configuration interaction calculations. This dissertation is also concerned with the prediction of atomic spectra. In principle spectra can be computed by the methods of ab initio quantum chemistry. In practice these computations are difficult, expensive, time consuming, and not uniformly successful. In this dissertation, the author employs a semi-empirical group theoretical analysis of discrete spectra is the exact analog of the Fourier analysis of continuous functions. In particular, he focuses on the spectra of atoms with incomplete p, d, and f shells. The formulas and techniques are derived in a fashion that apply equally well for more complex systems, as well as the isofreeon model of spherical nuclei

  17. Using of Quantum Dots in Biology and Medicine.

    Science.gov (United States)

    Pleskova, Svetlana; Mikheeva, Elza; Gornostaeva, Ekaterina

    2018-01-01

    Quantum dots are nanoparticles, which due to their unique physical and chemical (first of all optical) properties, are promising in biology and medicine. There are many ways for quantum dots synthesis, both in the form of nanoislands self-forming on the surfaces, which can be used as single-photon emitters in electronics for storing information, and in the form of colloidal quantum dots for diagnostic and therapeutic purposes in living systems. The paper describes the main methods of quantum dots synthesis and summarizes medical and biological ways of their use. The main emphasis is laid on the ways of quantum dots surface modification. Influence of the size and form of nanoparticles, charge on the surfaces of quantum dots, and cover type on the efficiency of internalization by cells and cell compartments is shown. The main mechanisms of penetration are considered.

  18. Life's Biological Chemistry: A Destiny or Destination Starting from Prebiotic Chemistry?

    Science.gov (United States)

    Krishnamurthy, Ramanarayanan

    2018-06-05

    Research into understanding the origins -and evolution- of life has long been dominated by the concept of taking clues from extant biology and extrapolating its molecules and pathways backwards in time. This approach has also guided the search for solutions to the problem of how contemporary biomolecules would have arisen directly from prebiotic chemistry on early earth. However, the continuing difficulties in finding universally convincing solutions in connecting prebiotic chemistry to biological chemistry should give us pause, and prompt us to rethink this concept of treating extant life's chemical processes as the sole end goal and, therefore, focusing only -and implicitly- on the respective extant chemical building blocks. Rather, it may be worthwhile "to set aside the goal" and begin with what would have been plausible prebiotic reaction mixtures (which may have no obvious or direct connection to life's chemical building blocks and processes) - and allow their chemistries and interactions, under different geochemical constraints, to guide and illuminate as to what processes and systems can emerge. Such a conceptual approach gives rise to the prospect that chemistry of life-as-we-know-it is not the only result (not a "destiny"), but one that has emerged among many potential possibilities (a "destination"). This postulate, in turn, could impact the way we think about chemical signatures and criteria used in the search for alternative and extraterrestrial "life". As a bonus, we may discover the chemistries and pathways naturally that led to the emergence of life as we know it. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Can quantum approaches benefit biology of decision making?

    Science.gov (United States)

    Takahashi, Taiki

    2017-11-01

    Human decision making has recently been focused in the emerging fields of quantum decision theory and neuroeconomics. The former discipline utilizes mathematical formulations developed in quantum theory, while the latter combines behavioral economics and neurobiology. In this paper, the author speculates on possible future directions unifying the two approaches, by contrasting the roles of quantum theory in the birth of molecular biology of the gene. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    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. 2010 Elsevier Ltd. All rights reserved.

  1. The biology and chemistry of the zoanthamine alkaloids.

    Science.gov (United States)

    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.

  2. Quantum entanglement and quantum information in biological systems (DNA)

    Science.gov (United States)

    Hubač, Ivan; Švec, Miloslav; Wilson, Stephen

    2017-12-01

    Recent studies of DNA show that the hydrogen bonds between given base pairs can be treated as diabatic systems with spin-orbit coupling. For solid state systems strong diabaticity and spin-orbit coupling the possibility of forming Majorana fermions has been discussed. We analyze the hydrogen bonds in the base pairs in DNA from this perspective. Our analysis is based on a quasiparticle supersymmetric transformation which couples electronic and vibrational motion and includes normal coordinates and the corresponding momenta. We define qubits formed by Majorana fermions in the hydrogen bonds and also discuss the entangled states in base pairs. Quantum information and quantum entropy are introduced. In addition to the well-known classical information connected with the DNA base pairs, we also consider quantum information and show that the classical and quantum information are closely connected.

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

    Science.gov (United States)

    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.

  4. Organic Chemistry and Biology: Chemical Biology Through the Eyes of Collaboration

    Science.gov (United States)

    Hruby, Victor J.

    2011-01-01

    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. PMID:20000552

  5. Solved and unsolved problems in relativistic quantum chemistry

    International Nuclear Information System (INIS)

    Kutzelnigg, Werner

    2012-01-01

    Graphical abstract: The graphical abstract represents the Dirac-Coulomb Hamiltonian in Fock space in a diagrammatic notation. A line (vertical or slanted) with an upgoing arrow represents an eletron, with a downgoing arrow a positron. A cross in the first line means the potential created by a nucleus, a broken line represents the Coulomb interaction between electrons and positrons. Highlights: ► Relativistic many-electron theory needs a Fock space and a field-dependent vacuum. ► A good starting point is QED in Coulomb gauge without transversal photons. ► The Dirac underworld picture is obsolete. ► A kinetically balanced even-tempered Gaussian basis is complete. ► ‘Quantum chemistry in Fock space is preferable over QED. - Abstract: A hierarchy of approximations in relativistic many-electron theory is discussed that starts with the Dirac equation and its expansion in a kinetically balanced basis, via a formulation of non-interacting electrons in Fock space (which is the only consistent way to deal with negative-energy states). The most straightforward approximate Hamiltonian for interacting electrons is derived from quantum electrodynamics (QED) in Coulomb gauge with the neglect of transversal photons. This allows an exact (non-perturbative) decoupling of the electromagnetic field from the fermionic field. The electric interaction of the fermions is non-retarded and non-quantized. The quantization of the fermionic field leads to a polarizable vacuum. The simplest (but somewhat problematic) approximation is a no-pair projected theory with external-field projectors. The Dirac-Coulomb operator in configuration space (first quantization) is not acceptable, even if the Brown–Ravenhall disease is much less virulent than often claimed. Effects of transversal photons, such as the Breit interaction and renormalized self-interaction can be taken care of perturbatively at the end, but there are still many open questions.

  6. Proceedings of the meeting on tunneling reaction and low temperature chemistry, 97 October. Tunneling reaction and quantum medium

    Energy Technology Data Exchange (ETDEWEB)

    Miyazaki, Tetsuo; Aratono, Yasuyuki; Ichikawa, Tsuneki; Shiotani, Masaru [eds.

    1998-02-01

    Present report is the proceedings of the 3rd Meeting on Tunneling Reaction and Low Temperature Chemistry held in Oct. 13 and 14, 1997. The main subject of the meeting is `Tunneling Reaction and Quantum Medium`. In the meeting, the physical and chemical phenomena in the liquid helium such as quantum nucleation, spectroscopy of atoms and molecules, and tunneling abstraction reaction of tritium atom were discussed as the main topics as well as the tunneling reactions in the solid hydrogen and organic compounds. Through the meetings held in 1995, 1996, and 1997, the tunneling phenomena proceeding at various temperatures (room temperature to mK) in the wide fields of chemistry, biology, and physics were discussed intensively and the importance of the tunneling phenomena in the science has been getting clear. The 12 of the presented papers are indexed individually. (J.P.N.)

  7. Proceedings of the meeting on tunneling reaction and low temperature chemistry, 97 October. Tunneling reaction and quantum medium

    International Nuclear Information System (INIS)

    Miyazaki, Tetsuo; Aratono, Yasuyuki; Ichikawa, Tsuneki; Shiotani, Masaru

    1998-02-01

    Present report is the proceedings of the 3rd Meeting on Tunneling Reaction and Low Temperature Chemistry held in Oct. 13 and 14, 1997. The main subject of the meeting is 'Tunneling Reaction and Quantum Medium'. In the meeting, the physical and chemical phenomena in the liquid helium such as quantum nucleation, spectroscopy of atoms and molecules, and tunneling abstraction reaction of tritium atom were discussed as the main topics as well as the tunneling reactions in the solid hydrogen and organic compounds. Through the meetings held in 1995, 1996, and 1997, the tunneling phenomena proceeding at various temperatures (room temperature to mK) in the wide fields of chemistry, biology, and physics were discussed intensively and the importance of the tunneling phenomena in the science has been getting clear. The 12 of the presented papers are indexed individually. (J.P.N.)

  8. 2010 Tetrapyrroles, Chemistry & Biology of Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    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.

  9. Dynamic light scattering with applications to chemistry, biology, and physics

    CERN Document Server

    Berne, Bruce J

    2000-01-01

    Lasers play an increasingly important role in a variety of detection techniques, making inelastic light scattering a tool of growing value in the investigation of dynamic and structural problems in chemistry, biology, and physics. Until the initial publication of this work, however, no monograph treated the principles behind current developments in the field.This volume presents a comprehensive introduction to the principles underlying laser light scattering, focusing on the time dependence of fluctuations in fluid systems; it also serves as an introduction to the theory of time correlation f

  10. Application of the CRAY-1 for quantum chemistry calculations

    International Nuclear Information System (INIS)

    Saunders, V.R.; Guest, M.F.

    1982-01-01

    The following steps in a typical quantum chemistry calculation will be considered: 1. Gaussian integrals evaluation. 2. Hartree-Fock computation of an uncorrelated wavefunction. 3. 4-index transformation of two-electron integrals. 4. Configuration interaction calculations of a correlated wavefunction. In all the above steps we have found that algorithms may be devised which formulate the problem as being dominated by a series of matrix multiplications: R=AB, where A (or B) is sparse. A routine for performing the sparse matrix multiply has been prepared with a maximum measured performance of 147 M flops. When this routine is used in our applications packages, overall performance of approximately 50, 100 and 120 M flops are observed for steps 1, 3 and 4, respectively. The result in step 2 is not so successful, as effective implementation of the matrix multiplication requires efficient performance of data gather and scatter sequences (not vectorisable on the CRAY-1), and a performance of 10 M flops is observed. The importance of gather/scatter sequences in such operations as file sorting is pointed out. The present performance is compared with that previously obtained on CDC 7600 equipment and from this data we deduce the cost-effectiveness of the CRAY-1 in our field. (orig.)

  11. Quantum Information Biology: From Theory of Open Quantum Systems to Adaptive Dynamics

    Science.gov (United States)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    This chapter reviews quantum(-like) information biology (QIB). Here biology is treated widely as even covering cognition and its derivatives: psychology and decision making, sociology, and behavioral economics and finances. QIB provides an integrative description of information processing by bio-systems at all scales of life: from proteins and cells to cognition, ecological and social systems. Mathematically QIB is based on the theory of adaptive quantum systems (which covers also open quantum systems). Ideologically QIB is based on the quantum-like (QL) paradigm: complex bio-systems process information in accordance with the laws of quantum information and probability. This paradigm is supported by plenty of statistical bio-data collected at all bio-scales. QIB re ects the two fundamental principles: a) adaptivity; and, b) openness (bio-systems are fundamentally open). In addition, quantum adaptive dynamics provides the most generally possible mathematical representation of these principles.

  12. Energy Connections and Misconnections across Chemistry and Biology.

    Science.gov (United States)

    Kohn, Kathryn P; Underwood, Sonia M; Cooper, Melanie M

    2018-01-01

    Despite the number of university students who take courses in multiple science disciplines, little is known about how they connect concepts between disciplines. Energy is a concept that underlies all scientific phenomena and, as such, provides an appropriate context in which to investigate student connections and misconnections across disciplines. In this study, university students concurrently enrolled in introductory chemistry and biology were interviewed to explore their perceptions of the integration of energy both within and across the disciplines, and how they attempted to accommodate and reconcile different disciplinary approaches to energy, to inform future, interdisciplinary course reform. Findings suggest that, while students believed energy to be important to the scientific world and to the disciplines of biology and chemistry, the extent to which it was seen as central to success in their courses varied. Differences were also apparent in students' descriptions of the molecular-level mechanisms by which energy transfer occurs. These findings reveal a disconnect between how energy is understood and used in introductory science course work and uncovers opportunities to make stronger connections across the disciplines. We recommend that instructors engage in interdisciplinary conversations and consider the perspectives and goals of other disciplines when teaching introductory science courses. © 2018 K. P. Kohn et al. CBE—Life Sciences Education © 2018 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  13. Roles of radiation chemistry in development and research of radiation biology

    International Nuclear Information System (INIS)

    Min Rui

    2009-01-01

    Radiation chemistry acts as a bridge connecting radiation physics with radiation biology in spatial and temporal insight. The theory, model, and methodology coming from radiation chemistry play an important role in the research and development of radiation biology. The chemical changes induced by ionizing radiation are involved not only in early event of biological effects caused by ionizing radiation but in function radiation biology, such as DNA damage and repair, sensitive modification, metabolism and function of active oxygen and so on. Following the research development of radiation biology, systems radiation biology, accurate quality and quantity of radiation biology effects need more methods and perfect tools from radiation chemistry. (authors)

  14. Quantum effects in biological electron transfer

    Czech Academy of Sciences Publication Activity Database

    de la Lande, A.; Babcock, N. S.; Řezáč, Jan; Levy, B.; Sanders, B. C.; Salahub, D.

    2012-01-01

    Roč. 14, č. 17 (2012), s. 5902-5918 ISSN 1463-9076 Institutional research plan: CEZ:AV0Z40550506 Keywords : electron transfer * tunnelling * decoherence * semi-classical molecular dynamics * density functional theory Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.829, year: 2012

  15. Ethnobotany, chemistry, and biological activities of the genus Tithonia (Asteraceae).

    Science.gov (United States)

    Chagas-Paula, Daniela A; Oliveira, Rejane B; Rocha, Bruno A; Da Costa, Fernando B

    2012-02-01

    The genus Tithonia is an important source of diverse natural products, particularly sesquiterpene lactones, diterpenes, and flavonoids. The collected information in this review attempts to summarize the recent developments in the ethnobotany, biological activities, and secondary metabolite chemistry of this genus. More than 100 structures of natural products from Tithonia are reported in this review. The species that has been most investigated in this genus is T. diversifolia, from which ca. 150 compounds were isolated. Biological studies are described to evaluate the anti-inflammatory, analgesic, antimalarial, antiviral, antidiabetic, antidiarrhoeal, antimicrobial, antispasmodic, vasorelaxant, cancer-chemopreventive, cytotoxic, toxicological, bioinsecticide, and repellent activities. A few of these studies have been carried out with isolated compounds from Tithonia species, but the majority has been conducted with different extracts. The relationship between the biological activity and the toxicity of compounds isolated from the plants of this genus as well as T. diversifolia extracts still remains unclear, and mechanisms of action remain to be determined. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.

  16. Model of biological quantum logic in DNA.

    Science.gov (United States)

    Mihelic, F Matthew

    2013-08-02

    The DNA molecule has properties that allow it to act as a quantum logic processor. It has been demonstrated that there is coherent conduction of electrons longitudinally along the DNA molecule through pi stacking interactions of the aromatic nucleotide bases, and it has also been demonstrated that electrons moving longitudinally along the DNA molecule are subject to a very efficient electron spin filtering effect as the helicity of the DNA molecule interacts with the spin of the electron. This means that, in DNA, electrons are coherently conducted along a very efficient spin filter. Coherent electron spin is held in a logically and thermodynamically reversible chiral symmetry between the C2-endo and C3-endo enantiomers of the deoxyribose moiety in each nucleotide, which enables each nucleotide to function as a quantum gate. The symmetry break that provides for quantum decision in the system is determined by the spin direction of an electron that has an orbital angular momentum that is sufficient to overcome the energy barrier of the double well potential separating the C2-endo and C3-endo enantiomers, and that enantiomeric energy barrier is appropriate to the Landauer limit of the energy necessary to randomize one bit of information.

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

    Science.gov (United States)

    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. Micro-segmented flow applications in chemistry and biology

    CERN Document Server

    Cahill, Brian

    2014-01-01

    The book is dedicated to the method and application potential of micro segmented flow. The recent state of development of this powerful technique is presented in 12 chapters by leading researchers from different countries. In the first section, the principles of generation and manipulation of micro-fluidic segments are explained. In the second section, the micro continuous-flow synthesis of different types of nanomaterials is shown as a typical example for the use of advantages of the technique in chemistry. In the third part, the particular importance of the technique in biotechnical applications is presented demonstrating the progress for miniaturized cell-free processes, for molecular biology and DNA-based diagnostis and sequencing as well as for the development of antibiotics and the evaluation of toxic effects in medicine and environment.

  19. Rabi model as a quantum coherent heat engine: From quantum biology to superconducting circuits

    Science.gov (United States)

    Altintas, Ferdi; Hardal, Ali Ü. C.; Müstecaplıoǧlu, Özgür E.

    2015-02-01

    We propose a multilevel quantum heat engine with a working medium described by a generalized Rabi model which consists of a two-level system coupled to a single-mode bosonic field. The model is constructed to be a continuum limit of a quantum biological description of light-harvesting complexes so that it can amplify quantum coherence by a mechanism which is a quantum analog of classical Huygens clocks. The engine operates in a quantum Otto cycle where the working medium is coupled to classical heat baths in the isochoric processes of the four-stroke cycle, while either the coupling strength or the resonance frequency is changed in the adiabatic stages. We found that such an engine can produce work with an efficiency close to the Carnot bound when it operates at low temperatures and in the ultrastrong-coupling regime. The interplay of the effects of quantum coherence and quantum correlations on the engine performance is discussed in terms of second-order coherence, quantum mutual information, and the logarithmic negativity of entanglement. We point out that the proposed quantum Otto engine can be implemented experimentally with modern circuit quantum electrodynamic systems where flux qubits can be coupled ultrastrongly to superconducting transmission-line resonators.

  20. Enabling new capabilities and insights from quantum chemistry by using component architectures

    International Nuclear Information System (INIS)

    Janssen, C L; Kenny, J P; Nielsen, I M B; Krishnan, M; Gurumoorthi, V; Valeev, E F; Windus, T L

    2006-01-01

    Steady performance gains in computing power, as well as improvements in Scientific computing algorithms, are making possible the study of coupled physical phenomena of great extent and complexity. The software required for such studies is also very complex and requires contributions from experts in multiple disciplines. We have investigated the use of the Common Component Architecture (CCA) as a mechanism to tackle some of the resulting software engineering challenges in quantum chemistry, focusing on three specific application areas. In our first application, we have developed interfaces permitting solvers and quantum chemistry packages to be readily exchanged. This enables our quantum chemistry packages to be used with alternative solvers developed by specialists, remedying deficiencies we discovered in the native solvers provided in each of the quantum chemistry packages. The second application involves development of a set of components designed to improve utilization of parallel machines by allowing multiple components to execute concurrently on subsets of the available processors. This was found to give substantial improvements in parallel scalability. Our final application is a set of components permitting different quantum chemistry packages to interchange intermediate data. These components enabled the investigation of promising new methods for obtaining accurate thermochemical data for reactions involving heavy elements

  1. Problems and solutions in quantum chemistry and physics

    CERN Document Server

    Johnson, Charles S

    1988-01-01

    Unusually varied problems, with detailed solutions, cover quantum mechanics, wave mechanics, angular momentum, molecular spectroscopy, scattering theory, more. 280 problems, plus 139 supplementary exercises.

  2. Interactive Simulations to Support Quantum Mechanics Instruction for Chemistry Students

    Science.gov (United States)

    Kohnle, Antje; Benfield, Cory; Hahner, Georg; Paetkau, Mark

    2017-01-01

    The QuVis Quantum Mechanics Visualization Project provides freely available research-based interactive simulations with accompanying activities for the teaching and learning of quantum mechanics across a wide range of topics and levels. This article gives an overview of some of the simulations and describes their use in an introductory physical…

  3. Students’ experienced coherence between chemistry and biology in context-based secondary science education

    NARCIS (Netherlands)

    Boer, H.J.; Prins, Gjalt; Goedhart, M.J.; Boersma, Kerst

    2014-01-01

    In current biology and chemistry secondary school practice, coherence between the subjects chemistry and biology is underexposed or even ignored. This is incongruent with the current scientific practice, in which the emphasis is shifting towards inter- and multidisciplinarity. These problems have

  4. 8. International Conference on Pulse Investigations in Chemistry, Biology and Physics - PULS'2008. Abstracts

    International Nuclear Information System (INIS)

    2008-01-01

    The Report comprises abstracts of 68 communications (oral and posters) presented during the 8. International Conference on Pulse Investigations in Chemistry, Biology and Physics - PULS'2008, held on September 6 - 12, 2008 in Cracow. Presentations cover a variety of research fields representing different fields of pulse radiolysis in chemistry, biology and physics

  5. 8. International Conference on Pulse Investigations in Chemistry, Biology and Physics - PULS'2008. Abstracts

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2008-07-01

    The Report comprises abstracts of 68 communications (oral and posters) presented during the 8. International Conference on Pulse Investigations in Chemistry, Biology and Physics - PULS'2008, held on September 6 - 12, 2008 in Cracow. Presentations cover a variety of research fields representing different fields of pulse radiolysis in chemistry, biology and physics.

  6. Using quantum chemistry muscle to flex massive systems: How to respond to something perturbing

    Energy Technology Data Exchange (ETDEWEB)

    Bertoni, Colleen [Iowa State Univ., Ames, IA (United States)

    2016-12-17

    Computational chemistry uses the theoretical advances of quantum mechanics and the algorithmic and hardware advances of computer science to give insight into chemical problems. It is currently possible to do highly accurate quantum chemistry calculations, but the most accurate methods are very computationally expensive. Thus it is only feasible to do highly accurate calculations on small molecules, since typically more computationally efficient methods are also less accurate. The overall goal of my dissertation work has been to try to decrease the computational expense of calculations without decreasing the accuracy. In particular, my dissertation work focuses on fragmentation methods, intermolecular interactions methods, analytic gradients, and taking advantage of new hardware.

  7. Indirect Radiohalogenation of Targeting Proteins: Labelling Chemistry and Biological Characterisation

    Energy Technology Data Exchange (ETDEWEB)

    Orlova, Anna

    2003-03-01

    In about half of all newly diagnosed cancer cases, conventional treatment is not adequately curative, mainly due to the failure of conventional techniques to find and kill residual cells and metastases, which might consist of only a few malignant cells, without causing unacceptable complications to healthy tissue. To solve the problem a more selective delivery of cytotoxic substances to tumour cells is needed. The approach applied here is called 'tumour targeting' and implies the use of biomolecules that recognise specific molecular structures on the malignant cell surface. Such molecules are then used for a selective transport of toxic agents to the cancer cells. The use of radionuclides as cytotoxic substances has a number of advantages: 1) radiation does not cause severe resistance; 2) there is a cross-fire effect and 3) smaller amounts of nuclides are required than other cytotoxic substances to cause the same damage. Such an approach is called radionuclide tumour therapy. Several factors are important for the success of radionuclide therapy, such as the pharmacokinetics of the radiolabelled substance and its radiocatabolites, as well as the physical and chemical properties of the radiolabel used. Nuclear properties of the label should be consistent with the problem to be solved: primary diagnostics; quantification of pharmacokinetics and dose planning; or therapy. From this point of view, radiohalogens are an attractive group of radiolabels. Halogens have nuclides with a variety of physical properties while the chemical and biological properties of halogens are very similar. The same labelling procedures can be used for all heavy halogens, i.e. bromine, iodine and astatine. It has been demonstrated that the biodistribution of proteins labelled with different heavy halogens is quite similar. The main goal of the study was to develop protein radiohalogenation methods that provide a stable halogen-protein bond, convenient labelling chemistry that

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

    Science.gov (United States)

    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.

  9. Quantum Processes and Dynamic Networks in Physical and Biological Systems.

    Science.gov (United States)

    Dudziak, Martin Joseph

    Quantum theory since its earliest formulations in the Copenhagen Interpretation has been difficult to integrate with general relativity and with classical Newtonian physics. There has been traditionally a regard for quantum phenomena as being a limiting case for a natural order that is fundamentally classical except for microscopic extrema where quantum mechanics must be applied, more as a mathematical reconciliation rather than as a description and explanation. Macroscopic sciences including the study of biological neural networks, cellular energy transports and the broad field of non-linear and chaotic systems point to a quantum dimension extending across all scales of measurement and encompassing all of Nature as a fundamentally quantum universe. Theory and observation lead to a number of hypotheses all of which point to dynamic, evolving networks of fundamental or elementary processes as the underlying logico-physical structure (manifestation) in Nature and a strongly quantized dimension to macroscalar processes such as are found in biological, ecological and social systems. The fundamental thesis advanced and presented herein is that quantum phenomena may be the direct consequence of a universe built not from objects and substance but from interacting, interdependent processes collectively operating as sets and networks, giving rise to systems that on microcosmic or macroscopic scales function wholistically and organically, exhibiting non-locality and other non -classical phenomena. The argument is made that such effects as non-locality are not aberrations or departures from the norm but ordinary consequences of the process-network dynamics of Nature. Quantum processes are taken to be the fundamental action-events within Nature; rather than being the exception quantum theory is the rule. The argument is also presented that the study of quantum physics could benefit from the study of selective higher-scale complex systems, such as neural processes in the brain

  10. Students' Energy Understanding Across Biology, Chemistry, and Physics Contexts

    Science.gov (United States)

    Opitz, S. T.; Neumann, K.; Bernholt, S.; Harms, U.

    2017-07-01

    Energy is considered both as a disciplinary core idea and as a concept cutting across science disciplines. Most previous approaches studied progressing energy understanding in specific disciplinary contexts, while disregarding the relation of understanding across them. Hence, this study provides a systematic analysis of cross-disciplinary energy learning. On the basis of a cross-sectional study with n = 742 students from grades 6, 8, and 10, we analyze students' progression in understanding energy across biology, chemistry, and physics contexts. The study is guided by three hypothetical scenarios that describe how the connection between energy understanding in the three disciplinary contexts changes across grade levels. These scenarios are compared using confirmatory factor analysis (CFA). The results suggest that, from grade 6 to grade 10, energy understanding in the three disciplinary contexts is highly interrelated, thus indicating a parallel progression of energy understanding in the three disciplinary contexts. In our study, students from grade 6 onwards appeared to have few problems to apply one energy understanding across the three disciplinary contexts. These findings were unexpected, as previous research concluded that students likely face difficulties in connecting energy learning across disciplinary boundaries. Potential reasons for these results and the characteristics of the observed cross-disciplinary energy understanding are discussed in the light of earlier findings and implications for future research, and the teaching of energy as a core idea and a crosscutting concept are addressed.

  11. Contextual analysis of Biology and Chemistry academic graphical abstracts

    Directory of Open Access Journals (Sweden)

    Cristiane Salete Florek

    2016-10-01

    Full Text Available http://dx.doi.org/10.5007/1984-8412.2016v13n3p1363 The Graphical Abstract (GA is a non-regular discursive practice held in the academic context, and that, when occurs, coexists with the academic abstract (AA in the table of contents of scientific journals, and in HTML versions of academic articles, materializing by the combination of the verbal and visual semiotics. In this paper, in the light of the Critical Analysis genres (MEURER, 2002; BHATIA, 2004; MOTTA-ROTH, 2006, 2008, which allow us to study a text based on the investigation of its context’s critical research, we present the results of the contextual analysis of GAs in the areas of Biology and Chemistry. This analysis was done by: i interviews with researchers of the investigated areas; and ii documentary analysis. Results show that, in general, GA: i is highlighted by presenting an advertising nature, which seeks to attract the reader’s attention; ii: summarizes the topic and the main findings of scientific research; and iii does not replace the academia abstract (AA.

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

    Science.gov (United States)

    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). Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Macroscopic Quantum-Type Potentials in Theoretical Systems Biology

    Directory of Open Access Journals (Sweden)

    Laurent Nottale

    2013-12-01

    Full Text Available We review in this paper the use of the theory of scale relativity and fractal space-time as a tool particularly well adapted to the possible development of a future genuine systems theoretical biology. We emphasize in particular the concept of quantum-type potentials, since, in many situations, the effect of the fractality of space—or of the underlying medium—can be reduced to the addition of such a potential energy to the classical equations of motion. Various equivalent representations—geodesic, quantum-like, fluid mechanical, stochastic—of these equations are given, as well as several forms of generalized quantum potentials. Examples of their possible intervention in high critical temperature superconductivity and in turbulence are also described, since some biological processes may be similar in some aspects to these physical phenomena. These potential extra energy contributions could have emerged in biology from the very fractal nature of the medium, or from an evolutive advantage, since they involve spontaneous properties of self-organization, morphogenesis, structuration and multi-scale integration. Finally, some examples of applications of the theory to actual biological-like processes and functions are also provided.

  14. Quantum Interference and Selectivity through Biological Ion Channels.

    Science.gov (United States)

    Salari, Vahid; Naeij, Hamidreza; Shafiee, Afshin

    2017-01-30

    The mechanism of selectivity in ion channels is still an open question in biology for more than half a century. Here, we suggest that quantum interference can be a solution to explain the selectivity mechanism in ion channels since interference happens between similar ions through the same size of ion channels. In this paper, we simulate two neighboring ion channels on a cell membrane with the famous double-slit experiment in physics to investigate whether there is any possibility of matter-wave interference of ions via movement through ion channels. Our obtained decoherence timescales indicate that the quantum states of ions can only survive for short times, i.e. ≈100 picoseconds in each channel and ≈17-53 picoseconds outside the channels, giving the result that the quantum interference of ions seems unlikely due to environmental decoherence. However, we discuss our results and raise few points, which increase the possibility of interference.

  15. Theoretical discussion for quantum computation in biological systems

    Science.gov (United States)

    Baer, Wolfgang

    2010-04-01

    Analysis of the brain as a physical system, that has the capacity of generating a display of every day observed experiences and contains some knowledge of the physical reality which stimulates those experiences, suggests the brain executes a self-measurement process described by quantum theory. Assuming physical reality is a universe of interacting self-measurement loops, we present a model of space as a field of cells executing such self-measurement activities. Empty space is the observable associated with the measurement of this field when the mass and charge density defining the material aspect of the cells satisfy the least action principle. Content is the observable associated with the measurement of the quantum wave function ψ interpreted as mass-charge displacements. The illusion of space and its content incorporated into cognitive biological systems is evidence of self-measurement activity that can be associated with quantum operations.

  16. Quantum and classical dynamics in biologically inspired systems

    International Nuclear Information System (INIS)

    Guerreschi, G.

    2012-01-01

    Quantum biology is an emerging field in which traditional believes and paradigms are under examination. Typically, quantum effects are witnessed inside quantum optics or atomic physics laboratories in systems which are kept under control and isolated from any noise source by means of very advanced technology. Biological systems exhibit opposite characteristics: They are usually constituted of macromolecules continuously exposed to a warm and wet environment, well beyond our control; but at the same time, they operate far away from equilibrium. Recently, the experimental observation of excitonic coherence in photosynthetic complexes has con firmed that, in non-equilibrium scenarios, quantum phenomena can survive even in presence of a noisy environment. The challenge faced by the ongoing research is twofold: On one side, considering biological molecules as effective nanomachines, one has to address questions of principle regarding their design and functioning; on the other side, one has to investigate real systems which are experimentally accessible and identify such features in these concrete scenarios. The present thesis contributes to both of these aspects. In Part I, we demonstrate how entanglement can be persistently generated even under unfavorable environmental conditions. The physical mechanism is modeled after the idea of conformational changes, and it relies on the interplay of classical oscillations of large structures with the quantum dynamics of a few interacting degrees of freedom. In a similar context, we show that the transfer of an excitation through a linear chain of sites can be enhanced when the inter-site distances oscillate periodically. This enhancement is present even in comparison with the static con figuration which is optimal in the classical case and, therefore, it constitutes a clear signature of the underlying quantum dynamics. In Part II of this thesis, we study the radical pair mechanism from the perspective of quantum control and

  17. Quantum Biology at the Cellular Level - elements of the research program

    OpenAIRE

    Bordonaro, Michael; Ogryzko, Vasily

    2013-01-01

    Quantum Biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (Quantum Biology at Cellular Level), a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. Key words. decoherence, macroscopic superpositions, basis-dependence, formal superposition, non-classical correlations,...

  18. Self-assembling hybrid diamond–biological quantum devices

    International Nuclear Information System (INIS)

    Albrecht, A; B Plenio, M; Koplovitz, G; Yochelis, S; Paltiel, Y; Retzker, A; Nevo, Y; Shoseyov, O; Jelezko, F; Porath, D

    2014-01-01

    The realization of scalable arrangements of nitrogen vacancy (NV) centers in diamond remains a key challenge on the way towards efficient quantum information processing, quantum simulation and quantum sensing applications. Although technologies based on implanting NV-centers in bulk diamond crystals or hybrid device approaches have been developed, they are limited by the achievable spatial resolution and by the intricate technological complexities involved in achieving scalability. We propose and demonstrate a novel approach for creating an arrangement of NV-centers, based on the self-assembling capabilities of biological systems and their beneficial nanometer spatial resolution. Here, a self-assembled protein structure serves as a structural scaffold for surface functionalized nanodiamonds, in this way allowing for the controlled creation of NV-structures on the nanoscale and providing a new avenue towards bridging the bio–nano interface. One-, two- as well as three-dimensional structures are within the scope of biological structural assembling techniques. We realized experimentally the formation of regular structures by interconnecting nanodiamonds using biological protein scaffolds. Based on the achievable NV-center distances of 11 nm, we evaluate the expected dipolar coupling interaction with neighboring NV-centers as well as the expected decoherence time. Moreover, by exploiting these couplings, we provide a detailed theoretical analysis on the viability of multiqubit quantum operations, suggest the possibility of individual addressing based on the random distribution of the NV intrinsic symmetry axes and address the challenges posed by decoherence and imperfect couplings. We then demonstrate in the last part that our scheme allows for the high-fidelity creation of entanglement, cluster states and quantum simulation applications. (papers)

  19. Self-assembling hybrid diamond-biological quantum devices

    Science.gov (United States)

    Albrecht, A.; Koplovitz, G.; Retzker, A.; Jelezko, F.; Yochelis, S.; Porath, D.; Nevo, Y.; Shoseyov, O.; Paltiel, Y.; Plenio, M. B.

    2014-09-01

    The realization of scalable arrangements of nitrogen vacancy (NV) centers in diamond remains a key challenge on the way towards efficient quantum information processing, quantum simulation and quantum sensing applications. Although technologies based on implanting NV-centers in bulk diamond crystals or hybrid device approaches have been developed, they are limited by the achievable spatial resolution and by the intricate technological complexities involved in achieving scalability. We propose and demonstrate a novel approach for creating an arrangement of NV-centers, based on the self-assembling capabilities of biological systems and their beneficial nanometer spatial resolution. Here, a self-assembled protein structure serves as a structural scaffold for surface functionalized nanodiamonds, in this way allowing for the controlled creation of NV-structures on the nanoscale and providing a new avenue towards bridging the bio-nano interface. One-, two- as well as three-dimensional structures are within the scope of biological structural assembling techniques. We realized experimentally the formation of regular structures by interconnecting nanodiamonds using biological protein scaffolds. Based on the achievable NV-center distances of 11 nm, we evaluate the expected dipolar coupling interaction with neighboring NV-centers as well as the expected decoherence time. Moreover, by exploiting these couplings, we provide a detailed theoretical analysis on the viability of multiqubit quantum operations, suggest the possibility of individual addressing based on the random distribution of the NV intrinsic symmetry axes and address the challenges posed by decoherence and imperfect couplings. We then demonstrate in the last part that our scheme allows for the high-fidelity creation of entanglement, cluster states and quantum simulation applications.

  20. Learning Quantum Chemistry via a Visual-Conceptual Approach: Students' Bidirectional Textual and Visual Understanding

    Science.gov (United States)

    Dangur, Vered; Avargil, Shirly; Peskin, Uri; Dori, Yehudit Judy

    2014-01-01

    Most undergraduate chemistry courses and a few high school honors courses, which focus on physical chemistry and quantum mechanics, are highly mathematically-oriented. At the Technion, Israel Institute of Technology, we developed a new module for high school students, titled "Chemistry--From 'the Hole' to 'the Whole': From the Nanoscale to…

  1. Students' Levels of Explanations, Models, and Misconceptions in Basic Quantum Chemistry: A Phenomenographic Study

    Science.gov (United States)

    Stefani, Christina; Tsaparlis, Georgios

    2009-01-01

    We investigated students' knowledge constructions of basic quantum chemistry concepts, namely atomic orbitals, the Schrodinger equation, molecular orbitals, hybridization, and chemical bonding. Ausubel's theory of meaningful learning provided the theoretical framework and phenomenography the method of analysis. The semi-structured interview with…

  2. A photoelectron imaging and quantum chemistry study of the deprotonated indole anion.

    Science.gov (United States)

    Parkes, Michael A; Crellin, Jonathan; Henley, Alice; Fielding, Helen H

    2018-05-29

    Indole is an important molecular motif in many biological molecules and exists in its deprotonated anionic form in the cyan fluorescent protein, an analogue of green fluorescent protein. However, the electronic structure of the deprotonated indole anion has been relatively unexplored. Here, we use a combination of anion photoelectron velocity-map imaging measurements and quantum chemistry calculations to probe the electronic structure of the deprotonated indole anion. We report vertical detachment energies (VDEs) of 2.45 ± 0.05 eV and 3.20 ± 0.05 eV, respectively. The value for D0 is in agreement with recent high-resolution measurements whereas the value for D1 is a new measurement. We find that the first electronically excited singlet state of the anion, S1(ππ*), lies above the VDE and has shape resonance character with respect to the D0 detachment continuum and Feshbach resonance character with respect to the D1 continuum.

  3. Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach.

    Science.gov (United States)

    Ramakrishnan, Raghunathan; Dral, Pavlo O; Rupp, Matthias; von Lilienfeld, O Anatole

    2015-05-12

    Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10% of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy.

  4. Innovative quantum technologies for microgravity fundamental physics and biological research

    Science.gov (United States)

    Kierk, I. K.

    2002-01-01

    This paper presents a new technology program, within the fundamental physics, focusing on four quantum technology areas: quantum atomics, quantum optics, space superconductivity and quantum sensor technology, and quantum field based sensor and modeling technology.

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

    Science.gov (United States)

    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.

  6. Molecular physics and chemistry applications of quantum Monte Carlo

    International Nuclear Information System (INIS)

    Reynolds, P.J.; Barnett, R.N.; Hammond, B.L.; Lester, W.A. Jr.

    1985-09-01

    We discuss recent work with the diffusion quantum Monte Carlo (QMC) method in its application to molecular systems. The formal correspondence of the imaginary time Schroedinger equation to a diffusion equation allows one to calculate quantum mechanical expectation values as Monte Carlo averages over an ensemble of random walks. We report work on atomic and molecular total energies, as well as properties including electron affinities, binding energies, reaction barriers, and moments of the electronic charge distribution. A brief discussion is given on how standard QMC must be modified for calculating properties. Calculated energies and properties are presented for a number of molecular systems, including He, F, F - , H 2 , N, and N 2 . Recent progress in extending the basic QMC approach to the calculation of ''analytic'' (as opposed to finite-difference) derivatives of the energy is presented, together with an H 2 potential-energy curve obtained using analytic derivatives. 39 refs., 1 fig., 2 tabs

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

    Science.gov (United States)

    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…

  8. Linking soil biology and chemistry in biological soil crust using isolate exometabolomics.

    Science.gov (United States)

    Swenson, Tami L; Karaoz, Ulas; Swenson, Joel M; Bowen, Benjamin P; Northen, Trent R

    2018-01-02

    Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.

  9. Single Molecule Spectroscopy in Chemistry, Physics and Biology Nobel Symposium

    CERN Document Server

    Gräslund, Astrid; Widengren, Jerker

    2010-01-01

    Written by the leading experts in the field, this book describes the development and current state-of-the-art in single molecule spectroscopy. The application of this technique, which started 1989, in physics, chemistry and biosciences is displayed.

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

    Science.gov (United States)

    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'.

  11. Quantum Dots: Proteomics characterization of the impact on biological systems

    Science.gov (United States)

    Pozzi-Mucelli, Stefano; Boschi, F.; Calderan, L.; Sbarbati, A.; Osculati, F.

    2009-05-01

    Over the past few years, Quantum Dots have been tested in most biotechnological applications that use fluorescence, including DNA array technology, immunofluorescence assays, cell and animal biology. Quantum Dots tend to be brighter than conventional dyes, because of the compounded effects of extinction coefficients that are an order of magnitude larger than those of most dyes. Their main advantage resides in their resistance to bleaching over long periods of time (minutes to hours), allowing the acquisition of images that are crisp and well contrasted. This increased photostability is especially useful for three-dimensional (3D) optical sectioning, where a major issue is bleaching of fluorophores during acquisition of successive z-sections, which compromises the correct reconstruction of 3D structures. The long-term stability and brightness of Quantum Dots make them ideal candidates also for live animal targeting and imaging. The vast majority of the papers published to date have shown no relevant effects on cells viability at the concentration used for imaging applications; higher concentrations, however, caused some issues on embryonic development. Adverse effects are due to be caused by the release of cadmium, as surface PEGylation of the Quantum Dots reduces these issues. A recently published paper shows evidences of an epigenetic effect of Quantum Dots treatment, with general histones hypoacetylation, and a translocation to the nucleus of p53. In this study, mice treated with Quantum Dots for imaging purposes were analyzed to investigate the impact on protein expression and networking. Differential mono-and bidimensional electrophoresis assays were performed, with the individuation of differentially expressed proteins after intravenous injection and imaging analysis; further, as several authors indicate an increase in reactive oxygen species as a possible mean of damage due to the Quantum Dots treatment, we investigated the signalling pathway of APE1/Ref1, a

  12. Quantum Dots: Proteomics characterization of the impact on biological systems

    International Nuclear Information System (INIS)

    Pozzi-Mucelli, Stefano; Osculati, F; Boschi, F; Calderan, L; Sbarbati, A

    2009-01-01

    Over the past few years, Quantum Dots have been tested in most biotechnological applications that use fluorescence, including DNA array technology, immunofluorescence assays, cell and animal biology. Quantum Dots tend to be brighter than conventional dyes, because of the compounded effects of extinction coefficients that are an order of magnitude larger than those of most dyes. Their main advantage resides in their resistance to bleaching over long periods of time (minutes to hours), allowing the acquisition of images that are crisp and well contrasted. This increased photostability is especially useful for three-dimensional (3D) optical sectioning, where a major issue is bleaching of fluorophores during acquisition of successive z-sections, which compromises the correct reconstruction of 3D structures. The long-term stability and brightness of Quantum Dots make them ideal candidates also for live animal targeting and imaging. The vast majority of the papers published to date have shown no relevant effects on cells viability at the concentration used for imaging applications; higher concentrations, however, caused some issues on embryonic development. Adverse effects are due to be caused by the release of cadmium, as surface PEGylation of the Quantum Dots reduces these issues. A recently published paper shows evidences of an epigenetic effect of Quantum Dots treatment, with general histones hypoacetylation, and a translocation to the nucleus of p53. In this study, mice treated with Quantum Dots for imaging purposes were analyzed to investigate the impact on protein expression and networking. Differential mono-and bidimensional electrophoresis assays were performed, with the individuation of differentially expressed proteins after intravenous injection and imaging analysis; further, as several authors indicate an increase in reactive oxygen species as a possible mean of damage due to the Quantum Dots treatment, we investigated the signalling pathway of APE1/Ref1, a

  13. Electron spin interactions in chemistry and biology fundamentals, methods, reactions mechanisms, magnetic phenomena, structure investigation

    CERN Document Server

    Likhtenshtein, Gertz

    2016-01-01

    This book presents the versatile and pivotal role of electron spin interactions in nature. It provides the background, methodologies and tools for basic areas related to spin interactions, such as spin chemistry and biology, electron transfer, light energy conversion, photochemistry, radical reactions, magneto-chemistry and magneto-biology. The book also includes an overview of designing advanced magnetic materials, optical and spintronic devices and photo catalysts. This monograph appeals to scientists and graduate students working in the areas related to spin interactions physics, biophysics, chemistry and chemical engineering.

  14. EFFECTS OF 5E LEARNING CYCLE ON STUDENTS ACHIEVEMENT IN BIOLOGY AND CHEMISTRY

    Directory of Open Access Journals (Sweden)

    Patrick Osawaru Ajaja,

    2012-01-01

    Full Text Available The major purpose of this study was to determine the effects of learning cycle as an instructional strategy on biology andchemistry students achievement. To guide this study, six research hypotheses were stated and tested at 0.05 level ofsignificance. The design of this study was 2x2x3x6 Pre-test Post-test non-equivalent control group quasi experimental design.These included two instructional groups (experimental and control groups, sex (male and female, repeated testing (Pre,Post and follow-up tests, and six weeks of experience. The samples of the study included six senior secondary schools, 112science students, and 12 biology and chemistry teachers. The instruments used for this study were: teacher’s questionnaireon knowledge and use of learning cycle (KULC; and Biology and Chemistry Achievement Test (BCAT. The data collected wereanalyzed with simple percentage, Analysis of Covariance (ANCOVA and student t-test statistics. The major findings of thestudy included that only 30.43% and 26.31% of biology and chemistry teachers have the knowledge that learning cycle is aninstructional method; all the biology and chemistry teachers sampled have never used learning cycle as an instructionalmethod; learning cycle had a significant effect on students achievement in biology and chemistry; students taught withlearning cycle significantly achieved better in biology/chemistry Post-test than those taught with lecture method; the posttestscores of students in the learning cycle group increased over the period of experience; non-significant difference in Posttestscores between males and females taught with learning cycle; non-significant interaction effect between method andsex on achievement; and a significant higher retention of biology and chemistry knowledge by students taught with learningcycle than those taught with lecture method. It was concluded that the method seems an appropriate instructional modelthat could be used to solve the problems of

  15. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    Science.gov (United States)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  16. Quantum Chemistry of Solids The LCAO First Principles Treatment of Crystals

    CERN Document Server

    Evarestov, Robert A

    2007-01-01

    Quantum Chemistry of Solids delivers a comprehensive account of the main features and possibilities of LCAO methods for the first principles calculations of electronic structure of periodic systems. The first part describes the basic theory underlying the LCAO methods applied to periodic systems and the use of wave-function-based (Hartree-Fock), density-based (DFT) and hybrid hamiltonians. The translation and site symmetry consideration is included to establish connection between k-space solid-state physics and real-space quantum chemistry methods in the framework of cyclic model of an infinite crystal. The inclusion of electron correlation effects for periodic systems is considered on the basis of localized crystalline orbitals. The possibilities of LCAO methods for chemical bonding analysis in periodic systems are discussed. The second part deals with the applications of LCAO methods for calculations of bulk crystal properties, including magnetic ordering and crystal structure optimization. The discussion o...

  17. The integration of the contents of the subject Physics-Chemistry (I in Biology-Chemistry specialty

    Directory of Open Access Journals (Sweden)

    M. Sc. Luis AZCUY LORENZ

    2017-12-01

    Full Text Available This work is the result of a research task developed in the Natural Sciences Education Department during 2013-2014 academic year, and it emerged from the necessity of solving some insufficiencies in the use of the real potentialities offered by the content of the subject Physics-Chemistry (I, that is part of the curriculum of the Biology-Chemistry career. Its main objective is to offer a set of exercises to contribute to achieve the integration of contents from the subject Physics-chemistry (I in the mentioned career at «Ignacio Agramonte Loynaz» University of Camaguey. The exercises proposed are characterized for being related to the real practice and to other subjects of the career. Their implementation through review lessons, partial tests and final evaluations during the formative experiment made possible a better academic result in the learners overall performance.

  18. A tracer aided study on silicon chemistry in biological systems

    NARCIS (Netherlands)

    Brasser, H.J.

    2009-01-01

    Silicon (Si) is omnipresent in nature, and it is involved in important but diverse roles in a broad range of organisms, including diatoms, higher plants and humans. Some organisms, like the diatoms, need high amounts of silicon, and master silicon chemistry to a high extend using several enzymes.

  19. Emerging trends at the interface of chemistry and biology ...

    Indian Academy of Sciences (India)

    Administrator

    Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012. 2. Molecular ... cussed. Methods for gene and siRNA delivery are presented along with challenges and opportunities for ..... to engineer mutations in the Fc region of an anti- ... potentially be applied to design immunogens and vaccines for ...

  20. Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry.

    Science.gov (United States)

    Arshad, Junaid; Hoffmann, Alexander; Gesing, Sandra; Grunzke, Richard; Krüger, Jens; Kiss, Tamas; Herres-Pawlis, Sonja; Terstyanszky, Gabor

    2016-01-01

    In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows. Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows. We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository.Graphical AbstractMeta-workflows and embedded workflows in the template representation.

  1. Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree-Fock.

    Science.gov (United States)

    Tamayo-Mendoza, Teresa; Kreisbeck, Christoph; Lindh, Roland; Aspuru-Guzik, Alán

    2018-05-23

    Automatic differentiation (AD) is a powerful tool that allows calculating derivatives of implemented algorithms with respect to all of their parameters up to machine precision, without the need to explicitly add any additional functions. Thus, AD has great potential in quantum chemistry, where gradients are omnipresent but also difficult to obtain, and researchers typically spend a considerable amount of time finding suitable analytical forms when implementing derivatives. Here, we demonstrate that AD can be used to compute gradients with respect to any parameter throughout a complete quantum chemistry method. We present DiffiQult , a Hartree-Fock implementation, entirely differentiated with the use of AD tools. DiffiQult is a software package written in plain Python with minimal deviation from standard code which illustrates the capability of AD to save human effort and time in implementations of exact gradients in quantum chemistry. We leverage the obtained gradients to optimize the parameters of one-particle basis sets in the context of the floating Gaussian framework.

  2. Exploration of the Central Dogma at the Interface of Chemistry and Biology

    Science.gov (United States)

    Zhou, Alice Qinhua

    2010-01-01

    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. PMID:20885900

  3. Exploration of the Central Dogma at the Interface of Chemistry and Biology

    OpenAIRE

    Zhou, Alice Qinhua

    2010-01-01

    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.

  4. Quantum chemistry of the minimal CdSe clusters

    Science.gov (United States)

    Yang, Ping; Tretiak, Sergei; Masunov, Artëm E.; Ivanov, Sergei

    2008-08-01

    Colloidal quantum dots are semiconductor nanocrystals (NCs) which have stimulated a great deal of research and have attracted technical interest in recent years due to their chemical stability and the tunability of photophysical properties. While internal structure of large quantum dots is similar to bulk, their surface structure and passivating role of capping ligands (surfactants) are not fully understood to date. We apply ab initio wavefunction methods, density functional theory, and semiempirical approaches to study the passivation effects of substituted phosphine and amine ligands on the minimal cluster Cd2Se2, which is also used to benchmark different computational methods versus high level ab initio techniques. Full geometry optimization of Cd2Se2 at different theory levels and ligand coverage is used to understand the affinities of various ligands and the impact of ligands on cluster structure. Most possible bonding patterns between ligands and surface Cd/Se atoms are considered, including a ligand coordinated to Se atoms. The degree of passivation of Cd and Se atoms (one or two ligands attached to one atom) is also studied. The results suggest that B3LYP/LANL2DZ level of theory is appropriate for the system modeling, whereas frequently used semiempirical methods (such as AM1 and PM3) produce unphysical results. The use of hydrogen atom for modeling of the cluster passivating ligands is found to yield unphysical results as well. Hence, the surface termination of II-VI semiconductor NCs with hydrogen atoms often used in computational models should probably be avoided. Basis set superposition error, zero-point energy, and thermal corrections, as well as solvent effects simulated with polarized continuum model are found to produce minor variations on the ligand binding energies. The effects of Cd-Se complex structure on both the electronic band gap (highest occupied molecular orbital-lowest unoccupied molecular orbital energy difference) and ligand binding

  5. Photodissociation of quantum state-selected diatomic molecules yields new insight into ultracold chemistry

    Science.gov (United States)

    McDonald, Mickey; McGuyer, Bart H.; Lee, Chih-Hsi; Apfelbeck, Florian; Zelevinsky, Tanya

    2016-05-01

    When a molecule is subjected to a sufficiently energetic photon it can break apart into fragments through a process called ``photodissociation''. For over 70 years this simple chemical reaction has served as a vital experimental tool for acquiring information about molecular structure, since the character of the photodissociative transition can be inferred by measuring the 3D photofragment angular distribution (PAD). While theoretical understanding of this process has gradually evolved from classical considerations to a fully quantum approach, experiments to date have not yet revealed the full quantum nature of this process. In my talk I will describe recent experiments involving the photodissociation of ultracold, optical lattice-trapped, and fully quantum state-resolved 88Sr2 molecules. Optical absorption images of the PADs produced in these experiments reveal features which are inherently quantum mechanical in nature, such as matter-wave interference between output channels, and are sensitive to the quantum statistics of the molecular wavefunctions. The results of these experiments cannot be predicted using quasiclassical methods. Instead, we describe our results with a fully quantum mechanical model yielding new intuition about ultracold chemistry.

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

    Science.gov (United States)

    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.

  7. Crystal density predictions for nitramines based on quantum chemistry

    International Nuclear Information System (INIS)

    Qiu Ling; Xiao Heming; Gong Xuedong; Ju Xuehai; Zhu Weihua

    2007-01-01

    An efficient and convenient method for predicting the crystalline densities of energetic materials was established based on the quantum chemical computations. Density functional theory (DFT) with four different basis sets (6-31G**, 6-311G**, 6-31+G**, and 6-311++G**) and various semiempirical molecular orbital (MO) methods have been employed to predict the molecular volumes and densities of a series of energetic nitramines including acyclic, monocyclic, and polycyclic/cage molecules. The relationships between the calculated values and experimental data were discussed in detail, and linear correlations were suggested and compared at different levels. The calculation shows that if the selected basis set is larger, it will expend more CPU (central processing unit) time, larger molecular volume and smaller density will be obtained. And the densities predicted by the semiempirical MO methods are all systematically larger than the experimental data. In comparison with other methods, B3LYP/6-31G** is most accurate and economical to predict the solid-state densities of energetic nitramines. This may be instructive to the molecular designing and screening novel HEDMs

  8. On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

    Science.gov (United States)

    Turi, László

    2016-04-01

    We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

  9. On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

    Energy Technology Data Exchange (ETDEWEB)

    Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, P.O. Box 32, H-1518 Budapest 112 (Hungary)

    2016-04-21

    We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

  10. Introduction to the Thematic Minireview Series: Green biological chemistry.

    Science.gov (United States)

    Jez, Joseph M

    2018-04-06

    Plants and their green cousins cyanobacteria and algae use sunlight to drive the chemistry that lets them grow, survive, and perform an amazing range of biochemical reactions. The ability of these organisms to use a freely available energy source makes them attractive as sustainable and renewable platforms for more than just food production. They are also a source of metabolic tools for engineering microbes for "green" chemistry. This Thematic Minireview Series discusses how green organisms capture light and protect their photosynthetic machinery from too much light; new structural snapshots of the clock complex that orchestrates signaling during the light/dark cycle; challenges for improving stress responses in crops; harnessing cyanobacteria as biofactories; and efforts to engineer microbes for "green" biopolymer production. © 2018 Jez.

  11. The molecular electron density distribution meeting place of X-ray diffraction and quantum chemistry intermediate - between theory and experiment

    NARCIS (Netherlands)

    Feil, D.; Feil, Dirk

    1992-01-01

    Quantum chemistry and the concepts used daily in chemistry are increasingly growing apart. Among the concepts that are able to bridge the gap between theory and experimental practice, electron density distribution has an important place. The study of this distribution has led to new developments in

  12. Adaptation of quantum chemistry software for the electronic structure calculations on GPU for solid-state systems

    International Nuclear Information System (INIS)

    Gusakov, V.E.; Bel'ko, V.I.; Dorozhkin, N.N.

    2015-01-01

    We report on adaptation of quantum chemistry software - Quantum Espresso and LASTO - for the electronic structure calculations for the complex solid-state systems on the GeForce series GPUs using the nVIDIA CUDA technology. Specifically, protective covering based on transition metal nitrides are considered. (authors)

  13. The use of quantum chemistry in pharmaceutical research as illustrated by case studies of indometacin and carbamazepine

    DEFF Research Database (Denmark)

    Gordon, Keith C; McGoverin, Cushla M; Strachan, Clare J

    2007-01-01

    A number of case studies that illustrate how quantum chemistry may be used in studying pharmaceutical systems are reviewed. A brief introduction to quantum methods is provided and the use of these methods in understanding the structure and properties of indometacin and carbamazepine is discussed...

  14. Scandium: its occurrence, chemistry, physics, metallurgy, biology, and technology

    International Nuclear Information System (INIS)

    Horovitz, C.T.

    1975-01-01

    This book describes the following aspects of scandium: discovery and history, occurrence in nature, geochemistry and mineralogy, chemical, physical and technological properties, fabrication and metallurgy, its biological significance and toxicology, and its uses. (Extensive references for each chapter)

  15. Impact of Theoretical Chemistry on Chemical and Biological Sciences

    Indian Academy of Sciences (India)

    IAS Admin

    theory as applied to biological systems. ... methods to follow the course of chemical reactions devised by. K Fukui and R .... optimize the structure of organic molecules using classical-em- pirical potential ..... science or engineering dis- ciplines.

  16. Laboratory study of nitrate photolysis in Antarctic snow. I. Observed quantum yield, domain of photolysis, and secondary chemistry

    DEFF Research Database (Denmark)

    Meusinger, Carl; Berhanu, Tesfaye A.; Erbland, Joseph

    2014-01-01

    undergoing secondary (recombination) chemistry. Modeled NOx emissions may increase significantly above measured values due to the observed quantum yield in this study. The apparent quantum yield in the 200 nm band was found to be ∼ 1%, much lower than reported for aqueous chemistry. A companion paper...... are understood. It has been shown that photolysis of nitrate in the snowpack plays a major role in nitrate loss and that the photolysis products have a significant influence on the local troposphere as well as on other species in the snow. Reported quantum yields for the main reaction spans orders of magnitude...

  17. Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation

    Directory of Open Access Journals (Sweden)

    Jiyoung Kang

    2012-01-01

    Full Text Available Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs and molecular mechanics (MMs calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

  18. Quantum Chemistry beyond Born–Oppenheimer Approximation on a Quantum Computer: A Simulated Phase Estimation Study

    Czech Academy of Sciences Publication Activity Database

    Veis, Libor; Višňák, Jakub; Nishizawa, H.; Nakai, H.; Pittner, Jiří

    2016-01-01

    Roč. 116, č. 18 (2016), s. 1328-1336 ISSN 0020-7608 R&D Projects: GA ČR GA203/08/0626 Institutional support: RVO:61388955 Keywords : Born-Oppenheimer approximation * nuclear orbital plus molecular orbital method * phase estimation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.920, year: 2016

  19. Can We Describe Biological Systems with Quantum Mechanics?

    International Nuclear Information System (INIS)

    Granados-Ramírez, C G; Benítez-Cardoza, C G; Carbajal-Tinoco, M D

    2016-01-01

    Quantum Mechanics is the favourite theory to predict the structure of any group of atoms, including biological molecules. Due to numerous difficulties, however, it is necessary to introduce a series of approximations to overcome such impediments. We present a coarse-grained model of circular dichroism (CD) that is based on the theory of optical activity, developed by DeVoe, in order to predict CD spectra. In first stage, we determine the polarisability of individual monomers (residues, in the case of peptides) from experiments of molar absorptivity. The complex polarisabilities are used together with peptide structures obtained by density functional theory and other methods to determine their corresponding CD spectra, which are in reasonable agreement with their experimental counterparts. (paper)

  20. Biological Actions of Artemisinin: Insights from Medicinal Chemistry Studies

    Directory of Open Access Journals (Sweden)

    Jian Li

    2010-03-01

    Full Text Available Artemisinins have become essential antimalarial drugs for increasingly widespread drug-resistant malaria strains. Although tremendous efforts have been devoted to decipher how this class of molecules works, their exact antimalarial mechanism is still an enigma. Several hypotheses have been proposed to explain their actions, including alkylation of heme by carbon-centered free radicals, interference with proteins such as the sarcoplasmic/endoplasmic calcium ATPase (SERCA, as well as damaging of normal mitochondrial functions. Besides artemisinins, other endoperoxides with various backbones have also been synthesized, some of which showed comparable or even higher antimalarial effects. It is noteworthy that among these artemisinin derivatives, some enantiomers displayed similar in vitro malaria killing efficacy. In this article, the proposed mechanisms of action of artemisinins are reviewed in light of medicinal chemistry findings characterized by efficacy-structure studies, with the hope of gaining more insight into how these potent drugs work.

  1. Click chemistry mediated functionalization of vertical nanowires for biological applications

    DEFF Research Database (Denmark)

    Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica

    2016-01-01

    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...

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

    Science.gov (United States)

    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. © 2015 The International Union of Biochemistry and Molecular Biology.

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

    Science.gov (United States)

    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. © 2013 by The International Union of Biochemistry and Molecular Biology.

  4. Simple glycolipids of microbes: Chemistry, biological activity and metabolic engineering

    Directory of Open Access Journals (Sweden)

    Ahmad Mohammad Abdel-Mawgoud

    2018-03-01

    Full Text Available Glycosylated lipids (GLs are added-value lipid derivatives of great potential. Besides their interesting surface activities that qualify many of them to act as excellent ecological detergents, they have diverse biological activities with promising biomedical and cosmeceutical applications. Glycolipids, especially those of microbial origin, have interesting antimicrobial, anticancer, antiparasitic as well as immunomodulatory activities. Nonetheless, GLs are hardly accessing the market because of their high cost of production. We believe that experience of metabolic engineering (ME of microbial lipids for biofuel production can now be harnessed towards a successful synthesis of microbial GLs for biomedical and other applications. This review presents chemical groups of bacterial and fungal GLs, their biological activities, their general biosynthetic pathways and an insight on ME strategies for their production.

  5. The Gravity of Regenerative Medicine; Physics, Chemistry & Biology behind it

    Directory of Open Access Journals (Sweden)

    Dedeepiya V

    2008-01-01

    Full Text Available The in-vitro expansion of cells of the organs/tissues and their re-implantation into the affected region/ tissue for treating cell/organ failure have been in practice for long, but in limited specialties. The in-vitro cell culture protocols use variety of biological reagents derived from animal sources and recombinant technologies. However, the optimal quantity of such biological components such as growth factors, cytokines etc.,needed for such cells to be grown in a non-physiological environment is still unknown. The use of such biological components have started to stir a controversy of late, due to the recognition of its potential hazards such as spread of prion diseases and contamination with non-human sialic acid proteins. Therefore synthetic reproducible biomaterials are gaining popularity in cell culture and tissue engineering. The biomaterials made of several chemical components based on physical parameters are starting to change certain concepts about the niche of cell culture and that of stem cell expansion and differentiation to specific lineages. Engler et al have already proven that a simple change in the matrix elasticity alone could change the lineage of the cells. Spencer et al have reported that a change in bioelectricity could change the morphogenesis during development. NCRM has been involved in cell culture and tissue engineering using approximately 240 different materials ranging from polymer hydrogel, gel with adherent inserts, nano composite materials, nano-coating technologies, nano-sheets and nano-films. These materials are used in cell culture in different hybrid combinations such as Floating 3D cell culture without adherent components in a homogenous hydrogel. Floating 3D cell culture with anchorage inserts. Flat surface- 2D adherent cell culture. Combined flat surface 2D cell culture (for differentiating cells and floating 3D culture (for undifferentiated cells. These combinations have started yielding several

  6. Quantum Chemistry, and Eclectic Mix: From Silicon Carbide to Size Consistency

    Energy Technology Data Exchange (ETDEWEB)

    Rintelman, Jamie Marie [Iowa State Univ., Ames, IA (United States)

    2004-12-19

    Chemistry is a field of great breadth and variety. It is this diversity that makes for both an interesting and challenging field. My interests have spanned three major areas of theoretical chemistry: applications, method development, and method evaluation. The topics presented in this thesis are as follows: (1) a multi-reference study of the geometries and relative energies of four atom silicon carbide clusters in the gas phase; (2) the reaction of acetylene on the Si(100)-(2x1) surface; (3) an improvement to the Effective Fragment Potential (EFP) solvent model to enable the study of reactions in both aqueous and nonaqueous solution; and (4) an evaluation of the size consistency of Multireference Perturbation Theory (MRPT). In the following section, the author briefly discusses two topics central to, and present throughout, this thesis: Multi-reference methods and Quantum Mechanics/Molecular Mechanics (QM/MM) methods.

  7. The surface chemistry determines the spatio-temporal interaction dynamics of quantum dots in atherosclerotic lesions.

    Science.gov (United States)

    Uhl, Bernd; Hirn, Stephanie; Mildner, Karina; Coletti, Raffaele; Massberg, Steffen; Reichel, Christoph A; Rehberg, Markus; Zeuschner, Dagmar; Krombach, Fritz

    2018-03-01

    To optimize the design of nanoparticles for diagnosis or therapy of vascular diseases, it is mandatory to characterize the determinants of nano-bio interactions in vascular lesions. Using ex vivo and in vivo microscopy, we analyzed the interactive behavior of quantum dots with different surface functionalizations in atherosclerotic lesions of ApoE-deficient mice. We demonstrate that quantum dots with different surface functionalizations exhibit specific interactive behaviors with distinct molecular and cellular components of the injured vessel wall. Moreover, we show a role for fibrinogen in the regulation of the spatio-temporal interaction dynamics in atherosclerotic lesions. Our findings emphasize the relevance of surface chemistry-driven nano-bio interactions on the differential in vivo behavior of nanoparticles in diseased tissue.

  8. A novel POSS-coated quantum dot for biological application

    Directory of Open Access Journals (Sweden)

    Rizvi SB

    2012-08-01

    Full Text Available Sarwat B Rizvi,1 Lara Yildirimer,1 Shirin Ghaderi,1 Bala Ramesh,1 Alexander M Seifalian,1,2 Mo Keshtgar1,21UCL Centre for Nanotechnology and Regenerative Medicine, Division of Surgery and Interventional Science, University College London, United Kingdom; 2Royal Free Hampstead NHS Trust Hospital, London, United KingdomAbstract: Quantum dots (QDs are fluorescent semiconductor nanocrystals that have the potential for major advancements in the field of nanomedicine through their unique photophysical properties. They can potentially be used as fluorescent probes for various biomedical imaging applications, including cancer localization, detection of micrometastasis, image guided surgery, and targeted drug delivery. Their main limitation is toxicity, which requires a biologically compatible surface coating to shield the toxic core from the surrounding environment. However, this leads to an increase in QD size that may lead to problems of excretion and systemic sequestration. We describe a one pot synthesis, characterization, and in vitro cytotoxicity of a novel polyhedral oligomeric silsesquioxane (POSS-coated CdTe-cored QD using mercaptosuccinic acid (MSA and D-cysteine as stabilizing agents. Characterization was performed using transmission electron microscopy Fourier transform infrared spectroscopy, and photoluminescence studies. POSS-coated QDs demonstrated high colloidal stability and enhanced photostability on high degrees of ultraviolet (UV excitation compared to QDs coated with MSA and D-cysteine alone (P value < 0.05. In vitro toxicity studies showed that both POSS and MSA-QDs were significantly less toxic than ionized salts of Cd+2 and Te-2. Confocal microscopy confirmed high brightness of POSS-QDs in cells at both 1 and 24 hours, indicating that these QDs are rapidly taken up by cells and remain photostable in a biological environment. We therefore conclude that a POSS coating confers biological compatibility, photostability, and colloidal

  9. Biological forcing controls the chemistry of the coral exoskeleton

    Science.gov (United States)

    Meibom, A.; Mostefaoui, S.; Cuif, J.; Yurimoto, H.; Dauphin, Y.; Houlbreque, F.; Dunbar, R.; Constantz, B.

    2006-12-01

    A multitude of marine organisms produce calcium carbonate skeletons that are used extensively to reconstruct water temperature variability of the tropical and subtropical oceans - a key parameter in global climate-change models. Such paleo-climate reconstructions are based on the notion that skeletal oxygen isotopic composition and certain trace-element abundances (e.g., Sr/Ca and Mg/Ca ratios) vary in response to changes in the water temperature. However, it is a fundamental problem that poorly understood biological processes introduce large compositional deviations from thermodynamic equilibrium and hinder precise calibrations of many paleo-climate proxies. Indeed, the role of water temperature in controlling the composition of the skeleton is far from understood. We have studied trace-element abundances as well as oxygen and carbon isotopic compositions of individual skeletal components in the zooxanthellate and non-zooxanthellate corals at ultra-structural, i.e. micrometer to sub-micrometer length scales. From this body of work we draw the following, generalized conclusions: 1) Centers of calcification (COC) are not in equilibrium with seawater. Notably, the Sr/Ca ratio is higher than expected for aragonite equilibrium with seawater at the temperature at which the skeleton was formed. Furthermore, the COC are further away from equilibrium with seawater than fibrous skeleton in terms of stable isotope composition. 2) COC are dramatically different from the fibrous aragonite skeleton in terms of trace element composition. 3) Neither trace element nor stable isotope variations in the fibrous (bulk) part of the skeleton are directly related to changes in SST. In fact, changes in SST can have very little to do with the observed compositional variations. 4) Trace element variations in the fibrous (bulk) part of the skeleton are not related to the activity of zooxanthellae. These observations are directly relevant to the issue of biological versus non-biological

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

    Science.gov (United States)

    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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

    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,…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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…

  16. Where Is Earth Science? Mining for Opportunities in Chemistry, Physics, and Biology

    Science.gov (United States)

    Thomas, Julie; Ivey, Toni; Puckette, Jim

    2013-01-01

    The Earth sciences are newly marginalized in K-12 classrooms. With few high schools offering Earth science courses, students' exposure to the Earth sciences relies on the teacher's ability to incorporate Earth science material into a biology, chemistry, or physics course. ''G.E.T. (Geoscience Experiences for Teachers) in the Field'' is an…

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

    Science.gov (United States)

    Kaski, K.; Salomaa, M.

    1990-01-01

    ), physics (fluid-dynamical and quantum-mechanical calculations; extensive numerical simulations of various condensed-matter systems; the development of stellar constellations, even the early Universe), chemistry (quantum-chemical calculations on the structures of new chemical compounds; chemical reactions and reaction dynamics), and biology (various models, for example, in population dynamics). We succeeded in our effort to assemble several internationally recognized researchers of Computational Science to deliver invited talks on a couple of exceptionally beautiful late-summer days in the modern premises of the Adult Education Center at Lahti. Among the plenary speakers, Per Bak described his highly original work on self-organized criticality. David Ceperley discussed pioneering numerical simulations of superfluid helium in which, for the first time, Feynman's path-integral formulation of quantum mechanics has been implemented on a computer. Jim Gunton presented his comprehensive studies of the Cahn-Hilliard equation for the dynamics of ordering in a condensed-matter system far from equilibrium, while Alex Hansen explained those on nonlinear breakdown in disordered materials. Representing the important field of computational chemistry, Bo Jönsson dealt with attractive forces between polyelectrolytes. Kurt Kremer gave an interesting account on computer-simulation studies of complex polymer systems, while Ole Mouritsen reviewed studies of interfacial fluctuations in lipid membranes. Pekka Pyykkö introduced his pioneering work which has led to predictions of completely novel chemical species. Annette Zippelius gave an expert introduction to the highly active field of neural networks. It is evident from each of these intriguing plenary contributions that, indeed, the computational approach is a frontier field of science, possibly providing the most versatile research method available today. We also arranged a competition for the best Posters presented at the Symposium; the

  18. Nonlinear optical polarization analysis in chemistry and biology

    CERN Document Server

    Simpson, Garth J

    2017-01-01

    This rigorous yet accessible guide presents a molecular-based description of nonlinear optical polarization analysis of chemical and biological assemblies. It includes discussion of the most common nonlinear optical microscopy and interfacial measurements used for quantitative analysis, specifically second harmonic generation (SHG), two-photon excited fluorescence (2PEF), vibrational sum frequency generation (SFG), and coherent anti-Stokes Raman spectroscopy/stimulated Raman spectroscopy (CARS/SRS). A linear algebra mathematical framework is developed, allowing step-wise systematic connections to be made between the observable measurements and the molecular response. Effects considered include local field corrections, the molecular orientation distribution, rotations between the molecular frame, the local frame and the laboratory frame, and simplifications from molecular and macromolecular symmetry. Specific examples are provided throughout the book, working from the common and relatively simple case studies ...

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

    Science.gov (United States)

    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…

  20. Analysis of temporal evolution of quantum dot surface chemistry by surface-enhanced Raman scattering.

    Science.gov (United States)

    Doğan, İlker; Gresback, Ryan; Nozaki, Tomohiro; van de Sanden, Mauritius C M

    2016-07-08

    Temporal evolution of surface chemistry during oxidation of silicon quantum dot (Si-QD) surfaces were probed using surface-enhanced Raman scattering (SERS). A monolayer of hydrogen and chlorine terminated plasma-synthesized Si-QDs were spin-coated on silver oxide thin films. A clearly enhanced signal of surface modes, including Si-Clx and Si-Hx modes were observed from as-synthesized Si-QDs as a result of the plasmonic enhancement of the Raman signal at Si-QD/silver oxide interface. Upon oxidation, a gradual decrease of Si-Clx and Si-Hx modes, and an emergence of Si-Ox and Si-O-Hx modes have been observed. In addition, first, second and third transverse optical modes of Si-QDs were also observed in the SERS spectra, revealing information on the crystalline morphology of Si-QDs. An absence of any of the abovementioned spectral features, but only the first transverse optical mode of Si-QDs from thick Si-QD films validated that the spectral features observed from Si-QDs on silver oxide thin films are originated from the SERS effect. These results indicate that real-time SERS is a powerful diagnostic tool and a novel approach to probe the dynamic surface/interface chemistry of quantum dots, especially when they involve in oxidative, catalytic, and electrochemical surface/interface reactions.

  1. Chemistry and Biological Activities of Flavonoids: An Overview

    Science.gov (United States)

    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

    Directory of Open Access Journals (Sweden)

    Shashank Kumar

    2013-01-01

    Full Text Available 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. Life as physics and chemistry: A system view of biology.

    Science.gov (United States)

    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. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Density functional representation of quantum chemistry. II. Local quantum field theories of molecular matter in terms of the charge density operator do not work

    International Nuclear Information System (INIS)

    Primas, H.; Schleicher, M.

    1975-01-01

    A comprehensive review of the attempts to rephrase molecular quantum mechanics in terms of the particle density operator and the current density or phase density operator is given. All pertinent investigations which have come to attention suffer from severe mathematical inconsistencies and are not adequate to the few-body problem of quantum chemistry. The origin of the failure of these attempts is investigated, and it is shown that a realization of a local quantum field theory of molecular matter in terms of observables would presuppose the solution of many highly nontrivial mathematical problems

  5. 2013 Gordon Research Conference on metals in biology and seminar on bioinorganic chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Rosenzweig, Amy C. [Northwestern Univ., Evanston, IL (United States)

    2013-01-25

    Typical topics for lectures and posters include: biochemical and biophysical characterization of new metal containing proteins, enzymes, nucleic acids, factors, and chelators from all forms of life; synthesis, detailed characterization, and reaction chemistry of biomimetic compounds; novel crystal and solution structures of biological molecules and synthetic metal-chelates; discussions of the roles that metals play in medicine, maintenance of the environment, and biogeochemical processes; metal homeostasis; application of theory and computations to the structure and mechanism of metal-containing biological systems; and novel applications of spectroscopy to metals in biological systems.

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

    Science.gov (United States)

    Gautier, Arnaud; Rodriguez, Raphaël

    2017-05-18

    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. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Quantum-chemistry based calibration of the alkali metal cation series (Li(+)-Cs(+)) for large-scale polarizable molecular mechanics/dynamics simulations.

    Science.gov (United States)

    Dudev, Todor; Devereux, Mike; Meuwly, Markus; Lim, Carmay; Piquemal, Jean-Philip; Gresh, Nohad

    2015-02-15

    The alkali metal cations in the series Li(+)-Cs(+) act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum-chemistry (QC) energy-decomposition analyses of their monoligated complexes with representative O-, N-, S-, and Se- ligands, performed with the aug-cc-pVTZ(-f) basis set at the Hartree-Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation-specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O- ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported. © 2014 Wiley Periodicals, Inc.

  8. The sea surface microlayer: biology, chemistry and anthropogenic enrichment

    Energy Technology Data Exchange (ETDEWEB)

    Hardy, J T

    1982-01-01

    Recent studies increasingly point to the interface between the world's atmosphere and hydrosphere (the sea-surface microlayer) as an important biological habitat and a collection point for anthropogenic materials. Newly developed sampling techniques collect different qualitative and quantitative fractions of the upper sea surface from depths of less than one micron to several centimeters. The microlayer provides a habitat for a biota, including the larvae of many commercial fishery species, which are often highly enriched in density compared to subsurface water only a few cm below. Common enrichments for bacterioneuston, phytoneuston, and zooneuston are 10/sup 2/-10/sup 4/, 1-10/sup 2/, and 1-10, respectively. The trophic relationships or intergrated functioning of these neustonic communities have not been examined. Surface tension forces provide a physically stable microlayer, but one which is subjected to greater environmental and climatic variation than the water column. A number of poorly understood physical processes control the movement and flux of materials within and through the microlayer. The microlayer is generally coated with a natural organic film of lipid and fatty acid material overlying a polysaccharide protein complex. The microlayer serves as both a source and a sink for materials in the atmosphere and the water column. Among these materials are large quantities of anthropogenic substances which frequently occur at concentrations 10/sup 2/-10/sup 4/ greater than those in the water column. These include plastics, tar lumps, polyaromatic hydrocarbons, chlorinated hydrocarbons, and potentially toxic metals, such as, lead, copper, zinc, and nickel. How the unique processes occurring in the microlayer affect the fate of anthropogenic substances is not yet clear.

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

    Science.gov (United States)

    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.

  10. A Synthesis of Fluid Dynamics and Quantum Chemistry for the Design of Nanoelectronics

    Science.gov (United States)

    MacDougall, Preston J.

    1998-01-01

    In 1959, during a famous lecture entitled "There's Plenty of Room at the Bottom", Richard Feynman focused on the startling technical possibilities that would exist at the limit of miniaturization, that being atomically precise devices with dimensions in the nanometer range. A nanometer is both a convenient unit of length for medium to large sized molecules, and the root of the name of the new interdisciplinary field of "nanotechnology". Essentially, "nanoelectronics" denotes the goal of shrinking electronic devices, such as diodes and transistors, as well as integrated circuits of such devices that can perform logical operations, down to dimensions in the range of 100 nanometers. The thirty-year hiatus in the development of nanotechnology can figuratively be seen as a period of waiting for the bottom-up and atomically precise construction skills of synthetic chemistry to meet the top-down reductionist aspirations of device physics. The sub-nanometer domain of nineteenth-century classical chemistry has steadily grown, and state-of-the-art supramolecular chemistry can achieve atomic precision in non-repeating molecular assemblies of the size desired for nanotechnology. For nanoelectronics in particular, a basic understanding of the electron transport properties of molecules must also be developed. Quantum chemistry provides powerful computational methods that can accurately predict the properties of small to medium sized molecules on a desktop workstation, and those of large molecules if one has access to a supercomputer. Of the many properties of a molecule that quantum chemistry routinely predicts, the ability to carry a current is one that had not even been considered until recently. "Currently", there is a controversy over just how to define this key property. Reminiscent of the situation in high-Tc superconductivity, much of the difficulty arises from the different models that are used to simplify the complex electronic structure of real materials. A model

  11. Parallel algorithms for quantum chemistry. I. Integral transformations on a hypercube multiprocessor

    International Nuclear Information System (INIS)

    Whiteside, R.A.; Binkley, J.S.; Colvin, M.E.; Schaefer, H.F. III

    1987-01-01

    For many years it has been recognized that fundamental physical constraints such as the speed of light will limit the ultimate speed of single processor computers to less than about three billion floating point operations per second (3 GFLOPS). This limitation is becoming increasingly restrictive as commercially available machines are now within an order of magnitude of this asymptotic limit. A natural way to avoid this limit is to harness together many processors to work on a single computational problem. In principle, these parallel processing computers have speeds limited only by the number of processors one chooses to acquire. The usefulness of potentially unlimited processing speed to a computationally intensive field such as quantum chemistry is obvious. If these methods are to be applied to significantly larger chemical systems, parallel schemes will have to be employed. For this reason we have developed distributed-memory algorithms for a number of standard quantum chemical methods. We are currently implementing these on a 32 processor Intel hypercube. In this paper we present our algorithm and benchmark results for one of the bottleneck steps in quantum chemical calculations: the four index integral transformation

  12. Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution

    Directory of Open Access Journals (Sweden)

    Ivan B. Djordjevic

    2015-08-01

    Full Text Available Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i Markovian classical model, (ii Markovian-like quantum model, and (iii hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage Markov chain-like models of aging, which

  13. A model of biological neuron with terminal chaos and quantum-like features

    International Nuclear Information System (INIS)

    Conte, Elio; Pierri, GianPaolo; Federici, Antonio; Mendolicchio, Leonardo; Zbilut, Joseph P.

    2006-01-01

    A model of biological neuron is proposed combining terminal dynamics with quantum-like mechanical features, assuming the spin to be an important entity in neurodynamics, and, in particular, in synaptic transmission

  14. Coupled effects of solution chemistry and hydrodynamics on the mobility and transport of quantum dot nanomaterials in the Vadose Zone

    Science.gov (United States)

    To investigate the coupled effects of solution chemistry and vadose zone processes on the mobility of quantum dot (QD) nanoparticles, laboratory scale transport experiments were performed. The complex coupled effects of ionic strength, size of QD aggregates, surface tension, contact angle, infiltrat...

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

    Science.gov (United States)

    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. Designing a 'neotissue' using the principles of biology, chemistry and engineering.

    Science.gov (United States)

    Nannaparaju, Madhusudhan; Oragui, Emeka; Khan, Wasim S

    2012-01-01

    The traditional methods of treating musculoskeletal injuries and disorders are not completely effective and have several limitations. Tissue engineering involves using the principles of biology, chemistry and engineering to design a 'neotissue' that augments a malfunctioning in vivo tissue. The main requirements for functional engineered tissue include reparative cellular components that proliferate on a scaffold grown within a bioreactor that provides specific biochemical and physical signals to regulate cell differentiation and tissue assembly. In this review we provide an overview of the biology of common musculoskeletal tissue and discuss their common pathologies. We also describe the commonly used stem cells, scaffolds and bioreactors and evaluate their role in issue engineering.

  17. An Unprecedented Revolution in Medicinal Chemistry Driven by the Progress of Biological Science.

    Science.gov (United States)

    Chou, Kuo-Chen

    2017-01-01

    The eternal or ultimate goal of medicinal chemistry is to find most effective ways to treat various diseases and extend human beings' life as long as possible. Human being is a biological entity. To realize such an ultimate goal, the inputs or breakthroughs from the advances in biological science are no doubt most important that may even drive medicinal science into a revolution. In this review article, we are to address this from several different angles. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  18. Living GenoChemetics by hyphenating synthetic biology and synthetic chemistry in vivo.

    Science.gov (United States)

    Sharma, Sunil V; Tong, Xiaoxue; Pubill-Ulldemolins, Cristina; Cartmell, Christopher; Bogosyan, Emma J A; Rackham, Emma J; Marelli, Enrico; Hamed, Refaat B; Goss, Rebecca J M

    2017-08-09

    Marrying synthetic biology with synthetic chemistry provides a powerful approach toward natural product diversification, combining the best of both worlds: expediency and synthetic capability of biogenic pathways and chemical diversity enabled by organic synthesis. Biosynthetic pathway engineering can be employed to insert a chemically orthogonal tag into a complex natural scaffold affording the possibility of site-selective modification without employing protecting group strategies. Here we show that, by installing a sufficiently reactive handle (e.g., a C-Br bond) and developing compatible mild aqueous chemistries, synchronous biosynthesis of the tagged metabolite and its subsequent chemical modification in living culture can be achieved. This approach can potentially enable many new applications: for example, assay of directed evolution of enzymes catalyzing halo-metabolite biosynthesis in living cells or generating and following the fate of tagged metabolites and biomolecules in living systems. We report synthetic biological access to new-to-nature bromo-metabolites and the concomitant biorthogonal cross-coupling of halo-metabolites in living cultures.Coupling synthetic biology and chemical reactions in cells is a challenging task. The authors engineer bacteria capable of generating bromo-metabolites, develop a mild Suzuki-Miyaura cross-coupling reaction compatible with cell growth and carry out the cross-coupling chemistry in live cell cultures.

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Multireference quantum chemistry through a joint density matrix renormalization group and canonical transformation theory.

    Science.gov (United States)

    Yanai, Takeshi; Kurashige, Yuki; Neuscamman, Eric; Chan, Garnet Kin-Lic

    2010-01-14

    We describe the joint application of the density matrix renormalization group and canonical transformation theory to multireference quantum chemistry. The density matrix renormalization group provides the ability to describe static correlation in large active spaces, while the canonical transformation theory provides a high-order description of the dynamic correlation effects. We demonstrate the joint theory in two benchmark systems designed to test the dynamic and static correlation capabilities of the methods, namely, (i) total correlation energies in long polyenes and (ii) the isomerization curve of the [Cu(2)O(2)](2+) core. The largest complete active spaces and atomic orbital basis sets treated by the joint DMRG-CT theory in these systems correspond to a (24e,24o) active space and 268 atomic orbitals in the polyenes and a (28e,32o) active space and 278 atomic orbitals in [Cu(2)O(2)](2+).

  1. The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age.

    Science.gov (United States)

    Adams, Sam; de Castro, Pablo; Echenique, Pablo; Estrada, Jorge; Hanwell, Marcus D; Murray-Rust, Peter; Sherwood, Paul; Thomas, Jens; Townsend, Joe

    2011-10-14

    Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication.In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today.Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other

  2. The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age

    Directory of Open Access Journals (Sweden)

    Adams Sam

    2011-10-01

    Full Text Available Abstract Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication. In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today. Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of

  3. Molecular Studies of Complex Soil Organic Matter Interactions with Metal Ions and Mineral Surfaces using Classical Molecular Dynamics and Quantum Chemistry Methods

    Science.gov (United States)

    Andersen, A.; Govind, N.; Laskin, A.

    2017-12-01

    Mineral surfaces have been implicated as potential protectors of soil organic matter (SOM) against decomposition and ultimate mineralization to small molecules which can provide nutrients for plants and soil microbes and can also contribute to the Earth's elemental cycles. SOM is a complex mixture of organic molecules of biological origin at varying degrees of decomposition and can, itself, self-assemble in such a way as to expose some biomolecule types to biotic and abiotic attack while protecting other biomolecule types. The organization of SOM and SOM with mineral surfaces and solvated metal ions is driven by an interplay of van der Waals and electrostatic interactions leading to partitioning of hydrophilic (e.g. sugars) and hydrophobic (e.g., lipids) SOM components that can be bridged with amphiphilic molecules (e.g., proteins). Classical molecular dynamics simulations can shed light on assemblies of organic molecules alone or complexation with mineral surfaces. The role of chemical reactions is also an important consideration in potential chemical changes of the organic species such as oxidation/reduction, degradation, chemisorption to mineral surfaces, and complexation with solvated metal ions to form organometallic systems. For the study of chemical reactivity, quantum chemistry methods can be employed and combined with structural insight provided by classical MD simulations. Moreover, quantum chemistry can also simulate spectroscopic signatures based on chemical structure and is a valuable tool in interpreting spectra from, notably, x-ray absorption spectroscopy (XAS). In this presentation, we will discuss our classical MD and quantum chemistry findings on a model SOM system interacting with mineral surfaces and solvated metal ions.

  4. GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations.

    Science.gov (United States)

    Maia, Julio Daniel Carvalho; Urquiza Carvalho, Gabriel Aires; Mangueira, Carlos Peixoto; Santana, Sidney Ramos; Cabral, Lucidio Anjos Formiga; Rocha, Gerd B

    2012-09-11

    In this study, we present some modifications in the semiempirical quantum chemistry MOPAC2009 code that accelerate single-point energy calculations (1SCF) of medium-size (up to 2500 atoms) molecular systems using GPU coprocessors and multithreaded shared-memory CPUs. Our modifications consisted of using a combination of highly optimized linear algebra libraries for both CPU (LAPACK and BLAS from Intel MKL) and GPU (MAGMA and CUBLAS) to hasten time-consuming parts of MOPAC such as the pseudodiagonalization, full diagonalization, and density matrix assembling. We have shown that it is possible to obtain large speedups just by using CPU serial linear algebra libraries in the MOPAC code. As a special case, we show a speedup of up to 14 times for a methanol simulation box containing 2400 atoms and 4800 basis functions, with even greater gains in performance when using multithreaded CPUs (2.1 times in relation to the single-threaded CPU code using linear algebra libraries) and GPUs (3.8 times). This degree of acceleration opens new perspectives for modeling larger structures which appear in inorganic chemistry (such as zeolites and MOFs), biochemistry (such as polysaccharides, small proteins, and DNA fragments), and materials science (such as nanotubes and fullerenes). In addition, we believe that this parallel (GPU-GPU) MOPAC code will make it feasible to use semiempirical methods in lengthy molecular simulations using both hybrid QM/MM and QM/QM potentials.

  5. Quantum chemistry calculation and experimental study on coal ash fusion characteristics of coal blend

    Energy Technology Data Exchange (ETDEWEB)

    Chen Yushuang; Zhang Zhong-xiao; Wu Xiao-jiang; Li Jie; Guang Rong-qing; Yan Bo [University of Shanghai for Science and Technology, Shanghai (China). Department of Power Engineering

    2009-07-01

    The coal ash fusion characteristics of high fusibility coal blending with two low fusibility coals respectively were studied. The data were analyzed using quantum chemistry methods and experiment from micro-and macro-molecular structures. The results show that Ca{sup 2+}, as the electron acceptor, easily enters into the lattice of mullite, causing a transition from mullite to anorthite. Mullite is much more stable than anorthite. Ca{sup 2+} of anorthite occupies the larger cavities with the (SiO{sub 4}){sup 4-} tetrahedral or (AlO{sub 4}){sup 5-} tetrahedral rings respectively. Ca atom linked O weakens Si-O bond, leading ash fusion point to reduce effectively. The chemistry, reactivity sites and bond-formation characteristics of minerals can well explain the reaction mechanism refractory minerals and flux ash melting process at high temperature. The results of experiment are agreed with the theory analysis by using ternary phase diagrams and quantitative calculation. 27 refs., 9 figs., 3 tabs.

  6. Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

    Science.gov (United States)

    Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

    2018-06-13

    An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

  7. The structural chemistry of metallocorroles: combined X-ray crystallography and quantum chemistry studies afford unique insights.

    Science.gov (United States)

    Thomas, Kolle E; Alemayehu, Abraham B; Conradie, Jeanet; Beavers, Christine M; Ghosh, Abhik

    2012-08-21

    Although they share some superficial structural similarities with porphyrins, corroles, trianionic ligands with contracted cores, give rise to fundamentally different transition metal complexes in comparison with the dianionic porphyrins. Many metallocorroles are formally high-valent, although a good fraction of them are also noninnocent, with significant corrole radical character. These electronic-structural characteristics result in a variety of fascinating spectroscopic behavior, including highly characteristic, paramagnetically shifted NMR spectra and textbook cases of charge-transfer spectra. Although our early research on corroles focused on spectroscopy, we soon learned that the geometric structures of metallocorroles provide a fascinating window into their electronic-structural characteristics. Thus, we used X-ray structure determinations and quantum chemical studies, chiefly using DFT, to obtain a comprehensive understanding of metallocorrole geometric and electronic structures. This Account describes our studies of the structural chemistry of metallocorroles. At first blush, the planar or mildly domed structure of metallocorroles might appear somewhat uninteresting particularly when compared to metalloporphyrins. Metalloporphyrins, especially sterically hindered ones, are routinely ruffled or saddled, but the missing meso carbon apparently makes the corrole skeleton much more resistant to nonplanar distortions. Ruffling, where the pyrrole rings are alternately twisted about the M-N bonds, is energetically impossible for metallocorroles. Saddling is also uncommon; thus, a number of sterically hindered, fully substituted metallocorroles exhibit almost perfectly planar macrocycle cores. Against this backdrop, copper corroles stand out as an important exception. As a result of an energetically favorable Cu(d(x2-y2))-corrole(π) orbital interaction, copper corroles, even sterically unhindered ones, are inherently saddled. Sterically hindered substituents

  8. Isoprostanes, neuroprostanes and phytoprostanes: An overview of 25years of research in chemistry and biology.

    Science.gov (United States)

    Galano, Jean-Marie; Lee, Yiu Yiu; Oger, Camille; Vigor, Claire; Vercauteren, Joseph; Durand, Thierry; Giera, Martin; Lee, Jetty Chung-Yung

    2017-10-01

    Since the beginning of the 1990's diverse types of metabolites originating from polyunsaturated fatty acids, formed under autooxidative conditions were discovered. Known as prostaglandin isomers (or isoprostanoids) originating from arachidonic acid, neuroprostanes from docosahexaenoic acid, and phytoprostanes from α-linolenic acid proved to be prevalent in biology. The syntheses of these compounds by organic chemists and the development of sophisticated mass spectrometry methods has boosted our understanding of the isoprostanoid biology. In recent years, it has become accepted that these molecules not only serve as markers of oxidative damage but also exhibit a wide range of bioactivities. In addition, isoprostanoids have emerged as indicators of oxidative stress in humans and their environment. This review explores in detail the isoprostanoid chemistry and biology that has been achieved in the past three decades. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Medicinal and Biological Chemistry (MBC) Library: An Efficient Source of New Hits.

    Science.gov (United States)

    Sebastián-Pérez, Víctor; Roca, Carlos; Awale, Mahendra; Reymond, Jean-Louis; Martinez, Ana; Gil, Carmen; Campillo, Nuria E

    2017-09-25

    Identification of new hits is one of the biggest challenges in drug discovery. Creating a library of well-characterized drug-like compounds is a key step in this process. Our group has developed an in-house chemical library called the Medicinal and Biological Chemistry (MBC) library. This collection has been successfully used to start several medicinal chemistry programs and developed in an accumulation of more than 30 years of experience in drug design and discovery of new drugs for unmet diseases. It contains over 1000 compounds, mainly heterocyclic scaffolds. In this work, analysis of drug-like properties and comparative study with well-known libraries by using different computer software are presented here.

  10. Materials of 4. international meeting on pulse investigations in physics, chemistry and biology. PULS'94

    International Nuclear Information System (INIS)

    1994-01-01

    4. International Meeting on Pulse Investigations in Physics, Chemistry and Biology, PULS'94 has been organized in honor of Professor Jerzy Kroh, the precursor of radiation chemistry in Poland. The meeting has been divided into three sessions: the historical session (H) with four review lectures, lecture session (L) collected 23 papers and poster session (P) with 39 posters. The fundamental studies on early stages of radiolysis have been presented for different systems being irradiated. The pulse radiolysis and flash photolysis methods has been predominantly used in reported experimental works. The reaction of intermediate products of radiolysis and photolysis such a trapped and solvated electrons, ions and radicals has been extensively studied. The reaction mechanisms and kinetics have been also discussed

  11. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

    Science.gov (United States)

    2013-01-01

    Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

  12. Interconnection of reactive oxygen species chemistry across the interfaces of atmospheric, environmental, and biological processes.

    Science.gov (United States)

    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

  13. 2-Aminothiophene scaffolds: Diverse biological and pharmacological attributes in medicinal chemistry.

    Science.gov (United States)

    Bozorov, Khurshed; Nie, Li Fei; Zhao, Jiangyu; Aisa, Haji A

    2017-11-10

    2-Aminothiophenes are important five-membered heterocyclic building blocks in organic synthesis, and the chemistry of these small molecules is still developing based on the discovery of cyclization by Gewald. Another attractive feature of 2-aminothiophene scaffolds is their ability to act as synthons for the synthesis of biological active thiophene-containing heterocycles, conjugates and hybrids. Currently, the biological actions of 2-aminothiophenes or their 2-N-substituted analogues are still being investigated because of their various mechanisms of action (e.g., pharmacophore and pharmacokinetic properties). Likewise, the 2-aminothiophene family is used as diverse promising selective inhibitors, receptors, and modulators in medicinal chemistry, and these compounds even exhibit effective pharmacological properties in the various clinical phases of appropriate diseases. In this review, major biological and pharmacological reports on 2-aminothiophenes and related compounds have been highlighted; most perspective drug-candidate hits were selected for discussion and described, along with additional synthetic pathways. In addition, we focused on the literature dedicated to 2-aminothiophenes and 2-N-substituted derivatives, which have been published from 2010 to 2017. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  14. Student selection: are the school-leaving A-level grades in biology and chemistry important?

    Science.gov (United States)

    Green, A; Peters, T J; Webster, D J

    1993-01-01

    This study determined the relationships of grades in A-level biology and chemistry with examination success or failure during the medical course. By inspection of medical student records, A-level grades at entry to medical school and examination performance were obtained for 128 (91%) of the students who sat their final MBBCh examination at the University of Wales College of Medicine in June 1988. The majority, 92 (72%), completed their medical school careers with no professional examination failures; 15 failed examinations just in the period up to 2nd MB; 11 failed examinations in the clinical period only and 10 failed examinations in both periods. Whereas grade achieved in A-level chemistry was not associated with undergraduate examination performance, students with a grade A or B in A-level biology were less likely to have problems than the others (21% compared with 47%; the difference of 26% has a 95% confidence interval of 7% to 44%). Specifically, there appears to be a strong relationship between a low grade in biology and difficulties in the preclinical examinations. Moreover, for those who have difficulties at this stage, this association continues later in the course.

  15. Quantum annealing versus classical machine learning applied to a simplified computational biology problem

    Science.gov (United States)

    Li, Richard Y.; Di Felice, Rosa; Rohs, Remo; Lidar, Daniel A.

    2018-01-01

    Transcription factors regulate gene expression, but how these proteins recognize and specifically bind to their DNA targets is still debated. Machine learning models are effective means to reveal interaction mechanisms. Here we studied the ability of a quantum machine learning approach to predict binding specificity. Using simplified datasets of a small number of DNA sequences derived from actual binding affinity experiments, we trained a commercially available quantum annealer to classify and rank transcription factor binding. The results were compared to state-of-the-art classical approaches for the same simplified datasets, including simulated annealing, simulated quantum annealing, multiple linear regression, LASSO, and extreme gradient boosting. Despite technological limitations, we find a slight advantage in classification performance and nearly equal ranking performance using the quantum annealer for these fairly small training data sets. Thus, we propose that quantum annealing might be an effective method to implement machine learning for certain computational biology problems. PMID:29652405

  16. Quantum annealing versus classical machine learning applied to a simplified computational biology problem

    Science.gov (United States)

    Li, Richard Y.; Di Felice, Rosa; Rohs, Remo; Lidar, Daniel A.

    2018-03-01

    Transcription factors regulate gene expression, but how these proteins recognize and specifically bind to their DNA targets is still debated. Machine learning models are effective means to reveal interaction mechanisms. Here we studied the ability of a quantum machine learning approach to classify and rank binding affinities. Using simplified data sets of a small number of DNA sequences derived from actual binding affinity experiments, we trained a commercially available quantum annealer to classify and rank transcription factor binding. The results were compared to state-of-the-art classical approaches for the same simplified data sets, including simulated annealing, simulated quantum annealing, multiple linear regression, LASSO, and extreme gradient boosting. Despite technological limitations, we find a slight advantage in classification performance and nearly equal ranking performance using the quantum annealer for these fairly small training data sets. Thus, we propose that quantum annealing might be an effective method to implement machine learning for certain computational biology problems.

  17. N-acylsulfonamides: Synthetic routes and biological potential in medicinal chemistry.

    Science.gov (United States)

    Ammazzalorso, Alessandra; De Filippis, Barbara; Giampietro, Letizia; Amoroso, Rosa

    2017-12-01

    Sulfonamide is a common structural motif in naturally occurring and synthetic medicinal compounds. The rising interest in sulfonamides and N-acyl derivatives is attested by the large number of drugs and lead compounds identified in last years, explored in different fields of medicinal chemistry and showing biological activity. Many acylsulfonamide derivatives were designed and synthesized as isosteres of carboxylic acids, being the characteristics of these functional groups very close. Starting from chemical routes to N-acylsulfonamides, this review explores compounds of pharmaceutical interest, developed as enzymatic inhibitors or targeting receptors. © 2017 John Wiley & Sons A/S.

  18. Chemistry

    International Nuclear Information System (INIS)

    Ferris, L.M.

    1975-01-01

    The chemical research and development efforts related to the design and ultimate operation of molten-salt breeder reactor systems are concentrated on fuel- and coolant-salt chemistry, including the development of analytical methods for use in these systems. The chemistry of tellurium in fuel salt is being studied to help elucidate the role of this element in the intergranular cracking of Hastelloy N. Studies were continued of the effect of oxygen-containing species on the equilibrium between dissolved UF 3 and dissolved UF 4 , and, in some cases, between the dissolved uranium fluorides and graphite, and the UC 2 . Several aspects of coolant-salt chemistry are under investigation. Hydroxy and oxy compounds that could be formed in molten NaBF 4 are being synthesized and characterized. Studies of the chemistry of chromium (III) compounds in fluoroborate melts were continued as part of a systematic investigation of the corrosion of structural alloys by coolant salt. An in-line voltammetric method for determining U 4+ /U 3+ ratios in fuel salt was tested in a forced-convection loop over a six-month period. (LK)

  19. Fluorescent porous silicon biological probes with high quantum efficiency and stability.

    Science.gov (United States)

    Tu, Chang-Ching; Chou, Ying-Nien; Hung, Hsiang-Chieh; Wu, Jingda; Jiang, Shaoyi; Lin, Lih Y

    2014-12-01

    We demonstrate porous silicon biological probes as a stable and non-toxic alternative to organic dyes or cadmium-containing quantum dots for imaging and sensing applications. The fluorescent silicon quantum dots which are embedded on the porous silicon surface are passivated with carboxyl-terminated ligands through stable Si-C covalent bonds. The porous silicon bio-probes have shown photoluminescence quantum yield around 50% under near-UV excitation, with high photochemical and thermal stability. The bio-probes can be efficiently conjugated with antibodies, which is confirmed by a standard enzyme-linked immunosorbent assay (ELISA) method.

  20. A Component Approach to Collaborative Scientific Software Development: Tools and Techniques Utilized by the Quantum Chemistry Science Application Partnership

    Directory of Open Access Journals (Sweden)

    Joseph P. Kenny

    2008-01-01

    Full Text Available Cutting-edge scientific computing software is complex, increasingly involving the coupling of multiple packages to combine advanced algorithms or simulations at multiple physical scales. Component-based software engineering (CBSE has been advanced as a technique for managing this complexity, and complex component applications have been created in the quantum chemistry domain, as well as several other simulation areas, using the component model advocated by the Common Component Architecture (CCA Forum. While programming models do indeed enable sound software engineering practices, the selection of programming model is just one building block in a comprehensive approach to large-scale collaborative development which must also address interface and data standardization, and language and package interoperability. We provide an overview of the development approach utilized within the Quantum Chemistry Science Application Partnership, identifying design challenges, describing the techniques which we have adopted to address these challenges and highlighting the advantages which the CCA approach offers for collaborative development.

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

    Science.gov (United States)

    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)

  2. Teleology in biology, chemistry and physics education: what primary teachers should know

    Directory of Open Access Journals (Sweden)

    KOSTAS KAMPOURAKIS

    2007-01-01

    Full Text Available Recent research in cognitive psychology suggests that children develop intuitions that may clash with what is accepted by scientists, thus making certain scientific concepts difficult to understand. Children possess intuitions about design and purpose that make them provide teleological explanations to many different sorts of tasks. One possible explanation for the origin of the bias to view objects as made for something derives from an early sensitivity to intentional agents and to their behavior as intentional object users and object makers. What is important is that teleological explanations may not be exclusively restricted in biological phenomena, as commonly assumed. Consequently, primary school teachers should take that into account when teaching biology, chemistry or physics concepts and try to refrain from enforcing students’ teleological intuitions.

  3. Review of the genus Ipomoea: traditional uses, chemistry and biological activities

    Directory of Open Access Journals (Sweden)

    Marilena Meira

    Full Text Available Approximately 600-700 species of Ipomoea, Convolvulaceae, are found throughout tropical and subtropical regions of the world. Several of those species have been used as ornamental plants, food, medicines or in religious ritual. The present work reviews the traditional uses, chemistry and biological activities of Ipomoea species and illustrates the potential of the genus as a source of therapeutic agents. These species are used in different parts of the world for the treatment of several diseases, such as, diabetes, hypertension, dysentery, constipation, fatigue, arthritis, rheumatism, hydrocephaly, meningitis, kidney ailments and inflammations. Some of these species showed antimicrobial, analgesic, spasmolitic, spasmogenic, hypoglycemic, hypotensive, anticoagulant, anti-inflammatory, psychotomimetic and anticancer activities. Alkaloids, phenolics compounds and glycolipids are the most common biologically active constituents from these plant extracts.

  4. [Research progress and trend analysis of biology and chemistry of Taxus medicinal resources].

    Science.gov (United States)

    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.

  5. Review and needs in actinide chemistry in relation with biological purposes

    Energy Technology Data Exchange (ETDEWEB)

    Ansoborlo, E.; Moulin, V.; Bion, L.; Doizi, D.; Moulin, C.; Cote, G.; Madic, C.; Van der Lee, J

    2004-07-01

    In case of accidental release of radionuclides in the environment, actinides could occur and may present an healthy risk for human beings. In order to study their behavior in human organism (metabolism, retention, excretion), it is of prime importance to know solution actinide chemistry, and more particularly thermodynamic constants, which will allow to determine their speciation: speciation governs biological availability and toxicity of elements and is also of great interest for decorporation purposes. In this framework, a CEA working group on speciation has been created in order to share data both on thermodynamic constants and on speciation analytical methods, interesting chemists, environmentalists and biologists. It has been focused, in a first time, on actinides. The purpose of this paper is to present the state of the art on actinide speciation within biological media and to focus on the lack of information in order to orientate future research. (authors)

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

    Directory of Open Access Journals (Sweden)

    Ryan P Womack

    Full Text Available 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.

  7. Spectral methods in chemistry and physics applications to kinetic theory and quantum mechanics

    CERN Document Server

    Shizgal, Bernard

    2015-01-01

    This book is a pedagogical presentation of the application of spectral and pseudospectral methods to kinetic theory and quantum mechanics. There are additional applications to astrophysics, engineering, biology and many other fields. The main objective of this book is to provide the basic concepts to enable the use of spectral and pseudospectral methods to solve problems in diverse fields of interest and to a wide audience. While spectral methods are generally based on Fourier Series or Chebychev polynomials, non-classical polynomials and associated quadratures are used for many of the applications presented in the book. Fourier series methods are summarized with a discussion of the resolution of the Gibbs phenomenon. Classical and non-classical quadratures are used for the evaluation of integrals in reaction dynamics including nuclear fusion, radial integrals in density functional theory, in elastic scattering theory and other applications. The subject matter includes the calculation of transport coefficient...

  8. Implications of causality for quantum biology - I: topology change

    Science.gov (United States)

    Scofield, D. F.; Collins, T. C.

    2018-06-01

    A framework for describing the causal, topology changing, evolution of interacting biomolecules is developed. The quantum dynamical manifold equations (QDMEs) derived from this framework can be related to the causality restrictions implied by a finite speed of light and to Planck's constant to set a transition frequency scale. The QDMEs imply conserved stress-energy, angular-momentum and Noether currents. The functional whose extremisation leads to this result provides a causal, time-dependent, non-equilibrium generalisation of the Hohenberg-Kohn theorem. The system of dynamical equations derived from this functional and the currents J derived from the QDMEs are shown to be causal and consistent with the first and second laws of thermodynamics. This has the potential of allowing living systems to be quantum mechanically distinguished from non-living ones.

  9. Quantum confinement and surface chemistry of 0.8–1.6 nm hydrosilylated silicon nanocrystals

    International Nuclear Information System (INIS)

    Pi Xiao-Dong; Wang Rong; Yang De-Ren

    2014-01-01

    In the framework of density functional theory (DFT), we have studied the electronic properties of alkene/alkyne-hydrosilylated silicon nanocrystals (Si NCs) in the size range from 0.8 nm to 1.6 nm. Among the alkenes with all kinds of functional groups considered in this work, only those containing —NH 2 and —C 4 H 3 S lead to significant hydrosilylation-induced changes in the gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of an Si NC at the ground state. The quantum confinement effect is dominant for all of the alkene-hydrosilylated Si NCs at the ground state. At the excited state, the prevailing effect of surface chemistry only occurs at the smallest (0.8 nm) Si NCs hydrosilylated with alkenes containing —NH 2 and —C 4 H 3 S. Although the alkyne hydrosilylation gives rise to a more significant surface chemistry effect than alkene hydrosilylation, the quantum confinement effect remains dominant for alkyne-hydrosilylated Si NCs at the ground state. However, at the excited state, the effect of surface chemistry induced by the hydrosilylation with conjugated alkynes is strong enough to prevail over that of quantum confinement. (condensed matter: structural, mechanical, and thermal properties)

  10. Performance Optimization of Tensor Contraction Expressions for Many Body Methods in Quantum Chemistry

    International Nuclear Information System (INIS)

    Hartono, Albert; Lu, Qingda; Henretty, Thomas; Krishnamoorthy, Sriram; Zhang, Huaijian; Baumgartner, Gerald; Bernholdt, David E.; Nooijen, Marcel; Pitzer, Russell M.; Ramanujam, J.; Sadayappan, Ponnuswamy

    2009-01-01

    Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to significantly decrease the number of arithmetic operations required for evaluation of these expressions. The identification of common subexpressions among a set of tensor contraction expressions can result in a reduction of the total number of operations required to evaluate the tensor contractions. The first part of the paper describes an effective algorithm for operation minimization with common subexpression identification and demonstrates its effectiveness on tensor contraction expressions for coupled cluster equations. The second part of the paper highlights the importance of data layout transformation in the optimization of tensor contraction computations on modern processors. A number of considerations such as minimization of cache misses and utilization of multimedia vector instructions are discussed. A library for efficient index permutation of multi-dimensional tensors is described and experimental performance data is provided that demonstrates its effectiveness.

  11. Performance Optimization of Tensor Contraction Expressions for Many Body Methods in Quantum Chemistry

    International Nuclear Information System (INIS)

    Krishnamoorthy, Sriram; Bernholdt, David E.; Pitzer, R.M.; Sadayappan, Ponnuswamy

    2009-01-01

    Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to significantly decrease the number of arithmetic operations required for evaluation of these expressions. The identification of common subexpressions among a set of tensor contraction expressions can result in a reduction of the total number of operations required to evaluate the tensor contractions. The first part of the paper describes an effective algorithm for operation minimization with common subexpression identification and demonstrates its effectiveness on tensor contraction expressions for coupled cluster equations. The second part of the paper highlights the importance of data layout transformation in the optimization of tensor contraction computations on modern processors. A number of considerations, such as minimization of cache misses and utilization of multimedia vector instructions, are discussed. A library for efficient index permutation of multidimensional tensors is described, and experimental performance data is provided that demonstrates its effectiveness.

  12. Time-dependent quantum chemistry of laser driven many-electron molecules

    International Nuclear Information System (INIS)

    Nguyen-Dang, Thanh-Tung; Couture-Bienvenue, Étienne; Viau-Trudel, Jérémy; Sainjon, Amaury

    2014-01-01

    A Time-Dependent Configuration Interaction approach using multiple Feshbach partitionings, corresponding to multiple ionization stages of a laser-driven molecule, has recently been proposed [T.-T. Nguyen-Dang and J. Viau-Trudel, J. Chem. Phys. 139, 244102 (2013)]. To complete this development toward a fully ab-initio method for the calculation of time-dependent electronic wavefunctions of an N-electron molecule, we describe how tools of multiconfiguration quantum chemistry such as the management of the configuration expansion space using Graphical Unitary Group Approach concepts can be profitably adapted to the new context, that of time-resolved electronic dynamics, as opposed to stationary electronic structure. The method is applied to calculate the detailed, sub-cycle electronic dynamics of BeH 2 , treated in a 3–21G bound-orbital basis augmented by a set of orthogonalized plane-waves representing continuum-type orbitals, including its ionization under an intense λ = 800 nm or λ = 80 nm continuous-wave laser field. The dynamics is strongly non-linear at the field-intensity considered (I ≃ 10 15 W/cm 2 ), featuring important ionization of an inner-shell electron and strong post-ionization bound-electron dynamics

  13. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

    Science.gov (United States)

    Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny; Gilbert, Andrew T. B.; Wormit, Michael; Kussmann, Joerg; Lange, Adrian W.; Behn, Andrew; Deng, Jia; Feng, Xintian; Ghosh, Debashree; Goldey, Matthew; Horn, Paul R.; Jacobson, Leif D.; Kaliman, Ilya; Khaliullin, Rustam Z.; Kuś, Tomasz; Landau, Arie; Liu, Jie; Proynov, Emil I.; Rhee, Young Min; Richard, Ryan M.; Rohrdanz, Mary A.; Steele, Ryan P.; Sundstrom, Eric J.; Woodcock, H. Lee, III; Zimmerman, Paul M.; Zuev, Dmitry; Albrecht, Ben; Alguire, Ethan; Austin, Brian; Beran, Gregory J. O.; Bernard, Yves A.; Berquist, Eric; Brandhorst, Kai; Bravaya, Ksenia B.; Brown, Shawn T.; Casanova, David; Chang, Chun-Min; Chen, Yunqing; Chien, Siu Hung; Closser, Kristina D.; Crittenden, Deborah L.; Diedenhofen, Michael; DiStasio, Robert A., Jr.; Do, Hainam; Dutoi, Anthony D.; Edgar, Richard G.; Fatehi, Shervin; Fusti-Molnar, Laszlo; Ghysels, An; Golubeva-Zadorozhnaya, Anna; Gomes, Joseph; Hanson-Heine, Magnus W. D.; Harbach, Philipp H. P.; Hauser, Andreas W.; Hohenstein, Edward G.; Holden, Zachary C.; Jagau, Thomas-C.; Ji, Hyunjun; Kaduk, Benjamin; Khistyaev, Kirill; Kim, Jaehoon; Kim, Jihan; King, Rollin A.; Klunzinger, Phil; Kosenkov, Dmytro; Kowalczyk, Tim; Krauter, Caroline M.; Lao, Ka Un; Laurent, Adèle D.; Lawler, Keith V.; Levchenko, Sergey V.; Lin, Ching Yeh; Liu, Fenglai; Livshits, Ester; Lochan, Rohini C.; Luenser, Arne; Manohar, Prashant; Manzer, Samuel F.; Mao, Shan-Ping; Mardirossian, Narbe; Marenich, Aleksandr V.; Maurer, Simon A.; Mayhall, Nicholas J.; Neuscamman, Eric; Oana, C. Melania; Olivares-Amaya, Roberto; O'Neill, Darragh P.; Parkhill, John A.; Perrine, Trilisa M.; Peverati, Roberto; Prociuk, Alexander; Rehn, Dirk R.; Rosta, Edina; Russ, Nicholas J.; Sharada, Shaama M.; Sharma, Sandeep; Small, David W.; Sodt, Alexander; Stein, Tamar; Stück, David; Su, Yu-Chuan; Thom, Alex J. W.; Tsuchimochi, Takashi; Vanovschi, Vitalii; Vogt, Leslie; Vydrov, Oleg; Wang, Tao; Watson, Mark A.; Wenzel, Jan; White, Alec; Williams, Christopher F.; Yang, Jun; Yeganeh, Sina; Yost, Shane R.; You, Zhi-Qiang; Zhang, Igor Ying; Zhang, Xing; Zhao, Yan; Brooks, Bernard R.; Chan, Garnet K. L.; Chipman, Daniel M.; Cramer, Christopher J.; Goddard, William A., III; Gordon, Mark S.; Hehre, Warren J.; Klamt, Andreas; Schaefer, Henry F., III; Schmidt, Michael W.; Sherrill, C. David; Truhlar, Donald G.; Warshel, Arieh; Xu, Xin; Aspuru-Guzik, Alán; Baer, Roi; Bell, Alexis T.; Besley, Nicholas A.; Chai, Jeng-Da; Dreuw, Andreas; Dunietz, Barry D.; Furlani, Thomas R.; Gwaltney, Steven R.; Hsu, Chao-Ping; Jung, Yousung; Kong, Jing; Lambrecht, Daniel S.; Liang, WanZhen; Ochsenfeld, Christian; Rassolov, Vitaly A.; Slipchenko, Lyudmila V.; Subotnik, Joseph E.; Van Voorhis, Troy; Herbert, John M.; Krylov, Anna I.; Gill, Peter M. W.; Head-Gordon, Martin

    2015-01-01

    A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

  14. Using machine learning and quantum chemistry descriptors to predict the toxicity of ionic liquids.

    Science.gov (United States)

    Cao, Lingdi; Zhu, Peng; Zhao, Yongsheng; Zhao, Jihong

    2018-06-15

    Large-scale application of ionic liquids (ILs) hinges on the advancement of designable and eco-friendly nature. Research of the potential toxicity of ILs towards different organisms and trophic levels is insufficient. Quantitative structure-activity relationships (QSAR) model is applied to evaluate the toxicity of ILs towards the leukemia rat cell line (ICP-81). The structures of 57 cations and 21 anions were optimized by quantum chemistry. The electrostatic potential surface area (S EP ) and charge distribution area (S σ-profile ) descriptors are calculated and used to predict the toxicity of ILs. The performance and predictive aptitude of extreme learning machine (ELM) model are analyzed and compared with those of multiple linear regression (MLR) and support vector machine (SVM) models. The highest R 2 and the lowest AARD% and RMSE of the training set, test set and total set for the ELM are observed, which validates the superior performance of the ELM than that of obtained by the MLR and SVM. The applicability domain of the model is assessed by the Williams plot. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Interest in STEM is contagious for students in biology, chemistry, and physics classes.

    Science.gov (United States)

    Hazari, Zahra; Potvin, Geoff; Cribbs, Jennifer D; Godwin, Allison; Scott, Tyler D; Klotz, Leidy

    2017-08-01

    We report on a study of the effect of peers' interest in high school biology, chemistry, and physics classes on students' STEM (science, technology, engineering, and mathematics)-related career intentions and course achievement. We define an interest quorum as a science class where students perceive a high level of interest for the subject matter from their classmates. We hypothesized that students who experience such an interest quorum are more likely to choose STEM careers. Using data from a national survey study of students' experiences in high school science, we compared the effect of five levels of peer interest reported in biology, chemistry, and physics courses on students' STEM career intentions. The results support our hypothesis, showing a strong, positive effect of an interest quorum even after controlling for differences between students that pose competing hypotheses such as previous STEM career interest, academic achievement, family support for mathematics and science, and gender. Smaller positive effects of interest quorums were observed for course performance in some cases, with no detrimental effects observed across the study. Last, significant effects persisted even after controlling for differences in teaching quality. This work emphasizes the likely importance of interest quorums for creating classroom environments that increase students' intentions toward STEM careers while enhancing or maintaining course performance.

  16. Interest in STEM is contagious for students in biology, chemistry, and physics classes

    Science.gov (United States)

    Hazari, Zahra; Potvin, Geoff; Cribbs, Jennifer D.; Godwin, Allison; Scott, Tyler D.; Klotz, Leidy

    2017-01-01

    We report on a study of the effect of peers’ interest in high school biology, chemistry, and physics classes on students’ STEM (science, technology, engineering, and mathematics)–related career intentions and course achievement. We define an interest quorum as a science class where students perceive a high level of interest for the subject matter from their classmates. We hypothesized that students who experience such an interest quorum are more likely to choose STEM careers. Using data from a national survey study of students‘ experiences in high school science, we compared the effect of five levels of peer interest reported in biology, chemistry, and physics courses on students‘ STEM career intentions. The results support our hypothesis, showing a strong, positive effect of an interest quorum even after controlling for differences between students that pose competing hypotheses such as previous STEM career interest, academic achievement, family support for mathematics and science, and gender. Smaller positive effects of interest quorums were observed for course performance in some cases, with no detrimental effects observed across the study. Last, significant effects persisted even after controlling for differences in teaching quality. This work emphasizes the likely importance of interest quorums for creating classroom environments that increase students’ intentions toward STEM careers while enhancing or maintaining course performance. PMID:28808678

  17. Quantum biology at the cellular level--elements of the research program.

    Science.gov (United States)

    Bordonaro, Michael; Ogryzko, Vasily

    2013-04-01

    Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) - a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the 'basis-dependent' nature of these concepts. We introduce the notion of 'formal superposition' and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular 'decision-making' and adaptation. We stress that the interpretation of the notion of 'formal superposition' should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., 'Basis-Dependent Selection', BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the 'evolvability mechanism' loophole are also discussed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  18. The Unicellular State as a Point Source in a Quantum Biological System

    Directory of Open Access Journals (Sweden)

    John S. Torday

    2016-05-01

    Full Text Available A point source is the central and most important point or place for any group of cohering phenomena. Evolutionary development presumes that biological processes are sequentially linked, but neither directed from, nor centralized within, any specific biologic structure or stage. However, such an epigenomic entity exists and its transforming effects can be understood through the obligatory recapitulation of all eukaryotic lifeforms through a zygotic unicellular phase. This requisite biological conjunction can now be properly assessed as the focal point of reconciliation between biology and quantum phenomena, illustrated by deconvoluting complex physiologic traits back to their unicellular origins.

  19. Chemistry

    International Nuclear Information System (INIS)

    Ferris, L.M.

    1976-01-01

    Research progress is reported in programs on fuel-salt chemistry, properties of compounds in the Li--Te system, Te spectroscopy UF 4 --H equilibria, porous electrode studies of molten salts, fuel salt-coolant salt reactions, thermodynamic properties of transition-metal fluorides, and properties of sodium fluoroborate. Developmental work on analytical methods is summarized including in-line analysis of molten MSBR fuel, analysis of coolant-salts for tritium, analysis of molten LiF--BeF 2 --ThF 4 for Fe and analysis of LiF--BeF--ThF 4 for Te

  20. Bioscience methodologies in physical chemistry an engineering and molecular approach

    CERN Document Server

    D'Amore, Alberto

    2013-01-01

    The field of bioscience methodologies in physical chemistry stands at the intersection of the power and generality of classical and quantum physics with the minute molecular complexity of chemistry and biology. This book provides an application of physical principles in explaining and rationalizing chemical and biological phenomena. It does not stick to the classical topics that are conventionally considered as part of physical chemistry; instead it presents principles deciphered from a modern point of view, which is the strength of this book.

  1. Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry.

    Science.gov (United States)

    Loquais, Yohan; Gloaguen, Eric; Habka, Sana; Vaquero-Vara, Vanesa; Brenner, Valérie; Tardivel, Benjamin; Mons, Michel

    2015-06-11

    The intrinsic conformational landscape of two phenylalanine-containing protein chain models (-Gly-Phe- and -Ala-Phe- sequences) has been investigated theoretically and experimentally in the gas phase. The near UV spectroscopy (first ππ* transition of the Phe ring) is obtained experimentally under jet conditions where the conformational features can be resolved. Single-conformation IR spectroscopy in the NH stretch region is then obtained by IR/UV double resonance in the ground state, leading to resolved vibrational spectra that are assigned in terms of conformation and H-bonding content from comparison with quantum chemistry calculations. For the main conformer, whose UV spectrum exhibits a significant Franck-Condon activity in low frequency modes involving peptide backbone motions relative to the Phe chromophore, excited state IR spectroscopy has also been recorded in a UV/IR/UV experiment. The NH stretch spectral changes observed in such a ππ* labeling experiment enable us to determine those NH bonds that are coupled to the phenyl ring; they are compared to CC2 excited state calculations to quantify the geometry change upon ππ* excitation. The complete and consistent series of data obtained enable us to propose an unambiguous assignment for the gallery of conformers observed and to demonstrate that, in these two sequences, three conceptually important local structural motifs of proteins (β-strands, 27 ribbons, and β-turns) are represented. The satisfactory agreement between the experimental conformational distribution and the predicted landscape anticipated from the DFT-D approach demonstrates the capabilities of a theoretical method that accounts for dispersive interactions. It also shows that the flaws, inherent to a resonant two-photon ionization detection scheme, often evoked for aromatic chromophores, do not seem to be significant in the case of Phe.

  2. Conjugation of nano and quantum materials with bovine serum albumin (BSA) to study their biological potential

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Suman, E-mail: sumansingh01@gmail.com [Central Scientific Instruments Organisation (CSIR-CSIO), Chandigarh (India); Kaur, Rajnish; Chahal, Jitender; Devi, P. [Central Scientific Instruments Organisation (CSIR-CSIO), Chandigarh (India); Jain, D.V.S. [Panjab University, Chandigarh (India); Singla, M.L., E-mail: singla_min@yahoo.co.in [Central Scientific Instruments Organisation (CSIR-CSIO), Chandigarh (India)

    2013-09-15

    Conjugates of gold nanoparticles (AuNPs) and semiconductor quantum dots (CdS/T) have been synthesized with bovine serum albumin (BSA) using wet chemistry. The optical properties of nano and quantum materials and their BSA conjugate have been studied using UV–Visible and Fluorescence spectroscopy. UV–Visible spectrum of pure BSA showed an absorption maximum at 278 nm, which showed blue shift after its conjugation with nano and quantum materials. Increased concentration of AuNPs during conjugation resulted in broadening of BSA peak (278 nm), which can be related to the formation of ground state complex formation, caused by the partial adsorption of BSA on the surface of NPs. However, increased concentrations of BSA resulted in decrease in SPR intensity of gold nanoparticles (528 nm) and absorbance peak of BSA started diminishing. AuNPs acted as quencher for BSA fluorescence intensity, when excited at 280 nm. The binding constant (K) and the number of binding sites (n) between AuNPs and BSA have been found to be 1.97×10{sup 2} LM{sup −1} and 0.6 respectively. With quantum dots, conjugation resulted in enhancement of fluorescence emission of quantum dots when excited at 300 nm, which might be due to the stabilizing effect of BSA on QDs or due to energy transfer from tryptophan moieties of albumin to quantum dots. -- Highlights: • Synthesis of nanoparticles (AuNPs) and quantum dots (CdS). • Conjugation of these materials with bovine serum albumin. • Optical behavioral studies.

  3. Integrating Biological Perspectives:. a Quantum Leap for Microarray Expression Analysis

    Science.gov (United States)

    Wanke, Dierk; Kilian, Joachim; Bloss, Ulrich; Mangelsen, Elke; Supper, Jochen; Harter, Klaus; Berendzen, Kenneth W.

    2009-02-01

    Biologists and bioinformatic scientists cope with the analysis of transcript abundance and the extraction of meaningful information from microarray expression data. By exploiting biological information accessible in public databases, we try to extend our current knowledge over the plant model organism Arabidopsis thaliana. Here, we give two examples of increasing the quality of information gained from large scale expression experiments by the integration of microarray-unrelated biological information: First, we utilize Arabidopsis microarray data to demonstrate that expression profiles are usually conserved between orthologous genes of different organisms. In an initial step of the analysis, orthology has to be inferred unambiguously, which then allows comparison of expression profiles between orthologs. We make use of the publicly available microarray expression data of Arabidopsis and barley, Hordeum vulgare. We found a generally positive correlation in expression trajectories between true orthologs although both organisms are only distantly related in evolutionary time scale. Second, extracting clusters of co-regulated genes implies similarities in transcriptional regulation via similar cis-regulatory elements (CREs). Vice versa approaches, where co-regulated gene clusters are found by investigating on CREs were not successful in general. Nonetheless, in some cases the presence of CREs in a defined position, orientation or CRE-combinations is positively correlated with co-regulated gene clusters. Here, we make use of genes involved in the phenylpropanoid biosynthetic pathway, to give one positive example for this approach.

  4. Mentha suaveolens Ehrh. (Lamiaceae) Essential Oil and Its Main Constituent Piperitenone Oxide: Biological Activities and Chemistry.

    Science.gov (United States)

    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.

  5. Calamintha nepeta (L.) Savi and its Main Essential Oil Constituent Pulegone: Biological Activities and Chemistry.

    Science.gov (United States)

    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.

  6. Calamintha nepeta (L. Savi and its Main Essential Oil Constituent Pulegone: Biological Activities and Chemistry

    Directory of Open Access Journals (Sweden)

    Mijat Božović

    2017-02-01

    Full Text Available 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

  7. Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

    Science.gov (United States)

    Smith, Daniel G A; Burns, Lori A; Sirianni, Dominic A; Nascimento, Daniel R; Kumar, Ashutosh; James, Andrew M; Schriber, Jeffrey B; Zhang, Tianyuan; Zhang, Boyi; Abbott, Adam S; Berquist, Eric J; Lechner, Marvin H; Cunha, Leonardo A; Heide, Alexander G; Waldrop, Jonathan M; Takeshita, Tyler Y; Alenaizan, Asem; Neuhauser, Daniel; King, Rollin A; Simmonett, Andrew C; Turney, Justin M; Schaefer, Henry F; Evangelista, Francesco A; DePrince, A Eugene; Crawford, T Daniel; Patkowski, Konrad; Sherrill, C David

    2018-06-11

    Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

  8. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine.

    Science.gov (United States)

    Grimme, Stefan; Bauer, Christopher Alexander

    2015-01-01

    The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.

  9. Processes that Drove the Transition from Chemistry to Biology: Concepts and Evidence

    Science.gov (United States)

    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

  10. Chemistry

    International Nuclear Information System (INIS)

    Ferris, L.M.

    1975-01-01

    Research and development activities dealing with the chemical problems related to design and ultimate operation of molten-salt reactor systems are described. An experimental test stand was constructed to expose metallurgical test specimens to Te 2 vapor at defined temperatures and deposition rates. To better define the chemistry of fluoroborate coolant, several aspects are being investigated. The behavior of hydroxy and oxy compounds in molten NaBF 4 is being investigated to define reactions and compounds that may be involved in corrosion and/or could be involved in methods for trapping tritium. Two corrosion products of Hastelloy N, Na 3 CrF 6 and Na 5 Cr 3 F 14 , were identified from fluoroborate systems. The evaluation of fluoroborate and alternate coolants continued. Research on the behavior of hydrogen and its isotopes is summarized. The solubilities of hydrogen, deuterium, and helium in Li 2 BeF 4 are very low. The sorption of tritium on graphite was found to be significant (a few milligrams of tritium per kilogram of graphite), possibly providing a means of sequestering a portion of the tritium produced. Development of analytical methods continued with emphasis on voltammetric and spectrophotometric techniques for the in-line analysis of corrosion products such as Fe 2+ and Cr 3+ and the determination of the U 3+ /U 4+ ratio in MSBR fuel salt. Similar studies were conducted with the NaBF 4 --NaF coolant salt. Information developed during the previous operation of the CSTF has been assessed and used to formulate plans for evaluation of in-line analytical methods in future CSTF operations. Electroanalytical and spectrophotometric research suggests that an electroactive protonic species is present in molten NaBF 4 --NaF, and that this species rapidly equilibrates with a volatile proton-containing species. Data obtained from the CSTF indicated that tritium was concentrated in the volatile species. (JGB)

  11. Quantum information and the problem of mechanisms of biological evolution.

    Science.gov (United States)

    Melkikh, Alexey V

    2014-01-01

    One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  12. Laboratory study of nitrate photolysis in Antarctic snow. I. Observed quantum yield, domain of photolysis, and secondary chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Meusinger, Carl; Johnson, Matthew S. [Department of Chemistry, University of Copenhagen, Copenhagen (Denmark); Berhanu, Tesfaye A.; Erbland, Joseph; Savarino, Joel, E-mail: jsavarino@lgge.obs.ujf-grenoble.fr [Univ. Grenoble Alpes, LGGE, F-38000 Grenoble (France); CNRS, LGGE, F-38000 Grenoble (France)

    2014-06-28

    Post-depositional processes alter nitrate concentration and nitrate isotopic composition in the top layers of snow at sites with low snow accumulation rates, such as Dome C, Antarctica. Available nitrate ice core records can provide input for studying past atmospheres and climate if such processes are understood. It has been shown that photolysis of nitrate in the snowpack plays a major role in nitrate loss and that the photolysis products have a significant influence on the local troposphere as well as on other species in the snow. Reported quantum yields for the main reaction spans orders of magnitude – apparently a result of whether nitrate is located at the air-ice interface or in the ice matrix – constituting the largest uncertainty in models of snowpack NO{sub x} emissions. Here, a laboratory study is presented that uses snow from Dome C and minimizes effects of desorption and recombination by flushing the snow during irradiation with UV light. A selection of UV filters allowed examination of the effects of the 200 and 305 nm absorption bands of nitrate. Nitrate concentration and photon flux were measured in the snow. The quantum yield for loss of nitrate was observed to decrease from 0.44 to 0.003 within what corresponds to days of UV exposure in Antarctica. The superposition of photolysis in two photochemical domains of nitrate in snow is proposed: one of photolabile nitrate, and one of buried nitrate. The difference lies in the ability of reaction products to escape the snow crystal, versus undergoing secondary (recombination) chemistry. Modeled NO{sub x} emissions may increase significantly above measured values due to the observed quantum yield in this study. The apparent quantum yield in the 200 nm band was found to be ∼1%, much lower than reported for aqueous chemistry. A companion paper presents an analysis of the change in isotopic composition of snowpack nitrate based on the same samples as in this study.

  13. Two Methods of Determining Total Phenolic Content of Foods and Juices in a General, Organic, and Biological (GOB) Chemistry Lab

    Science.gov (United States)

    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…

  14. Connecting Structure-Property and Structure-Function Relationships across the Disciplines of Chemistry and Biology: Exploring Student Perceptions

    Science.gov (United States)

    Kohn, Kathryn P.; Underwood, Sonia M.; Cooper, Melanie M.

    2018-01-01

    While many university students take science courses in multiple disciplines, little is known about how they perceive common concepts from different disciplinary perspectives. Structure-property and structure-function relationships have long been considered important explanatory concepts in the disciplines of chemistry and biology, respectively.…

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

    Science.gov (United States)

    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…

  16. Water as Life, Death, and Power: Building an Integrated Interdisciplinary Course Combining Perspectives from Anthropology, Biology, and Chemistry

    Science.gov (United States)

    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…

  17. Research on condensed matter and atomic physics using major experimental facilities and devices: Physics, chemistry, biology. Reports on results. Vol. 3. 4. Chemistry. 5. Biology. 6. Development of methods and instruments

    International Nuclear Information System (INIS)

    1993-01-01

    This report in three volumes substantiates the contents of the programme survey published in September 1989. The progress reports cover the following research areas: Vol. I, (1). Atomic and molecular physics - free atoms, molecules, macromolecules, clusters, matrix-isolated atoms and molecules. (2) Physics and chemistry of surfaces and interfaces - epitaxy, surface structure, adsorption, electrical, magnetic, and optical properties, thin films, synthetic layer structure. Vol. II, (3). Solid-state physics, and materials science -structural research, lattice dynamics, magnetic structure and dynamics, electronic states; load; spin and pulse density fluctuations; diffusion and internal motion, defects, unordered systems and liquids. Vol. III, (4). Chemistry - bonding and structure, kinetics and reaction mechanisms, polymer research, analysis and synthesis. (5). Biology, - structure and dynamics of biological macromolecules, membrane and cell biology. (6) Development of methods and instruments - neutron sources, synchrotron sources, special accelerators, research with interlinked systems and devices. (orig.) [de

  18. Relativistic quantum chemistry of the superheavy elements. Closed-shell element 114 as a case study

    International Nuclear Information System (INIS)

    Schwerdtfeger, Peter; Seth, Michael

    2002-01-01

    The chemistry of superheavy element 114 is reviewed. The ground state of element 114 is closed shell [112]7s 2 7p 1/2 2 and shows a distinct chemical inertness (low reactivity). This inertness makes it rather difficult to study the atom-at-a-time chemistry of 114 in the gas or liquid phase. (author)

  19. The Biological Nature of Geochemical Proxies: algal symbionts affect coral skeletal chemistry

    Science.gov (United States)

    Owens, K.; Cohen, A. L.; Shimizu, N.

    2001-12-01

    The strontium-calcium ratio (Sr/Ca) of reef coral skeleton is an important ocean temperature proxy that has been used to address some particularly controversial climate change issues. However, the paleothermometer has sometimes proven unreliable and there are indications that the temperature-dependence of Sr/Ca in coral aragonite is linked to the photosynthetic activity of algal symbionts (zooxanthellae) in coral tissue. We examined the effect of algal symbiosis on skeletal chemistry using Astrangia danae, a small colonial temperate scleractinian that occurs naturally with and without zooxanthellae. Live symbiotic (deep brown) and asymbiotic (white) colonies of similar size were collected in Woods Hole where water temperatures fluctuate seasonally between -2oC and 23oC. We used a microbeam technique (Secondary Ion Mass Spectrometry) and a 30 micron diameter sampling beam to construct high-resolution Sr/Ca profiles, 2500 microns long, down the growth axes of the outer calical (thecal) walls. Profiles generated from co-occuring symbiotic and asymbiotic colonies are remarkably different despite their exposure to identical water temperatures. Symbiotic coral Sr/Ca displays four large-amplitude annual cycles with high values in the winter, low values in the summer and a temperature dependence similar to that of tropical reef corals. By comparison, Sr/Ca profiles constructed from asymbiotic coral skeleton display little variability over the same time period. Asymbiont Sr/Ca is relatively insensitive to the enormous temperature changes experienced over the year; the temperature dependence is similar to that of nighttime skeletal deposits in tropical reef corals and non-biological aragonite precipitates. We propose that the large variations in skeletal Sr/Ca observed in all symbiont-hosting coral species are not related to SST variability per se but are driven primarily by large seasonal variations in skeletal calcification rate associated with symbiont photosynthesis. Our

  20. On the measurements of molecular similarity: a connection between quantum chemistry and artificial intelligence

    International Nuclear Information System (INIS)

    Carbo, R.; Calabuig, B.

    1988-01-01

    Molecular similarity measures within the quantum concept of density functions are described and analyzed. It is intended to show how artificial intelligence techniques can be used within the framework of quantum theory, in order to study and classify the molecular structures and their properties. (A.C.A.S) [pt

  1. Combinatorial chemistry

    DEFF Research Database (Denmark)

    Nielsen, John

    1994-01-01

    An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds.......An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds....

  2. Quantum chemistry and dynamics of the abstraction reaction of H atoms from formaldehyde

    Energy Technology Data Exchange (ETDEWEB)

    Siaï, A. [Faculté des Sciences de Tunis, Département de Physique, (LPMC), Université de Tunis El Manar, 2092 Tunis (Tunisia); Oueslati, I. [Faculté des Sciences de Tunis, Département de Physique, (LPMC), Université de Tunis El Manar, 2092 Tunis (Tunisia); Observatoire de Paris-Meudon, Sorbonne Universités, UPMC Univ Paris 06, UMR8112 du CNRS, LERMA, 5 Place Jules Janssen, 92195 Meudon cedex (France); Académie Militaire, Fondouk Jedid, 8012 Nabeul (Tunisia); Kerkeni, Boutheïna, E-mail: Boutheina.kerkeni@obspm.fr [Faculté des Sciences de Tunis, Département de Physique, (LPMC), Université de Tunis El Manar, 2092 Tunis (Tunisia); Observatoire de Paris-Meudon, Sorbonne Universités, UPMC Univ Paris 06, UMR8112 du CNRS, LERMA, 5 Place Jules Janssen, 92195 Meudon cedex (France); Institut Supérieur des Arts Multimédia de la Manouba, Université de la Manouba, 2010 la Manouba (Tunisia)

    2016-08-02

    This work reports a reduced dimensionality rate constant calculation of the H-abstraction reaction from formaldehyde. Quantum scattering calculations are performed treating explicitly the bonds being broken and formed. Geometry optimisations and frequency calculations are done at the MP2/cc-pVTZ level while energies are calculated with the CCSD(T) method. An analytical potential energy surface was developed from a relatively small number of grid points. When compared to semi-classical approaches, the quantum scattering calculations show that quantum tunnelling yields large contributions at low temperatures. At 200 K, we note a difference of about 5 orders of magnitude between transition state theory (TST) and quantum rate constants. Our predicted results show that the quantum and the CVT/SCT rate constants are in reasonable agreement with the available experiment at high temperatures, but that the last one gives better agreement to experimental results at low temperatures.

  3. Quantum Chemistry on Quantum Computers: A Polynomial-Time Quantum Algorithm for Constructing the Wave Functions of Open-Shell Molecules.

    Science.gov (United States)

    Sugisaki, Kenji; Yamamoto, Satoru; Nakazawa, Shigeaki; Toyota, Kazuo; Sato, Kazunobu; Shiomi, Daisuke; Takui, Takeji

    2016-08-18

    Quantum computers are capable to efficiently perform full configuration interaction (FCI) calculations of atoms and molecules by using the quantum phase estimation (QPE) algorithm. Because the success probability of the QPE depends on the overlap between approximate and exact wave functions, efficient methods to prepare accurate initial guess wave functions enough to have sufficiently large overlap with the exact ones are highly desired. Here, we propose a quantum algorithm to construct the wave function consisting of one configuration state function, which is suitable for the initial guess wave function in QPE-based FCI calculations of open-shell molecules, based on the addition theorem of angular momentum. The proposed quantum algorithm enables us to prepare the wave function consisting of an exponential number of Slater determinants only by a polynomial number of quantum operations.

  4. XVIII Mendeleev congress on general and applied chemistry. Summaries of reports in five volumes. Volume 5. IV Russian-French symposium Supramolecular systems in chemistry and biology. II Russian-Indian symposium on organic chemistry. International symposium on present-day radiochemistry Radiochemistry: progress and prospects. International symposium Green chemistry, stable evolution and social responsibility of chemists. Symposium Nucleophilic hydrogen substitution in aromatic systems and related reactions

    International Nuclear Information System (INIS)

    2007-01-01

    The 5 volume of the XVIII Mendeleev congress on general and applied chemistry includes summaries of reports on the subjects of sypramolecular systems in chemistry and biology, organic chemistry, modern radiochemistry, green chemistry - development and social responsibility of chemists, nucleophilic hydrogen substitution in aromatic systems and related chemical reactions [ru

  5. Effects of quantum chemistry models for bound electrons on positron annihilation spectra for atoms and small molecules

    International Nuclear Information System (INIS)

    Wang Feng; Ma Xiaoguang; Selvam, Lalitha; Gribakin, Gleb; Surko, Clifford M

    2012-01-01

    The Doppler-shift spectra of the γ-rays from positron annihilation in molecules were determined by using the momentum distribution of the annihilation electron–positron pair. The effect of the positron wavefunction on spectra was analysed in a recent paper (Green et al 2012 New J. Phys. 14 035021). In this companion paper, we focus on the dominant contribution to the spectra, which arises from the momenta of the bound electrons. In particular, we use computational quantum chemistry models (Hartree–Fock with two basis sets and density functional theory (DFT)) to calculate the wavefunctions of the bound electrons. Numerical results are presented for noble gases and small molecules such as H 2 , N 2 , O 2 , CH 4 and CF 4 . The calculations reveal relatively small effects on the Doppler-shift spectra from the level of inclusion of electron correlation energy in the models. For atoms, the difference in the full-width at half-maximum of the spectra obtained using the Hartree–Fock and DFT models does not exceed 2%. For molecules the difference can be much larger, reaching 8% for some molecular orbitals. These results indicate that the predicted positron annihilation spectra for molecules are generally more sensitive to inclusion of electron correlation energies in the quantum chemistry model than the spectra for atoms are. (paper)

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

    Science.gov (United States)

    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. © 2016 The Author(s).

  7. Biology and chemistry of three Pennsylvania lakes: responses to acid precipitation

    Energy Technology Data Exchange (ETDEWEB)

    Bradt, P.T.; Dudley, J.L.; Berg, M.B.; Barrasso, D.S.

    1986-09-01

    The biology and chemistry of three northeastern Pennsylvania lakes was studied from summer 1981 through summer 1983 to evaluate lakes with different sensitivities to acidification. At the acidified lake there were fewer phytoplankton and zooplankton species than at the moderately sensitive lakes. The most numerous plankton species in all three lakes are reportedly acid tolerant. Among the benthic macro-invertebrates (BMI) there were more acid tolerant Chironomidae at the acidified lake, but more acid intolerant Ephemeroptera and Mollusca and a higher wet weight at the least sensitive lake. There were no differences among the lakes' BMI mean total numbers or mean number of taxa. The fish community at the acidified lake was dominated by stunted Lepomis gibbosus, but L. machrochirous were most abundant in the other lakes. Principal component analysis suggested a shift in all three lakes over the sampling period toward combined lower pH, alkalinity, specific conductance, Ca and Mg and higher Al and Mn. Such chemical changes have been associated with acidification. The rate and extent of acidification appeared to be controlled by geological and hydrological characteristics of the drainage basins. 38 refs.

  8. Biology and chemistry of tree Pennsylvania lakes: responses to acid precipitation. [Lepomis gibbosus; Lepomis machrochirous

    Energy Technology Data Exchange (ETDEWEB)

    Bradt, P.T.; Dudley, J.L.; Berg, M.B.; Barrasso, D.S.

    1986-01-01

    The biology and chemistry of three northeastern Pennsylvania lakes was studied from summer 1981 through summer 1983 to evaluate lakes with different sensitivities to acidification. At the acidifies lake (total alkalinity par. delta 0.0 ..mu..eq L/sup -1/) there were fewer phytoplankton and zooplankton species than at the moderately sensitive lakes. The most numerous plankton species in all three lakes are reportedly acid tolerant. Among the benthic macro- invertebrates (BMI) there were more acid tolerant Chironomidae at the acidified lake, but more acid intolerant Ephemeroptera and Mollusca and a higher wet weight at the least sensitive lake. There were no differences among the lakes' BMI mean total numbers or mean number of taxa. The fish community at the acidified lake was dominated by stunted Lepomis gibbosus, but L. machrochirous were most abundant in the other lakes. Principal component analysis suggested a shift in all three lakes over the sampling period toward combined lower pH, alkalinity, specific conductance, Ca, and Mg and higher Al and Mn. Such chemical changes have been associated with acidification. The rate and extent of acidification appeared to be controlled by geological and hydrological characteristics of the drainage basins.

  9. Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology.

    Science.gov (United States)

    Zhang, Liqin; Wan, Shuo; Jiang, Ying; Wang, Yanyue; Fu, Ting; Liu, Qiaoling; Cao, Zhijuan; Qiu, Liping; Tan, Weihong

    2017-02-22

    Disease-related biomarkers are objectively measurable molecular signatures of physiological status that can serve as disease indicators or drug targets in clinical diagnosis and therapy, thus acting as a tool in support of personalized medicine. For example, the prostate-specific antigen (PSA) biomarker is now widely used to screen patients for prostate cancer. However, few such biomarkers are currently available, and the process of biomarker identification and validation is prolonged and complicated by inefficient methods of discovery and few reliable analytical platforms. Therefore, in this Perspective, we look at the advanced chemistry of aptamer molecules and their significant role as molecular probes in biomarker studies. As a special class of functional nucleic acids evolved from an iterative technology termed Systematic Evolution of Ligands by Exponential Enrichment (SELEX), these single-stranded oligonucleotides can recognize their respective targets with selectivity and affinity comparable to those of protein antibodies. Because of their fast turnaround time and exceptional chemical properties, aptamer probes can serve as novel molecular tools for biomarker investigations, particularly in assisting identification of new disease-related biomarkers. More importantly, aptamers are able to recognize biomarkers from complex biological environments such as blood serum and cell surfaces, which can provide direct evidence for further clinical applications. This Perspective highlights several major advancements of aptamer-based biomarker discovery strategies and their potential contribution to the practice of precision medicine.

  10. Role of Precursor-Conversion Chemistry in the Crystal-Phase Control of Catalytically Grown Colloidal Semiconductor Quantum Wires.

    Science.gov (United States)

    Wang, Fudong; Buhro, William E

    2017-12-26

    Crystal-phase control is one of the most challenging problems in nanowire growth. We demonstrate that, in the solution-phase catalyzed growth of colloidal cadmium telluride (CdTe) quantum wires (QWs), the crystal phase can be controlled by manipulating the reaction chemistry of the Cd precursors and tri-n-octylphosphine telluride (TOPTe) to favor the production of either a CdTe solute or Te, which consequently determines the composition and (liquid or solid) state of the Bi x Cd y Te z catalyst nanoparticles. Growth of single-phase (e.g., wurtzite) QWs is achieved only from solid catalysts (y ≪ z) that enable the solution-solid-solid growth of the QWs, whereas the liquid catalysts (y ≈ z) fulfill the solution-liquid-solid growth of the polytypic QWs. Factors that affect the precursor-conversion chemistry are systematically accounted for, which are correlated with a kinetic study of the composition and state of the catalyst nanoparticles to understand the mechanism. This work reveals the role of the precursor-reaction chemistry in the crystal-phase control of catalytically grown colloidal QWs, opening the possibility of growing phase-pure QWs of other compositions.

  11. Complex chemistry

    International Nuclear Information System (INIS)

    Kim, Bong Gon; Kim, Jae Sang; Kim, Jin Eun; Lee, Boo Yeon

    2006-06-01

    This book introduces complex chemistry with ten chapters, which include development of complex chemistry on history coordination theory and Warner's coordination theory and new development of complex chemistry, nomenclature on complex with conception and define, chemical formula on coordination compound, symbol of stereochemistry, stereo structure and isomerism, electron structure and bond theory on complex, structure of complex like NMR and XAFS, balance and reaction on solution, an organo-metallic chemistry, biology inorganic chemistry, material chemistry of complex, design of complex and calculation chemistry.

  12. The common extremalities in biology and physics maximum energy dissipation principle in chemistry, biology, physics and evolution

    CERN Document Server

    Moroz, Adam

    2011-01-01

    This book is the first unified systemic description of dissipative phenomena, taking place in biology, and non-dissipative (conservative) phenomena, which is more relevant to physics. Fully updated and revised, this new edition extends our understanding of nonlinear phenomena in biology and physics from the extreme / optimal perspective. The first book to provide understanding of physical phenomena from a biological perspective and biological phenomena from a physical perspective Discusses emerging fields and analysis Provides examples.

  13. Teaching Introductory Quantum Physics and Chemistry: Caveats from the History of Science and Science Teaching to the Training of Modern Chemists

    Science.gov (United States)

    Greca, Ileana M.; Freire, Olival, Jr.

    2014-01-01

    Finding the best ways to introduce quantum physics to undergraduate students in all scientific areas, in particular for chemistry students, is a pressing, but hardly a simple task. In this paper, we discuss the relevance of taking into account lessons from the history of the discipline and the ongoing controversy over its interpretations and…

  14. Infrared and Raman spectroscopy and quantum chemistry calculation studies of C-H...O hydrogen bondings and thermal behavior of biodegradable polyhydroxyalkanoate

    Czech Academy of Sciences Publication Activity Database

    Sato, H.; Dybal, Jiří; Murakami, R.; Noda, I.; Ozaki, Y.

    744-747, - (2005), s. 35-46 ISSN 0022-2860 R&D Projects: GA AV ČR IAA4050208 Keywords : infrared and Raman spectroscopy * quantum chemical calculation * C-H...O hydrogen bonding Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.440, year: 2005

  15. Understanding schizophrenia as a disorder of consciousness: biological correlates and translational implications from quantum theory perspectives.

    Science.gov (United States)

    Venkatasubramanian, Ganesan

    2015-04-30

    From neurophenomenological perspectives, schizophrenia has been conceptualized as "a disorder with heterogeneous manifestations that can be integrally understood to involve fundamental perturbations in consciousness". While these theoretical constructs based on consciousness facilitate understanding the 'gestalt' of schizophrenia, systematic research to unravel translational implications of these models is warranted. To address this, one needs to begin with exploration of plausible biological underpinnings of "perturbed consciousness" in schizophrenia. In this context, an attractive proposition to understand the biology of consciousness is "the orchestrated object reduction (Orch-OR) theory" which invokes quantum processes in the microtubules of neurons. The Orch-OR model is particularly important for understanding schizophrenia especially due to the shared 'scaffold' of microtubules. The initial sections of this review focus on the compelling evidence to support the view that "schizophrenia is a disorder of consciousness" through critical summary of the studies that have demonstrated self-abnormalities, aberrant time perception as well as dysfunctional intentional binding in this disorder. Subsequently, these findings are linked with 'Orch-OR theory' through the research evidence for aberrant neural oscillations as well as microtubule abnormalities observed in schizophrenia. Further sections emphasize the applicability and translational implications of Orch-OR theory in the context of schizophrenia and elucidate the relevance of quantum biology to understand the origins of this puzzling disorder as "fundamental disturbances in consciousness".

  16. Synthesis, crystal structure, vibrational spectra and theoretical calculations of quantum chemistry of a potential antimicrobial Meldrum's acid derivative

    Science.gov (United States)

    Campelo, M. J. M.; Freire, P. T. C.; Mendes Filho, J.; de Toledo, T. A.; Teixeira, A. M. R.; da Silva, L. E.; Bento, R. R. F.; Faria, J. L. B.; Pizani, P. S.; Gusmão, G. O. M.; Coutinho, H. D. M.; Oliveira, M. T. A.

    2017-10-01

    A new derivative of Meldrum's acid 5-((5-chloropyridin-2-ylamino)methylene)-2,2-dimethyl-1,3-dioxane-4,6-dione (CYMM) of molecular formula C12H11ClN2O4 was synthesized and structurally characterized using single crystal X-ray diffraction technique. The vibrational properties of the crystal were studied by Fourier Transform infrared (FT-IR), Fourier Transform Raman (FT-Raman) techniques and theoretical calculations of quantum chemistry using Density functional theory (DFT) and Density functional perturbation theory (DFPT). A comparison with experimental spectra allowed the assignment of all the normal modes. The descriptions of the normal modes were carried by means of potential energy distribution (PED). Additionally, analysis of the antimicrobial activity and antibiotic resistance modulatory activity was carried out to evaluate the antibacterial potential of the CYMM.

  17. Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

    Science.gov (United States)

    Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

  18. Combinatorial computational chemistry approach of tight-binding quantum chemical molecular dynamics method to the design of the automotive catalysts

    International Nuclear Information System (INIS)

    Ito, Yuki; Jung, Changho; Luo, Yi; Koyama, Michihisa; Endou, Akira; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira

    2006-01-01

    Recently, we have developed a new tight-binding quantum chemical molecular dynamics program 'Colors' for combinatorial computational chemistry approach. This methodology is based on our original tight-binding approximation and realized over 5000 times acceleration compared to the conventional first-principles molecular dynamics method. In the present study, we applied our new program to the simulations on various realistic large-scale models of the automotive three-way catalysts, ultrafine Pt particle/CeO 2 (111) support. Significant electron transfer from the Pt particle to the CeO 2 (111) surface was observed and it was found to strongly depend on the size of the Pt particle. Furthermore, our simulation results suggest that the reduction of the Ce atom due to the electron transfer from the Pt particle to the CeO 2 surface is a main reason for the strong interaction of the Pt particle and CeO 2 (111) support

  19. Quantum Dots in a Polymer Composite: A Convenient Particle-in-a-Box Laboratory Experiment

    Science.gov (United States)

    Rice, Charles V.; Giffin, Guinevere A.

    2008-01-01

    Semiconductor quantum dots are at the forefront of materials science chemistry with applications in biological imaging and photovoltaic technologies. We have developed a simple laboratory experiment to measure the quantum-dot size from fluorescence spectra. A major roadblock of quantum-dot based exercises is the particle synthesis and handling;…

  20. Picture this: The value of multiple visual representations for student learning of quantum concepts in general chemistry

    Science.gov (United States)

    Allen, Emily Christine

    Mental models for scientific learning are often defined as, "cognitive tools situated between experiments and theories" (Duschl & Grandy, 2012). In learning, these cognitive tools are used to not only take in new information, but to help problem solve in new contexts. Nancy Nersessian (2008) describes a mental model as being "[loosely] characterized as a representation of a system with interactive parts with representations of those interactions. Models can be qualitative, quantitative, and/or simulative (mental, physical, computational)" (p. 63). If conceptual parts used by the students in science education are inaccurate, then the resulting model will not be useful. Students in college general chemistry courses are presented with multiple abstract topics and often struggle to fit these parts into complete models. This is especially true for topics that are founded on quantum concepts, such as atomic structure and molecular bonding taught in college general chemistry. The objectives of this study were focused on how students use visual tools introduced during instruction to reason with atomic and molecular structure, what misconceptions may be associated with these visual tools, and how visual modeling skills may be taught to support students' use of visual tools for reasoning. The research questions for this study follow from Gilbert's (2008) theory that experts use multiple representations when reasoning and modeling a system, and Kozma and Russell's (2005) theory of representational competence levels. This study finds that as students developed greater command of their understanding of abstract quantum concepts, they spontaneously provided additional representations to describe their more sophisticated models of atomic and molecular structure during interviews. This suggests that when visual modeling with multiple representations is taught, along with the limitations of the representations, it can assist students in the development of models for reasoning about

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  3. The Variation Theorem Applied to H-2+: A Simple Quantum Chemistry Computer Project

    Science.gov (United States)

    Robiette, Alan G.

    1975-01-01

    Describes a student project which requires limited knowledge of Fortran and only minimal computing resources. The results illustrate such important principles of quantum mechanics as the variation theorem and the virial theorem. Presents sample calculations and the subprogram for energy calculations. (GS)

  4. Bridging quantum chemistry and nuclear structure theory: Coupled-cluster calculations for closed- and open-shell nuclei

    International Nuclear Information System (INIS)

    Piecuch, Piotr; Wloch, Marta; Gour, Jeffrey R.; Dean, David J.; Papenbrock, Thomas; Hjorth-Jensen, Morten

    2005-01-01

    We review basic elements of the single-reference coupled-cluster theory and discuss large scale ab initio calculations of ground and excited states of 15O, 16O, and 17O using coupled-cluster methods and algorithms developed in quantum chemistry. By using realistic two-body interactions and the renormalized form of the Hamiltonian obtained with a no-core G-matrix approach, we obtain the converged results for 16O and promising preliminary results for 15O and 17O at the level of two-body interactions. The calculated properties other than energies include matter density, charge radius, and charge form factor. The relatively low costs of coupled-cluster calculations, which are characterized by the low-order polynomial scaling with the system size, enable us to probe large model spaces with up to 7 or 8 major oscillator shells, for which non-truncated shell-model calculations for nuclei with A = 15 17 active particles are presently not possible. We argue that the use of coupled-cluster methods and computer algorithms developed by quantum chemists to calculate properties of nuclei is an important step toward the development of accurate and affordable many-body theories that cross the boundaries of various physical sciences

  5. Mössbauer spectroscopy: applications in chemistry, biology, industry, and nanotechnology

    National Research Council Canada - National Science Library

    Sharma, Virender K; Klingelhofer, Gostar; Nishida, Tetsuaki

    2013-01-01

    "A one-stop reference for determining the oxidation states of elements so that oxidation eduction chemistry can be studied across a wide variety of systems, this book presents advances in the field...

  6. Sustainable Materials Management (SMM) Web Academy Webinar: Compost from Food Waste: Understanding Soil Chemistry and Soil Biology on a College/University Campus

    Science.gov (United States)

    This page contains information about the Sustainable Materials Management (SMM) Web Academy Webinar Series titled Compost from Food Waste:Understanding Soil Chemistry and Soil Biology on a College/University Campus

  7. The Effect of Isotopic Substitution on Quantum Proton Transfer Across Short Water Bridges in Biological Systems

    Science.gov (United States)

    Blazejewski, Jacob; Schultz, Chase; Mazzuca, James

    2015-03-01

    Many biological systems utilize water chains to transfer charge over long distances by means of an excess proton. This study examines how quantum effects impact these reactions in a small model system. The model consists of a water molecule situated between an imidazole donor and acceptor group, which simulate a fixed amino acid backbone. A one dimensional energy profile is evaluated using density functional theory at the 6-31G*/B3LYP level, which generates a barrier with a width of 0.6 Å and a height of 20.7 kcal/mol. Quantum transmission probability is evaluated by solving the time dependent Schrödinger equation on a grid. Isotopic effects are examined by performing calculations with both hydrogen and deuterium. The ratio of hydrogen over the deuterium shows a 130-fold increase in transmission probability at low temperatures. This indicates a substantial quantum tunneling effect. The study of higher dimensional systems as well as increasing the number of water molecules in the chain will be necessary to fully describe the proton transfer process. Alma College Provost's Office.

  8. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology.

    Science.gov (United States)

    Galdeano, Carles; Ciulli, Alessio

    2016-09-01

    Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.

  9. Electron Bifurcation: Thermodynamics and Kinetics of Two-Electron Brokering in Biological Redox Chemistry.

    Science.gov (United States)

    Zhang, Peng; Yuly, Jonathon L; Lubner, Carolyn E; Mulder, David W; King, Paul W; Peters, John W; Beratan, David N

    2017-09-19

    processes of their own. We dissect the thermodynamics and kinetics of electron bifurcation in Nfn and find that the key features of electron bifurcation are (1) spatially separated transfer pathways that diverge from a two-electron donor, (2) one thermodynamically uphill and one downhill redox pathway, with a large negative shift in the donor's reduction potential after departure of the first electron, and (3) electron tunneling and activation factors that enable bifurcation, producing a 1:1 partitioning of electrons onto the two pathways. Electron bifurcation is found in the CO 2 reducing pathways of methanogenic archaea, in the hydrogen pathways of hydrogenases, in the nitrogen fixing pathway of Fix, and in the mitochondrial charge transfer chain of complex III, cytochrome bc 1 . While crossed potentials may offer the biological advantage of producing tightly regulated high energy reactive species, neither kinetic nor thermodynamic considerations mandate crossed potentials to generate successful electron bifurcation. Taken together, the theoretical framework established here, focusing on the underpinning electron tunneling barriers and activation free energies, explains the logic of electron bifurcation that enables energy conversion and conservation in Nfn, points toward bioinspired schemes to execute multielectron redox chemistry, and establishes a roadmap for examining novel electron bifurcation networks in nature.

  10. Yb-based heavy fermion compounds and field tuned quantum chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Mun, Eundeok [Iowa State Univ., Ames, IA (United States)

    2010-01-01

    The motivation of this dissertation was to advance the study of Yb-based heavy fermion (HF) compounds especially ones related to quantum phase transitions. One of the topics of this work was the investigation of the interaction between the Kondo and crystalline electric field (CEF) energy scales in Yb-based HF systems by means of thermoelectric power (TEP) measurements. In these systems, the Kondo interaction and CEF excitations generally give rise to large anomalies such as maxima in ρ(T) and as minima in S(T). The TEP data were use to determine the evolution of Kondo and CEF energy scales upon varying transition metals for YbT2Zn20 (T = Fe, Ru, Os, Ir, Rh, and Co) compounds and applying magnetic fields for YbAgGe and YbPtBi. For YbT2Zn20 and YbPtBi, the Kondo and CEF energy scales could not be well separated in S(T), presumably because of small CEF level splittings. A similar effect was observed for the magnetic contribution to the resistivity. For YbAgGe, S(T) has been successfully applied to determine the Kondo and CEF energy scales due to the clear separation between the ground state and thermally excited CEF states. The Kondo temperature, TK, inferred from the local maximum in S(T), remains finite as magnetic field increases up to 140 kOe. In this dissertation we have examined the heavy quasi-particle behavior, found near the field tuned AFM quantum critical point (QCP), with YbAgGe and YbPtBi. Although the observed nFL behaviors in the vicinity of the QCP are different between YbAgGe and YbPtBi, the constructed H-T phase diagram including the two crossovers are similar. For both YbAgGe and YbPtBi, the details of the quantum criticality turn out to be complicated. We expect that YbPtBi will provide an additional example of field tuned quantum criticality, but clearly there are further experimental investigations left and more ideas needed to understand the basic physics of field-induced quantum

  11. Chemistry and physics

    International Nuclear Information System (INIS)

    Broerse, J.J.; Barendsen, G.W.; Kal, H.B.; Kogel, A.J. van der

    1983-01-01

    This book contains the extended abstracts of the contributions of the poster workshop sessions on chemistry and physics of the 7th international congress of radiation research. They cover the following main topics: primary processes in radiation physics and chemistry, general chemistry in radiation chemistry, DNA and model systems in radiation chemistry, molecules of biological interest in radiation chemistry, techniques in radiation chemistry, hot atom chemistry. refs.; figs.; tabs

  12. Capping biological quantum dots with the peptide CLPFFD to increase stability and to reduce effects on cell viability

    Energy Technology Data Exchange (ETDEWEB)

    Riveros, A. L., E-mail: ariveros@postqyf.uchile.cl [Universidad de Chile, Facultad de Ciencias Químicas y Farmacéuticas (Chile); Astudillo, J., E-mail: jason.astudillo@usach.cl; Vásquez, C. C., E-mail: claudio.vasquez@usach.cl [Universidad de Santiago de Chile, Facultad de Química y Biología (Chile); Jara, Danilo H., E-mail: Danilo.H.JaraQuinteros.1@nd.edu [University of Notre Dame, Radiation Laboratory, Department of Chemistry and Biochemistry (United States); Guerrero, Ariel R. [Universidad de Chile, Facultad de Ciencias Químicas y Farmacéuticas (Chile); Guzman, F., E-mail: fanny.guzman@ucv.cl [Pontificia Universidad Católica de Valparaíso, Núcleo de Biotecnología Curauma (Chile); Osorio-Roman, I. O., E-mail: igor.orlando@gmail.com [University of Windsor, Department of Chemistry and Biochemistry (Canada); Kogan, M. J., E-mail: mkogan@ciq.uchile.cl [Universidad de Chile, Facultad de Ciencias Químicas y Farmacéuticas (Chile)

    2016-08-15

    Highly fluorescent nanoparticles, or quantum dots, have multiple applications in biology and biomedicine; however, in most cases, it is necessary to functionalize them to enhance their biocompatibility and selectivity. Generally, functionalization is performed after nanoparticle synthesis and involves the use of molecules or macromolecules having two important traits: specific biological activity and functional groups that facilitate nanoparticle capping (i.e. atom–atom interaction). For this reason, we carried out a simple protocol for the chemical synthesis of cadmium telluride quantum dots capped with glutathione, and we then functionalized these nanoparticles with the amphipathic peptide CLPFFD. This peptide attaches selectively to β-Amyloid fibres, which are involved in Alzheimer’s disease. Our results show that the optical properties of the quantum dots are not affected by functionalization with this peptide. Infrared spectra showed that cadmium telluride quantum dots were functionalized with the peptide CLPFFD. In addition, no significant differences were observed between the surface charge of the quantum dots with or without CLPFFD and the nanocrystal size calculated for HR-TEM was 4.2 nm. Finally, our results show that quantum dots with CLPFFD are stable and that they resulted in a significantly reduced cytotoxicity with respect to that induced by quantum dots not conjugated with the peptide. Moreover, the results show that the CLPFFD-functionalized nanoparticles bind to β-Amyloid fibres.

  13. Application of Ion Mobility Spectrometry (IMS) in forensic chemistry and toxicology with focus on biological matrices

    Science.gov (United States)

    Bernhard, Werner; Keller, Thomas; Regenscheit, Priska

    1995-01-01

    The IMS (Ion Mobility Spectroscopy) instrument 'Ionscan' takes advantage of the fact that trace quantities of illicit drugs are adsorbed on dust particles on clothes, in cars and on other items of evidence. The dust particles are collected on a membrane filter by a special attachment on a vacuum cleaner. The sample is then directly inserted into the spectrometer and can be analyzed immediately. We show casework applications of a forensic chemistry and toxicology laboratory. One new application of IMS in forensic chemistry is the detection of psilocybin in dried mushrooms without any further sample preparation.

  14. Oxygen chemistry in biology: Vibrational spectroscopy, stable isotopes, and future applications

    Energy Technology Data Exchange (ETDEWEB)

    Babcock, G.T. [Michigan State Univ., East Lansing, MI (United States)

    1994-12-01

    Dioxygen is an ideally suited substrate for enzymatic manipulation in oxidation-reduction chemistry and in substrate transformation. It is a powerful oxidant with a midpoint potential of 0.815 at neutral pH; at the same time, however, it exists in a triplet state in its most stable electronic configuration. This latter property confers kinetic inertness as a result of spin-conservation restrictions on reaction chemistry. If these restrictions can be overcome and controlled, dioxygen`s high redox potential can be used to maximize efficiency in free-energy conversion processes and to effect activation of relatively inert substrates.

  15. Science Academies' Refresher Course in Quantum Mechanics Post ...

    Indian Academy of Sciences (India)

    Physics Dept

    2016-02-20

    Feb 20, 2016 ... Quantum Mechanics is essential for understanding Physics, Chemistry and even modern Biology. A brief outline of the course is as follows: Schrödinger equation, Hydrogen atom, mathematics of linear vector space, principles and postulates of quantum mechanics, angular momentum, perturbation theory.

  16. Research into condensed matter using large-scale apparatus. Physics, chemistry, biology. Progress report 1992-1995. Summarizing reports

    International Nuclear Information System (INIS)

    1996-01-01

    Activities for research into condensed matter have been supported by the German BMBF with approx. 102 million Deutschmarks in the years 1992 through 1995. These financial means have been distributed among 314 research projects in the fields of physics, chemistry, biology, materials science, and other fields, which all rely on the intensive utilization of photon and particle beams generated in large-scale apparatus of institutions for basic research. The volume in hand first gives information of a general kind and statistical data on the distribution of financial means, for a number of priority research projects. The project reports are summarizing reports on the progress achieved in the various projects. (CB) [de

  17. Solid-state quantum chemistry and materials science: Solid compounds of the d and f elements

    International Nuclear Information System (INIS)

    Gubanov, V.A.

    1989-01-01

    Methods have been developed for calculating electron structures for solid compounds of d and f elements and for simulating physicochemical properties of materials based on them. Cluster and band calculations are considered for refractory compounds of d metals formed with light elements. There are bond and property regularities in doping by meals and metalloids, and defects and impurities have certain effects, where studies have been made on the electron structures for disordered phases and solid solutions in relation to sublattice compositions. Quantum-chemical simulation methods have been developed for optically active and fluorescent materials based on d and f metal oxides, fluorides, and chalcogenides, and compositions have been proposed for new optically active composites and protective coatings. New approaches have been defined to the magnetic parameters of metals, alloys, and compounds; these can be applied in simulating new magnetic materials. Calculations are given on energy spectra for high-temperature oxide superconductors. There is interesting scope for quantum-chemical methods in application to many topics in materials science

  18. Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks.

    Science.gov (United States)

    Kastrup, Christian J; Runyon, Matthew K; Lucchetta, Elena M; Price, Jessica M; Ismagilov, Rustem F

    2008-04-01

    Understanding the spatial dynamics of biochemical networks is both fundamentally important for understanding life at the systems level and also has practical implications for medicine, engineering, biology, and chemistry. Studies at the level of individual reactions provide essential information about the function, interactions, and localization of individual molecular species and reactions in a network. However, analyzing the spatial dynamics of complex biochemical networks at this level is difficult. Biochemical networks are nonequilibrium systems containing dozens to hundreds of reactions with nonlinear and time-dependent interactions, and these interactions are influenced by diffusion, flow, and the relative values of state-dependent kinetic parameters. To achieve an overall understanding of the spatial dynamics of a network and the global mechanisms that drive its function, networks must be analyzed as a whole, where all of the components and influential parameters of a network are simultaneously considered. Here, we describe chemical concepts and microfluidic tools developed for network-level investigations of the spatial dynamics of these networks. Modular approaches can be used to simplify these networks by separating them into modules, and simple experimental or computational models can be created by replacing each module with a single reaction. Microfluidics can be used to implement these models as well as to analyze and perturb the complex network itself with spatial control on the micrometer scale. We also describe the application of these network-level approaches to elucidate the mechanisms governing the spatial dynamics of two networkshemostasis (blood clotting) and early patterning of the Drosophila embryo. To investigate the dynamics of the complex network of hemostasis, we simplified the network by using a modular mechanism and created a chemical model based on this mechanism by using microfluidics. Then, we used the mechanism and the model to

  19. Some aspects of the organic, biological and inorganic chemistry of astatine

    International Nuclear Information System (INIS)

    Visser, G.W.M.

    1982-01-01

    Astatine has no stable isotopes and the radioactive isotopes with half-lives sufficiently long for chemical experiments ( 209 At, 210 At, 211 At) must be produced artificially with a cyclotron or with a high energy accelerator by spallation of Th. This thesis deals with the synthesis and chemistry of At-compounds and the determination of some of their properties. (C.F.)

  20. Integrating Biology into the General Chemistry Laboratory: Fluorometric Analysis of Chlorophyll "a"

    Science.gov (United States)

    Wesolowski, Meredith C.

    2014-01-01

    A laboratory experiment that introduces fluorometry of chlorophyll "a" at the general chemistry level is described. The use of thin-layer chromatography to isolate chlorophyll "a" from spirulina and leaf matter enables quantification of small amounts of chlorophyll "a" via fluorometry. Student results were reasonably…

  1. Derivatization chemistry of the double-decker dicobalt sandwich ion targeted to design biologically active substances

    Czech Academy of Sciences Publication Activity Database

    Grüner, Bohumír; Švec, Petr; Hájková, Zuzana; Císařová, I.; Pokorná, Jana; Konvalinka, Jan

    2012-01-01

    Roč. 84, č. 11 (2012), s. 2243-2262 ISSN 0033-4545 R&D Projects: GA AV ČR IAAX00320901 Institutional support: RVO:61388980 ; RVO:61388963 Keywords : AIDS treatment * boranes * canastide ion * carboranes * dicarbollides * HIV -protease Subject RIV: CA - Inorganic Chemistry Impact factor: 3.386, year: 2012

  2. Scale relativity theory and integrative systems biology: 2. Macroscopic quantum-type mechanics.

    Science.gov (United States)

    Nottale, Laurent; Auffray, Charles

    2008-05-01

    In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, which aims at describing the effects of a non-differentiable and fractal (i.e., explicitly scale dependent) geometry of space-time. The first paper of this series was devoted, in this new framework, to the construction from first principles of scale laws of increasing complexity, and to the discussion of some tentative applications of these laws to biological systems. In this second review and perspective paper, we describe the effects induced by the internal fractal structures of trajectories on motion in standard space. Their main consequence is the transformation of classical dynamics into a generalized, quantum-like self-organized dynamics. A Schrödinger-type equation is derived as an integral of the geodesic equation in a fractal space. We then indicate how gauge fields can be constructed from a geometric re-interpretation of gauge transformations as scale transformations in fractal space-time. Finally, we introduce a new tentative development of the theory, in which quantum laws would hold also in scale space, introducing complexergy as a measure of organizational complexity. Initial possible applications of this extended framework to the processes of morphogenesis and the emergence of prokaryotic and eukaryotic cellular structures are discussed. Having founded elements of the evolutionary, developmental, biochemical and cellular theories on the first principles of scale relativity theory, we introduce proposals for the construction of an integrative theory of life and for the design and implementation of novel macroscopic quantum-type experiments and devices, and discuss their potential

  3. Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol

    Science.gov (United States)

    Lounnas, Valère; Wedler, Henry B.; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G.; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J.; Vriend, Gert

    2014-11-01

    In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted—from published articles, via printed results of computational chemistry experiments, to 3D models—is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

  4. Polarizabilities of Ba and Ba2: Comparison of molecular beam experiments with relativistic quantum chemistry

    International Nuclear Information System (INIS)

    Schaefer, Sascha; Mehring, Max; Schaefer, Rolf; Schwerdtfeger, Peter

    2007-01-01

    The dielectric response to an inhomogeneous electric field has been investigated for Ba and Ba 2 within a molecular beam experiment. The ratio of the polarizabilities per atom of Ba 2 and Ba is determined to be 1.30±0.13. The experimental result is compared to a high level ab initio quantum chemical coupled cluster calculation with an energy-consistent scalar relativistic small-core pseudopotential for Ba. For the barium atom a polarizability of 40.82 A 3 is obtained and the isotropic value of the polarizability calculated for Ba 2 is 97.88 A 3 , which is in good agreement with the experimental results, demonstrating that a quantitative understanding of the interaction between two closed-shell heavy element metal atoms has been achieved

  5. High-throughput quantum chemistry and virtual screening for OLED material components

    Science.gov (United States)

    Halls, Mathew D.; Giesen, David J.; Hughes, Thomas F.; Goldberg, Alexander; Cao, Yixiang

    2013-09-01

    Computational structure enumeration, analysis using an automated simulation workflow and filtering of large chemical structure libraries to identify lead systems, has become a central paradigm in drug discovery research. Transferring this paradigm to challenges in materials science is now possible due to advances in the speed of computational resources and the efficiency and stability of chemical simulation packages. State-of-the-art software tools that have been developed for drug discovery can be applied to efficiently explore the chemical design space to identify solutions for problems such as organic light-emitting diode material components. In this work, virtual screening for OLED materials based on intrinsic quantum mechanical properties is illustrated. Also, a new approach to more reliably identify candidate systems is introduced that is based on the chemical reaction energetics of defect pathways for OLED materials.

  6. Design of SGLT2 Inhibitors for the Treatment of Type 2 Diabetes: A History Driven by Biology to Chemistry.

    Science.gov (United States)

    Cai, Wenqing; Jiang, Linlin; Xie, Yafei; Liu, Yuqiang; Liu, Wei; Zhao, Guilong

    2015-01-01

    A brief history of the design of sodium-dependent glucose cotransporter 2 (SGLT2) inhibitors is reviewed. The design of O-glucoside SGLT2 inhibitors by structural modification of phlorizin, a naturally occurring O-glucoside, in the early stage was a process mainly driven by biology with anticipation of improving SGLT2/SGLT1 selectivity and increasing metabolic stability. Discovery of dapagliflozin, a pioneering C-glucoside SGLT2 inhibitor developed by Bristol-Myers Squibb, represents an important milestone in this history. In the second stage, the design of C-glycoside SGLT2 inhibitors by modifications of the aglycone and glucose moiety of dapagliflozin, an original structural template for almost all C-glycoside SGLT2 inhibitors, was mainly driven by synthetic organic chemistry due to the challenge of designing dapagliflozin derivatives that are patentable, biologically active and synthetically accessible. Structure-activity relationships (SAR) of the SGLT2 inhibitors are also discussed.

  7. State of Academic Knowledge on Toxicity and Biological Fate of Quantum Dots

    Science.gov (United States)

    Pelley, Jennifer L.; Daar, Abdallah S.; Saner, Marc A.

    2009-01-01

    Quantum dots (QDs), an important class of emerging nanomaterial, are widely anticipated to find application in many consumer and clinical products in the near future. Premarket regulatory scrutiny is, thus, an issue gaining considerable attention. Previous review papers have focused primarily on the toxicity of QDs. From the point of view of product regulation, however, parameters that determine exposure (e.g., dosage, transformation, transportation, and persistence) are just as important as inherent toxicity. We have structured our review paper according to regulatory risk assessment practices, in order to improve the utility of existing knowledge in a regulatory context. Herein, we summarize the state of academic knowledge on QDs pertaining not only to toxicity, but also their physicochemical properties, and their biological and environmental fate. We conclude this review with recommendations on how to tailor future research efforts to address the specific needs of regulators. PMID:19684286

  8. Evaluation of the Biological Effects of Externally Tunable, Hydrogel Encapsulated Quantum Dot Nanospheres in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Somesree GhoshMitra

    2011-08-01

    Full Text Available Quantum Dots (QDs have become an interesting subject of study for labeling and drug delivery in biomedical research due to their unique responses to external stimuli. In this paper, the biological effects of a novel hydrogel based QD nano-structure on E. coli bacteria are presented. The experimental evidence reveals that cadmium telluride (CdTe QDs that are encapsulated inside biocompatible polymeric shells have reduced or negligible toxicity to this model cell system, even when exposed at higher dosages. Furthermore, a preliminary gene expression study indicates that QD-hydrogel nanospheres do not inhibit the Green Fluorescent Protein (GFP gene expression. As the biocompatible and externally tunable polymer shells possess the capability to control the QD packing density at nanometer scales, the resulting luminescence efficiency of the nanostructures, besides reducing the cytotoxic potential, may be suitable for various biomedical applications.

  9. Factor analysis for instruments of science learning motivation and its implementation for the chemistry and biology teacher candidates

    Science.gov (United States)

    Prasetya, A. T.; Ridlo, S.

    2018-03-01

    The purpose of this study is to test the learning motivation of science instruments and compare the learning motivation of science from chemistry and biology teacher candidates. Kuesioner Motivasi Sains (KMS) in Indonesian adoption of the Science Motivation Questionnaire II (SMQ II) consisting of 25 items with a 5-point Likert scale. The number of respondents for the Exploratory Factor Analysis (EFA) test was 312. The Kaiser-Meyer-Olkin (KMO), determinant, Bartlett’s Sphericity, Measures of Sampling Adequacy (MSA) tests against KMS using SPSS 20.0, and Lisrel 8.51 software indicate eligible indications. However testing of Communalities obtained results that there are 4 items not qualified, so the item is discarded. The second test, all parameters of eligibility and has a magnitude of Root Mean Square Error of Approximation (RMSEA), P-Value for the Test of Close Fit (RMSEA <0.05), Goodness of Fit Index (GFI) was good. The new KMS with 21 valid items and composite reliability of 0.9329 can be used to test the level of learning motivation of science which includes Intrinsic Motivation, Sefl-Efficacy, Self-Determination, Grade Motivation and Career Motivation for students who master the Indonesian language. KMS trials of chemistry and biology teacher candidates obtained no significant difference in the learning motivation between the two groups.

  10. The exposure of bacteria to CdTe-core quantum dots: the importance of surface chemistry on cytotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Raphael [DCPR, Departement de Chimie Physique de Reactions, Nancy Universite, CNRS, 1 rue Grandville, BP 20451, F-54001 Nancy (France); Wolpert, Cecile; Guilloteau, Helene; Lambert, Jacques; Merlin, Christophe [LCPME, Laboratoire de Chimie Physique et Microbiologie pour l' Environnement, Nancy-Universite, CNRS, 405 rue de Vandoeuvre, F-54600 Villers-les-Nancy (France); Balan, Lavinia [DPG, Departement de Photochimie Generale, UMR CNRS 7525, Universite de Haute Alsace, ENSCMu, 3 rue Alfred Werner, F-68093 Mulhouse (France)], E-mail: Christophe.Merlin@pharma.uhp-nancy.fr

    2009-06-03

    A series of water-soluble CdTe-core quantum dots (QDs) with diameters below 5.0 nm and functionalized at their surface with polar ligands such as thioglycolic acid (TGA) or the tripeptide glutathione (GSH) were synthesized and characterized by UV-vis absorption spectroscopy, their photoluminescence measurements, atomic force microscopy (AFM) and transmission electron microscopy (TEM). Because cell elongations and growth inhibitions were observed during labeling experiments, the cytotoxicity of CdTe-core QDs was investigated. Using growth inhibition tests combining different bacterial strains with different CdTe-core QDs, it was possible to demonstrate that the cytotoxicity of QDs towards bacteria depends on exposure concentrations, surface chemistry and coating, and that it varied with the strain considered. Growth inhibition tests carried out with heavy-metal-resistant bacteria, as well as ICP-AES analyses of cadmium species released by CdTe-TGA QDs, demonstrated that the leakage of Cd{sup 2+} is not the main source of QD toxicity. Our study suggests that QD cytotoxicity is rather due to the formation of TeO{sub 2} and probably the existence of CdO formed by surface oxidation. In this respect, QDs possessing a CdO shell appeared very toxic.

  11. Biological Fate of Fe3O4 Core-Shell Mesoporous Silica Nanoparticles Depending on Particle Surface Chemistry

    Science.gov (United States)

    Rascol, Estelle; Daurat, Morgane; Da Silva, Afitz; Maynadier, Marie; Dorandeu, Christophe; Charnay, Clarence; Garcia, Marcel; Lai-Kee-Him, Joséphine; Bron, Patrick; Auffan, Mélanie; Angeletti, Bernard; Devoisselle, Jean-Marie; Guari, Yannick; Gary-Bobo, Magali; Chopineau, Joël

    2017-01-01

    The biological fate of nanoparticles (NPs) for biomedical applications is highly dependent of their size and charge, their aggregation state and their surface chemistry. The chemical composition of the NPs surface influences their stability in biological fluids, their interaction with proteins, and their attraction to the cell membranes. In this work, core-shell magnetic mesoporous silica nanoparticles (Fe3O4@MSN), that are considered as potential theranostic candidates, are coated with polyethylene glycol (PEG) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer. Their biological fate is studied in comparison to the native NPs. The physicochemical properties of these three types of NPs and their suspension behavior in different media are investigated. The attraction to a membrane model is also evaluated using a supported lipid bilayer. The surface composition of NPs strongly influences their dispersion in biological fluids mimics, protein binding and their interaction with cell membrane. While none of these types of NPs is found to be toxic on mice four days after intravenous injection of a dose of 40 mg kg−1 of NPs, their surface coating nature influences the in vivo biodistribution. Importantly, NP coated with DMPC exhibit a strong accumulation in liver and a very low accumulation in lung in comparison with nude or PEG ones. PMID:28665317

  12. The synergistic use of computation, chemistry and biology to discover novel peptide-based drugs: the time is right.

    Science.gov (United States)

    Audie, J; Boyd, C

    2010-01-01

    The case for peptide-based drugs is compelling. Due to their chemical, physical and conformational diversity, and relatively unproblematic toxicity and immunogenicity, peptides represent excellent starting material for drug discovery. Nature has solved many physiological and pharmacological problems through the use of peptides, polypeptides and proteins. If nature could solve such a diversity of challenging biological problems through the use of peptides, it seems reasonable to infer that human ingenuity will prove even more successful. And this, indeed, appears to be the case, as a number of scientific and methodological advances are making peptides and peptide-based compounds ever more promising pharmacological agents. Chief among these advances are powerful chemical and biological screening technologies for lead identification and optimization, methods for enhancing peptide in vivo stability, bioavailability and cell-permeability, and new delivery technologies. Other advances include the development and experimental validation of robust computational methods for peptide lead identification and optimization. Finally, scientific analysis, biology and chemistry indicate the prospect of designing relatively small peptides to therapeutically modulate so-called 'undruggable' protein-protein interactions. Taken together a clear picture is emerging: through the synergistic use of the scientific imagination and the computational, chemical and biological methods that are currently available, effective peptide therapeutics for novel targets can be designed that surpass even the proven peptidic designs of nature.

  13. Ab initio quantum chemistry in parallel-portable tools and applications

    International Nuclear Information System (INIS)

    Harrison, R.J.; Shepard, R.; Kendall, R.A.

    1991-01-01

    In common with many of the computational sciences, ab initio chemistry faces computational constraints to which a partial solution is offered by the prospect of highly parallel computers. Ab initio codes are large and complex (O(10 5 ) lines of FORTRAN), representing a significant investment of communal effort. The often conflicting requirements of portability and efficiency have been successfully resolved on vector computers by reliance on matrix oriented kernels. This proves inadequate even upon closely-coupled shared-memory parallel machines. We examine the algorithms employed during a typical sequence of calculations. Then we investigate how efficient portable parallel implementations may be derived, including the complex multi-reference singles and doubles configuration interaction algorithm. A portable toolkit, modeled after the Intel iPSC and the ANL-ACRF PARMACS, is developed, using shared memory and TCP/IP sockets. The toolkit is used as an initial platform for programs portable between LANS, Crays and true distributed-memory MIMD machines. Timings are presented. 53 refs., 4 tabs

  14. RM1 Semiempirical Quantum Chemistry: Parameters for Trivalent Lanthanum, Cerium and Praseodymium.

    Directory of Open Access Journals (Sweden)

    José Diogo L Dutra

    Full Text Available The RM1 model for the lanthanides is parameterized for complexes of the trications of lanthanum, cerium, and praseodymium. The semiempirical quantum chemical model core stands for the [Xe]4fn electronic configuration, with n =0,1,2 for La(III, Ce(III, and Pr(III, respectively. In addition, the valence shell is described by three electrons in a set of 5d, 6s, and 6p orbitals. Results indicate that the present model is more accurate than the previous sparkle models, although these are still very good methods provided the ligands only possess oxygen or nitrogen atoms directly coordinated to the lanthanide ion. For all other different types of coordination, the present RM1 model for the lanthanides is much superior and must definitely be used. Overall, the accuracy of the model is of the order of 0.07Å for La(III and Pr(III, and 0.08Å for Ce(III for lanthanide-ligand atom distances which lie mostly around the 2.3Å to 2.6Å interval, implying an error around 3% only.

  15. Aggregation and growth of ZnO quantum dots prepared from sol-gel chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Santilli, C.V.; Pulcinelli, S.H.; Caetano, B.L. [Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Araraquara, SP (Brazil); Briois, V.B [Synchrotron SOLEIL, Saint-Aubin (France)

    2016-07-01

    Full text: Herein we discuss in depth the mechanisms of growth control of ZnO quantum dots (Q-dot) prepared from the zinc oxy-acetate ethanolic solution by the addition of LiOH. Through in situ monitoring of Q-dot radii and of aggregation index calculated from UV-Vis absorption spectra and small-angle X-ray scattering (SAXS) the aggregation and growth of ZnO nanocrystal was well described from two kinetic models: during the first step (t< 50 min) the structural evolution is controlled by the coalescence caused by the oriented attachment between the nanocrystal aggregates while at the advanced time (t> 50 min) the Q-dot coarsening follows the Ostwald ripening (OR) mechanism. From the higher oriented attachment efficiency observed here as compared with early reported synthesis using NaOH and KOH, we propose an universal mechanism to control coalescence and coarsening of ZnO nanocrystal provided from the shield caused by the adsorption of the alkali cation. From X-ray diffraction and transmission electron microscopy results we demonstrate that this mechanism is also useful to prepare Q-dot powders with controlled size. (author)

  16. Electron Transfer in Chemistry and Biology – The Primary Events in ...

    Indian Academy of Sciences (India)

    molecular unit to another. This reaction, accompanied by proton and hydrogen atom trans- fers, occurs in a cascade in many biological processes, includ- ing photosynthesis. The key chemical steps involved in photo- synthesis and the many ...

  17. Evaluation of Anti-Inflammatory Drug-Conjugated Silicon Quantum Dots: Their Cytotoxicity and Biological Effect

    Directory of Open Access Journals (Sweden)

    Kenji Yamamoto

    2013-01-01

    Full Text Available Silicon quantum dots (Si-QDs have great potential for biomedical applications, including their use as biological fluorescent markers and carriers for drug delivery systems. Biologically inert Si-QDs are less toxic than conventional cadmium-based QDs, and can modify the surface of the Si-QD with covalent bond. We synthesized water-soluble alminoprofen-conjugated Si-QDs (Ap-Si. Alminoprofen is a non-steroid anti-inflammatory drug (NSAID used as an analgesic for rheumatism. Our results showed that the “silicon drug” is less toxic than the control Si-QD and the original drug. These phenomena indicate that the condensed surface integration of ligand/receptor-type drugs might reduce the adverse interaction between the cells and drug molecules. In addition, the medicinal effect of the Si-QDs (i.e., the inhibition of COX-2 enzyme was maintained compared to that of the original drug. The same drug effect is related to the integration ratio of original drugs, which might control the binding interaction between COX-2 and the silicon drug. We conclude that drug conjugation with biocompatible Si-QDs is a potential method for functional pharmaceutical drug development.

  18. Etymology of transition metal biomolecules as a learning aid in Biological Chemistry

    International Nuclear Information System (INIS)

    Silva, Jose A.L. da

    2013-01-01

    Numerous functional biomolecules are associated with metals, i.e. the metallobiomolecules; more specifically, some are dependent on transition metals required for several crucial biological roles. Nevertheless, their names can lead to ambiguous interpretations concerning the properties and performances of this group of biological molecules. Their etymology may be useful by providing a more perceptive insight into their features. However, etymology can lead to incongruous conclusions, requiring an especially careful approach to prevent errors. Examples illustrating these subjects shall be examined (author)

  19. Radiation biology using synchrotron radiation. In relation to radiation chemistry as an initial process

    International Nuclear Information System (INIS)

    Kobayashi, Katsumi

    1995-01-01

    Radiation biology using synchrotron radiation have been investigated, focusing on the mechanism of the formation of molecular damage. This paper introduces recent outcome of these studies. First, the process from imparted energy to the formation of molecular damage is outlined. The previous studies can be largely categorized as dealing with (1) biological effects of inner-shell ionization on elements composing the living body and (2) X-ray energy dependence of biological effects. Bromine and phosphorus are used as elements for the study of inner-cell ionization. In the study on lethal effects of monochromatic soft X-rays on the BrdUMP-incorporated yeast cells, Auger enhancement was found to occur. The first report on the effects of K-shell absorption of cellular phosphorus atoms has revealed that biological effects on cellular lethality and genetic changes was enhanced by 40%. Plasmid DNA and oligonucleotide have been used to study biological effects of vacuum ultraviolet rays to monochromatic soft X-ray, which makes it possible to study strand breaks. Because experimental production of energy required for the formation of double strand breaks has become possible, synchrotron radiation plays a very important role in radiation biological studies. Finally, future issues are presented. (N.K.)

  20. Radical cations in radiation chemistry of aldehydes. ESR study and quantum chemical analysis

    International Nuclear Information System (INIS)

    Belevskii, V.N.; Tyurin, D.A.; Chuvilkin, N.D.

    1998-01-01

    Quantum-chemical (MNDO-UHF) calculations of electronic, spin and energy characteristics of radical cations (RC) of ethanal, propanal, butanal, and pentanal and their distonic isomers were performed. The calculations both with 'frozen' (vertical ionization) and completely optimize geometry (adiabatic approximation) were made. It was been shown that the most positive charge and spin population are localized at O atoms and adjacent C atom as well as at aldehyde protons. The C-H bonds corresponding to those protons as well as neighboring C-O and C-C bonds are considerable weaker (longer) in radical cations as compared to their neutral precursors. That is why such reaction centers are apt to deprotonation with the formation of acyl radical as well as to α- and β-splitting (scission) which are well-known from aldehydes mass-spectra. Our calculations shown that distonic RC (products of intramolecular H-atom transfer) are more stable as compare to their classical isomers: e.g. the difference in energy ΔE = -0.95 eV, -1.2 eV, and -1.5 eV for tree distonic isomers of butanal RC as compare to classical isomer, ΔE -1.2 eV for distonic RC of ethanal. The results of calculations are effectively correlated with ESR data obtained in freonic solutions, X- and gamma-irradiated at 77 K and in liquid aldehydes, X-irradiated by using 2,4,6-tri-tert-burylnitrosobenzene (BNB) and t-BuNO (NtB) as a spin traps. (author)

  1. Correlating labeling chemistry and in-vitro test results with the biological behavior of radiolabeled proteins

    International Nuclear Information System (INIS)

    Srivastava, S.C.; Meinken, G.E.

    1985-01-01

    Monoclonal antibodies possess enormous potential for delivery of therapeutic amounts of radionuclides to target antigens in vivo, in particular for tumor imaging and therapy. Translation of this concept into practice has encountered numerous problems. Specifically whereas general protein radiolabeling methods are applicable to antibodies, immunological properties of the antibodies are often compromised resulting in reduced in-vivo specificity for the target antigens. The bifunctional chelating agent approach shows the most promise, however, development of other agents will be necessary for widespread usefulness of this technique. The effects of labeling chemistry on the in-vivo behavior of several monoclonal antibodies are described. 30 refs., 4 figs., 10 tabs

  2. Quantum

    CERN Document Server

    Al-Khalili, Jim

    2003-01-01

    In this lively look at quantum science, a physicist takes you on an entertaining and enlightening journey through the basics of subatomic physics. Along the way, he examines the paradox of quantum mechanics--beautifully mathematical in theory but confoundingly unpredictable in the real world. Marvel at the Dual Slit experiment as a tiny atom passes through two separate openings at the same time. Ponder the peculiar communication of quantum particles, which can remain in touch no matter how far apart. Join the genius jewel thief as he carries out a quantum measurement on a diamond without ever touching the object in question. Baffle yourself with the bizzareness of quantum tunneling, the equivalent of traveling partway up a hill, only to disappear then reappear traveling down the opposite side. With its clean, colorful layout and conversational tone, this text will hook you into the conundrum that is quantum mechanics.

  3. Information carriers and (reading them through) information theory in quantum chemistry.

    Science.gov (United States)

    Geerlings, Paul; Borgoo, Alex

    2011-01-21

    This Perspective discusses the reduction of the electronic wave function via the second-order reduced density matrix to the electron density ρ(r), which is the key ingredient in density functional theory (DFT) as a basic carrier of information. Simplifying further, the 1-normalized density function turns out to contain essentially the same information as ρ(r) and is even of preferred use as an information carrier when discussing the periodic properties along Mendeleev's table where essentially the valence electrons are at stake. The Kullback-Leibler information deficiency turns out to be the most interesting choice to obtain information on the differences in ρ(r) or σ(r) between two systems. To put it otherwise: when looking for the construction of a functional F(AB) = F[ζ(A)(r),ζ(B)(r)] for extracting differences in information from an information carrier ζ(r) (i.e. ρ(r), σ(r)) for two systems A and B the Kullback-Leibler information measure ΔS is a particularly adequate choice. Examples are given, varying from atoms, to molecules and molecular interactions. Quantum similarity of atoms indicates that the shape function based KL information deficiency is the most appropriate tool to retrieve periodicity in the Periodic Table. The dissimilarity of enantiomers for which different information measures are presented at global and local (i.e. molecular and atomic) level leads to an extension of Mezey's holographic density theorem and shows numerical evidence that in a chiral molecule the whole molecule is pervaded by chirality. Finally Kullback-Leibler information profiles are discussed for intra- and intermolecular proton transfer reactions and a simple S(N)2 reaction indicating that the theoretical information profile can be used as a companion to the energy based Hammond postulate to discuss the early or late transition state character of a reaction. All in all this Perspective's answer is positive to the question of whether an even simpler carrier of

  4. Heats of formation of phosphorus compounds determined by current methods of computational quantum chemistry

    Science.gov (United States)

    Haworth, Naomi L.; Bacskay, George B.

    2002-12-01

    The heats of formation of a range of phosphorus containing molecules (P2, P4, PH, PH2, PH3, P2H2, P2H4, PO, PO2, PO3, P2O, P2O2, HPO, HPOH, H2POH, H3PO, HOPO, and HOPO2) have been determined by high level quantum chemical calculations. The equilibrium geometries and vibrational frequencies were computed via density functional theory, utilizing the B3LYP/6-31G(2df,p) functional and basis set. Atomization energies were obtained by the application of ab initio coupled cluster theory with single and double excitations from (spin)-restricted Hartree-Fock reference states with perturbative correction for triples [CCSD(T)], in conjunction with cc-pVnZ basis sets (n=T, Q, 5) which include an extra d function on the phosphorus atoms and diffuse functions on the oxygens, as recommended by Bauschlicher [J. Phys. Chem. A 103, 11126 (1999)]. The valence correlated atomization energies were extrapolated to the complete basis limit and corrected for core-valence (CV) correlation and scalar relativistic effects, as well as for basis set superposition errors (BSSE) in the CV terms. This methodology is effectively the same as the one adopted by Bauschlicher in his study of PO, PO2, PO3, HPO, HOPO, and HOPO2. Consequently, for these molecules the results of this work closely match Bauschlicher's computed values. The theoretical heats of formation, whose accuracy is estimated as ranging from ±1.0 to ±2.5 kcal mol-1, are consistent with the available experimental data. The current set of theoretical data represent a convenient benchmark, against which the results of other computational procedures, such as G3, G3X, and G3X2, can be compared. Despite the fact that G3X2 [which is an approximation to the quadratic CI procedure QCISD(T,Full)/G3Xlarge] is a formally higher level theory than G3X, the heats of formation obtained by these two methods are found to be of comparable accuracy. Both reproduce the benchmark heats of formation on the average to within ±2 kcal mol-1 and, for these

  5. Chemistry and biology of reactive species with special reference to the antioxidative defence status in pancreatic β-cells.

    Science.gov (United States)

    Lenzen, Sigurd

    2017-08-01

    Diabetes mellitus is a serious metabolic disease. Dysfunction and subsequent loss of the β-cells in the islets of Langerhans through apoptosis ultimately cause a life-threatening insulin deficiency. The underlying reason for the particular vulnerability of the β-cells is an extraordinary sensitivity to the toxicity of reactive oxygen and nitrogen species (ROS and RNS) due to its low antioxidative defense status. This review considers the different aspects of the chemistry and biology of the biologically most important reactive species and their chemico-biological interactions in the β-cell toxicity of proinflammatory cytokines in type 1 diabetes and of lipotoxicity in type 2 diabetes development. The weak antioxidative defense equipment in the different subcellular organelles makes the β-cells particularly vulnerable and prone to mitochondrial, peroxisomal and ER stress. Looking upon the enzyme deficiencies which are responsible for the low antioxidative defense status of the pancreatic β-cells it is the lack of enzymatic capacity for H 2 O 2 inactivation at all major subcellular sites. Diabetes is the most prevalent metabolic disorder with a steadily increasing incidence of both type 1 and type 2 diabetes worldwide. The weak protection of the pancreatic β-cells against oxidative stress is a major reason for their particular vulnerability. Thus, careful protection of the β-cells is required for prevention of the disease. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Biological sensing and control of emission dynamics of quantum dot bioconjugates using arrays of long metallic nanorods.

    Science.gov (United States)

    Sadeghi, Seyed M; Gutha, Rithvik R; Wing, Waylin J; Sharp, Christina; Capps, Lucas; Mao, Chuanbin

    2017-01-01

    We study biological sensing using plasmonic and photonic-plasmonic resonances of arrays of ultralong metallic nanorods and analyze the impact of these resonances on emission dynamics of quantum dot bioconjugates. We demonstrate that the LSPRs and plasmonic lattice modes of such array can be used to detect a single self-assembled monolayer of alkanethiol at the visible (550 nm) and near infrared (770 nm) range with well resolved shifts. We study adsorption of streptavidin-quantum dot conjugates to this monolayer, demonstrating that formation of nearly two dimensional arrays of quantum dots with limited emission blinking can lead to extra well-defined wavelength shifts in these modes. Using spectrally-resolved lifetime measurements we study the emission dynamics of such quantum dot bioconjugates within their monodispersed size distribution. We show that, despite their close vicinity to the nanorods, the rate of energy transfer from these quantum dots to nanorods is rather weak, while the plasmon field enhancement can be strong. Our results reveal that the nanorods present a strongly wavelength or size-dependent non-radiative decay channel to the quantum dot bioconjugates.

  7. Lee Pedersen’s work in theoretical and computational chemistry and biochemistry

    OpenAIRE

    Pedersen, Lee G

    2011-01-01

    Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics. In many cases, a reasonable approximation to quantum mechanics is classical mechanics realized through Newton’s equations of motion. Dr. Pedersen began his career using quantum mechanics to describe the properties of small molecular complexes that could serve as models for biochemical systems. To describe large molecular systems required a drop-back to classical means and this led surpri...

  8. Marine Natural Product Bis-indole Alkaloid Caulerpin: Chemistry and Biology.

    Science.gov (United States)

    Lunagariya, Jignesh; Bhadja, Poonam; Zhong, Shenghui; Vekariya, Rohit; Xu, Shihai

    2017-09-27

    Marine bis-indole alkaloids comprise a large and increasingly growing class of secondary metabolites, and continue to deliver a great variety of structural templates. The alkaloids derived from marine resources play a crucial role in medicinal chemistry and as chemical agents. In particular, bis-indole alkaloid caulerpin isolated from marine green algae Caulerpa and a red algae Chondria armata at various places around the world, and tested against several therapeutic areas such as anti-diabetic, antinociceptive, anti-inflammatory, anti-tumor, anti-larvicidal, anti-herpes, anti-tubercular, anti-microbial and immunostimulating activity as well as means of other chemical agents. Herein, we summarized discovery of caulerpin, and its potential medicinal and chemical applications in chronological order with various aspects. Additionally, synthesis of caulerpin, its functional analogues, and structural isomer have also been reviewed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  9. Chemistry and the worm: Caenorhabditis elegans as a platform for integrating chemical and biological research.

    Science.gov (United States)

    Hulme, S Elizabeth; Whitesides, George M

    2011-05-16

    This Review discusses the potential usefulness of the worm Caenorhabditis elegans as a model organism for chemists interested in studying living systems. C. elegans, a 1 mm long roundworm, is a popular model organism in almost all areas of modern biology. The worm has several features that make it attractive for biology: it is small (1000 cells), transparent, and genetically tractable. Despite its simplicity, the worm exhibits complex phenotypes associated with multicellularity: the worm has differentiated cells and organs, it ages and has a well-defined lifespan, and it is capable of learning and remembering. This Review argues that the balance between simplicity and complexity in the worm will make it a useful tool in determining the relationship between molecular-scale phenomena and organism-level phenomena, such as aging, behavior, cognition, and disease. Following an introduction to worm biology, the Review provides examples of current research with C. elegans that is chemically relevant. It also describes tools-biological, chemical, and physical-that are available to researchers studying the worm. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Investigating Membranes: Using Artificial Membranes to Convey Chemistry and Biology Concepts

    Science.gov (United States)

    Zrelak, Yoshi; McCallister, Gary

    2009-01-01

    While not organic in nature, quick-"growing" artificial membranes can be a profound visual aid when teaching students about cellular processes and the chemical nature of membranes. Students are often intrigued when they see biological and chemical concepts come to life before their eyes. In this article, the authors share their approach to growing…

  11. On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry.

    Science.gov (United States)

    Long, Marcus J C; Poganik, Jesse R; Aye, Yimon

    2016-03-23

    Proximity enhancement is a central chemical tenet underpinning an exciting suite of small-molecule toolsets that have allowed us to unravel many biological complexities. The leitmotif of this opus is "tethering"-a strategy in which a multifunctional small molecule serves as a template to bring proteins/biomolecules together. Scaffolding approaches have been powerfully applied to control diverse biological outcomes such as protein-protein association, protein stability, activity, and improve imaging capabilities. A new twist on this strategy has recently appeared, in which the small-molecule probe is engineered to unleash controlled amounts of reactive chemical signals within the microenvironment of a target protein. Modification of a specific target elicits a precisely timed and spatially controlled gain-of-function (or dominant loss-of-function) signaling response. Presented herein is a unique personal outlook conceptualizing the powerful proximity-enhanced chemical biology toolsets into two paradigms: "multifunctional scaffolding" versus "on-demand targeting". By addressing the latest advances and challenges in the established yet constantly evolving multifunctional scaffolding strategies as well as in the emerging on-demand precision targeting (and related) systems, this Perspective is aimed at choosing when it is best to employ each of the two strategies, with an emphasis toward further promoting novel applications and discoveries stemming from these innovative chemical biology platforms.

  12. Chemistry and biology of radiotracers that target changes in sympathetic and parasympathetic nervous systems in heart disease.

    Science.gov (United States)

    Eckelman, William C; Dilsizian, Vasken

    2015-06-01

    Following the discovery of the sympathetic and parasympathetic nervous system, numerous adrenoceptor drugs were radiolabeled and potent radioligands were prepared in order to image the β-adrenergic and the muscarinic systems. But the greatest effort has been in preparing noradrenaline analogs, such as norepinephrine, (11)C-metahydroxyephedrine, and (123)I-metaiodobenzylguanidine that measure cardiac sympathetic nerve varicosities. Given the technical and clinical challenges in designing and validating targeted adrenoceptor-binding radiotracers, namely the heavily weighted flow dependence and relatively low target-to-background ratio, both requiring complicated mathematic analysis, and the inability of targeted adrenoceptor radioligands to have an impact on clinical care of heart disease, the emphasis has been on radioligands monitoring the norepinephrine pathway. The chemistry and biology of such radiotracers, and the clinical and prognostic impact of these innervation imaging studies in patients with heart disease, are examined. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

  13. 'Nothing of chemistry disappears in biology': the Top 30 damage-prone endogenous metabolites.

    Science.gov (United States)

    Lerma-Ortiz, Claudia; Jeffryes, James G; Cooper, Arthur J L; Niehaus, Thomas D; Thamm, Antje M K; Frelin, Océane; Aunins, Thomas; Fiehn, Oliver; de Crécy-Lagard, Valérie; Henry, Christopher S; Hanson, Andrew D

    2016-06-15

    Many common metabolites are intrinsically unstable and reactive, and hence prone to chemical (i.e. non-enzymatic) damage in vivo Although this fact is widely recognized, the purely chemical side-reactions of metabolic intermediates can be surprisingly hard to track down in the literature and are often treated in an unprioritized case-by-case way. Moreover, spontaneous chemical side-reactions tend to be overshadowed today by side-reactions mediated by promiscuous ('sloppy') enzymes even though chemical damage to metabolites may be even more prevalent than damage from enzyme sloppiness, has similar outcomes, and is held in check by similar biochemical repair or pre-emption mechanisms. To address these limitations and imbalances, here we draw together and systematically integrate information from the (bio)chemical literature, from cheminformatics, and from genome-scale metabolic models to objectively define a 'Top 30' list of damage-prone metabolites. A foundational part of this process was to derive general reaction rules for the damage chemistries involved. The criteria for a 'Top 30' metabolite included predicted chemical reactivity, essentiality, and occurrence in diverse organisms. We also explain how the damage chemistry reaction rules ('operators') are implemented in the Chemical-Damage-MINE (CD-MINE) database (minedatabase.mcs.anl.gov/#/top30) to provide a predictive tool for many additional potential metabolite damage products. Lastly, we illustrate how defining a 'Top 30' list can drive genomics-enabled discovery of the enzymes of previously unrecognized damage-control systems, and how applying chemical damage reaction rules can help identify previously unknown peaks in metabolomics profiles. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  14. Nanoscience The Science of the Small in Physics, Engineering, Chemistry, Biology and Medicine

    CERN Document Server

    Schaefer, Hans-Eckhardt

    2010-01-01

    Nanoscience stands out for its interdisciplinarity. Barriers between disciplines disappear and the fields tend to converge at the very smallest scale, where basic principles and tools are universal. Novel properties are inherent to nanosized systems due to quantum effects and a reduction in dimensionality: nanoscience is likely to continue to revolutionize many areas of human activity, such as materials science, nanoelectronics, information processing, biotechnology and medicine. This textbook spans all fields of nanoscience, covering its basics and broad applications. After an introduction to the physical and chemical principles of nanoscience, coverage moves on to the adjacent fields of microscopy, nanoanalysis, synthesis, nanocrystals, nanowires, nanolayers, carbon nanostructures, bulk nanomaterials, nanomechanics, nanophotonics, nanofluidics, nanomagnetism, nanotechnology for computers, nanochemistry, nanobiology, and nanomedicine. Consequently, this broad yet unified coverage addresses research in academ...

  15. Elucidating reaction mechanisms on quantum computers

    Science.gov (United States)

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

    2017-07-01

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

  16. Elucidating reaction mechanisms on quantum computers

    Science.gov (United States)

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

    2017-01-01

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources. PMID:28674011

  17. Elucidating reaction mechanisms on quantum computers.

    Science.gov (United States)

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M; Wecker, Dave; Troyer, Matthias

    2017-07-18

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

  18. Natural Proline-Rich Cyclopolypeptides from Marine Organisms: Chemistry, Synthetic Methodologies and Biological Status.

    Science.gov (United States)

    Fang, Wan-Yin; Dahiya, Rajiv; Qin, Hua-Li; Mourya, Rita; Maharaj, Sandeep

    2016-10-26

    Peptides have gained increased interest as therapeutics during recent years. More than 60 peptide drugs have reached the market for the benefit of patients and several hundreds of novel therapeutic peptides are in preclinical and clinical development. The key contributor to this success is the potent and specific, yet safe, mode of action of peptides. Among the wide range of biologically-active peptides, naturally-occurring marine-derived cyclopolypeptides exhibit a broad range of unusual and potent pharmacological activities. Because of their size and complexity, proline-rich cyclic peptides (PRCPs) occupy a crucial chemical space in drug discovery that may provide useful scaffolds for modulating more challenging biological targets, such as protein-protein interactions and allosteric binding sites. Diverse pharmacological activities of natural cyclic peptides from marine sponges, tunicates and cyanobacteria have encouraged efforts to develop cyclic peptides with well-known synthetic methods, including solid-phase and solution-phase techniques of peptide synthesis. The present review highlights the natural resources, unique structural features and the most relevant biological properties of proline-rich peptides of marine-origin, focusing on the potential therapeutic role that the PRCPs may play as a promising source of new peptide-based novel drugs.

  19. Research on condensed matter and atomic physics, using major experimental facilities and devices: Physics, chemistry, biology. Reports on results. Vol. 1. 1. Atomic and molecular physics. 2. Physics and chemistry of surfaces and interfaces

    International Nuclear Information System (INIS)

    1993-01-01

    This report in three volumes substantiates the contents of the programme survey published in September 1989. The progress reports cover the following research areas: Vol. I, (1). Atomic and molecular physics - free atoms, molecules, macromolecules, clusters, matrix-isolated atoms and molecules. (2) Physics and chemistry of surfaces and interfaces - epitaxy, surface structure, adsorption, electrical, magnetic, and optical properties, thin films, synthetic layer structure. Vol. II, (3). Solid-state physics, and materials science -structural research, lattice dynamics, magnetic structure and dynamics, electronic states; load; spin and pulse density fluctuations; diffusion and internal motion, defects, unordered systems and liquids. Vol. III, (4). Chemistry - bonding and structure, kinetics and reaction mechanisms, polymer research, analysis and synthesis. (5). Biology, - structure and dynamics of biological macromolecules, membrane and cell biology. (6) Development of methods and instruments - neutron sources, synchrotron sources, special accelerators, research with interlinked systems and devices. (orig.) [de

  20. "Solvent-in-salt" systems for design of new materials in chemistry, biology and energy research.

    Science.gov (United States)

    Azov, Vladimir A; Egorova, Ksenia S; Seitkalieva, Marina M; Kashin, Alexey S; Ananikov, Valentine P

    2018-02-21

    Inorganic and organic "solvent-in-salt" (SIS) systems have been known for decades but have attracted significant attention only recently. Molten salt hydrates/solvates have been successfully employed as non-flammable, benign electrolytes in rechargeable lithium-ion batteries leading to a revolution in battery development and design. SIS with organic components (for example, ionic liquids containing small amounts of water) demonstrate remarkable thermal stability and tunability, and present a class of admittedly safer electrolytes, in comparison with traditional organic solvents. Water molecules tend to form nano- and microstructures (droplets and channel networks) in ionic media impacting their heterogeneity. Such microscale domains can be employed as microreactors for chemical and enzymatic synthesis. In this review, we address known SIS systems and discuss their composition, structure, properties and dynamics. Special attention is paid to the current and potential applications of inorganic and organic SIS systems in energy research, chemistry and biochemistry. A separate section of this review is dedicated to experimental methods of SIS investigation, which is crucial for the development of this field.

  1. What Are They Thinking? Automated Analysis of Student Writing about Acid–Base Chemistry in Introductory Biology

    Science.gov (United States)

    Haudek, Kevin C.; Prevost, Luanna B.; Moscarella, Rosa A.; Merrill, John; Urban-Lurain, Mark

    2012-01-01

    Students’ writing can provide better insight into their thinking than can multiple-choice questions. However, resource constraints often prevent faculty from using writing assessments in large undergraduate science courses. We investigated the use of computer software to analyze student writing and to uncover student ideas about chemistry in an introductory biology course. Students were asked to predict acid–base behavior of biological functional groups and to explain their answers. Student explanations were rated by two independent raters. Responses were also analyzed using SPSS Text Analysis for Surveys and a custom library of science-related terms and lexical categories relevant to the assessment item. These analyses revealed conceptual connections made by students, student difficulties explaining these topics, and the heterogeneity of student ideas. We validated the lexical analysis by correlating student interviews with the lexical analysis. We used discriminant analysis to create classification functions that identified seven key lexical categories that predict expert scoring (interrater reliability with experts = 0.899). This study suggests that computerized lexical analysis may be useful for automatically categorizing large numbers of student open-ended responses. Lexical analysis provides instructors unique insights into student thinking and a whole-class perspective that are difficult to obtain from multiple-choice questions or reading individual responses. PMID:22949425

  2. Key discoveries in bile acid chemistry and biology and their clinical applications: history of the last eight decades.

    Science.gov (United States)

    Hofmann, Alan F; Hagey, Lee R

    2014-08-01

    During the last 80 years there have been extraordinary advances in our knowledge of the chemistry and biology of bile acids. We present here a brief history of the major achievements as we perceive them. Bernal, a physicist, determined the X-ray structure of cholesterol crystals, and his data together with the vast chemical studies of Wieland and Windaus enabled the correct structure of the steroid nucleus to be deduced. Today, C24 and C27 bile acids together with C27 bile alcohols constitute most of the bile acid "family". Patterns of bile acid hydroxylation and conjugation are summarized. Bile acid measurement encompasses the techniques of GC, HPLC, and MS, as well as enzymatic, bioluminescent, and competitive binding methods. The enterohepatic circulation of bile acids results from vectorial transport of bile acids by the ileal enterocyte and hepatocyte; the key transporters have been cloned. Bile acids are amphipathic, self-associate in solution, and form mixed micelles with polar lipids, phosphatidylcholine in bile, and fatty acids in intestinal content during triglyceride digestion. The rise and decline of dissolution of cholesterol gallstones by the ingestion of 3,7-dihydroxy bile acids is chronicled. Scientists from throughout the world have contributed to these achievements. Copyright © 2014 by the American Society for Biochemistry and Molecular Biology, Inc.

  3. Environmental chemistry. Seventh edition

    Energy Technology Data Exchange (ETDEWEB)

    Manahan, S.E. [Univ. of Missouri, Columbia, MO (United States)

    1999-11-01

    This book presents a basic understanding of environmental chemistry and its applications. In addition to providing updated materials in this field, the book emphasizes the major concepts essential to the practice of environmental chemistry. Topics of discussion include the following: toxicological chemistry; toxicological chemistry of chemical substances; chemical analysis of water and wastewater; chemical analysis of wastes and solids; air and gas analysis; chemical analysis of biological materials and xenobiotics; fundamentals of chemistry; and fundamentals of organic chemistry.

  4. Integrated Ecological River Health Assessments, Based on Water Chemistry, Physical Habitat Quality and Biological Integrity

    Directory of Open Access Journals (Sweden)

    Ji Yoon Kim

    2015-11-01

    Full Text Available This study evaluated integrative river ecosystem health using stressor-based models of physical habitat health, chemical water health, and biological health of fish and identified multiple-stressor indicators influencing the ecosystem health. Integrated health responses (IHRs, based on star-plot approach, were calculated from qualitative habitat evaluation index (QHEI, nutrient pollution index (NPI, and index of biological integrity (IBI in four different longitudinal regions (Groups I–IV. For the calculations of IHRs values, multi-metric QHEI, NPI, and IBI models were developed and their criteria for the diagnosis of the health were determined. The longitudinal patterns of the river were analyzed by a self-organizing map (SOM model and the key major stressors in the river were identified by principal component analysis (PCA. Our model scores of integrated health responses (IHRs suggested that mid-stream and downstream regions were impaired, and the key stressors were closely associated with nutrient enrichment (N and P and organic matter pollutions from domestic wastewater disposal plants and urban sewage. This modeling approach of IHRs may be used as an effective tool for evaluations of integrative ecological river health..

  5. Site-selective protein-modification chemistry for basic biology and drug development.

    Science.gov (United States)

    Krall, Nikolaus; da Cruz, Filipa P; Boutureira, Omar; Bernardes, Gonçalo J L

    2016-02-01

    Nature has produced intricate machinery to covalently diversify the structure of proteins after their synthesis in the ribosome. In an attempt to mimic nature, chemists have developed a large set of reactions that enable post-expression modification of proteins at pre-determined sites. These reactions are now used to selectively install particular modifications on proteins for many biological and therapeutic applications. For example, they provide an opportunity to install post-translational modifications on proteins to determine their exact biological roles. Labelling of proteins in live cells with fluorescent dyes allows protein uptake and intracellular trafficking to be tracked and also enables physiological parameters to be measured optically. Through the conjugation of potent cytotoxicants to antibodies, novel anti-cancer drugs with improved efficacy and reduced side effects may be obtained. In this Perspective, we highlight the most exciting current and future applications of chemical site-selective protein modification and consider which hurdles still need to be overcome for more widespread use.

  6. The Solomon Sea: its circulation, chemistry, geochemistry and biology explored during two oceanographic cruises

    Directory of Open Access Journals (Sweden)

    Alexandre Ganachaud

    2017-06-01

    Full Text Available The semi-enclosed Solomon Sea in the southwestern tropical Pacific is on the pathway of a major oceanic circuit connecting the subtropics to the equator via energetic western boundary currents. Waters transiting through this area replenish the Pacific Warm Pool and ultimately feed the equatorial current system, in particular the equatorial undercurrent. In addition to dynamical transformations, water masses undergo nutrient and micronutrient enrichment when coming in contact with the coasts, impacting the productivity of the downstream equatorial region. Broadscale observing systems are not well suited for describing the fine-scale currents and water masses properties in the Solomon Sea, leaving it relatively unexplored. Two multidisciplinary oceanographic cruises were conducted in the Solomon Sea region, the first in July–August 2012 and the second in March 2014, by investigators from France and the United States. The experimental approach combined physical, chemical, geochemical and biogeochemical analyses, providing access to a wide range of space and time scales of the circulation. This collection of data allows describing the fine-scale structure of the currents and the water properties, transformations and mixing from the surface to the sill depth in the Solomon Sea and in the straits connecting it to the equator. Ocean-margin exchanges were documented through a comprehensive sampling of trace elements and isotopes as efficient tracers of natural fertilization processes. As air chemistry is largely impacted by the regional volcanic plumes, rainwater pH was also sampled. Dinitrogen fixation rates were measured and found to be among the highest in the global ocean, highlighting this region as a hot spot of nitrogen fixation. This study provides an overview of the climatic context during both cruises and the physical circulation and water masses properties. It provides a comprehensive description of all measurements made onboard, and

  7. Actin Immobilization on Chitin for Purifying Myosin II: A Laboratory Exercise That Integrates Concepts of Molecular Cell Biology and Protein Chemistry

    Science.gov (United States)

    de Souza, Marcelle Gomes; Grossi, Andre Luiz; Pereira, Elisangela Lima Bastos; da Cruz, Carolina Oliveira; Mendes, Fernanda Machado; Cameron, Luiz Claudio; Paiva, Carmen Lucia Antao

    2008-01-01

    This article presents our experience on teaching biochemical sciences through an innovative approach that integrates concepts of molecular cell biology and protein chemistry. This original laboratory exercise is based on the preparation of an affinity chromatography column containing F-actin molecules immobilized on chitin particles for purifying…

  8. A Case-Based Scenario with Interdisciplinary Guided-Inquiry in Chemistry and Biology: Experiences of First Year Forensic Science Students

    Science.gov (United States)

    Cresswell, Sarah L.; Loughlin, Wendy A.

    2017-01-01

    In this paper, insight into forensic science students' experiences of a case-based scenario with an interdisciplinary guided-inquiry experience in chemistry and biology is presented. Evaluation of student experiences and interest showed that the students were engaged with all aspects of the case-based scenario, including the curriculum theory…

  9. We Don't Get Any Training: The Impact of a Professional Development Model on Teaching Practices of Chemistry and Biology Graduate Teaching Assistants

    Science.gov (United States)

    Mutambuki, Jacinta M.; Schwartz, Renee

    2018-01-01

    This study investigated the implementation of best teaching practices by science graduate teaching assistants [GTAs] (3 chemists and 2 biologists) in five inquiry-based, interdisciplinary chemistry-biology experiments during a six-week professional development (PD) program, Engage PD. Additionally, we examined GTAs' experiences in implementing…

  10. Structural and Conformational Chemistry from Electrochemical Molecular Machines. Replicating Biological Functions. A Review.

    Science.gov (United States)

    Otero, Toribio F

    2017-12-14

    Each constitutive chain of a conducting polymer electrode acts as a reversible multi-step electrochemical molecular motor: reversible reactions drive reversible conformational movements of the chain. The reaction-driven cooperative actuation of those molecular machines generates, or destroys, inside the film the free volume required to lodge/expel balancing counterions and solvent: reactions drive reversible film volume variations, which basic structural components are here identified and quantified from electrochemical responses. The content of the reactive dense gel (chemical molecular machines, ions and water) mimics that of the intracellular matrix in living functional cells. Reaction-driven properties (composition-dependent properties) and devices replicate biological functions and organs. An emerging technological world of soft, wet, reaction-driven, multifunctional and biomimetic devices and the concomitant zoomorphic or anthropomorphic robots is presented. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Electron Bifurcation: Thermodynamics and Kinetics of Two-Electron Brokering in Biological Redox Chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Peng; Yuly, Jonathon L.; Lubner, Carolyn E. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; Mulder, David W. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; King, Paul W. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; Peters, John W. [Institute; Beratan, David N. [Department

    2017-08-23

    How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently. This Account provides an exegesis of the biophysical principles that underpin electron bifurcation.

  12. Combustion chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Brown, N.J. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    This research is concerned with the development and use of sensitivity analysis tools to probe the response of dependent variables to model input variables. Sensitivity analysis is important at all levels of combustion modeling. This group`s research continues to be focused on elucidating the interrelationship between features in the underlying potential energy surface (obtained from ab initio quantum chemistry calculations) and their responses in the quantum dynamics, e.g., reactive transition probabilities, cross sections, and thermal rate coefficients. The goals of this research are: (i) to provide feedback information to quantum chemists in their potential surface refinement efforts, and (ii) to gain a better understanding of how various regions in the potential influence the dynamics. These investigations are carried out with the methodology of quantum functional sensitivity analysis (QFSA).

  13. Deposition kinetics of quantum dots and polystyrene latex nanoparticles onto alumina: role of water chemistry and particle coating.

    Science.gov (United States)

    Quevedo, Ivan R; Olsson, Adam L J; Tufenkji, Nathalie

    2013-03-05

    A clear understanding of the factors controlling the deposition behavior of engineered nanoparticles (ENPs), such as quantum dots (QDs), is necessary for predicting their transport and fate in natural subsurface environments and in water filtration processes. A quartz crystal microbalance with dissipation monitoring (QCM-D) was used to study the effect of particle surface coatings and water chemistry on the deposition of commercial QDs onto Al2O3. Two carboxylated QDs (CdSe and CdTe) with different surface coatings were compared with two model nanoparticles: sulfate-functionalized (sPL) and carboxyl-modified (cPL) polystyrene latex. Deposition rates were assessed over a range of ionic strengths (IS) in simple electrolyte (KCl) and in electrolyte supplemented with two organic molecules found in natural waters; namely, humic acid and rhamnolipid. The Al2O3 collector used here is selected to be representative of oxide patches found on the surface of aquifer or filter grains. Deposition studies showed that ENP deposition rates on bare Al2O3 generally decreased with increasing salt concentration, with the exception of the polyacrylic-acid (PAA) coated CdTe QD which exhibited unique deposition behavior due to changes in the conformation of the PAA coating. QD deposition rates on bare Al2O3 were approximately 1 order of magnitude lower than those of the polystyrene latex nanoparticles, likely as a result of steric stabilization imparted by the QD surface coatings. Adsorption of humic acid or rhamnolipid on the Al2O3 surface resulted in charge reversal of the collector and subsequent reduction in the deposition rates of all ENPs. Moreover, the ratio of the two QCM-D output parameters, frequency and dissipation, revealed key structural information of the ENP-collector interface; namely, on bare Al2O3, the latex particles were rigidly attached as compared to the more loosely attached QDs. This study emphasizes the importance of considering the nature of ENP coatings as well

  14. Vectorization in quantum chemistry

    International Nuclear Information System (INIS)

    Saunders, V.R.

    1987-01-01

    It is argued that the optimal vectorization algorithm for many steps (and sub-steps) in a typical ab initio calculation of molecular electronic structure is quite strongly dependent on the target vector machine. Details such as the availability (or lack) of a given vector construct in the hardware, vector startup times and asymptotic rates must all be considered when selecting the optimal algorithm. Illustrations are drawn from: gaussian integral evaluation, fock matrix construction, 4-index transformation of molecular integrals, direct-CI methods, the matrix multiply operation. A cross comparison of practical implementations on the CDC Cyber 205, the Cray-IS and Cray-XMP machines is presented. To achieve portability while remaining optimal on a wide range of machines it is necessary to code all available algorithms in a machine independent manner, and to select the appropriate algorithm using a procedure which is based on machine dependent parameters. Most such parameters concern the timing of certain vector loop kernals, which can usually be derived from a 'bench-marking' routine executed prior to the calculation proper

  15. Mathematics for quantum chemistry

    CERN Document Server

    Anderson, Jay Martin

    2005-01-01

    This concise volume offers undergraduates an introduction to mathematical formalism in problems of molecular structure and motion. The main topics cover the calculus of orthogonal functions, algebra of vector spaces, and Lagrangian and Hamiltonian formulation of classical mechanics and applications to molecular motion. Answers to problems. 1966 edition.

  16. Biological chemistry as a foundation of DNA genealogy: the emergence of "molecular history".

    Science.gov (United States)

    Klyosov, A A

    2011-05-01

    This paper presents the basis of DNA genealogy, a new field of science, which is currently emerging as an unusual blend of biochemistry, history, linguistics, and chemical kinetics. The methodology of the new approach is comprised of chemical (biological) kinetics applied to a pattern of mutations in non-recombinant fragments of DNA (Y chromosome and mtDNA, the latter not being considered in this overview). The goal of the analysis is to translate DNA mutation patterns into time spans to the most recent common ancestors of a given population or tribe and to the dating of ancient migration routes. To illustrate this approach, time spans to the common ancestors are calculated for ethnic Russians, that is Eastern Slavs (R1a1 tribe), Western Slavs (I1 and I2 tribes), and Northern (or Uralic) Slavs (N1c tribe), which were found to live around 4600 years before present (R1a1), 3650 ybp (I1), 3000 and 10,500 ybp (I2, two principal DNA lineages), and 3525 ybp (N1c) (confidence intervals are given in the main text). The data were compared with the respective dates for the nearest common ancestor of the R1a1 "Indo-European" population in India, who lived 4050 years before present, whose descendants represent the majority of the upper castes in India today (up to 72%). Furthermore, it was found that the haplotypes of ethnic Russians of the R1a1 haplogroup (up to 62% of the population in the Russian Federation) and those of the R1a1 Indians (more than 100 million today) are practically identical to each other, up to 67-marker haplotypes. This essentially solves a 200-year-old mystery of who were the Aryans who arrived in India around 3500 years before the present. Haplotypes and time spans to the ancient common ancestors were also compared for the ethnic Russians of haplogroups I1 and I2, on one hand, and the respective I1 and I2 populations in Eastern and Western Europe and Scandinavia, on the other. It is suggested that the approach described in this overview lays the

  17. The Chemistry and Flow Dynamics of Molecular Biological Tools Used to Confirm In Situ Bioremediation of Benzene, TBA, and MTBE

    Science.gov (United States)

    North, K. P.; Mackay, D. M.; Scow, K. M.

    2010-12-01

    In situ bioremediation has typically been confirmed by collecting sediment and groundwater samples to directly demonstrate a degradation process in a laboratory microcosm. However, recent advances in molecular biological tools present options for demonstrating degradation processes with field-based tools that are less time-consuming. We have been investigating the capability of some of these molecular biological tools to evaluate in situ biodegradation of tert-butyl alcohol (TBA), methyl tert-butyl ether (MTBE), and benzene at two field sites in California. At both sites, we have deployed Bio-Traps® (“traps”), made of Bio-Sep® beads in slotted PVC pipe, which provide ideal environments for microbial colonization. Stable Isotope Probing can be accomplished by sorbing the13C-labeled organic contaminant of concern onto Bio-Sep® beads (“baiting”); incorporation of 13C into the biomass collected by the trap would indicate that the microbial community was capable of degrading the labeled compound. In addition, we examined the chemistry and flow dynamics of these traps and present those results here. We performed a field experiment and a lab experiment to, in part, define the rate that different baits leached off various traps. At a TBA- and MTBE-contaminated site at Vandenberg AFB, Lompoc, CA, the TBA-dominant plume was effectively treated by recirculation/oxygenation of groundwater, decreasing TBA and MTBE concentrations to detection limits along predicted flowpaths created by two pairs of recirculation wells. We used the generated aerobic treatment zone to deploy traps baited with 13C-labeled MTBE or TBA in a novel, ex situ experimental setup. The groundwater flow extracted from the aerobic treatment zone was split through several chambers, each containing a trap and monitoring of influent and effluent. The chamber effluent was measured throughout a six-week deployment and analyzed for both TBA and MTBE; the majority of mass leached from the baited traps did

  18. Modular Synthesis of Biologically Active Phosphatidic Acid Probes Using Click Chemistry

    Science.gov (United States)

    Smith, Matthew D.; Sudhahar, Christopher G.; Gong, Denghuang; Stahelin, Robert V.

    2018-01-01

    Phosphatidic acid (PA) is an important signaling lipid that plays roles in a range of biological processes including both physiological and pathophysiological events. PA is one of a number of signaling lipids that can act as site-specific ligands for protein receptors in binding events that enforce membrane-association and generally regulate both receptor function and subcellular localization. However, elucidation of the full scope of PA activities has proven problematic, primarily due to the lack of a consensus sequence among PA-binding receptors. Thus, experimental approaches, such as those employing lipid probes, are necessary for characterizing interactions at the molecular level. Herein, we describe an efficient modular approach to the synthesis of a range of PA probes that employs a late stage introduction of reporter groups. This strategy was exploited in the synthesis of PA probes bearing fluorescent and photoaffinity tags as well as a bifunctional probe containing both a photoaffinity moiety and an azide as a secondary handle for purification purposes. To discern the ability of these PA analogues to mimic the natural lipid in protein binding properties, each compound was incorporated into vesicles for binding studies using a known PA receptor, the C2 domain of PKCα. In these studies, each compound exhibited binding properties that were comparable to those of synthetic PA, indicating their viability as probes for effectively studying the activities of PA in cellular processes. PMID:19668861

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Electrophoretic separation techniques and their hyphenation to mass spectrometry in biological inorganic chemistry.

    Science.gov (United States)

    Holtkamp, Hannah; Grabmann, Gerlinde; Hartinger, Christian G

    2016-04-01

    Electrophoretic methods have been widely applied in research on the roles of metal complexes in biological systems. In particular, CE, often hyphenated to a sensitive MS detector, has provided valuable information on the modes of action of metal-based pharmaceuticals, and more recently new methods have been added to the electrophoretic toolbox. The range of applications continues to expand as a result of enhanced CE-to-MS interfacing, with sensitivity often at picomolar level, and evolved separation modes allowing for innovative sample analysis. This article is a followup to previous reviews about CE methods in metallodrug research (Electrophoresis, 2003, 24, 2023-2037; Electrophoresis, 2007, 28, 3436-3446; Electrophoresis, 2012, 33, 622-634), also providing a comprehensive overview of metal species studied by electrophoretic methods hyphenated to MS. It highlights the latest CE developments, takes a sneak peek into gel electrophoresis, traces biomolecule labeling, and focuses on the importance of early-stage drug development. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Research on condensed matter and atomic physics using major experimental facilities and devices: Physics, chemistry, biology. Reports on results. Vol. 2. 3. Solid state physics and materials science

    International Nuclear Information System (INIS)

    1993-01-01

    This report in three volumes substantiates the contents of the programme survey published in September 1989. The progress reports cover the following research areas: Vol. I, (1). Atomic and molecular physics - free atoms, molecules, macromolecules, clusters, matrix-isolated atoms and molecules. (2) Physics and chemistry of surfaces and interfaces - epitaxy, surface structure, adsorption, electrical, magnetic, and optical properties, thin films, synthetic layer structure. Vol. II, (3). Solid-state physics, and materials science -structural research, lattice dynamics, magnetic structure and dynamics, electronic states; load; spin and pulse density fluctuations; diffusion and internal motion, defects, unordered systems and liquids. Vol. III, (4). Chemistry - bonding and structure, kinetics and reaction mechanisms, polymer research, analysis and synthesis. (5). Biology, - structure and dynamics of biological macromolecules, membrane and cell biology. (6) Development of methods and instruments - neutron sources, synchrotron sources, special accelerators, research with interlinked systems and devices. (orig.) [de

  2. Some aspects of radiation-induced free-radical chemistry of biologically important molecules

    International Nuclear Information System (INIS)

    Sonntag, C. von

    1992-01-01

    Biologically relevant material is usually associated with considerable amounts of water. When ionizing radiation interacts with such material one must consider two modes of energy deposition: the direct effect (ionizing radiation is absorbed by the biomolecules) and the indirect effect (ionizing radiation is absorbed by the surrounding water). In the direct effect, radical cations plus electrons, and excited states of the biomolecules are formed. In the indirect effect the water is decomposed resulting in the formation of the water radicals OH,H and e aq - . These reactive intermediates then interact with the biomolecules. When such systems are irradiated oxygen is often present. As a result of this, the radicals formed in the biomolecules by the various routes are converted into the corresponding peroxyl radicals. In certain cases, e.g. with the nucleobases of DNA, radical cations can be produced in dilute aqueous solutions by radiation-generated SO 4 - radicals, and the fate of these nucleobase radical cations studied by pulse radiolysis and product analysis. Attention will be drawn to the fact that frequently some of the reaction products of the radical cations with water are identical to those formed by OH radical attack, but that there are also marked differences. Similarly, protonation of radical anions (formed by the reaction of solvated electrons with the biomolecules) and the reaction of H-atoms with these molecules can lead to radical intermediates with considerably differing characteristics. Our present knowledge of the variety of reactions of the peroxyl radicals occurring in aqueous solutions will be briefly discussed, emphasizing the large variety of HO 2 /O 2 - elimination reactions and pointing to the reversibility of the oxygen addition (RO 2 →R + O 2 ) in some systems recently studied. (author)

  3. General chemistry

    International Nuclear Information System (INIS)

    Kwon, Yeong Sik; Lee, Dong Seop; Ryu, Haung Ryong; Jang, Cheol Hyeon; Choi, Bong Jong; Choi, Sang Won

    1993-07-01

    The book concentrates on the latest general chemistry, which is divided int twenty-three chapters. It deals with basic conception and stoichiometry, nature of gas, structure of atoms, quantum mechanics, symbol and structure of an electron of ion and molecule, chemical thermodynamics, nature of solid, change of state and liquid, properties of solution, chemical equilibrium, solution and acid-base, equilibrium of aqueous solution, electrochemistry, chemical reaction speed, molecule spectroscopy, hydrogen, oxygen and water, metallic atom; 1A, IIA, IIIA, carbon and atom IVA, nonmetal atom and an inert gas, transition metals, lanthanons, and actinoids, nuclear properties and radioactivity, biochemistry and environment chemistry.

  4. AN INTEGRATIVE WAY OF TEACHING MOLECULAR CELL BIOLOGY AND PROTEIN CHEMISTRY USING ACTIN IMMOBILIZATION ON CHITIN FOR PURIFYING MYOSIN II.

    Directory of Open Access Journals (Sweden)

    M.G. Souza

    2007-05-01

    Full Text Available Our intent is to present our experience on teaching Molecular Cell Biology andProtein Chemistry at UNIRIO through an innovative approach that includes myosin IIextraction and purification. We took advantage of the properties of muscle contractionand propose a simple method for purifying myosin II by affinity chromatography. Thisoriginal method is based on the preparation of an affinity column containing actinmolecules covalently bound to chitin particles. We propose a three-week syllabus thatincludes lectures and bench experimental work. The syllabus favors the activelearning of protein extraction and purification, as well as, of scientific concepts suchas muscle contraction, cytoskeleton structure and its importance for the living cell. Italso promotes the learning of the biotechnological applications of chitin and theapplications of protein immobilization in different industrial fields. Furthermore, theactivities also target the development of laboratorial technical abilities, thedevelopment of problem solving skills and the ability to write up a scientific reportfollowing the model of a scientific article. It is very important to mention that thissyllabus can be used even in places where a facility such as ultra-centrifugation islacking.

  5. Key discoveries in bile acid chemistry and biology and their clinical applications: history of the last eight decades

    Science.gov (United States)

    Hofmann, Alan F.; Hagey, Lee R.

    2014-01-01

    During the last 80 years there have been extraordinary advances in our knowledge of the chemistry and biology of bile acids. We present here a brief history of the major achievements as we perceive them. Bernal, a physicist, determined the X-ray structure of cholesterol crystals, and his data together with the vast chemical studies of Wieland and Windaus enabled the correct structure of the steroid nucleus to be deduced. Today, C24 and C27 bile acids together with C27 bile alcohols constitute most of the bile acid “family”. Patterns of bile acid hydroxylation and conjugation are summarized. Bile acid measurement encompasses the techniques of GC, HPLC, and MS, as well as enzymatic, bioluminescent, and competitive binding methods. The enterohepatic circulation of bile acids results from vectorial transport of bile acids by the ileal enterocyte and hepatocyte; the key transporters have been cloned. Bile acids are amphipathic, self-associate in solution, and form mixed micelles with polar lipids, phosphatidylcholine in bile, and fatty acids in intestinal content during triglyceride digestion. The rise and decline of dissolution of cholesterol gallstones by the ingestion of 3,7-dihydroxy bile acids is chronicled. Scientists from throughout the world have contributed to these achievements. PMID:24838141

  6. NATO Advanced Study Institute on Mixed-Valence Compounds : Theory and Applications in Chemistry, Physics, Geology, and Biology

    CERN Document Server

    1980-01-01

    It has been a decade since two seminal reviews demonstrated that mixed-valence compounds share many unique and fascinating features. The insight pro­ vided by those early works has promoted a great deal of both experimental and theoretical study. As a result of extensive efforts, our understanding of the bonding and properties of mixed-valence compounds has advanced substantially. There has been no compre­ hensive treatment of mixed-valence compounds since 1967, and the meeting convened at Oxford in September, 1979, provided a unique opportunity to examine the subject and its many ramifications. Mixed-valence compounds play an important role in many fields. Although the major impact of the subject has been in chemistry, its importance has become increasingly clear in solid state physics, geology, and biology. Extensive interest and effort in the field of molecular metals has demonstrated that mixed-valency is a prerequisite for high elec­ trical conductivity. The intense colors of many minerals have been s...

  7. Secondary Physics, Chemistry, and Biology (PCB Teachers’ Views about In-service Training Related to Curricular Change

    Directory of Open Access Journals (Sweden)

    Fatih Çağlayan Mercan

    2015-04-01

    Full Text Available In Turkey the Physics, Chemistry and Biology (PCB curricula were renewed in 2008. However, little in-service training for teachers has been conducted to disseminate the ideas in the new curricula. The purpose of this study was to investigate PCB teachers’ views on in-service training, which may serve as the base knowledge of educational change in Turkey that can be used in further curricular development. In Istanbul 99 teachers voluntarily participated in this qualitative case study. Data were collected utilizing semi-structured interviews and analyzed by employing constant comparative analysis. The data showed that for 40% of the teachers the in-service training was insufficient: the new curricula were not introduced to them adequately. Only 7% of the teachers expressed positive views towards the in-service training. The teachers were concerned about the incompetence of the trainers and the low quality of the training programs. 20% of the teachers felt that they need to keep up to date with the new curricula and establish ways of cooperation among teachers. The results imply that educational change is more than changing the curriculum, which requires serious planning for implementation requiring a reconceptualization of in-service training as part of a larger professional development framework.

  8. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    Energy Technology Data Exchange (ETDEWEB)

    Bylaska, Eric J., E-mail: Eric.Bylaska@pnnl.gov [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States); Weare, Jonathan Q., E-mail: weare@uchicago.edu [Department of Mathematics, University of Chicago, Chicago, Illinois 60637 (United States); Weare, John H., E-mail: jweare@ucsd.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 (United States)

    2013-08-21

    to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H{sub 2}O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

  9. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.

    Science.gov (United States)

    Bylaska, Eric J; Weare, Jonathan Q; Weare, John H

    2013-08-21

    distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

  10. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    International Nuclear Information System (INIS)

    Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

    2013-01-01

    distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H 2 O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step

  11. Bio-templated CdSe quantum dots green synthesis in the functional protein, lysozyme, and biological activity investigation

    International Nuclear Information System (INIS)

    Wang, Qisui; Li, Song; Liu, Peng; Min, Xinmin

    2012-01-01

    Bifunctional fluorescence (CdSe Quantum Dots) – protein (Lysozyme) nanocomposites were synthesized at room temperature by a protein-directed, solution-phase, green-synthetic method. Fluorescence (FL) and absorption spectra showed that CdSe QDs were prepared successfully with Lyz. The average particle size and crystalline structure of QDs were investigated by high-resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD), respectively. With attenuated total reflection-fourier transform infrared (ATR-FTIR) spectra and thermogravimetric (TG) analysis, it was confirmed that there is interaction between QDs and amide I, amide II groups in Lyz. FL polarization was measured and FL imaging was done to monitor whether QDs could be responsible for possible changes in the conformation and activity of Lyz. Interestingly, the results showed Lyz still retain the biological activity after formation of QDs, but the secondary structure of the Lyz was changed. And the advantage of this synthesis method is producing excellent fluorescent QDs with specifically biological function. -- Highlights: ► Lysozyme-directed green synthesis of CdSe quantum dots. ► Lysozyme still retain the biological activity after formation of CdSe. ► The method is the production of fluorescent QDs with highly specific and functions.

  12. Radiation chemistry

    International Nuclear Information System (INIS)

    Swallow, A.J.

    1983-01-01

    The subject is covered in chapters, entitled: introduction (defines scope of article as dealing with the chemistry of reactive species, (e.g. excess electrons, excited states, free radicals and inorganic ions in unusual valency states) as studied using radiation with radiation chemistry in its traditional sense and with biological and industrial applications); gases; water and simple inorganic systems; aqueous metallo-organic compounds and metalloproteins; small organic molecules in aqueous solution; microheterogeneous systems; non-aqueous liquids and solutions; solids; biological macromolecules; synthetic polymers. (U.K.)

  13. Quantum Physics for Scientists and Technologists Fundamental Principles and Applications for Biologists, Chemists, Computer Scientists, and Nanotechnologists

    CERN Document Server

    Sanghera, Paul

    2011-01-01

    Presenting quantum physics for the non-physicists, Quantum Physics for Scientists and Technologists is a self-contained, cohesive, concise, yet comprehensive, story of quantum physics from the fields of science and technology, including computer science, biology, chemistry, and nanotechnology. The authors explain the concepts and phenomena in a practical fashion with only a minimum amount of math. Examples from, and references to, computer science, biology, chemistry, and nanotechnology throughout the book make the material accessible to biologists, chemists, computer scientists, and non-techn

  14. “Biotecnological War” - A Conceptual And Perceptual Assessment Tool For Teaching Biotechnology And Protein Chemistry For Undergraduate Students In Biological Sciences.

    OpenAIRE

    C. R. C. Cruz et al.

    2017-01-01

    "Biotecnological War" board game, a conceptual and perceptual assessment tool for biotechnology and protein chemistry teaching for undergraduate students in biological sciences and related areas. It is a proposal initially conceived as an alternative complementary tool for biochemistry teaching of proteins and peptides, challenging students, aiming to review concepts transmitted in classroom, stimulating diverse student’s abilities, such as their creativity, competitiveness and resource manag...

  15. Adapting to large-scale changes in Advanced Placement Biology, Chemistry, and Physics: the impact of online teacher communities

    Science.gov (United States)

    Frumin, Kim; Dede, Chris; Fischer, Christian; Foster, Brandon; Lawrenz, Frances; Eisenkraft, Arthur; Fishman, Barry; Jurist Levy, Abigail; McCoy, Ayana

    2018-03-01

    Over the past decade, the field of teacher professional learning has coalesced around core characteristics of high quality professional development experiences (e.g. Borko, Jacobs, & Koellner, 2010. Contemporary approaches to teacher professional development. In P. L. Peterson, E. Baker, & B. McGaw (Eds.), International encyclopedia of education (Vol. 7, pp. 548-556). Oxford: Elsevier.; Darling-Hammond, Hyler, & Gardner, 2017. Effective teacher professional development. Palo Alto, CA: Learning Policy Institute). Many countries have found these advances of great interest because of a desire to build teacher capacity in science education and across the full curriculum. This paper continues this progress by examining the role and impact of an online professional development community within the top-down, large-scale curriculum and assessment revision of Advanced Placement (AP) Biology, Chemistry, and Physics. This paper is part of a five-year, longitudinal, U.S. National Science Foundation-funded project to study the relative effectiveness of various types of professional development in enabling teachers to adapt to the revised AP course goals and exams. Of the many forms of professional development our research has examined, preliminary analyses indicated that participation in the College Board's online AP Teacher Community (APTC) - where teachers can discuss teaching strategies, share resources, and connect with each other - had positive, direct, and statistically significant association with teacher self-reported shifts in practice and with gains in student AP scores (Fishman et al., 2014). This study explored how usage of the online APTC might be useful to teachers and examined a more robust estimate of these effects. Findings from the experience of AP teachers may be valuable in supporting other large-scale curriculum changes, such as the U.S. Next Generation Science Standards or Common Core Standards, as well as parallel curricular shifts in other countries.

  16. Desalination Brine Discharge Impacts on Coastal Biology and Water Chemistry - A Case Study from Carlsbad Southern California

    Science.gov (United States)

    Petersen, K. L.; Heck, N.; Potts, D. C.; Paytan, A.

    2017-12-01

    Fresh water demand is increasing world-wide due to on-going droughts, climate change and increasing human population and associated demand for food and water. Desalination of seawater is a reliable source of potable water; however the effects of byproduct brine discharge from desalination plants on coastal areas have not been thoroughly assessed. Here we report results from in-situmeasurements of the effects of brine discharge on water chemistry and coastal biology from a desalination plant in Carlsbad, Southern California. We compared select parameters in the coastal zone around the discharge site before and after operation began and conducted additional controlled laboratory incubations with key coastal species and brine effluent. Our in-situ data shows differences in salinity and temperature between the discharge area and a control site both before and after the desalination plant started operation. The discharge water is warmer by 3-5 Co than the ambient seawater and a temperature gradient is seen around the discharge channel. This is likely a result of mixing of the desalination brine with power plant cooling water for dilution prior to discharge and the higher temperatures are not directly attributed to the desalination. Our post-discharge results show a decipherable salinity plume at the bottom of the water column ( 6 m depth) reaching up to 600 m offshore from the discharge site. This indicates inefficient mixing of the brine in the coastal discharge zone. No significant differences are found in nutrient levels, organic carbon or chlorophyll a concentrations around the discharge. The benthic biology assemblage post-discharge is significantly different from the pre-discharge organisms' assemblage. However, the role of seasonal changes in temperature may also have impacted the data as the sampling was conducted during different seasons. Controlled incubation experiments of brittle stars (Ophiothrix spiculata) shows no significant difference in growth or

  17. Low temperature synthesis of silicon quantum dots with plasma chemistry control in dual frequency non-thermal plasmas.

    Science.gov (United States)

    Sahu, Bibhuti Bhusan; Yin, Yongyi; Han, Jeon Geon; Shiratani, Masaharu

    2016-06-21

    The advanced materials process by non-thermal plasmas with a high plasma density allows the synthesis of small-to-big sized Si quantum dots by combining low-temperature deposition with superior crystalline quality in the background of an amorphous hydrogenated silicon nitride matrix. Here, we make quantum dot thin films in a reactive mixture of ammonia/silane/hydrogen utilizing dual-frequency capacitively coupled plasmas with high atomic hydrogen and nitrogen radical densities. Systematic data analysis using different film and plasma characterization tools reveals that the quantum dots with different sizes exhibit size dependent film properties, which are sensitively dependent on plasma characteristics. These films exhibit intense photoluminescence in the visible range with violet to orange colors and with narrow to broad widths (∼0.3-0.9 eV). The observed luminescence behavior can come from the quantum confinement effect, quasi-direct band-to-band recombination, and variation of atomic hydrogen and nitrogen radicals in the film growth network. The high luminescence yields in the visible range of the spectrum and size-tunable low-temperature synthesis with plasma and radical control make these quantum dot films good candidates for light emitting applications.

  18. Proceedings of the 17. Annual Meeting of the Brazilian Chemistry Society; 7. National Symposium on Inorganic Chemistry. Abstracts

    International Nuclear Information System (INIS)

    1994-01-01

    These 17. Annual Meeting of the Brazilian Chemistry Society and 7. National Symposium on Inorganic Chemistry present several subjects of different interests for the participants, including sections about inorganic chemistry; organic chemistry; environmental chemistry; technological chemistry; electrochemistry; physical chemistry; photochemistry; chemical education; natural products; analytical chemistry and biological chemistry. (C.G.C.)

  19. Molecular quantum dynamics. From theory to applications

    International Nuclear Information System (INIS)

    Gatti, Fabien

    2014-01-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the

  20. Molecular quantum dynamics. From theory to applications

    Energy Technology Data Exchange (ETDEWEB)

    Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253

    2014-09-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible

  1. Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

    Czech Academy of Sciences Publication Activity Database

    Vlček, L.; Uhlík, F.; Moučka, F.; Nezbeda, Ivo; Chialvo, L.

    2015-01-01

    Roč. 119, č. 3 (2015), s. 488-500 ISSN 1089-5639 Institutional support: RVO:67985858 Keywords : monte-carlo simulations * molecular-dynamic simulations * classical drude oscillators Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.883, year: 2015

  2. Exploring Do-It-Yourself Approaches in Computational Quantum Chemistry: The Pedagogical Benefits of the Classical Boys Algorithm

    Science.gov (United States)

    Orsini, Gabriele

    2015-01-01

    The ever-increasing impact of molecular quantum calculations over chemical sciences implies a strong and urgent need for the elaboration of proper teaching strategies in university curricula. In such perspective, this paper proposes an extensive project for a student-driven, cooperative, from-scratch implementation of a general Hartree-Fock…

  3. Interfacial chemistry and the design of solid-phase nucleic acid hybridization assays using immobilized quantum dots as donors in fluorescence resonance energy transfer.

    Science.gov (United States)

    Algar, W Russ; Krull, Ulrich J

    2011-01-01

    The use of quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET) offer several advantages for the development of multiplexed solid-phase QD-FRET nucleic acid hybridization assays. Designs for multiplexing have been demonstrated, but important challenges remain in the optimization of these systems. In this work, we identify several strategies based on the design of interfacial chemistry for improving sensitivity, obtaining lower limits of detection (LOD) and enabling the regeneration and reuse of solid-phase QD-FRET hybridization assays. FRET-sensitized emission from acceptor dyes associated with hybridization events at immobilized QD donors provides the analytical signal in these assays. The minimization of active sensing area reduces background from QD donor PL and allows the resolution of smaller amounts of acceptor emission, thus lowering the LOD. The association of multiple acceptor dyes with each hybridization event can enhance FRET efficiency, thereby improving sensitivity. Many previous studies have used interfacial protein layers to generate selectivity; however, transient destabilization of these layers is shown to prevent efficient regeneration. To this end, we report a protein-free interfacial chemistry and demonstrate the specific detection of as little as 2 pmol of target, as well as an improved capacity for regeneration.

  4. Determination of equilibrium structures of bromothymol blue revealed by using quantum chemistry with an aid of multivariate analysis of electronic absorption spectra.

    Science.gov (United States)

    Shimada, Toru; Hasegawa, Takeshi

    2017-10-05

    The pH dependent chemical structures of bromothymol blue (BTB), which have long been under controversy, are determined by employing a combined technique of multivariate analysis of electronic absorption spectra and quantum chemistry. Principle component analysis (PCA) of the pH dependent spectra apparently reveals that only two chemical species are adequate to fully account for the color changes, with which the spectral decomposition is readily performed by using augmented alternative least-squares (ALS) regression analysis. The quantity variation by the ALS analysis also reveals the practical acid dissociation constant, pK a '. The determination of pK a ' is performed for various ionic strengths, which reveals the thermodynamic acid constant (pK a =7.5) and the number of charge on each chemical species; the yellow form is negatively charged species of -1 and the blue form that of -2. On this chemical information, the quantum chemical calculation is carried out to find that BTB molecules take the pure quinoid form in an acid solution and the quinoid-phenolate form in an alkaline solution. The time-dependent density functional theory (TD-DFT) calculations for the theoretically determined chemical structures account for the peak shift of the electronic spectra. In this manner, the structures of all the chemical species appeared in equilibrium have finally been confirmed. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Determination of equilibrium structures of bromothymol blue revealed by using quantum chemistry with an aid of multivariate analysis of electronic absorption spectra

    Science.gov (United States)

    Shimada, Toru; Hasegawa, Takeshi

    2017-10-01

    The pH dependent chemical structures of bromothymol blue (BTB), which have long been under controversy, are determined by employing a combined technique of multivariate analysis of electronic absorption spectra and quantum chemistry. Principle component analysis (PCA) of the pH dependent spectra apparently reveals that only two chemical species are adequate to fully account for the color changes, with which the spectral decomposition is readily performed by using augmented alternative least-squares (ALS) regression analysis. The quantity variation by the ALS analysis also reveals the practical acid dissociation constant, pKa‧. The determination of pKa‧ is performed for various ionic strengths, which reveals the thermodynamic acid constant (pKa = 7.5) and the number of charge on each chemical species; the yellow form is negatively charged species of - 1 and the blue form that of - 2. On this chemical information, the quantum chemical calculation is carried out to find that BTB molecules take the pure quinoid form in an acid solution and the quinoid-phenolate form in an alkaline solution. The time-dependent density functional theory (TD-DFT) calculations for the theoretically determined chemical structures account for the peak shift of the electronic spectra. In this manner, the structures of all the chemical species appeared in equilibrium have finally been confirmed.

  6. Quantum information processing in the radical-pair mechanism: Haberkorn's theory violates the Ozawa entropy bound

    Science.gov (United States)

    Mouloudakis, K.; Kominis, I. K.

    2017-02-01

    Radical-ion-pair reactions, central for understanding the avian magnetic compass and spin transport in photosynthetic reaction centers, were recently shown to be a fruitful paradigm of the new synthesis of quantum information science with biological processes. We show here that the master equation so far constituting the theoretical foundation of spin chemistry violates fundamental bounds for the entropy of quantum systems, in particular the Ozawa bound. In contrast, a recently developed theory based on quantum measurements, quantum coherence measures, and quantum retrodiction, thus exemplifying the paradigm of quantum biology, satisfies the Ozawa bound as well as the Lanford-Robinson bound on information extraction. By considering Groenewold's information, the quantum information extracted during the reaction, we reproduce the known and unravel other magnetic-field effects not conveyed by reaction yields.

  7. Quantum information processing in the radical-pair mechanism: Haberkorn's theory violates the Ozawa entropy bound.

    Science.gov (United States)

    Mouloudakis, K; Kominis, I K

    2017-02-01

    Radical-ion-pair reactions, central for understanding the avian magnetic compass and spin transport in photosynthetic reaction centers, were recently shown to be a fruitful paradigm of the new synthesis of quantum information science with biological processes. We show here that the master equation so far constituting the theoretical foundation of spin chemistry violates fundamental bounds for the entropy of quantum systems, in particular the Ozawa bound. In contrast, a recently developed theory based on quantum measurements, quantum coherence measures, and quantum retrodiction, thus exemplifying the paradigm of quantum biology, satisfies the Ozawa bound as well as the Lanford-Robinson bound on information extraction. By considering Groenewold's information, the quantum information extracted during the reaction, we reproduce the known and unravel other magnetic-field effects not conveyed by reaction yields.

  8. Quantum mechanics

    International Nuclear Information System (INIS)

    Basdevant, J.L.; Dalibard, J.; Joffre, M.

    2008-01-01

    All physics is quantum from elementary particles to stars and to the big-bang via semi-conductors and chemistry. This theory is very subtle and we are not able to explain it without the help of mathematic tools. This book presents the principles of quantum mechanics and describes its mathematical formalism (wave function, Schroedinger equation, quantum operators, spin, Hamiltonians, collisions,..). We find numerous applications in the fields of new technologies (maser, quantum computer, cryptography,..) and in astrophysics. A series of about 90 exercises with their answers is included. This book is based on a physics course at a graduate level. (A.C.)

  9. Special report: a century of chemistry. History of sciences: Max Planck and the birth of quantum mechanics

    International Nuclear Information System (INIS)

    Boudenot, J.C.

    2000-01-01

    In 1892 Lord Kelvin said 'that the fundamental concepts of physics had been established'. However, quantum mechanics in 1900, and relativity in 1905 were going to profoundly upset this science. Jean-Claude Boudenot allows us to relive the essential discoveries, which have given rise to the majority of the technologies of the 20. century through the life of Max Planck (1858-1947). The first scientific hit of M.Planck was to solve the problem of the black body at the turn of last century, he postulated that the exchange of energy between radiation and the walls of the cavity had the form of a flow of very small and indivisible quantities of energy called energy quantum. This discovery allowed him to receive the Nobel prize of physics in 1918

  10. Multi-scale multi-physics computational chemistry simulation based on ultra-accelerated quantum chemical molecular dynamics method for structural materials in boiling water reactor

    International Nuclear Information System (INIS)

    Miyamoto, Akira; Sato, Etsuko; Sato, Ryo; Inaba, Kenji; Hatakeyama, Nozomu

    2014-01-01

    In collaboration with experimental experts we have reported in the present conference (Hatakeyama, N. et al., “Experiment-integrated multi-scale, multi-physics computational chemistry simulation applied to corrosion behaviour of BWR structural materials”) the results of multi-scale multi-physics computational chemistry simulations applied to the corrosion behaviour of BWR structural materials. In macro-scale, a macroscopic simulator of anode polarization curve was developed to solve the spatially one-dimensional electrochemical equations on the material surface in continuum level in order to understand the corrosion behaviour of typical BWR structural material, SUS304. The experimental anode polarization behaviours of each pure metal were reproduced by fitting all the rates of electrochemical reactions and then the anode polarization curve of SUS304 was calculated by using the same parameters and found to reproduce the experimental behaviour successfully. In meso-scale, a kinetic Monte Carlo (KMC) simulator was applied to an actual-time simulation of the morphological corrosion behaviour under the influence of an applied voltage. In micro-scale, an ultra-accelerated quantum chemical molecular dynamics (UA-QCMD) code was applied to various metallic oxide surfaces of Fe 2 O 3 , Fe 3 O 4 , Cr 2 O 3 modelled as same as water molecules and dissolved metallic ions on the surfaces, then the dissolution and segregation behaviours were successfully simulated dynamically by using UA-QCMD. In this paper we describe details of the multi-scale, multi-physics computational chemistry method especially the UA-QCMD method. This method is approximately 10,000,000 times faster than conventional first-principles molecular dynamics methods based on density-functional theory (DFT), and the accuracy was also validated for various metals and metal oxides compared with DFT results. To assure multi-scale multi-physics computational chemistry simulation based on the UA-QCMD method for

  11. Luminescent passive-oxidized silicon quantum dots as biological staining labels and their cytotoxicity effects at high concentration

    International Nuclear Information System (INIS)

    Fujioka, Kouki; Manabe, Noriyoshi; Hanada, Sanshiro; Hoshino, Akiyoshi; Yamamoto, Kenji; Hiruoka, Masaki; Sato, Keisuke; Hirakuri, Kenji; Miyasaka, Ryosuke; Tilley, Richard D; Manome, Yoshinobu

    2008-01-01

    Semiconductor quantum dots (QDs) hold some advantages over conventional organic fluorescent dyes. Due to these advantages, they are becoming increasingly popular in the field of bioimaging. However, recent work suggests that cadmium based QDs affect cellular activity. As a substitute for cadmium based QDs, we have developed photoluminescent stable silicon quantum dots (Si-QDs) with a passive-oxidation technique. Si-QDs (size: 6.5 ± 1.5 nm) emit green light, and they have been used as biological labels for living cell imaging. In order to determine the minimum concentration for cytotoxicity, we investigated the response of HeLa cells. We have shown that the toxicity of Si-QDs was not observed at 112 μg ml -1 and that Si-QDs were less toxic than CdSe-QDs at high concentration in mitochondrial assays and with lactate dehydrogenase (LDH) assays. Especially under UV exposure, Si-QDs were more than ten times safer than CdSe-QDs. We suggest that one mechanism for the cytotoxicity is that Si-QDs can generate oxygen radicals and these radicals are associated with membrane damages. This work has demonstrated the suitability of Si-QDs for bioimaging in lower concentration, and their cytotoxicity and one toxicity mechanism at high concentration

  12. Radiochemistry at the University of Missouri-Columbia. A joint venture with chemistry, nuclear engineering, molecular biology, biochemistry, and the Missouri University Research Reactor (MURR)

    International Nuclear Information System (INIS)

    Miller, W.H.; Duval, P.; Jurisson, S.S.; Robertson, J.D.; Wall, J.D.; Quinn, T.P.; Volkert, W.A.; Neumeyer, G.M.

    2005-01-01

    Missouri University, a recipient of a U.S. Department of Energy Radiochemistry Education Award Program (REAP) grant in 1999, has significantly expanded its education and research mission in radiochemistry. While MU had a viable radiochemistry program through existing faculty expertise and the utilization of the Missouri University Research Reactor, the REAP award allowed MU to leverage its resources in significantly expanding capabilities in radiochemistry. Specifically, the grant enabled the: (1) hiring of a new faculty member in actinide radiochemistry (Dr. Paul Duval); (2) support of six graduate students in radiochemistry; (3) purchase of new radiochemistry laboratory equipment; (4) more extensive collaboration with DOE scientists through interactions with faculty and graduate students, and (5) revised radiochemical curriculum (joint courses across disciplines and new courses in actinide chemistry). The most significant impact of this award has been in encouraging interdisciplinary education and research. The proposal was initiated by a joint effort between Nuclear Engineering and Chemistry, but also included faculty in biochemistry, radiology, and molecular biology. Specific outcomes of the REAP grant thus far are: (1) increased educational and research capabilities in actinide chemistry (faculty hire and equipment acquisition); (2) increased integration of biochemistry and radiochemistry (e.g., radiochemical analysis of uranium speciation in biological systems); (3) stronger interdisciplinary integration of molecular biology and radiochemical sciences (alpha-emitters for treating cancer); (4) new and more extensive interactions with national laboratory facilities (e.g., student internships at LANL and LLBL, faculty and lab scientist exchange visits, analytical measurements and collaboration with the Advanced Photon Source), and (7) new research funding opportunities based on REAP partnership. (author)

  13. Surface chemistry and density distribution influence on visible luminescence of silicon quantum dots: an experimental and theoretical approach.

    Science.gov (United States)

    Dutt, Ateet; Matsumoto, Yasuhiro; Santana-Rodríguez, G; Ramos, Estrella; Monroy, B Marel; Santoyo Salazar, J

    2017-01-04

    The impact of the surface reconstruction of the density distribution and photoluminescence of silicon quantum dots (QDs) embedded in a silicon oxide matrix (SiO x ) has been studied. Annealing treatments carried out on the as-deposited samples provoked the effusion of hydrogen species. Moreover, depending on the surrounding density and coalescence of QDs, they resulted in a change in the average size of the particles depending on the initial local environment. The shift in the luminescence spectra all over the visible region (blue, green and red) shows a strong dependence on the resultant change in the size and/or the passivation environment of QDs. Density functional theoretical (DFT) calculations support this fact and explain the possible electronic transitions (HOMO-LUMO gap) involved. Passivation in the presence of oxygen species lowers the band gap of Si 29 and Si 35 nanoclusters up to 1.7 eV, whereas, surface passivation in the environment of hydrogen species increases the band gap up to 4.4 eV. These results show a good agreement with the quantum confinement model described in this work and explain the shift in the luminescence all over the visible region. The results reported here offer vital insight into the mechanism of emission from silicon quantum dots which has been one of the most debated topics in the last two decades. QDs with multiple size distribution in different local environments (band gap) observed in this work could be used for the fabrication of light emission diodes (LEDs) or shift-conversion thin films in third generation efficient tandem solar cells for the maximum absorption of the solar spectrum in different wavelength regions.

  14. Cold chemistry with ionic partners: quantum features of HeH+(1Σ) with H(1S) at ultralow energies.

    Science.gov (United States)

    Bovino, S; Tacconi, M; Gianturco, F A

    2011-07-28

    Quantum reactive calculations are presented for an ion-atom reaction involving the HeH(+)cation and its destruction via a barrierless interaction with H atoms. The range of collision energies considered is that of a cold trap regime (around and below millikelvin) where the ionic partner could be spatially confined. Specific resonant features caused by the interplay of the strong ionic interaction with the very slow partners' dynamics are found and analyzed. Indications are also given on the consequences of the abstraction mechanism that acts for this reaction at low energies. © 2011 American Chemical Society

  15. Understanding the sequence preference of recurrent RNA building blocks using quantum chemistry: The intrastrand RNA dinucleotide platform

    Czech Academy of Sciences Publication Activity Database

    Mládek, Arnošt; Šponer, Judit E.; Kulhánek, P.; Lu, X.-J.; Olson, W.K.; Šponer, Jiří

    2012-01-01

    Roč. 8, č. 1 (2012), s. 335-347 ISSN 1549-9618 R&D Projects: GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GD203/09/H046 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : RNA dinucleotide platform * quantum-chemical calculation Subject RIV: BO - Biophysics Impact factor: 5.389, year: 2012

  16. Structural and optical properties of Mg doped ZnS quantum dots and biological applications

    Science.gov (United States)

    Ashokkumar, M.; Boopathyraja, A.

    2018-01-01

    Zn1-xMgxS (x = 0, 0.2 and 0.4) quantum dots (QDs) were prepared by co-precipitation method. The Mg dopant did not modify the cubic blende structure of ZnS QDs. The Mg related secondary phase was not detected even for 40% of Mg doping. The size mismatch between host Zn ion and dopant Mg ion created distortion around the dopant. The creation of distortion centres produced small changes in the lattice parameters and diffraction peak position. All the QDs showed small sulfur deficiency and the deficiency level were increased by Mg doping. Band gap of the QD was decreased due to the dominated quantum confinement effect over compositional effect at initial doping of Mg. But at higher doping the band gap was increased due to compositional effect, since there was no change in average crystallite size. The prepared QDs had three emission bands in the UV and Visible regions corresponding to near band edge emission and defect related emissions. The electron transport reaction chain which forms free radicals was broken by sulfur vacancy trap sites. Therefore, the ZnS QDs had better antioxidant activity and the antioxidant behaviour was enhanced by Mg doping. The enhanced UV absorption and emission of 20% of Mg doped ZnS QDs let to maximize the zone of inhibition against E. Coli bacterial strain.

  17. The quantum gamble

    CERN Document Server

    Boeyens, Jan C A

    2016-01-01

    This volume, written by a highly cited author, presents the history of quantum theory together with open questions and remaining problems in terms of the plausibility of quantum chemistry and physics. It also provides insights into the theory of matter-wave mechanics. The content is aimed at students and lecturers in chemistry, physics and the philosophy of science.

  18. The 54th International Meeting of Physical Chemistry; Fast Elementary Processes in Chemical and Biological Systems Proceedings

    International Nuclear Information System (INIS)

    Tramer, A.

    1996-01-01

    These proceedings represent papers presented at the 54th International Meeting of Physical Chemistry held in Villeneuve d'Ascq in France. Topics discussed include ultrafast studies in biophysics surface phenomena, photochemical processes, electron and proton transfer, crystalline and microdisperse media and isolated molecules. There were 80 papers presented at the meeting and 14 have been abstracted for the Energy Science and Technology database

  19. What Are They Thinking? Automated Analysis of Student Writing about Acid-Base Chemistry in Introductory Biology

    Science.gov (United States)

    Haudek, Kevin C.; Prevost, Luanna B.; Moscarella, Rosa A.; Merrill, John; Urban-Lurain, Mark

    2012-01-01

    Students' writing can provide better insight into their thinking than can multiple-choice questions. However, resource constraints often prevent faculty from using writing assessments in large undergraduate science courses. We investigated the use of computer software to analyze student writing and to uncover student ideas about chemistry in an…

  20. Quantum physics for beginners

    CERN Document Server

    Ficek, Zbigniew

    2016-01-01

    The textbook introduces students to the main ideas of quantum physics and the basic mathematical methods and techniques used in the fields of advanced quantum physics, atomic physics, laser physics, nanotechnology, quantum chemistry, and theoretical mathematics. The textbook explains how microscopic objects (particles) behave in unusual ways, giving rise to what's called quantum effects. It contains a wide range of tutorial problems from simple confidence-builders to fairly challenging exercises that provide adequate understanding of the basic concepts of quantum physics.

  1. Comparing Two Definitions of Work for a Biological Quantum Heat Engine

    International Nuclear Information System (INIS)

    Xu You-Yang; Zhao Shun-Cai; Liu Juan

    2015-01-01

    Systems of photosynthetic reaction centres have been modelled as heat engines, while it has also been reported that the efficiency and power of such heat engines can be enhanced by quantum interference — a trait that has attracted much interest. We compare two definitions of the work of such a photosynthetic heat engine, i.e. definition A used by Weimer et al. and B by Dorfman et al. We also introduce a coherent interaction between donor and acceptor (CIDA) to demonstrate a reversible energy transport. We show that these two definitions of work can impart contradictory results, that is, CIDA enhances the power and efficiency of the photosynthetic heat engine with definition B but not with A. Additionally, we find that both reversible and irreversible excitation-energy transport can be described with definition A, but definition B can only model irreversible transport. As a result, we conclude that definition A is more suitable for photosynthetic systems than definition B. (paper)

  2. Changes in stream chemistry and biology in response to reduced levels of acid deposition during 1987-2003 in the Neversink River Basin, Catskill Mountains

    Science.gov (United States)

    Burns, Douglas A.; Riva-Murray, K.; Bode, R.W.; Passy, S.

    2008-01-01

    Atmospheric acid deposition has decreased in the northeastern United States since the 1970s, resulting in modest increases in pH, acid-neutralizing capacity (ANC), and decreases in inorganic monomeric aluminum (AlIM) concentrations since stream chemistry monitoring began in the 1980s in the acid-sensitive upper Neversink River basin in the Catskill Mountains of New York. Stream pH has increased by 0.01 units/year during 1987-2003 at three sites in the Neversink basin as determined by Seasonal Kendall trend analysis. In light of this observed decrease in stream acidity, we sampled 12 stream sites within the Neversink River watershed for water chemistry, macroinvertebrates, fish, and periphytic diatoms in 2003 to compare with a similar data set collected in 1987. Metrics and indices that reflect sensitivity to stream acidity were developed with these biological data to determine whether changes in stream biota over the intervening 16 years parallel those of stream chemistry. Statistical comparisons of data on stream chemistry and an acid biological assessment profile (Acid BAP) derived from invertebrate data showed no significant differences between the two years. For pH and ANC, however, values in 2003 were generally lower than those in 1987; this difference likely resulted from higher streamflow in summer 2003. Despite these likely flow-induced changes in summer 2003, an ordination and cluster analysis of macroinvertebrate taxa based on the Acid BAP indicated that the most acidic sites in the upstream half of the East Branch Neversink River form a statistically significant separate cluster consistent with less acidic stream conditions. This analysis is consistent with limited recovery of invertebrate species in the most acidic reaches of the river, but will require additional improvement in stream chemistry before a stronger conclusion can be drawn. Data on the fish and periphytic diatom communities in 2003 indicate that slimy sculpin had not extended their habitat

  3. Quantum chemistry of solids and materials technology: solid-phase compounds of d- and f-elements

    International Nuclear Information System (INIS)

    Gubanov, V.A.

    1988-01-01

    The results of studies aimed at the development of methods of theoretical calculations of the electronic structure of solid phase compounds of α- and f-elements and the modelling of physicochemical properties of materials developed on their basis, are presented. The possibilities of cluster and zone calculations of the electronic structure of refractory compounds of d-metals with light elements are considered. The regularities of changes in the chemical bond and properties during crystal lattice alloying with metals, metalloids are found. The methods of quantum chemical modeling of optically active and luminescent materials on the base of oxides, fluorides, chalcogenides of d- and f-metals are developed. The compositions of new optically active compositions and protective coatings are suggested. New approaches to the study of magnetic properties of metals, alloys and compounds are developed. The results of calculations of the energy spectra of high-temperature oxide superconductors are given

  4. Large-scale calculations of solid oxide fuel cell cermet anode by tight-binding quantum chemistry method

    International Nuclear Information System (INIS)

    Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira

    2005-01-01

    Improvement of anode characteristics of solid oxide fuel cells is important for the better cell performance and especially the direct use of hydrocarbons. A mixture of ceramics and metal is generally used as anode, and different combinations of ceramics and metals lead to different electrode characteristics. We performed large-scale calculations to investigate the characteristics of Ni/CeO 2 and Cu/CeO 2 anodes at the electronic level using our tight-binding quantum chemical molecular dynamics program. Charge distribution analysis clarified the electron transfer from metal to oxide in both anodes. The calculations of density of states clarified different contributions of Ni and Cu orbitals to the energy levels at around Fermi level in each cermet. Based on the obtained results, we made considerations to explain different characteristics of both cermet anodes. The effectiveness of our approach for the investigation of complex cermet system was proved

  5. Prion-like nanofibrils of small molecules (PriSM): A new frontier at the intersection of supramolecular chemistry and cell biology.

    Science.gov (United States)

    Zhou, Jie; Du, Xuewen; Xu, Bing

    2015-01-01

    Formed by non-covalent interactions and not defined at genetic level, the assemblies of small molecules in biology are complicated and less explored. A common morphology of the supramolecular assemblies of small molecules is nanofibrils, which coincidentally resembles the nanofibrils formed by proteins such as prions. So these supramolecular assemblies are termed as prion-like nanofibrils of small molecules (PriSM). Emerging evidence from several unrelated fields over the past decade implies the significance of PriSM in biology and medicine. This perspective aims to highlight some recent advances of the research on PriSM. This paper starts with description of the intriguing similarities between PriSM and prions, discusses the paradoxical features of PriSM, introduces the methods for elucidating the biological functions of PriSM, illustrates several examples of beneficial aspects of PriSM, and finishes with the promises and current challenges in the research of PriSM. We anticipate that the research of PriSM will contribute to the fundamental understanding at the intersection of supramolecular chemistry and cell biology and ultimately lead to a new paradigm of molecular (or supramolecular) therapeutics for biomedicine.

  6. Adsorption Energies of Carbon, Nitrogen, and Oxygen Atoms on the Low-temperature Amorphous Water Ice: A Systematic Estimation from Quantum Chemistry Calculations

    Science.gov (United States)

    Shimonishi, Takashi; Nakatani, Naoki; Furuya, Kenji; Hama, Tetsuya

    2018-03-01

    We propose a new simple computational model to estimate the adsorption energies of atoms and molecules to low-temperature amorphous water ice, and we present the adsorption energies of carbon (3 P), nitrogen (4 S), and oxygen (3 P) atoms based on quantum chemistry calculations. The adsorption energies were estimated to be 14,100 ± 420 K for carbon, 400 ± 30 K for nitrogen, and 1440 ± 160 K for oxygen. The adsorption energy of oxygen is consistent with experimentally reported values. We found that the binding of a nitrogen atom is purely physisorption, while that of a carbon atom is chemisorption, in which a chemical bond to an O atom of a water molecule is formed. That of an oxygen atom has a dual character, with both physisorption and chemisorption. The chemisorption of atomic carbon also implies the possibility of further chemical reactions to produce molecules bearing a C–O bond, though this may hinder the formation of methane on water ice via sequential hydrogenation of carbon atoms. These properties would have a large impact on the chemical evolution of carbon species in interstellar environments. We also investigated the effects of newly calculated adsorption energies on the chemical compositions of cold dense molecular clouds with the aid of gas-ice astrochemical simulations. We found that abundances of major nitrogen-bearing molecules, such as N2 and NH3, are significantly altered by applying the calculated adsorption energy, because nitrogen atoms can thermally diffuse on surfaces, even at 10 K.

  7. Coupled-cluster calculations for ground and excited states of closed- and open-shell nuclei using methods of quantum chemistry

    International Nuclear Information System (INIS)

    Wloch, Marta; Gour, Jeffrey R; Piecuch, Piotr; Dean, David J; Hjorth-Jensen, Morten; Papenbrock, Thomas

    2005-01-01

    We discuss large-scale ab initio calculations of ground and excited states of 16 O and preliminary calculations for 15 O and 17 O using coupled-cluster methods and algorithms developed in quantum chemistry. By using realistic two-body interactions and the renormalized form of the Hamiltonian obtained with a no-core G-matrix approach, we are able to obtain the virtually converged results for 16 O and promising results for 15 O and 17 O at the level of two-body interactions. The calculated properties other than binding and excitation energies include charge radius and charge form factor. The relatively low costs of coupled-cluster calculations, which are characterized by the low-order polynomial scaling with the system size, enable us to probe large model spaces with up to seven or eight major oscillator shells, for which nontruncated shell-model calculations for nuclei with A = 15-17 active particles are presently not possible

  8. Tuning optical properties of water-soluble CdTe quantum dots for biological applications

    Energy Technology Data Exchange (ETDEWEB)

    Schulze, Anne S.; Tavernaro, Isabella; Machka, Friederike [Justus-Liebig-University Giessen, Institute of Inorganic and Analytical Chemistry (Germany); Dakischew, Olga; Lips, Katrin S. [Justus-Liebig-University Giessen, Laboratory of Experimental Trauma Surgery (Germany); Wickleder, Mathias S., E-mail: mathias.wickleder@anorg.chemie.uni-giessen.de [Justus-Liebig-University Giessen, Institute of Inorganic and Analytical Chemistry (Germany)

    2017-02-15

    In this study, two different synthetic methods in aqueous solution are presented to tune the optical properties of CdTe and CdSe semiconductor nanoparticles. Additionally, the influence of different temperatures, pressures, precursor ratios, surface ligands, bases, and core components in the synthesis was investigated with regard to the particle sizes and optical properties. As a result, a red shift of the emission and absorption maxima with increasing reaction temperature (100 to 220°C), pressure (1 to 25 bar), and different ratios of core components of alloyed semiconductor nanoparticles could be observed without a change of the particle size. An increase in particle size from 2.5 to 5 nm was only achieved by variation of the mercaptocarboxylic acid ligands in combination with the reaction time and used base. To get a first hint on the cytotoxic effects and cell uptake of the synthesized quantum dots, in vitro tests mesenchymal stem cells (MSCs) were carried out.

  9. Comparative studies of biological activity of cadmium-based quantum dots with different surface modifications

    Science.gov (United States)

    Kalinowska, D.; Grabowska-Jadach, I.; Drozd, M.; Pietrzak, M.

    2018-05-01

    This paper presents a modification of the surface of CdS/ZnS and CdSe x S1-x /ZnS quantum dots (QDs) with 3-mercaptopropionic and 6-mercaptohexanoic acid. The obtained QDs were characterized using TEM, DLS, UV-Vis, and fluorescence spectroscopy. Flow cytometry was applied to evaluate the cytotoxicity of QDs and examine the type of death caused by the tested nanoparticles. In addition, the generation of reactive oxygen species after incubation of the tested cells with CdSe x S1-x /ZnS-MPA and CdSe x S1-x /ZnS-MHA QDs was evaluated. The study was conducted on three cell lines: adherent (A549 and MRC-5) and suspension ones (K562). The conducted research demonstrated that the tested nanoparticles exhibit concentration-dependent toxicity. It was observed that the surface modification influences the toxicity level of the examined QDs, and modification of their surface with the use of the ligand of longer carbon chain (MHA) reduces the toxicity in comparison with QDs-MPA. It was also found that all tested QDs caused the death of cells in the course of necrosis. Based on obtained results, it was concluded that the cytotoxicity of QDs is to a large extent related to reactive oxygen species (ROS) generation.

  10. Miniaturized Quantum Semiconductor Surface Plasmon Resonance Platform for Detection of Biological Molecules

    Directory of Open Access Journals (Sweden)

    Jan J. Dubowski

    2013-06-01

    Full Text Available The concept of a portable, inexpensive and semi-automated biosensing platform, or lab-on-a-chip, is a vision shared by many researchers and venture industries. Under this scope, we have investigated the application of optical emission from quantum well (QW microstructures for monitoring surface phenomena on gold layers remaining in proximity (<300 nm with QW microstructures. The uncollimated QW radiation excites surface plasmons (SP and through the surface plasmon resonance (SPR effect allows for detection of small perturbation in the density surface adsorbates. The SPR technology is already commonly used for biochemical characterization in pharmaceutical industries, but the reduction of the distance between the SP exciting source and the biosensing platform to a few hundreds of nanometers is an innovative approach enabling us to achieve an ultimate miniaturization of the device. We evaluate the signal quality of this nanophotonic QW-SPR device using hyperspectral-imaging technology, and we compare its performance with that of a standard prism-based commercial system. Two standard biochemical agents are employed for this characterization study: bovine serum albumin and inactivated influenza A virus. With an innovative conical method of SPR data collection, we demonstrate that individually collected SPR scan, each in less than 2.2 s, yield a resolution of the detection at 1.5 × 10−6 RIU.

  11. Support vector machine regression (LS-SVM)--an alternative to artificial neural networks (ANNs) for the analysis of quantum chemistry data?

    Science.gov (United States)

    Balabin, Roman M; Lomakina, Ekaterina I

    2011-06-28

    A multilayer feed-forward artificial neural network (MLP-ANN) with a single, hidden layer that contains a finite number of neurons can be regarded as a universal non-linear approximator. Today, the ANN method and linear regression (MLR) model are widely used for quantum chemistry (QC) data analysis (e.g., thermochemistry) to improve their accuracy (e.g., Gaussian G2-G4, B3LYP/B3-LYP, X1, or W1 theoretical methods). In this study, an alternative approach based on support vector machines (SVMs) is used, the least squares support vector machine (LS-SVM) regression. It has been applied to ab initio (first principle) and density functional theory (DFT) quantum chemistry data. So, QC + SVM methodology is an alternative to QC + ANN one. The task of the study was to estimate the Møller-Plesset (MPn) or DFT (B3LYP, BLYP, BMK) energies calculated with large basis sets (e.g., 6-311G(3df,3pd)) using smaller ones (6-311G, 6-311G*, 6-311G**) plus molecular descriptors. A molecular set (BRM-208) containing a total of 208 organic molecules was constructed and used for the LS-SVM training, cross-validation, and testing. MP2, MP3, MP4(DQ), MP4(SDQ), and MP4/MP4(SDTQ) ab initio methods were tested. Hartree-Fock (HF/SCF) results were also reported for comparison. Furthermore, constitutional (CD: total number of atoms and mole fractions of different atoms) and quantum-chemical (QD: HOMO-LUMO gap, dipole moment, average polarizability, and quadrupole moment) molecular descriptors were used for the building of the LS-SVM calibration model. Prediction accuracies (MADs) of 1.62 ± 0.51 and 0.85 ± 0.24 kcal mol(-1) (1 kcal mol(-1) = 4.184 kJ mol(-1)) were reached for SVM-based approximations of ab initio and DFT energies, respectively. The LS-SVM model was more accurate than the MLR model. A comparison with the artificial neural network approach shows that the accuracy of the LS-SVM method is similar to the accuracy of ANN. The extrapolation and interpolation results show that LS-SVM is

  12. Nano-design of quantum dot-based photocatalysts for hydrogen generation using advanced surface molecular chemistry

    KAUST Repository

    Yu, Weili; Noureldine, Dalal; Isimjan, Tayirjan T.; Lin, Bin; Del Gobbo, Silvano; Abulikemu, Mutalifu; Hedhili, Mohamed N.; Anjum, Dalaver H.; Takanabe, Kazuhiro

    2015-01-01

    Efficient photocatalytic hydrogen generation in a suspension system requires a sophisticated nano-device that combines a photon absorber with effective redox catalysts. This study demonstrates an innovative molecular linking strategy for fabricating photocatalytic materials that allow effective charge separation of excited carriers, followed by efficient hydrogen evolution. The method for the sequential replacement of ligands with appropriate molecules developed in this study tethers both quantum dots (QDs), as photosensitizers, and metal nanoparticles, as hydrogen evolution catalysts, to TiO2 surfaces in a controlled manner at the nano-level. Combining hydrophobic and hydrophilic interactions on the surface, CdSe-ZnS core-shell QDs and an Au-Pt alloy were attached to TiO2 without overlapping during the synthesis. The resultant nano-photocatalysts achieved substantially high-performance visible-light-driven photocatalysis for hydrogen evolution. All syntheses were conducted at room temperature and in ambient air, providing a promising route for fabricating visible-light-responsive photocatalysts.

  13. Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Vlcek, Lukas [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Uhlik, Filip [Charles Univ., Prague (Czech Republic); Moucka, Filip [Purkinje Univ. (Czech Republic); Nezbeda, Ivo [Purkinje Univ. (Czech Republic); Academy of Sciences of the Czech Republic (ASCR), Prague (Czech Republic); Chialvo, Ariel A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-12-16

    We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge non-polarizable SPC/E, (ii) Drude point charge polarizable SWM4- DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ion hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration, but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.

  14. Lectures on quantum mechanics

    International Nuclear Information System (INIS)

    Weinberg, Steven

    2015-01-01

    Quantum mechanics represents the central revolution of modern natural science and reaches in its importance farely beyond physics. Neither chemistry nor biology on the molecular scale would be understandable without it. Modern information technology from the laptop over the mobile telephone and the flat screen until the supercomputer would be unthinkable without quantum-mechanical effects. It desribes the world on the atomic and subatomic scale and is by this the starting point of our modern worldview. The Nobel-prize carrier Steven Weinberg has done ever among others by his theory of the unification of the weak and the electromagnetic interaction one of the most important contributions to this revolution. In this book he reproduces his personal view of quantum mechanics, which captivates by its strictly logic construction, precise linguistic representation, and mathematical clearness and completeness. This book appeals to studyings of natural sciences, especially of physics. Accompanied is the test by exercise problems, which allow the studying to apply immediately the knowledge, but also test their understanding. Because of its precision and clearness ''Lectures on Quantum Mechanics'' by Weinberg is also essentially suited for the self-study.

  15. Biological interactions of quantum dot nanoparticles in skin and in human epidermal keratinocytes

    International Nuclear Information System (INIS)

    Zhang, Leshuai W.; Yu, William W.; Colvin, Vicki L.; Monteiro-Riviere, Nancy A.

    2008-01-01

    Quantum dots nanoparticles have novel optical properties for biomedical applications and electronics, but little is known about their skin permeability and interaction with cells. QD621 are nail-shaped nanoparticles that contain a cadmium/selenide core with a cadmium sulfide shell coated with polyethylene glycol (PEG) and are soluble in water. QD were topically applied to porcine skin flow-through diffusion cells to assess penetration at 1 μM, 2 μM and 10 μM for 24 h. QD were also studied in human epidermal keratinocytes (HEK) to determine cellular uptake, cytotoxicity and inflammatory potential. Confocal microscopy depicted the penetration of QD621 through the uppermost stratum corneum (SC) layers of the epidermis and fluorescence was found primarily in the SC and near hair follicles. QD were found in the intercellular lipid bilayers of the SC by transmission electron microscopy (TEM). Inductively coupled plasma-optical emission spectroscopy (ICP-OES) analysis for cadmium (Cd) and fluorescence for QD both did not detect Cd nor fluorescence signal in the perfusate at any time point or concentration. In HEK, viability decreased significantly (p < 0.05) from 1.25 nM to 10nM after 24 h and 48 h. There was a significant increase in IL-6 at 1.25 nM to 10 nM, while IL-8 increased from 2.5nM to 10nM after 24 h and 48 h. TEM of HEK treated with 10 nM of QD621 at 24 h depicted QD in cytoplasmic vacuoles and at the periphery of the cell membranes. These results indicate that porcine skin penetration of QD621 is minimal and limited primarily to the outer SC layers, yet if the skin were damaged allowing direct QD exposure to skin or keratinocytes, an inflammatory response could be initiated

  16. Radiation chemistry

    International Nuclear Information System (INIS)

    Rodgers, F.; Rodgers, M.A.

    1987-01-01

    The contents of this book include: Interaction of ionizing radiation with matter; Primary products in radiation chemistry; Theoretical aspects of radiation chemistry; Theories of the solvated electron; The radiation chemistry of gases; Radiation chemistry of colloidal aggregates; Radiation chemistry of the alkali halides; Radiation chemistry of polymers; Radiation chemistry of biopolymers; Radiation processing and sterilization; and Compound index

  17. Insight into the Extraction Mechanism of Americium(III) over Europium(III) with Pyridylpyrazole: A Relativistic Quantum Chemistry Study.

    Science.gov (United States)

    Kong, Xiang-He; Wu, Qun-Yan; Wang, Cong-Zhi; Lan, Jian-Hui; Chai, Zhi-Fang; Nie, Chang-Ming; Shi, Wei-Qun

    2018-05-10

    Separation of trivalent actinides (An(III)) and lanthanides (Ln(III)) is one of the most important steps in spent nuclear fuel reprocessing. However, it is very difficult and challenging to separate them due to their similar chemical properties. Recently the pyridylpyrazole ligand (PypzH) has been identified to show good separation ability toward Am(III) over Eu(III). In this work, to explore the Am(III)/Eu(III) separation mechanism of PypzH at the molecular level, the geometrical structures, bonding nature, and thermodynamic behaviors of the Am(III) and Eu(III) complexes with PypzH ligands modified by alkyl chains (Cn-PypzH, n = 2, 4, 8) have been systematically investigated using scalar relativistic density functional theory (DFT). According to the NBO (natural bonding orbital) and QTAIM (quantum theory of atoms in molecules) analyses, the M-N bonds exhibit a certain degree of covalent character, and more covalency appears in Am-N bonds compared to Eu-N bonds. Thermodynamic analyses suggest that the 1:1 extraction reaction, [M(NO 3 )(H 2 O) 6 ] 2+ + PypzH + 2NO 3 - → M(PypzH)(NO 3 ) 3 (H 2 O) + 5H 2 O, is the most suitable for Am(III)/Eu(III) separation. Furthermore, the extraction ability and the Am(III)/Eu(III) selectivity of the ligand PypzH is indeed enhanced by adding alkyl-substituted chains in agreement with experimental observations. Besides this, the nitrogen atom of pyrazole ring plays a more significant role in the extraction reactions related to Am(III)/Eu(III) separation compared to that of pyridine ring. This work could identify the mechanism of the Am(III)/Eu(III) selectivity of the ligand PypzH and provide valuable theoretical information for achieving an efficient Am(III)/Eu(III) separation process for spent nuclear fuel reprocessing.

  18. Spins in chemistry

    CERN Document Server

    McWeeny, Roy

    2004-01-01

    Originally delivered as a series of lectures, this volume systematically traces the evolution of the ""spin"" concept from its role in quantum mechanics to its assimilation into the field of chemistry. Author Roy McWeeny presents an in-depth illustration of the deductive methods of quantum theory and their application to spins in chemistry, following the path from the earliest concepts to the sophisticated physical methods employed in the investigation of molecular structure and properties. Starting with the origin and development of the spin concept, the text advances to an examination of sp

  19. Activation of CH4 by Th(+) as studied by guided ion beam mass spectrometry and quantum chemistry.

    Science.gov (United States)

    Cox, Richard M; Armentrout, P B; de Jong, Wibe A

    2015-04-06

    The reaction of atomic thorium cations with CH4 (CD4) and the collision-induced dissociation (CID) of ThCH4(+) with Xe are studied using guided ion beam tandem mass spectrometry. In the methane reactions at low energies, ThCH2(+) (ThCD2(+)) is the only product; however, the energy dependence of the cross-section is inconsistent with a barrierless exothermic reaction as previously assumed on the basis of ion cyclotron resonance mass spectrometry results. The dominant product at higher energies is ThH(+) (ThD(+)), with ThCH3(+) (ThCD3(+)) having a similar threshold energy. The latter product subsequently decomposes at still higher energies to ThCH(+) (ThCD(+)). CID of ThCH4(+) yields atomic Th(+) as the exclusive product. The cross-sections of all product ions are modeled to provide 0 K bond dissociation energies (in eV) of D0(Th(+)-H) ≥ 2.25 ± 0.18, D0(Th(+)-CH) = 6.19 ± 0.16, D0(Th(+)-CH2) ≥ 4.54 ± 0.09, D0(Th(+)-CH3) = 2.60 ± 0.30, and D0(Th(+)-CH4) = 0.47 ± 0.05. Quantum chemical calculations at several levels of theory are used to explore the potential energy surfaces for activation of methane by Th(+), and the effects of spin-orbit coupling are carefully considered. When spin-orbit coupling is explicitly considered, a barrier for C-H bond activation that is consistent with the threshold measured for ThCH2(+) formation (0.17 ± 0.02 eV) is found at all levels of theory, whereas this barrier is observed only at the BHLYP and CCSD(T) levels otherwise. The observation that the CID of the ThCH4(+) complex produces Th(+) as the only product with a threshold of 0.47 eV indicates that this species has a Th(+)(CH4) structure, which is also consistent with a barrier for C-H bond activation. This barrier is thought to exist as a result of the mixed ((4)F,(2)D) electronic character of the Th(+) J = (3)/2 ground level combined with extensive spin-orbit effects.

  20. Syntheses, structural elucidation, thermal properties, theoretical quantum chemical studies (DFT and biological studies of barbituric–hydrazone complexes

    Directory of Open Access Journals (Sweden)

    Amina A. Soayed

    2015-03-01

    Full Text Available Condensation of barbituric acid with hydrazine hydrate yielded barbiturichydrazone (L which was characterized using IR, 1H NMR and mass spectra. The Co(II, Ni(II and Cu(II complexes derived from this ligand have been synthesized and structurally characterized by elemental analyses, spectroscopic methods (IR, UV–Vis and ESR and thermal analyses (TGA, DTG and DTA and the structures were further elucidated using quantum chemical density functional theory. Complexes of L were found to have the ML.nH2O stoichiometry with either tetrahedral or octahedral geometry. The ESR data showed the Cu(II complex to be in a tetragonal geometry. Theoretical investigation of the electronic structure of metal complexes at the TD-DFT/B3LYP level of theory has been carried out and discussed. The fundamental vibrational wavenumbers were calculated and a good agreement between observed and scaled calculated wavenumbers was achieved. Thermal studies were performed to deduce the stabilities of the ligand and complexes. Thermodynamic parameters, such as the order of reactions (n, activation energy ΔE∗, enthalpy of reaction ΔH∗ and entropy ΔS∗ were calculated from DTA curves using Horowitz–Metzger method. The ligand L and its complexes have been screened for their antifungal and antibacterial activities and were found to possess better biological activities compared to those of unsubstituted barbituric acid complexes.

  1. Formation of Carbon Nanotube Based Gears: Quantum Chemistry and Molecular Mechanics Study of the Electrophilic Addition of o-Benzyne to Fullerenes, Graphene, and Nanotubes

    Science.gov (United States)

    Jaffe, Richard; Han, Jie; Globus, Al; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    Considerable progress has been made in recent years in chemical functionalization of fullerene molecules. In some cases, the predominant reaction products are different from those obtained (using the same reactants) from polycyclic aromatic hydrocarbons (PAHs). One such example is the cycloaddition of o-benzyne to C60. It is well established that benzyne adds across one of the rings in naphthalene, anthracene and other PAHs forming the [2+4] cycloaddition product (benzobicyclo[2.2.2.]-octatriene with naphthalene and triptycene with anthracene). However, Hoke et al demonstrated that the only reaction path for o-benzyne with C60 leads to the [2+2] cycloaddition product in which benzyne adds across one of the interpentagonal bonds (forming a cyclobutene ring in the process). Either reaction product results in a loss of aromaticity and distortion of the PAH or fullerene substrate, and in a loss of strain in the benzyne. It is not clear, however, why different products are preferred in these cases. In the current paper, we consider the stability of benzyne-nanotube adducts and the ability of Brenner's potential energy model to describe the structure and stability of these adducts. The Brenner potential has been widely used for describing diamondoid and graphitic carbon. Recently it has also been used for molecular mechanics and molecular dynamics simulations of fullerenes and nanotubes. However, it has not been tested for the case of functionalized fullerenes (especially with highly strained geometries). We use the Brenner potential for our companion nanogear simulations and believe that it should be calibrated to insure that those simulations are physically reasonable. In the present work, Density Functional theory (DFT) calculations are used to determine the preferred geometric structures and energetics for this calibration. The DFT method is a kind of ab initio quantum chemistry method for determining the electronic structure of molecules. For a given basis set

  2. Biological assessment and streambed-sediment chemistry of streams in the Indianapolis metropolitan area, Indiana, 2003–2008

    Science.gov (United States)

    Voelker, David C.

    2012-01-01

    During 2003–2008, the U.S. Geological Survey sampled 13 sites in the Indianapolis metropolitan area in Indiana for benthic invertebrates, fish communities, and streambed-sediment chemistry. Data from seven White River sites and six tributary sites complement surface-water chemistry data collected by the Indianapolis Department of Public Works. The information is being used to assess changes in water quality in conjunction with the City's programs to reduce combined sewer overflows and other point and nonpoint sources of pollution in the Indianapolis area. During the study, 233 benthic-invertebrate taxa were identified from which the Ephemeroptera, Plecoptera, and Trichoptera (EPT) Index, the Hilsenhoff Biotic Index (HBI), and the Invertebrate Community Index (ICI) were calculated. EPT index scores ranged from 2 to 16 on the White River and from 2 to 17 on the tributaries. EPT index scores indicate that these pollution-intolerant taxa are more prevalent upstream from and away from the combined-sewer areas of Indianapolis. HBI scores from sites on the White River ranged from 4.67 (good) to 9.55 (very poor), whereas on the tributaries, scores ranged from 4.21 (very good) to 8.14 (poor). Lower HBI scores suggest that less organic pollution was present and, like the EPT scores, indicate better conditions where combined-sewer overflows (CSOs) are not present. Similarly, ICI scores indicated better conditions upstream from the CSO outfalls on the White River. White River scores ranged from 12 to 46, where higher ICI scores indicate better conditions in the benthic-invertebrate community. ICI scores at the tributary sites ranged from 12 to 52, with the highest scores on streams without CSOs.

  3. "TAARgeting Addiction"--The Alamo Bears Witness to Another Revolution: An Overview of the Plenary Symposium of the 2015 Behavior, Biology and Chemistry Conference.

    Science.gov (United States)

    Grandy, David K; Miller, Gregory M; Li, Jun-Xu

    2016-02-01

    In keeping with the free-thinking tradition San Antonians are known for, the Scientific Program Committee of the Behavior, Biology and Chemistry: Translational Research in Addiction Conference chose trace amine-associated receptor 1 (TAAR1) as the focus of the plenary symposium for its 7th annual meeting held at the University of Texas Health Science Center at San Antonio on March 14 and 15, 2015. The timing of the meeting's plenary session on TAAR1 coincided with the Ides of March, an apt concurrence given the long association of this date with the overthrow of the status quo. And whether aware of the coincidence or not, those in attendance witnessed the plunging of the metaphorical dagger into the heart of the dopamine (DA) transporter (DAT)-centric view of psychostimulant action. The symposium's four plenary presentations focused on the molecular and cellular biology, genetics, medicinal chemistry and behavioral pharmacology of the TAAR1 system and the experimental use of newly developed selective TAAR1 ligands. The consensus was that TAAR1 is a DA and methamphetamine receptor, interacts with DAT and DA D2 receptors, and is essential in modulating addiction-related effects of psychostimulants. Collectively the findings presented during the symposium constitute a significant challenge to the current view that psychostimulants such as methamphetamine and amphetamine solely target DAT to interfere with normal DA signaling and provide a novel conceptual framework from which a more complete understanding of the molecular mechanisms underlying the actions of DA and METH is likely to emerge. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  4. The Breath of Chemistry

    DEFF Research Database (Denmark)

    Josephsen, Jens

    The present preliminary text is a short thematic presentation in biological inorganic chemistry meant to illustrate general and inorganic (especially coordination) chemistry in biochemistry. The emphasis is on molecular models to explain features of the complicated mechanisms essential to breathing...

  5. Review of the ethnobotany, chemistry, biological activity and safety of the botanical dietary supplement Morinda citrifolia (noni).

    Science.gov (United States)

    Pawlus, Alison D; Kinghorn, Douglas A

    2007-12-01

    Morinda citrifolia, commonly called noni, has a long history as a medicinal plant and its use as a botanical dietary supplement has grown tremendously in recent years. This has prompted a concomitant increase in research on the phytochemical constituents and biological activity of noni. A relatively large number of scientific publications on noni have been published in recent years, including a number of review articles. The goals of this review are to provide an updated categorization of the phytochemical constituents found in noni and to provide perspective for its extensive utilization as a major botanical dietary supplement. Included herein are a comprehensive list of known ethnobotanical uses and common names of M. citrifolia, a brief summary of relevant biological studies and a discussion of the safety of noni as a supplement.

  6. Quantum mechanics. Textbook for students of physics, mathematics and physical chemistry. 4. ed. Quantenmechanik. Studienbuch fuer Studierende der Physik, Mathematik und Physikalischen Chemie

    Energy Technology Data Exchange (ETDEWEB)

    Grawert, G.

    1985-01-01

    The aim of the textbook now present in fourth edition is the representation of the fundamental physical concepts of the theory of quantum mechanics. It is confined to the nonrelativistic quantum mechanics; however also themes are treated which are in an extended form important just for quantum field theory up to the modern development. (orig./HSI). With 22 figs.

  7. Quantum mechanics. Textbook for students of physics, mathematics and physical chemistry. Quantenmechanik. Studienbuch fuer Studierende der Physik, Mathematik und Physikalischen Chemie

    Energy Technology Data Exchange (ETDEWEB)

    Grawert, G. (Marburg Univ. (Germany, F.R.). Fachbereich 13 - Physik)

    1989-01-01

    The aim of the textbook now present in fifth edition is the representation of the fundamental physical concepts of the theory of quantum mechanics. It is confined to the nonrelativistic quantum mechanics; however also themes are treated which are in an extended form important just for quantum field theory up to the modern development. (orig.) With 22 figs.

  8. Discovery of a general method of solving the Schrödinger and dirac equations that opens a way to accurately predictive quantum chemistry.

    Science.gov (United States)

    Nakatsuji, Hiroshi

    2012-09-18

    Just as Newtonian law governs classical physics, the Schrödinger equation (SE) and the relativistic Dirac equation (DE) rule the world of chemistry. So, if we can solve these equations accurately, we can use computation to predict chemistry precisely. However, for approximately 80 years after the discovery of these equations, chemists believed that they could not solve SE and DE for atoms and molecules that included many electrons. This Account reviews ideas developed over the past decade to further the goal of predictive quantum chemistry. Between 2000 and 2005, I discovered a general method of solving the SE and DE accurately. As a first inspiration, I formulated the structure of the exact wave function of the SE in a compact mathematical form. The explicit inclusion of the exact wave function's structure within the variational space allows for the calculation of the exact wave function as a solution of the variational method. Although this process sounds almost impossible, it is indeed possible, and I have published several formulations and applied them to solve the full configuration interaction (CI) with a very small number of variables. However, when I examined analytical solutions for atoms and molecules, the Hamiltonian integrals in their secular equations diverged. This singularity problem occurred in all atoms and molecules because it originates from the singularity of the Coulomb potential in their Hamiltonians. To overcome this problem, I first introduced the inverse SE and then the scaled SE. The latter simpler idea led to immediate and surprisingly accurate solution for the SEs of the hydrogen atom, helium atom, and hydrogen molecule. The free complement (FC) method, also called the free iterative CI (free ICI) method, was efficient for solving the SEs. In the FC method, the basis functions that span the exact wave function are produced by the Hamiltonian of the system and the zeroth-order wave function. These basis functions are called complement

  9. Chemistry with bigger, better atoms

    Indian Academy of Sciences (India)

    DELL

    Anshu Pandey. Solid State and Structural Chemistry Unit. Indian Institute of Science. H. Cd. Hg. U ? Page 2. Quantum Dots: A Coarse-grained view. • Quantum Dot Electronic Structure can be approximated remarkably well as a Spherical. Particle in a Box Problem ... The concept of stoichiometry still holds!!! Rekha M. et. al.

  10. Radiation chemistry and bioradical chemistry

    International Nuclear Information System (INIS)

    Ferradini, C.

    1991-01-01

    Oxygen metabolism results, at the cellular level, in the formation of superoxyde radical O 2 - · and probably also of hydroxyl radical OH·. Other radical species can be produced from exogenous or endogenous molecules and nearly all of them have the possibility to react with oxygen giving peroxyradicals. Some of these transients play a role in various biological processes such as phagocytosis, inflammation or ischemy although the mechanisms invoked are poorly understood. Radiation chemistry is an invaluable tool for obtaining a quantitative view of these mechanisms. A description is given of this interaction [fr

  11. Study of a multitrophical integrated aquatic system for the teaching-learning of the subjects physics, chemistry and biology in the bachelor

    Science.gov (United States)

    Ramirez, Eva; Espinosa, Cecilia

    2017-04-01

    In Mexico exist due to the lack of water in the City, which is where the College of Sciences and Humanities Orient (at UNAM) is located. This is because a point of view from the Chemical, Physics and Biology subjects is important to find learning strategies that motivate students to seek solutions to problems such as these. As Science Mentors, students were asked to propose water treatment from the homes they live in. From these investigations the students concluded that it was necessary to study in depth the wetlands like Multi-trophic Aquatic System that allow the treatment of gray water, so that a prototype of Micro-scale Multitrophic Aquatic System was set up in the laboratory, where the pH was measured , The concentration of oxygen, phosphates, from a Chemical perspective. As for the subject of Biology, we worked on the search for mycorrhizal fungi associated with the growth of plants for the purification of water. In physics we worked the sedimentation system. Artificial wetlands are man-made zones in which, in a controlled manner, mechanisms for the removal of contaminants present in wastewater, occurring in natural wetlands through physical, biological and chemical processes, are constructed mechanically and Is waterproofed to prevent losses of water to the subsoil, the use of substrates different from the original land for rooting the plants and their selection that will colonize the wetland benefit the recovery of water. The present project aims to structure an Artificial Wetland to carry out didactic strategies, activities with students, as well as work on research projects in the sciences of Chemistry, Physics and Biology. Through the application of chemical, biological and physical concepts and processes, so that students of the different semesters of the College of Sciences and Humanities Plantel Oriente, appropriate the relevant knowledge in the area of experimental sciences, developing thinking skills and achieve Significant learning, which are

  12. Integrating Computational Chemistry into a Course in Classical Thermodynamics

    Science.gov (United States)

    Martini, Sheridan R.; Hartzell, Cynthia J.

    2015-01-01

    Computational chemistry is commonly addressed in the quantum mechanics course of undergraduate physical chemistry curricula. Since quantum mechanics traditionally follows the thermodynamics course, there is a lack of curricula relating computational chemistry to thermodynamics. A method integrating molecular modeling software into a semester long…

  13. Medicinal Chemistry/Pharmacology in Sophomore Organic Chemistry.

    Science.gov (United States)

    Harrison, Aline M.

    1989-01-01

    Discussed is a series of lectures designed to illustrate the use of general organic chemical principles in molecular biology, introduce current research in interdisciplinary areas to the beginner, increase interest in organic chemistry, and bridge the gap between traditional organic chemistry, biology, and the consumer. An outline is presented.…

  14. comparative assessment of university chemistry undergraduate

    African Journals Online (AJOL)

    Temechegn

    The areas of chemistry covered are Introductory, Inorganic, Physical, Organic, and Quantum and ... various specialisations like Pure and Applied Chemistry, Analytical ... even engineering disciplines, a degree in chemistry can be the starting point. .... It is also to show the relevance of the instructional methods relative to the.

  15. Dynamic Processes in Biology, Chemistry, and Materials Science: Opportunities for UltraFast Transmission Electron Microscopy - Workshop Summary Report

    Energy Technology Data Exchange (ETDEWEB)

    Kabius, Bernd C.; Browning, Nigel D.; Thevuthasan, Suntharampillai; Diehl, Barbara L.; Stach, Eric A.

    2012-07-25

    This report summarizes a 2011 workshop that addressed the potential role of rapid, time-resolved electron microscopy measurements in accelerating the solution of important scientific and technical problems. A series of U.S. Department of Energy (DOE) and National Academy of Science workshops have highlighted the critical role advanced research tools play in addressing scientific challenges relevant to biology, sustainable energy, and technologies that will fuel economic development without degrading our environment. Among the specific capability needs for advancing science and technology are tools that extract more detailed information in realistic environments (in situ or operando) at extreme conditions (pressure and temperature) and as a function of time (dynamic and time-dependent). One of the DOE workshops, Future Science Needs and Opportunities for Electron Scattering: Next Generation Instrumentation and Beyond, specifically addressed the importance of electron-based characterization methods for a wide range of energy-relevant Grand Scientific Challenges. Boosted by the electron optical advancement in the last decade, a diversity of in situ capabilities already is available in many laboratories. The obvious remaining major capability gap in electron microscopy is in the ability to make these direct in situ observations over a broad spectrum of fast (µs) to ultrafast (picosecond [ps] and faster) temporal regimes. In an effort to address current capability gaps, EMSL, the Environmental Molecular Sciences Laboratory, organized an Ultrafast Electron Microscopy Workshop, held June 14-15, 2011, with the primary goal to identify the scientific needs that could be met by creating a facility capable of a strongly improved time resolution with integrated in situ capabilities. The workshop brought together more than 40 leading scientists involved in applying and/or advancing electron microscopy to address important scientific problems of relevance to DOE’s research

  16. Simulation with Phast of the pore water chemistry experiment results (Mont Terri Url, Switzerland), including transport, thermodynamics, kinetics, and biological activity

    International Nuclear Information System (INIS)

    Tournassat, C.; Gaucher, E.; Pearson, F.J.; Mettler, S.; Wersin, P.

    2005-01-01

    Full text of publication follows: The Pore water Chemistry (PC-)experiment was initially designed to determine the processes that control the redox properties of pore water in the Opalinus Clay at the Mont Terri URL. However, changes in isotopic data and chemical parameters such as pH, alkalinity, dissolved methane, acetate and sulphate concentrations indicated unexpected microbial activity. The origin of the bacteria is not clear. In the light of published data, an indigenous origin cannot be ruled out. A combined biological and reactive transport model has been developed with the parallel PHAST software to simulate the processes that determine pore water chemistry. The influence of bacterial activity on the system is successfully modelled by considering different reaction pathways scenarios including aceto-genesis, methano-genesis, and methane/acetate oxidation coupled to sulphate reduction. Several conclusions can be clearly stated in the light of the simulation results: - The measured redox potentials (redox electrode) are in line with the S(-II)/S(+VI) redox system. - In the undisturbed pore water, S(-II) and S(+VI) activities are controlled by a mineral assemblage containing pyrite and a Fe carbonate (siderite or ankerite). pH is buffered by mineral phases and SO 4 2- concentration is inherited from the marine sedimentary rock. - Some local redox potentials in the sedimentary rock do not correspond to the measured redox potential; for instance, organic matter/HCO 3 - and CH 4 /HCO 3 - systems are not at equilibrium with the measured redox potential. - Redox disequilibrium can be exploited by micro-organisms as a source of energy for their metabolism. In this experiment CH 4 , acetate and other organic acids were produced and SO 4 2- was reduced to HS - . The redox properties of the system are then governed by kinetics rather than by thermodynamic equilibrium. The unexpected persistence of acetate in the borehole water is one of the consequences of these

  17. Herbal Therapies for Type 2 Diabetes Mellitus: Chemistry, Biology, and Potential Application of Selected Plants and Compounds

    Directory of Open Access Journals (Sweden)

    Cicero L. T. Chang

    2013-01-01

    Full Text Available Diabetes mellitus has been recognized since antiquity. It currently affects as many as 285 million people worldwide and results in heavy personal and national economic burdens. Considerable progress has been made in orthodox antidiabetic drugs. However, new remedies are still in great demand because of the limited efficacy and undesirable side effects of current orthodox drugs. Nature is an extraordinary source of antidiabetic medicines. To date, more than 1200 flowering plants have been claimed to have antidiabetic properties. Among them, one-third have been scientifically studied and documented in around 460 publications. In this review, we select and discuss blood glucose-lowering medicinal herbs that have the ability to modulate one or more of the pathways that regulate insulin resistance, β-cell function, GLP-1 homeostasis, and glucose (reabsorption. Emphasis is placed on phytochemistry, anti-diabetic bioactivities, and likely mechanism(s. Recent progress in the understanding of the biological actions, mechanisms, and therapeutic potential of compounds and extracts of plant origin in type 2 diabetes is summarized. This review provides a source of up-to-date information for further basic and clinical research into herbal therapy for type 2 diabetes. Emerging views on therapeutic strategies for type 2 diabetes are also discussed.

  18. Quantum computation and simulation with trapped ions using dissipation

    International Nuclear Information System (INIS)

    Schindler, P.

    2013-01-01

    current quantum systems do not allow for the required level of control. Nevertheless it seems promising to adapt the techniques developed for quantum information processing to build a quantum simulator. Such a device is able to efficiently reproduce the dynamics of any quantum system - a task that is only possible for small systems on existing classical computers. However, the quantum system of interest may be coupled to a classical environment where many examples for such systems can be found in quantum biology and quantum chemistry. These systems are often embedded in a thermal environment and, analogous to classical physics, show non-reversible, or dissipative, dynamics. Thus, also the quantum simulator should be able to reproduce dissipative dynamics which requires an extension of the usual quantum computing toolbox. In the context of quantum computing, such a coupling is usually treated as a noise process that defeats the possible gain from using such a device. Interestingly it has been shown that an environment can be engineered that drives the system towards a state that features entanglement and can serve as a resource for quantum information processing. In this thesis, an extended toolbox that goes beyond coherent operations is introduced in our small-scale ion-trap quantum information processor. This is then used to create an entangled state through dissipative dynamics. In the next step a quantum simulation of a dissipative many-body system is performed, demonstrating the hallmark feature of a novel type of quantum phase transitions. (author) [de

  19. Bad chemistry

    OpenAIRE

    Petsko, Gregory A

    2004-01-01

    General chemistry courses haven't changed significantly in forty years. Because most basic chemistry students are premedical students, medical schools have enormous influence and could help us start all over again to create undergraduate chemistry education that works.

  20. Overview of Stabilizing Ligands for Biocompatible Quantum Dot Nanocrystals

    Directory of Open Access Journals (Sweden)

    Aaron Clapp

    2011-11-01

    Full Text Available Luminescent colloidal quantum dots (QDs possess numerous advantages as fluorophores in biological applications. However, a principal challenge is how to retain the desirable optical properties of quantum dots in aqueous media while maintaining biocompatibility. Because QD photophysical properties are directly related to surface states, it is critical to control the surface chemistry that renders QDs biocompatible while maintaining electronic passivation. For more than a decade, investigators have used diverse strategies for altering the QD surface. This review summarizes the most successful approaches for preparing biocompatible QDs using various chemical ligands.

  1. Comparative chemistry and biological properties of the solid residues from hydrodistillation of Spanish populations of Rosmarinus officinalis L.

    Directory of Open Access Journals (Sweden)

    Sánchez-Vioque, R.

    2015-06-01

    Full Text Available Solid residues from the hydrodistillation of selected Spanish populations of rosemary (Rosmarinus officinalis L. have been analyzed for their polyphenol composition, and antioxidant and bioplaguicide activities. The objective was to evaluate and select the most suitable plant materials as sources of natural antioxidants and crop protectants. Total polyphenol content and polyphenol composition of rosemary populations were very dependent on the growth location: populations from Aranjuez showed a higher content of total polyphenols and were richer in rosmarinic acid as compared with their equivalent populations from Cuenca, whereas these latter were characterized by an overall higher content in genkwanin and carnosol. Most of the antioxidant activities were highly correlated with the total content of polyphenols although some polyphenols like carnosic acid and carnosol seemed to favor such activities. The extracts from R. officinalis were strong antifeedants against Leptinotarsa decemlineata Say and moderate against Spodoptera littoralis Boisd and Myzus persicae Sulzer, according to their feeding ecologies. The biological effects of the active samples cannot be accounted by their chemical composition, suggesting additive or synergistic effects. Both the phytotoxic and stimulating effects on Lactuca sativa L., and Lolium perenne L. leaf and/or root growth were observed.Se ha analizado la composición en polifenoles y las actividades antioxidante y bioplaguicida de los residuos sólidos procedentes de la hidrodestilación de poblaciones seleccionadas de romero (Rosmarinus officinalis L.. El objetivo fue evaluar y seleccionar los materiales vegetales más adecuados como fuente de antioxidantes y bioplaguicidas naturales. El contenido total y la composición en polifenoles de las poblaciones de romero dependieron mucho de la localidad de cultivo: las poblaciones de Aranjuez mostraron un mayor contenido en polifenoles y fueron más ricas en

  2. Iron-sulfur clusters as biological sensors: the chemistry of reactions with molecular oxygen and nitric oxide.

    Science.gov (United States)

    Crack, Jason C; Green, Jeffrey; Thomson, Andrew J; Le Brun, Nick E

    2014-10-21

    Iron-sulfur cluster proteins exhibit a range of physicochemical properties that underpin their functional diversity in biology, which includes roles in electron transfer, catalysis, and gene regulation. Transcriptional regulators that utilize iron-sulfur clusters are a growing group that exploit the redox and coordination properties of the clusters to act as sensors of environmental conditions including O2, oxidative and nitrosative stress, and metabolic nutritional status. To understand the mechanism by which a cluster detects such analytes and then generates modulation of DNA-binding affinity, we have undertaken a combined strategy of in vivo and in vitro studies of a range of regulators. In vitro studies of iron-sulfur cluster proteins are particularly challenging because of the inherent reactivity and fragility of the cluster, often necessitating strict anaerobic conditions for all manipulations. Nevertheless, and as discussed in this Account, significant progress has been made over the past decade in studies of O2-sensing by the fumarate and nitrate reduction (FNR) regulator and, more recently, nitric oxide (NO)-sensing by WhiB-like (Wbl) and FNR proteins. Escherichia coli FNR binds a [4Fe-4S] cluster under anaerobic conditions leading to a DNA-binding dimeric form. Exposure to O2 converts the cluster to a [2Fe-2S] form, leading to protein monomerization and hence loss of DNA binding ability. Spectroscopic and kinetic studies have shown that the conversion proceeds via at least two steps and involves a [3Fe-4S](1+) intermediate. The second step involves the release of two bridging sulfide ions from the cluster that, unusually, are not released into solution but rather undergo oxidation to sulfane (S(0)) subsequently forming cysteine persulfides that then coordinate the [2Fe-2S] cluster. Studies of other [4Fe-4S] cluster proteins that undergo oxidative cluster conversion indicate that persulfide formation and coordination may be more common than previously

  3. Introduction to quantum graphs

    CERN Document Server

    Berkolaiko, Gregory

    2012-01-01

    A "quantum graph" is a graph considered as a one-dimensional complex and equipped with a differential operator ("Hamiltonian"). Quantum graphs arise naturally as simplified models in mathematics, physics, chemistry, and engineering when one considers propagation of waves of various nature through a quasi-one-dimensional (e.g., "meso-" or "nano-scale") system that looks like a thin neighborhood of a graph. Works that currently would be classified as discussing quantum graphs have been appearing since at least the 1930s, and since then, quantum graphs techniques have been applied successfully in various areas of mathematical physics, mathematics in general and its applications. One can mention, for instance, dynamical systems theory, control theory, quantum chaos, Anderson localization, microelectronics, photonic crystals, physical chemistry, nano-sciences, superconductivity theory, etc. Quantum graphs present many non-trivial mathematical challenges, which makes them dear to a mathematician's heart. Work on qu...

  4. Alcohol combustion chemistry

    KAUST Repository

    Sarathy, Mani

    2014-10-01

    Alternative transportation fuels, preferably from renewable sources, include alcohols with up to five or even more carbon atoms. They are considered promising because they can be derived from biological matter via established and new processes. In addition, many of their physical-chemical properties are compatible with the requirements of modern engines, which make them attractive either as replacements for fossil fuels or as fuel additives. Indeed, alcohol fuels have been used since the early years of automobile production, particularly in Brazil, where ethanol has a long history of use as an automobile fuel. Recently, increasing attention has been paid to the use of non-petroleum-based fuels made from biological sources, including alcohols (predominantly ethanol), as important liquid biofuels. Today, the ethanol fuel that is offered in the market is mainly made from sugar cane or corn. Its production as a first-generation biofuel, especially in North America, has been associated with publicly discussed drawbacks, such as reduction in the food supply, need for fertilization, extensive water usage, and other ecological concerns. More environmentally friendly processes are being considered to produce alcohols from inedible plants or plant parts on wasteland. While biofuel production and its use (especially ethanol and biodiesel) in internal combustion engines have been the focus of several recent reviews, a dedicated overview and summary of research on alcohol combustion chemistry is still lacking. Besides ethanol, many linear and branched members of the alcohol family, from methanol to hexanols, have been studied, with a particular emphasis on butanols. These fuels and their combustion properties, including their ignition, flame propagation, and extinction characteristics, their pyrolysis and oxidation reactions, and their potential to produce pollutant emissions have been intensively investigated in dedicated experiments on the laboratory and the engine scale

  5. The physical basis of chemistry

    CERN Document Server

    Warren, Warren S

    2000-01-01

    If the text you're using for general chemistry seems to lack sufficient mathematics and physics in its presentation of classical mechanics, molecular structure, and statistics, this complementary science series title may be just what you're looking for. Written for the advanced lower-division undergraduate chemistry course, The Physical Basis of Chemistry, Second Edition, offers students an opportunity to understand and enrich the understanding of physical chemistry with some quantum mechanics, the Boltzmann distribution, and spectroscopy. Posed and answered are questions concerning eve

  6. Temperature-controlled micro-TLC: a versatile green chemistry and fast analytical tool for separation and preliminary screening of steroids fraction from biological and environmental samples.

    Science.gov (United States)

    Zarzycki, Paweł K; Slączka, Magdalena M; Zarzycka, Magdalena B; Bartoszuk, Małgorzata A; Włodarczyk, Elżbieta; Baran, Michał J

    2011-11-01

    whole range of target substances as well as chemo-taxonomic studies and fingerprinting of complex mixtures, which are present in biological or environmental samples. Due to low consumption of eluent (usually 0.3-1mL/run) mainly composed of water-alcohol binary mixtures, this method can be considered as environmentally friendly and green chemistry focused analytical tool, supplementary to analytical protocols involving column chromatography or planar micro-fluidic devices. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Silicon quantum dots: surface matters

    Czech Academy of Sciences Publication Activity Database

    Dohnalová, K.; Gregorkiewicz, T.; Kůsová, Kateřina

    2014-01-01

    Roč. 26, č. 17 (2014), 1-28 ISSN 0953-8984 R&D Projects: GA ČR GPP204/12/P235 Institutional support: RVO:68378271 Keywords : silicon quantum dots * quantum dot * surface chemistry * quantum confinement Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.346, year: 2014

  8. Sample collections from healthy volunteers for biological variation estimates' update: a new project undertaken by the Working Group on Biological Variation established by the European Federation of Clinical Chemistry and Laboratory Medicine.

    Science.gov (United States)

    Carobene, Anna; Strollo, Marta; Jonker, Niels; Barla, Gerhard; Bartlett, William A; Sandberg, Sverre; Sylte, Marit Sverresdotter; Røraas, Thomas; Sølvik, Una Ørvim; Fernandez-Calle, Pilar; Díaz-Garzón, Jorge; Tosato, Francesca; Plebani, Mario; Coşkun, Abdurrahman; Serteser, Mustafa; Unsal, Ibrahim; Ceriotti, Ferruccio

    2016-10-01

    Biological variation (BV) data have many fundamental applications in laboratory medicine. At the 1st Strategic Conference of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) the reliability and limitations of current BV data were discussed. The EFLM Working Group on Biological Variation is working to increase the quality of BV data by developing a European project to establish a biobank of samples from healthy subjects to be used to produce high quality BV data. The project involved six European laboratories (Milan, Italy; Bergen, Norway; Madrid, Spain; Padua, Italy; Istanbul, Turkey; Assen, The Netherlands). Blood samples were collected from 97 volunteers (44 men, aged 20-60 years; 43 women, aged 20-50 years; 10 women, aged 55-69 years). Initial subject inclusion required that participants completed an enrolment questionnaire to verify their health status. The volunteers provided blood specimens once per week for 10 weeks. A short questionnaire was completed and some laboratory tests were performed at each sampling consisting of blood collected under controlled conditions to provide serum, K2EDTA-plasma and citrated-plasma samples. Samples from six out of the 97 enroled subjects were discarded as a consequence of abnormal laboratory measurements. A biobank of 18,000 aliquots was established consisting of 120 aliquots of serum, 40 of EDTA-plasma, and 40 of citrated-plasma from each subject. The samples were stored at -80 °C. A biobank of well-characterised samples collected under controlled conditions has been established delivering a European resource to enable production of contemporary BV data.

  9. Identification of Di(oxymethylene)glycol in the Raman Spectrum of Formaldehyde Aqueous Solutions by ab lnitio Molecular Dynamics Simulations and Quantum Chemistry Calculations

    Czech Academy of Sciences Publication Activity Database

    Delcroix, Pauline; Pagliai, M.; Cardini, G.; Bégué, D.; Hanoune, B.

    2015-01-01

    Roč. 119, č. 38 (2015), s. 9785-9793 ISSN 1089-5639 Institutional support: RVO:61388963 Keywords : hydrogen bond dynamics * chemical equilibria * liquid water Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.883, year: 2015

  10. Quantum mechanics

    CERN Document Server

    Ghosh, P K

    2014-01-01

    Quantum mechanics, designed for advanced undergraduate and graduate students of physics, mathematics and chemistry, provides a concise yet self-contained introduction to the formal framework of quantum mechanics, its application to physical problems and the interpretation of the theory. Starting with a review of some of the necessary mathematics, the basic concepts are carefully developed in the text. After building a general formalism, detailed treatment of the standard material - the harmonic oscillator, the hydrogen atom, angular momentum theory, symmetry transformations, approximation methods, identical particle and many-particle systems, and scattering theory - is presented. The concluding chapter discusses the interpretation of quantum mechanics. Some of the important topics discussed in the book are the rigged Hilbert space, deformation quantization, path integrals, coherent states, geometric phases, decoherene, etc. This book is characterized by clarity and coherence of presentation.

  11. Solvent effects in chemistry

    CERN Document Server

    Buncel, Erwin

    2015-01-01

    This book introduces the concepts, theory and experimental knowledge concerning solvent effects on the rate and equilibrium of chemical reactions of all kinds.  It begins with basic thermodynamics and kinetics, building on this foundation to demonstrate how a more detailed understanding of these effects may be used to aid in determination of reaction mechanisms, and to aid in planning syntheses. Consideration is given to theoretical calculations (quantum chemistry, molecular dynamics, etc.), to statistical methods (chemometrics), and to modern day concerns such as ""green"" chemistry, where ut

  12. Mathematical Chemistry

    OpenAIRE

    Trinajstić, Nenad; Gutman, Ivan

    2002-01-01

    A brief description is given of the historical development of mathematics and chemistry. A path leading to the meeting of these two sciences is described. An attempt is made to define mathematical chemistry, and journals containing the term mathematical chemistry in their titles are noted. In conclusion, the statement is made that although chemistry is an experimental science aimed at preparing new compounds and materials, mathematics is very useful in chemistry, among other things, to produc...

  13. “Biotecnological War” - A Conceptual And Perceptual Assessment Tool For Teaching Biotechnology And Protein Chemistry For Undergraduate Students In Biological Sciences.

    Directory of Open Access Journals (Sweden)

    C. R. C. Cruz et al.

    2017-07-01

    Full Text Available "Biotecnological War" board game, a conceptual and perceptual assessment tool for biotechnology and protein chemistry teaching for undergraduate students in biological sciences and related areas. It is a proposal initially conceived as an alternative complementary tool for biochemistry teaching of proteins and peptides, challenging students, aiming to review concepts transmitted in classroom, stimulating diverse student’s abilities, such as their creativity, competitiveness and resource management. OBJECTIVES. Correlate biochemistry importance of proteins and peptides with the development of new products. MATERIAL AND METHODS. Firstly, theoretical-practical classes were given with seminars to be presented by the groups, including topics that will be addressed in game. Groups of 5 students, with previously viewed themes drawn a goal to be achieved. There are two drawn goals variations: Academic or Commercial. Board is divided into provinces, which must be bought with an initial resource to complete the goal. Before the beginning each group will have 15 minutes to plan their actions. The objective is to develop the entire objective drawn with appropriate methodology, having at least 1 territory in each province. RESULTS. This game proved to be an excellent tool for complementary evaluation of students, which stimulated teamwork and a strong competitive spirit within classroom, which allowed to analyze students' perception regarding the protein subject and team work. On the other hand, for teacher and students participating in compulsory traineeship program this game demonstrated new ways to approach complex subjects in biochemistry using creativity with the development of new activities such as this board game. CONCLUSION: Overall, students had a good impression of “Biotecnological war” game since it helped to secure and administer the protein and peptides biochemical subject in a competitive and team work way.

  14. Interactions between lithology and biology drive the long-term response of stream chemistry to major hurricanes in a tropical landscape

    Science.gov (United States)

    W.H. McDowell; R.L. Brereton; F.N. Scatena; J.B. Shanley; N.V. Brokaw; A.E. Lugo

    2013-01-01

    Humid tropical forests play a dominant role in many global biogeochemical cycles, yet long-term records of tropical stream chemistry and its response to disturbance events such as severe storms and droughts are rare. Here we document the long-term variability in chemistry of two streams in the Luquillo Mountains, Puerto Rico over a period of 27 years. Our two focal...

  15. Ancient chemistry fuels new biology.

    Science.gov (United States)

    Williams, N

    2001-04-03

    An enormous new greenhouse project in southern Britain aims to heighten awareness of the human relationship with plants and the growing potential of plant-derived compounds to find new uses, reports Nigel Williams

  16. Wilson and Gisvold's textbook of organic medicinal and pharmaceutical chemistry

    National Research Council Canada - National Science Library

    Wilson, Charles Owens; Beale, John Marlowe; Block, John H

    2011-01-01

    ... and chemistry students as well as practicing pharmacists. Fully updated for the Twelfth Edition, the book begins with the fundamental principles of chemistry, biochemistry, and biology that underlie the discipline of medicinal chemistry...

  17. Quorum sensing: a quantum perspective.

    Science.gov (United States)

    Majumdar, Sarangam; Pal, Sukla

    2016-09-01

    Quorum sensing is the efficient mode of communication in the bacterial world. After a lot of advancements in the classical theory of quorum sensing few basic questions of quorum sensing still remain unanswered. The sufficient progresses in quantum biology demands to explain these questions from the quantum perspective as non trivial quantum effects already have manifested in various biological processes like photosynthesis, magneto-reception etc. Therefore, it's the time to review the bacterial communications from the quantum view point. In this article we carefully accumulate the latest results and arguments to strengthen quantum biology through the addition of quorum sensing mechanism in the light of quantum mechanics.

  18. Elementary and brief introduction of hadronic chemistry

    Science.gov (United States)

    Tangde, Vijay M.

    2013-10-01

    The discipline, today known as Quantum Chemistry for atomic and subatomic level interactions has no doubt made a significant historical contributions to the society. Despite of its significant achievements, quantum chemistry is also known for its widespread denial of insufficiencies it inherits. An Italian-American Scientist Professor Ruggero Maria Santilli during his more than five decades of dedicated and sustained research has denounced the fact that quantum chemistry is mostly based on mere nomenclatures without any quantitative scientific contents. Professor R M Santilli first formulated the iso-, geno- and hyper-mathematics [1-4] that helped in understanding numerous diversified problems and removing inadequacies in most of the established and celebrated theories of 20th century physics and chemistry. This involves the isotopic, genotopic, etc. lifting of Lie algebra that generated Lie admissible mathematics to properly describe irreversible processes. The studies on Hadronic Mechanics in general and chemistry in particular based on Santilli's mathematics[3-5] for the first time has removed the very fundamental limitations of quantum chemistry [2, 6-8]. In the present discussion, we have briefly reviewed the conceptual foundations of Hadronic Chemistry that imparts the completeness to the Quantum Chemistry via an addition of effects at distances of the order of 1 fm (only) which are assumed to be Non-linear, Non-local, Non-potential, Non-hamiltonian and thus Non-unitary and its application in development of a new chemical species called Magnecules.

  19. Quantum optical rotatory dispersion

    Science.gov (United States)

    Tischler, Nora; Krenn, Mario; Fickler, Robert; Vidal, Xavier; Zeilinger, Anton; Molina-Terriza, Gabriel

    2016-01-01

    The phenomenon of molecular optical activity manifests itself as the rotation of the plane of linear polarization when light passes through chiral media. Measurements of optical activity and its wavelength dependence, that is, optical rotatory dispersion, can reveal information about intricate properties of molecules, such as the three-dimensional arrangement of atoms comprising a molecule. Given a limited probe power, quantum metrology offers the possibility of outperforming classical measurements. This has particular appeal when samples may be damaged by high power, which is a potential concern for chiroptical studies. We present the first experiment in which multiwavelength polarization-entangled photon pairs are used to measure the optical activity and optical rotatory dispersion exhibited by a solution of chiral molecules. Our work paves the way for quantum-enhanced measurements of chirality, with potential applications in chemistry, biology, materials science, and the pharmaceutical industry. The scheme that we use for probing wavelength dependence not only allows one to surpass the information extracted per photon in a classical measurement but also can be used for more general differential measurements. PMID:27713928

  20. Physics, radiology, and chemistry. 7. rev. ed.

    International Nuclear Information System (INIS)

    Linde, O.K.; Knigge, H.J.

    1986-01-01

    This book is an introduction to physics and chemistry especially for medical personnel. After a general introduction, measurement methods, mechanics including mechanics of solid bodies, fluids and gases, heat, optics, acoustics, electricity, radiations including their biological effects, general chemistry, inorganic and organic chemistry are treated. Every chapter contains exercises mostly in connection with medical and biological effects. Furthermore, connections with biology and medicine are considered. The chapters on physiological chemistry, computer and information theory, chemistry and ecology, and metabolism have been rewritten. (orig./HP) [de