Sample records for adamantyl-substituted retinoid-derived molecule

  1. Synthesis of Poly(aryl ether ketone) Copolymers Containing Adamantyl-substituted Naphthalene Rings

    Institute of Scientific and Technical Information of China (English)

    ZHU Xiao-liang; ZHANG Shu-ling; REN Dian-fu; GUAN Shao-wei; WANG Gui-bin; JIANG Zhen-hua


    @@ 1 Introduction High performance polymers have received considerable attention over the past decade owing to their increased demands as replacements for metals or ceramics in automotive,aerospace,and microelectronic industries.Poly(aryl ether ketone)s(PAEKs) are a class of important high-performance aromatic polymers with excellent mechanical properties,good solvent resistance,size-accuracy,electrical characteristics,and superior thermal stability[1-3].

  2. Molecule nanoweaver (United States)

    Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela


    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  3. Enumerating molecules.

    Energy Technology Data Exchange (ETDEWEB)

    Visco, Donald Patrick, Jr. (, . Tennessee Technological University, Cookeville, TN); Faulon, Jean-Loup Michel; Roe, Diana C.


    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  4. Hadron Molecules

    CERN Document Server

    Gutsche, Thomas; Faessler, Amand; Lee, Ian Woo; Lyubovitskij, Valery E


    We discuss a possible interpretation of the open charm mesons $D_{s0}^*(2317)$, $D_{s1}(2460)$ and the hidden charm mesons X(3872), Y(3940) and Y(4140) as hadron molecules. Using a phenomenological Lagrangian approach we review the strong and radiative decays of the $D_{s0}^* (2317)$ and $D_{s1}(2460)$ states. The X(3872) is assumed to consist dominantly of molecular hadronic components with an additional small admixture of a charmonium configuration. Determing the radiative ($\\gamma J/\\psi$ and $\\gamma \\psi(2s)$) and strong ($J/\\psi 2\\pi $ and $ J/\\psi 3\\pi$) decay modes we show that present experimental observation is consistent with the molecular structure assumption of the X(3872). Finally we give evidence for molecular interpretations of the Y(3940) and Y(4140) related to the observed strong decay modes $J/\\psi + \\omega$ or $J/\\psi + \\phi$, respectively.

  5. Effect of Am-80, A Novel Retinoid Derivative, On Contact Hypersensitivity Caused by Repeated Applications of Hapten in Mice

    Directory of Open Access Journals (Sweden)

    Satoru Niwa


    Full Text Available Some retinoids show an anti-inflammatory action through regulation of transcription of various genes. In the present study, the inhibitory effect of 4-((5,6,7,8- tetrahydro-5,5,8,8-tetramethyl-2-naphthyl carbamoyl benzoic acid (Am-80, a synthetic retinoid, on mouse contact hypersensitivity provoked by repeated applications of 2,4-dinitrofluorobenzene (DNFB to the ear was investigated. Five-fold applications of DNFB on ears once per week elicited severe contact dermatitis with marked infiltration of inflammatory cells and elevation of anti-dinitrophenyl (DNP-IgE antibody in the serum. The Am-80 significantly inhibited ear swelling in a dose-dependent manner. In the histopathologic study, infiltration of inflammatory cells was clearly decreased by Am-80. However, Am-80 did not affect the production of DNP-specific IgE antibody both at the transcriptional and post-transcriptional levels. The effects of Am-80 on the transcriptional level of cytokines, interferon (IFN-γ, interleukin (IL-1 and IL-4 in cervical lymph nodes were investigated. Marked elevation of mRNA for all cytokines was observed and Am-80 potently inhibited the expression of IFN-γ mRNA, but not IL-1 and IL-4 mRNA. These findings indicated that Am-80 may inhibit the contact dermatitis at the post-sensitization phase by inhibiting IFN-γ production at the transcriptional level in mice.

  6. Formation of Ultracold Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cote, Robin [Univ. of Connecticut, Storrs, CT (United States)


    Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

  7. Trapping molecules on chips

    CERN Document Server

    Santambrogio, Gabriele


    In the last years, it was demonstrated that neutral molecules can be loaded on a microchip directly from a supersonic beam. The molecules are confined in microscopic traps that can be moved smoothly over the surface of the chip. Once the molecules are trapped, they can be decelerated to a standstill, for instance, or pumped into selected quantum states by laser light or microwaves. Molecules are detected on the chip by time-resolved spatial imaging, which allows for the study of the distribution in the phase space of the molecular ensemble.

  8. [Endothelial cell adhesion molecules]. (United States)

    Ivanov, A N; Norkin, I A; Puchin'ian, D M; Shirokov, V Iu; Zhdanova, O Iu


    The review presents current data concerning the functional role of endothelial cell adhesion molecules belonging to different structural families: integrins, selectins, cadherins, and the immunoglobulin super-family. In this manuscript the regulatory mechanisms and factors of adhesion molecules expression and distribution on the surface of endothelial cells are discussed. The data presented reveal the importance of adhesion molecules in the regulation of structural and functional state of endothelial cells in normal conditions and in pathology. Particular attention is paid to the importance of these molecules in the processes of physiological and pathological angiogenesis, regulation of permeability of the endothelial barrier and cell transmigration.


    NARCIS (Netherlands)


    In this paper, some results obtained on the formation of isolated molecules of composition SnOx in silver and SnFx in copper-are reviewed. Hyperfine interaction and ion beam interaction techniques were used for the identification of these molecules.

  10. Algebraic theory of molecules

    CERN Document Server

    Iachello, F


    1. The Wave Mechanics of Diatomic Molecules. 2. Summary of Elements of Algebraic Theory. 3. Mechanics of Molecules. 4. Three-Body Algebraic Theory. 5. Four-Body Algebraic Theory. 6. Classical Limit and Coordinate Representation. 8. Prologue to the Future. Appendices. Properties of Lie Algebras; Coupling of Algebras; Hamiltonian Parameters

  11. Molecules in galaxies

    CERN Document Server

    Omont, Alain


    The main achievements, current developments and prospects of molecular studies in external galaxies are reviewed. They are put in the context of the results of several decades of studies of molecules in local interstellar medium, their chemistry and their importance for star formation. CO observations have revealed the gross structure of molecular gas in galaxies. Together with other molecules, they are among the best tracers of star formation at galactic scales. Our knowledge about molecular abundances in various local galactic environments is progressing. They trace physical conditions and metallicity, and they are closely related to dust processes and large aromatic molecules. Major recent developments include mega-masers, and molecules in Active Galactic Nuclei; millimetre emission of molecules at very high redshift; and infrared H2 emission as tracer of warm molecular gas, shocks and photodissociation regions. The advent of sensitive giant interferometers from the centimetre to sub-millimetre range, espe...

  12. Dynamics of Activated Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Mullin, Amy S. [Univ. of Maryland, College Park, MD (United States)


    Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

  13. Electron correlation in molecules

    CERN Document Server

    Wilson, S


    Electron correlation effects are of vital significance to the calculation of potential energy curves and surfaces, the study of molecular excitation processes, and in the theory of electron-molecule scattering. This text describes methods for addressing one of theoretical chemistry's central problems, the study of electron correlation effects in molecules.Although the energy associated with electron correlation is a small fraction of the total energy of an atom or molecule, it is of the same order of magnitude as most energies of chemical interest. If the solution of quantum mechanical equatio

  14. Heavy Exotic Molecules

    CERN Document Server

    Liu, Yizhuang


    We briefly review the formation of pion-mediated heavy-light exotic molecules with both charm and bottom, under the general strictures of chiral and heavy quark symmetries. The charm isosinglet exotic molecules with $J^{PC}=1^{++}$ binds, which we identify as the reported neutral $X(3872)$. The bottom isotriplet exotic with $J^{PC}=1^{+-}$ binds, and is identified as a mixed state of the reported charged exotics $Z^+_b(10610)$ and $Z^+_b(10650)$. The bound bottom isosinglet molecule with $J^{PC}=1^{++}$ is a possible neutral $X_b(10532)$ to be observed.

  15. Electron-molecule collisions

    CERN Document Server

    Takayanagi, Kazuo


    Scattering phenomena play an important role in modern physics. Many significant discoveries have been made through collision experiments. Amongst diverse kinds of collision systems, this book sheds light on the collision of an electron with a molecule. The electron-molecule collision provides a basic scattering problem. It is scattering by a nonspherical, multicentered composite particle with its centers having degrees of freedom of motion. The molecule can even disintegrate, Le., dissociate or ionize into fragments, some or all of which may also be molecules. Although it is a difficult problem, the recent theoretical, experimental, and computational progress has been so significant as to warrant publication of a book that specializes in this field. The progress owes partly to technical develop­ ments in measurements and computations. No less important has been the great and continuing stimulus from such fields of application as astrophysics, the physics of the earth's upper atmosphere, laser physics, radiat...

  16. Single molecules and nanotechnology

    CERN Document Server

    Vogel, Horst


    This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

  17. Adamantyl Retinoid-Related Molecules Induce Apoptosis in Pancreatic Cancer Cells by Inhibiting IGF-1R and Wnt/β-Catenin Pathways

    Directory of Open Access Journals (Sweden)

    Lulu Farhana


    Full Text Available Pancreatic carcinoma has a dismal prognosis as it often presents as locally advanced or metastatic. We have found that exposure to adamantyl-substituted retinoid-related (ARR compounds 3-Cl-AHPC and AHP3 resulted in growth inhibition and apoptosis induction in PANC-1, Capan-2, and MiaPaCa-2 pancreatic cancer cell lines. In addition, AHP3 and 3-Cl-AHPC inhibited growth and induced apoptosis in spheres derived from the CD44+/CD24+ (CD133+/EpCAM+ stem-like cell population isolated from the pancreatic cancer cell lines. 3-Cl-AHPC-induced apoptosis was preceded by decreasing expression of IGF-1R, cyclin D1, β-catenin, and activated Notch-1 in the pancreatic cancer cell lines. Decreased IGF-1R expression inhibited PANC-1 proliferation, enhanced 3-Cl-AHPC-mediated apoptosis, and significantly decreased sphere formation. 3-Cl-AHPC inhibited the Wnt/β-catenin pathway as indicated by decreased β-catenin nuclear localization and inhibited Wnt/β-catenin activation of transcription factor TCF/LEF. Knockdown of β-catenin using sh-RNA also induced apoptosis and inhibited growth in pancreatic cancer cells. Thus, 3-Cl-AHPC and AHP3 induce apoptosis in pancreatic cancer cells and cancer stem-like cells and may serve as an important potential therapeutic agent in the treatment of pancreatic cancer.

  18. Molecules in supernova ejecta

    CERN Document Server

    Cherchneff, Isabelle


    The first molecules detected at infrared wavelengths in the ejecta of a Type II supernova, namely SN1987A, consisted of CO and SiO. Since then, confirmation of the formation of these two species in several other supernovae a few hundred days after explosion has been obtained. However, supernova environments appear to hamper the synthesis of large, complex species due to the lack of microscopically-mixed hydrogen deep in supernova cores. Because these environments also form carbon and silicate dust, it is of importance to understand the role played by molecules in the depletion of elements and how chemical species get incorporated into dust grains. In the present paper, we review our current knowledge of the molecular component of supernova ejecta, and present new trends and results on the synthesis of molecules in these harsh, explosive events.


    Energy Technology Data Exchange (ETDEWEB)

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf [Max-Planck Institut fuer Radioastronomie, Auf dem Huegel 69, 53121 Bonn (Germany); Zapata, Luis A.; Rodriguez, Luis F. [Centro de Radioastronomia y Astrofisica, Universidad Nacional Autonoma de Mexico, Apartado Postal 3-72, 58090 Morelia, Michoacan (Mexico)


    We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  20. Molecules in \\eta\\ Carinae

    CERN Document Server

    Loinard, Laurent; Guesten, Rolf; Zapata, Luis A; Rodriguez, Luis F


    We report the detection toward \\eta\\ Carinae of six new molecules, CO, CN, HCO+, HCN, HNC, and N2H+, and of two of their less abundant isotopic counterparts, 13CO and H13CN. The line profiles are moderately broad (about 100 km /s) indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO+ do not appear to be under-abundant in \\eta\\ Carinae. On the other hand, molecules containing nitrogen or the 13C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of eta Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  1. Gated container molecules

    Institute of Scientific and Technical Information of China (English)

    LIU Fang; WANG Hao; HOUK K. N.


    Donald J.Cram,the great UCLA chemist,received the Nobel Prize for his discoveries about host-guest complexes [1].Both theoretical and experimental studies have been conducted about the nature and strength of interactions between the host and guest molecules.The concepts of constrictive binding (the activation energy of the binding process) and intrinsic binding (the free energy difference between the complex and the free host and guest molecules) were introduced to characterize different binding properties (Figure 1)[2].

  2. Enzyme molecules as nanomotors. (United States)

    Sengupta, Samudra; Dey, Krishna K; Muddana, Hari S; Tabouillot, Tristan; Ibele, Michael E; Butler, Peter J; Sen, Ayusman


    Using fluorescence correlation spectroscopy, we show that the diffusive movements of catalase enzyme molecules increase in the presence of the substrate, hydrogen peroxide, in a concentration-dependent manner. Employing a microfluidic device to generate a substrate concentration gradient, we show that both catalase and urease enzyme molecules spread toward areas of higher substrate concentration, a form of chemotaxis at the molecular scale. Using glucose oxidase and glucose to generate a hydrogen peroxide gradient, we induce the migration of catalase toward glucose oxidase, thereby showing that chemically interconnected enzymes can be drawn together.

  3. Disentangling DNA molecules (United States)

    Vologodskii, Alexander


    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  4. Properties of entanglement molecules

    Energy Technology Data Exchange (ETDEWEB)

    Huang Yanxia [Department of Physics, Hubei Normal University, Huangshi 435002 (China); Zhan Mingsheng [State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China)


    We propose a scheme to prepare a certain kind of N-atom entangled state that allows us to construct some possible types of entanglement molecules via cavity QED. The entanglement properties of entanglement molecules vertical bar {psi}{sub N}){sub {alpha}} are studied with respect to bipartite entanglement that is robust against the disposal of particles and are compared with entanglement molecules {rho}{sub I} introduced in Dur (2001 Phys. Rev. A 63 020303). We also give the maximal amount of entanglement achievable for two particular situations in two possible configurations. Meanwhile, we investigate the entanglement properties of entanglement molecules vertical bar {psi}{sub N}){sub {alpha}} in terms of local measurement using the maximum connectedness and persistency and compare them with other kinds of N-atom entangled states such as |GHZ), vertical bar W{sub N}) and vertical bar {phi}{sub N}). We show that the maximal value N - 1 of the persistency of the state vertical bar {psi}{sub N}){sub {alpha}} corresponds to the case that all atoms are pairwise entangled. If any pair of atoms {rho}{sub ij} is disentangled, the entanglement of the state vertical bar {psi}{sub N}){sub {alpha}} is very easy to destroy by a single local measurement.

  5. Properties of entanglement molecules (United States)

    Huang, Yan-Xia; Zhan, Ming-Sheng


    We propose a scheme to prepare a certain kind of N-atom entangled state that allows us to construct some possible types of entanglement molecules via cavity QED. The entanglement properties of entanglement molecules |psgrNrangagr are studied with respect to bipartite entanglement that is robust against the disposal of particles and are compared with entanglement molecules rgrI introduced in Dur (2001 Phys. Rev. A 63 020303). We also give the maximal amount of entanglement achievable for two particular situations in two possible configurations. Meanwhile, we investigate the entanglement properties of entanglement molecules |psgrNrangagr in terms of local measurement using the maximum connectedness and persistency and compare them with other kinds of N-atom entangled states such as |GHZrang, |WNrang and |phgrNrang. We show that the maximal value N - 1 of the persistency of the state |psgrNrangagr corresponds to the case that all atoms are pairwise entangled. If any pair of atoms rgrij is disentangled, the entanglement of the state |psgrNrangagr is very easy to destroy by a single local measurement.

  6. Atoms, Molecules, and Compounds

    CERN Document Server

    Manning, Phillip


    Explores the atoms that govern chemical processes. This book shows how the interactions between simple substances such as salt and water are crucial to life on Earth and how those interactions are predestined by the atoms that make up the molecules.

  7. Disentangling DNA molecules. (United States)

    Vologodskii, Alexander


    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  8. Diversity in Biological Molecules (United States)

    Newbury, H. John


    One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…

  9. Synthesis beyond the molecule

    NARCIS (Netherlands)

    Reinhoudt, D.N.; Crego-Calama, M.


    Weak, noncovalent interactions between molecules control many biological functions. In chemistry, noncovalent interactions are now exploited for the synthesis in solution of large supramolecular aggregates. The aim of these syntheses is not only the creation of a particular structure, but also the i

  10. Bacterial invasion reconstructed molecule by molecule

    Energy Technology Data Exchange (ETDEWEB)

    Werner, James H [Los Alamos National Laboratory


    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the

  11. Molecules in Magnetic Fields (United States)

    Berdyugina, Svetlana


    Molecules probe cool matter in the Universe and various astrophysical objects. Their ability to sense magnetic fields provides new insights into magnetic properties of these objects. During the past fifteen years we have carried out a theoretical study of molecular magnetic effects such as the Zeeman, Paschen-Back and Hanle effects and their applications for inferring magnetic structures and spatial inhomogeneities on the Sun, cool stars, brown dwarfs, and exoplanets from molecular spectro-polarimetry (e.g., Berdyugina 2011). Here, we present an overview of this study and compare our theoretical predictions with recent laboratory measurements of magnetic properties of some molecules. We present also a new web-based tool to compute molecular magnetic effects and polarized spectra which is supported by the ERC Advanced Grant HotMol.

  12. Atoms, molecules & elements

    CERN Document Server

    Graybill, George


    Young scientists will be thrilled to explore the invisible world of atoms, molecules and elements. Our resource provides ready-to-use information and activities for remedial students using simplified language and vocabulary. Students will label each part of the atom, learn what compounds are, and explore the patterns in the periodic table of elements to find calcium (Ca), chlorine (Cl), and helium (He) through hands-on activities.

  13. Model molecules mimicking asphaltenes. (United States)

    Sjöblom, Johan; Simon, Sébastien; Xu, Zhenghe


    Asphalthenes are typically defined as the fraction of petroleum insoluble in n-alkanes (typically heptane, but also hexane or pentane) but soluble in toluene. This fraction causes problems of emulsion formation and deposition/precipitation during crude oil production, processing and transport. From the definition it follows that asphaltenes are not a homogeneous fraction but is composed of molecules polydisperse in molecular weight, structure and functionalities. Their complexity makes the understanding of their properties difficult. Proper model molecules with well-defined structures which can resemble the properties of real asphaltenes can help to improve this understanding. Over the last ten years different research groups have proposed different asphaltene model molecules and studied them to determine how well they can mimic the properties of asphaltenes and determine the mechanisms behind the properties of asphaltenes. This article reviews the properties of the different classes of model compounds proposed and present their properties by comparison with fractionated asphaltenes. After presenting the interest of developing model asphaltenes, the composition and properties of asphaltenes are presented, followed by the presentation of approaches and accomplishments of different schools working on asphaltene model compounds. The presentation of bulk and interfacial properties of perylene-based model asphaltene compounds developed by Sjöblom et al. is the subject of the next part. Finally the emulsion-stabilization properties of fractionated asphaltenes and model asphaltene compounds is presented and discussed.

  14. Photonic Molecule Lasers Revisited (United States)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.


    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  15. Hydrogen molecules in semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Weber, Joerg [Technische Universitaet Dresden, 01062 Dresden (Germany)], E-mail:; Hiller, Martin; Lavrov, Edward V. [Technische Universitaet Dresden, 01062 Dresden (Germany)


    Molecular hydrogen, the simplest of all molecules, allows a direct insight into the fundamental properties of quantum mechanics. In the case of H{sub 2}, the Pauli principle leads to two different species, para-H{sub 2} and ortho-H{sub 2}. A conversion between these species is prohibited. Vibrational mode spectra reflect the fundamental properties and allow an unambiguous identification of the H{sub 2} molecules. Today, we have experimental evidence for the trapping of hydrogen molecules in the semiconductors Si, Ge and GaAs at the interstitial sites, within hydrogen-induced platelets, in voids and at impurities (interstitial oxygen in Si). Interstitial H{sub 2} is a nearly free rotor with a surprisingly simple behavior. We review on interstitial H{sub 2} in semiconductors and report on the unexpected preferential disappearance of the para-H{sub 2} or ortho-D{sub 2} species. The origin of the detected ortho-para conversion will be discussed.

  16. Molecules in crystals (United States)

    Spackman, Mark A.


    Hirshfeld surface analysis has developed from the serendipitous discovery of a novel partitioning of the crystal electron density into discrete molecular fragments, to a suite of computational tools used widely for the identification, analysis and discussion of intermolecular interactions in molecular crystals. The relationship between the Hirshfeld surface and very early ideas on the internal structure of crystals is outlined, and applications of Hirshfeld surface analysis are presented for three molecules of historical importance in the development of modern x-ray crystallography: hexamethylbenzene, hexamethylenetetramine and diketopiperazine.

  17. Molecules Best Paper Award 2013. (United States)

    McPhee, Derek J


    Molecules has started to institute a "Best Paper" award to recognize the most outstanding papers in the area of natural products, medicinal chemistry and molecular diversity published in Molecules. We are pleased to announce the second "Molecules Best Paper Award" for 2013.

  18. Passing Current through Touching Molecules

    DEFF Research Database (Denmark)

    Schull, G.; Frederiksen, Thomas; Brandbyge, Mads


    The charge flow from a single C-60 molecule to another one has been probed. The conformation and electronic states of both molecules on the contacting electrodes have been characterized using a cryogenic scanning tunneling microscope. While the contact conductance of a single molecule between two...

  19. Lanthanide single molecule magnets

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Jinkui; Zhang, Peng [Chinese Academy of Sciences, Changchun (China). Changchun Inst. of Applied Chemistry


    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures - an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and explore new directions.

  20. Forces in molecules. (United States)

    Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W


    Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another?

  1. Lanthanide single molecule magnets

    CERN Document Server

    Tang, Jinkui


    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs, and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures – an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and...

  2. Astrochemistry and Interstellar Molecules (United States)

    Minh, Y. C.


    Astrochemistry provides powerful tools to understand various cosmic phenomena, including those in our solar system to the large-scale structure of the universe. In addition, the chemical property of an astronomical body is a crucial factor which governs the evolution of the system. Recent progress in astrophysical theories, computational modelings, and observational techniques requires a detailed understanding of the interactions between the constituents of an astronomical system, which are atoms and molecules within the system. Especially the far-infrared/sub-millimeter wave range, which is called as the last frontier in astronomical observations, contains numerous molecular lines, which may provide a huge amount of new information. However, we need an astrochemical understanding to use this information fully. Although this review is very limited, I would like to stress the importance of astrochemical approach in this overview for the field, which is getting much more attention than ever before.

  3. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same (United States)

    Croteau, Rodney Bruce; Burke, Charles Cullen


    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  4. Molecule-based magnets

    Indian Academy of Sciences (India)

    J V Yakhmi


    The conventional magnetic materials used in current technology, such as, Fe, Fe2O3, Cr2O3, SmCo5, Nd2Fe14B etc are all atom-based, and their preparation/processing require high temperature routes. Employing self-assembly methods, it is possible to engineer a bulk molecular material with long-range magnetic order, mainly because one can play with the weak intermolecular interactions. Since the first successful synthesis of molecular magnets in 1986, a large variety of them have been synthesized, which can be categorized on the basis of the chemical nature of the magnetic units involved: organic-, metal-based systems, heterobimetallic assemblies, or mixed organic–inorganic systems. The design of molecule-based magnets has also been extended to the design of poly-functional molecular magnets, such as those exhibiting second-order optical nonlinearity, liquid crystallinity, or chirality simultaneously with long-range magnetic order. Solubility, low density and biocompatibility are attractive features of molecular magnets. Being weakly coloured, unlike their opaque classical magnet ‘cousins’ listed above, possibilities of photomagnetic switching exist. Persistent efforts also continue to design the ever-elusive polymer magnets towards applications in industry. While providing a brief overview of the field of molecular magnetism, this article highlights some recent developments in it, with emphasis on a few studies from the author’s own lab.

  5. Strongly interacting ultracold polar molecules

    CERN Document Server

    Gadway, Bryce


    This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole-dipole interactions. Ultracold samples of dipolar molecules with long-range interactions offer a unique platform for quantum simulations and the study of correlated many-body physics. We provide an introduction to the physics of dipolar quantum gases, both electric and magnetic, and summarize the multipronged efforts to bring dipolar molecules into the quantum regime. We discuss in detail the recent experimental progress in realizing and studying strongly interacting systems of polar molecules trapped in optical lattices, with particular emphasis on the study of interacting spin systems and non-equilibrium quantum magnetism. Finally, we conclude with a brief discussion of the future prospects for studies of strongly interacting dipolar molecules.

  6. STM investigation of surfactant molecules

    Institute of Scientific and Technical Information of China (English)


    Adsorption and self-organization of sodium alkyl sulfonates (STS and SHS) have been studied on HOPG by using the in situ scanning tunneling microscopy (STM). Both SHS and STS molecules adsorb on the HOPG surface and form long-range well-ordered monolayers. The neighboring molecules in different rows form a "head to head" configuration. In the high-resolution images of STS and SHS molecules, one end of the molecules shows bright spots which are attributed to the SO3- groups.

  7. Theoretical Investigations Regarding Single Molecules

    DEFF Research Database (Denmark)

    Pedersen, Kim Georg Lind

    Neoclassical Valence Bond Theory, Quantum Transport, Quantum Interference, Kondo Effect, and Electron Pumping. Trap a single organic molecule between two electrodes and apply a bias voltage across this "molecular junction". When electrons pass through the molecule, the different electron paths can...

  8. Micro-Kelvin cold molecules.

    Energy Technology Data Exchange (ETDEWEB)

    Strecker, Kevin E.; Chandler, David W.


    We have developed a novel experimental technique for direct production of cold molecules using a combination of techniques from atomic optical and molecular physics and physical chemistry. The ability to produce samples of cold molecules has application in a broad spectrum of technical fields high-resolution spectroscopy, remote sensing, quantum computing, materials simulation, and understanding fundamental chemical dynamics. Researchers around the world are currently exploring many techniques for producing samples of cold molecules, but to-date these attempts have offered only limited success achieving milli-Kelvin temperatures with low densities. This Laboratory Directed Research and Development project is to develops a new experimental technique for producing micro-Kelvin temperature molecules via collisions with laser cooled samples of trapped atoms. The technique relies on near mass degenerate collisions between the molecule of interest and a laser cooled (micro-Kelvin) atom. A subset of collisions will transfer all (nearly all) of the kinetic energy from the 'hot' molecule, cooling the molecule at the expense of heating the atom. Further collisions with the remaining laser cooled atoms will thermally equilibrate the molecules to the micro-Kelvin temperature of the laser-cooled atoms.

  9. Enzyme Molecules in Solitary Confinement

    Directory of Open Access Journals (Sweden)

    Raphaela B. Liebherr


    Full Text Available Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

  10. Enzyme molecules in solitary confinement. (United States)

    Liebherr, Raphaela B; Gorris, Hans H


    Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

  11. Single Molecule Electronics and Devices

    Directory of Open Access Journals (Sweden)

    Makusu Tsutsui


    Full Text Available The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule.

  12. When water molecules meet air


    Hsie, Cho-Shuen; Campen, R. Kramer; Verde, Ana Vila; Bolhuis, Peter; Nienhuys, Han-Kwang; Bonn, Mischa


    About 70% of our planet is covered in water. Most of that water exists as water in the bulk – the neighbors of water molecules are other water molecules – and only a small fraction of molecules are at the air-water interface. Despite the small relative abundance of interfacial water, it is of the utmost importance: it governs the chemistry involving the surface of oceans and seawater aerosols, or the small water droplets forming clouds. Reactions at the air-water interface are directly releva...

  13. Special Issue: Single Molecule Techniques

    Directory of Open Access Journals (Sweden)

    Hans H. Gorris


    Full Text Available Technological advances in the detection and manipulation of single molecules have enabled new insights into the function, structure and interactions of biomolecules. This Special Issue was launched to account for the rapid progress in the field of “Single Molecule Techniques”. Four original research articles and seven review articles provide an introduction, as well as an in-depth discussion, of technical developments that are indispensable for the characterization of individual biomolecules. Fluorescence microscopy takes center stage in this Special Issue because it is one of the most sensitive and flexible techniques, which has been adapted in many variations to the specific demands of single molecule analysis. Two additional articles are dedicated to single molecule detection based on atomic force microscopy.

  14. Absorption characteristics of bacteriorhodopsin molecules

    Indian Academy of Sciences (India)

    H K T Kumar; K Appaji Gowda


    The bacteriorhodopsin molecule absorbs light and undergoes a series of structural transformation following a well-defined photocycle. The complex photocycle is transformed to an equivalent level diagram by considering the lifetime of the intermediate states. Assuming that only and states are appreciably populated at any instant of time, the level diagram is further simplified to two-level system. Based on the rate equations for two-level system, an analytic expression for the absorption coefficient of bacteriorhodopsin molecule is derived. It is applied to study the behaviour of absorption coefficient of bacteriorhodopsin film in the visible wavelength region of 514 nm. The dependence of absorption coefficient of bacteriorhodopsin film on the thickness of the film, total number density of active molecules and initial number density of molecules in -state is presented in the graphical form.

  15. Quantum Transport Through Heterocyclic Molecules (United States)

    Maiti, Santanu K.; Karmakar, S. N.

    We explore electron transport properties in molecular wires made of heterocyclic molecules (pyrrole, furan and thiophene) by using the Green's function technique. Parametric calculations are given based on the tight-binding model to describe the electron transport in these wires. It is observed that the transport properties are significantly influenced by (a) the heteroatoms in the heterocyclic molecules and (b) the molecule-to-electrodes coupling strength. Conductance (g) shows sharp resonance peaks associated with the molecular energy levels in the limit of weak molecular coupling, while they get broadened in the strong molecular coupling limit. These resonances get shifted with the change of the heteroatoms in these heterocyclic molecules. All the essential features of the electron transfer through these molecular wires become much more clearly visible from the study of our current-voltage (I-V) characteristics, and they provide several key information in the study of molecular transport.

  16. Guidance molecules in lung cancer


    Nasarre, Patrick; Potiron, Vincent; Drabkin, Harry; Roche, Joëlle


    Guidance molecules were first described in the nervous system to control axon outgrowth direction. They are also widely expressed outside the nervous system where they control cell migration, tissue development and establishment of the vascular network. In addition, they are involved in cancer development, tumor angiogenesis and metastasis. This review is primarily focused on their functions in lung cancer and their involvement in lung development is also presented. Five guidance molecule fam...

  17. Plasmonic atoms and plasmonic molecules

    CERN Document Server

    Klimov, V V


    The proposed paradigm of plasmonic atoms and plasmonic molecules allows one to describe and predict the strongly localized plasmonic oscillations in the clusters of nanoparticles and some other nanostructures in uniform way. Strongly localized plasmonic molecules near the contacting surfaces might become the fundamental elements (by analogy with Lego bricks) for a construction of fully integrated opto-electronic nanodevices of any complexity and scale of integration.

  18. Plasmonic atoms and plasmonic molecules (United States)

    Klimov, V. V.; Guzatov, D. V.


    The proposed paradigm of plasmonic atoms and plasmonic molecules allows one to describe and predict the strongly localized plasmonic oscillations in the clusters of nanoparticles and some other nanostructures in uniform way. Strongly localized plasmonic molecules near the contacting surfaces might become the fundamental elements (by analogy with Lego bricks) for the construction of fully integrated opto-electronic nanodevices of any complexity and scale of integration.

  19. Optofluidic single molecule flow proteometry (United States)

    Jing, Nan; Chou, Chao-Kai; Hung, Mien-Chie; Kameoka, Jun


    A microfluidic single molecule fluorescence-based detection scheme is developed to identify target protein direct from cell lysate by using polyclonal antibody. Relative concentration of target protein in solution is determined by twodimensional (2D) photon burst analysis. Compared to conventional ensemble measurement assays, this microfluidic single molecule approach combines the advantages of higher sensitivity, fast processing time, small sample consumption and high resolution quantitative analysis.

  20. Raman Optical Activity Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach. (United States)

    Jovan Jose, K V; Raghavachari, Krishnan


    We present an efficient method for the calculation of the Raman optical activity (ROA) spectra for large molecules through the molecules-in-molecules (MIM) fragment-based method. The relevant higher energy derivatives from smaller fragments are used to build the property tensors of the parent molecule to enable the extension of the MIM method for evaluating ROA spectra (MIM-ROA). Two factors were found to be particularly important in yielding accurate results. First, the link-atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, yielding a mathematically rigorous method. Second, the long-range interactions between fragments are taken into account by using a less computationally expensive lower level of theory. The performance of the MIM-ROA model is calibrated on the enantiomeric pairs of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and ROA intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-ROA method is employed to predict the ROA spectra of d-maltose, α-D-cyclodextrin, and cryptophane-A, yielding spectra in excellent agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-ROA model for exploring ROA spectra of large molecules.

  1. The Molecule Cloud - compact visualization of large collections of molecules

    Directory of Open Access Journals (Sweden)

    Ertl Peter


    Full Text Available Abstract Background Analysis and visualization of large collections of molecules is one of the most frequent challenges cheminformatics experts in pharmaceutical industry are facing. Various sophisticated methods are available to perform this task, including clustering, dimensionality reduction or scaffold frequency analysis. In any case, however, viewing and analyzing large tables with molecular structures is necessary. We present a new visualization technique, providing basic information about the composition of molecular data sets at a single glance. Summary A method is presented here allowing visual representation of the most common structural features of chemical databases in a form of a cloud diagram. The frequency of molecules containing particular substructure is indicated by the size of respective structural image. The method is useful to quickly perceive the most prominent structural features present in the data set. This approach was inspired by popular word cloud diagrams that are used to visualize textual information in a compact form. Therefore we call this approach “Molecule Cloud”. The method also supports visualization of additional information, for example biological activity of molecules containing this scaffold or the protein target class typical for particular scaffolds, by color coding. Detailed description of the algorithm is provided, allowing easy implementation of the method by any cheminformatics toolkit. The layout algorithm is available as open source Java code. Conclusions Visualization of large molecular data sets using the Molecule Cloud approach allows scientists to get information about the composition of molecular databases and their most frequent structural features easily. The method may be used in the areas where analysis of large molecular collections is needed, for example processing of high throughput screening results, virtual screening or compound purchasing. Several example visualizations of large

  2. Molecule-by-Molecule Writing Using a Focused Electron Beam

    DEFF Research Database (Denmark)

    Van Dorp, Willem F.; Zhang, Xiaoyan; Feringa, Ben L.;


    on graphene can be followed molecule-by-molecule with FEBID. The results show that mechanisms that are inherent to the process inhibit a further increase in control over the process. Hence, our results present the resolution limit of (electron) optical lithography techniques. The writing of isolated...... atoms also be written with an electron beam? We verify this with focused electron-beam-induced deposition (FEBID), a direct-write technique that has the current record for the smallest feature written by (electron) optical lithography. We show that the deposition of an organometallic precursor...

  3. Electric Deflection of Rotating Molecules

    CERN Document Server

    Gershnabel, E


    We provide a theory of the deflection of polar and non-polar rotating molecules by inhomogeneous static electric field. Rainbow-like features in the angular distribution of the scattered molecules are analyzed in detail. Furthermore, we demonstrate that one may efficiently control the deflection process with the help of short and strong femtosecond laser pulses. In particular the deflection process may by turned-off by a proper excitation, and the angular dispersion of the deflected molecules can be substantially reduced. We study the problem both classically and quantum mechanically, taking into account the effects of strong deflecting field on the molecular rotations. In both treatments we arrive at the same conclusions. The suggested control scheme paves the way for many applications involving molecular focusing, guiding, and trapping by inhomogeneous fields.

  4. Single-molecule magnet engineering

    DEFF Research Database (Denmark)

    Pedersen, Kasper Steen; Bendix, Jesper; Clérac, Rodolphe


    to delicately tune, for instance, the properties of molecules that behave as "magnets", the so-called single-molecule magnets (SMMs). Although many interesting SMMs have been prepared by a more or less serendipitous approach, the assembly of predesigned, isolatable molecular entities into higher nuclearity...... complexes constitutes an elegant and fascinating strategy. This Feature article focuses on the use of building blocks or modules (both terms being used indiscriminately) to direct the structure, and therefore also the magnetic properties, of metal ion complexes exhibiting SMM behaviour. This journal...

  5. Technetium-aspirin molecule complexes

    Energy Technology Data Exchange (ETDEWEB)

    El-Shahawy, A.S.; Mahfouz, R.M.; Aly, A.A.M.; El-Zohry, M. (Assiut Univ. (Egypt))


    Technetium-aspirin and technetium-aspirin-like molecule complexes were prepared. The structure of N-acetylanthranilic acid (NAA) has been decided through CNDO calculations. The ionization potential and electron affinity of the NAA molecule as well as the charge densities were calculated. The electronic absorption spectra of Tc(V)-Asp and Tc(V)-ATS complexes have two characteristic absorption bands at 450 and 600 nm, but the Tc(V)-NAA spectrum has one characteristic band at 450 nm. As a comparative study, Mo-ATS complex was prepared and its electronic absorption spectrum is comparable with the Tc-ATS complex spectrum. (author).

  6. Recoiling DNA Molecule Simulation & Experiment

    CERN Document Server

    Neto, J C; Mesquita, O N; Neto, Jose Coelho; Dickman, Ronald


    Many recent experiments with single DNA molecules are based on force versus extension measurements and involve tethering a microsphere to one of its extremities and the other to a microscope coverglass. In this work we show that similar results can also be obtained by studying the recoil dynamics of the tethered microspheres. Computer simulations of the corresponding Langevin equation indicate which assumptions are required for a reliable analysis of the experimental recoil curves. We have measured the persistence length A of single naked DNA molecules and DNA-Ethidium Bromide complexes using this approach.

  7. Exotic helium molecules; Molecules exotiques d'helium

    Energy Technology Data Exchange (ETDEWEB)

    Portier, M


    We study the photo-association of an ultracold cloud of magnetically trapped helium atoms: pairs of colliding atoms interact with one or two laser fields to produce a purely long range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}P{sub 0}) molecule, or a {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) long range molecule. Light shifts in one photon photo-association spectra are measured and studied as a function of the laser polarization and intensity, and the vibrational state of the excited molecule. They result from the light-induced coupling between the excited molecule, and bound and scattering states of the interaction between two metastable atoms. Their analysis leads to the determination of the scattering length a = (7.2 {+-} 0.6) ruling collisions between spin polarized atoms. The two photon photo-association spectra show evidence of the production of polarized, long-range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) molecules. They are said to be exotic as they are made of two metastable atoms, each one carrying a enough energy to ionize the other. The corresponding lineshapes are calculated and decomposed in sums and products of Breit-Wigner and Fano profiles associated to one and two photon processes. The experimental spectra are fit, and an intrinsic lifetime {tau} = (1.4 {+-} 0.3) {mu}s is deduced. It is checked whether this lifetime could be limited by spin-dipole induced Penning autoionization. This interpretation requires that there is a quasi-bound state close to the dissociation threshold in the singlet interaction potential between metastable helium atoms for the theory to match the experiment. (author)

  8. Small Molecules Target Carcinogenic Proteins (United States)

    Gradinaru, Claudiu


    An ingenious cellular mechanism of effecting protein localization is prenylation: the covalent attachment of a hydrophobic prenyl group to a protein that facilitates protein association with cell membranes. Fluorescence microscopy was used to investigate whether the oncogenic Stat3 protein can undergo artificial prenylation via high-affinity prenylated small-molecule binding agents and thus be rendered inactive by localization at the plasma membrane instead of nucleus. The measurements were performed on a home-built instrument capable of recording simultaneously several optical parameters (lifetime, polarization, color, etc) and with single-molecule sensitivity. A pH-invariant fluorescein derivative with double moiety was designed to bridge a prenyl group and a small peptide that binds Stat3 with high affinity. Confocal fluorescence images show effective localization of the ligand to the membrane of liposomes. Stat3 predominantly localizes at the membrane only in the presence of the prenylated ligand. Single-molecule FRET (fluorescence resonance energy transfer) between donor-labeled prenylated agents and acceptor-labeled, surface tethered Stat3 protein is used to determine the dynamic heterogeneity of the protein-ligand interaction and follow individual binding-unbinding events in real time. The data indicates that molecules can effect protein localization, validating a therapeutic design that influences protein activity via induced localization.

  9. Azobenzene-functionalized cascade molecules

    DEFF Research Database (Denmark)

    Archut, A.; Vogtle, F.; De Cola, L.;


    Cascade molecules bearing up to 32 azobenzene groups in the periphery have been prepared from poly(propylene imine) dendrimers and N-hydroxysuccinimide esters. The dendritic azobenzene species show similar isomerization properties as the corresponding azobenzene monomers. The all-E azobenzene...

  10. Small Molecule PET-Radiopharmaceuticals

    NARCIS (Netherlands)

    Elsinga, Philip H.; Dierckx, Rudi A. J. O.


    This review describes several aspects required for the development of small molecule PET-tracers. Design and selection criteria are important to consider before starting to develop novel PET-tracers. Principles and latest trends in C-11 and F-18-radiochemistry are summarized. In addition an update o

  11. Pair Tunneling through Single Molecules (United States)

    Raikh, Mikhail


    Coupling to molecular vibrations induces a polaronic shift, and can lead to a negative charging energy, U. For negative U, the occupation of the ground state of the molecule is even. In this situation, virtual pair transitions between the molecule and the leads can dominate electron transport. At low temperature, T, these transitions give rise to the charge-Kondo effect [1]. We developed the electron transport theory through the negative-U molecule [2] at relatively high T, when the Kondo correlations are suppressed. Two physical ingredients distinguish our theory from the transport through a superconducting grain coupled to the normal leads [3]: (i) in parallel with sequential pair-tunneling processes, single-particle cotunneling processes take place; (ii) the electron pair on the molecule can be created (or annihilated) by two electrons tunneling in from (or out to) opposite leads. We found that, even within the rate-equation description, the behavior of differential conductance through the negative-U molecule as function of the gate voltage is quite peculiar: the height of the peak near the degeneracy point is independent of temperature, while its width is proportional to T. This is in contrast to the ordinary Coulomb-blockade conductance peak, whose integral strength is T-independent. At finite source-drain bias, V>>T, the width of the conductance peak is ˜V, whereas the conventional Coulomb-blockade peak at finite V splits into two sharp peaks at detunings V/2, and -V/2. Possible applications to the gate-controlled current rectification and switching will be discussed. [1] A. Taraphder and P. Coleman, Phys. Rev. Lett. 66, 2814 (1991). [2] J. Koch, M. E. Raikh, and F. von Oppen, Phys. Rev. Lett. 96, 056803 (2006). [3] F. W. J. Hekking, L. I. Glazman, K. A. Matveev, and R. I. Shekhter, Phys. Rev. Lett. 70, 4138 (1993).

  12. Ballonet String Model of Molecules

    Directory of Open Access Journals (Sweden)

    Gavril NIAC


    Full Text Available Strings of ballonets, modelling rows of orbitals, are assembled to molecule models by crossing them properly. The ballonets at the ends of the strings of 2, 3, 4 or 5 spheres represent bonding orbitals of hydrogen with other elements like C, N or O (the proton being inside the sphere, as well as nonbonding orbitals. The ballonets between them are modelling bonding orbitals among elements other than hydrogen - except the double bond in diborane, the atomic cores laying at the junction of two or more spheres.Advantages of elastic sphere models range from self-adjusting bond angles to resistance when closing cycles like cyclopropane or modeling double bonds.Examples comprise alkanes, including platonic hydrocarbons, ethene, acetylene, and some inorganic molecules.

  13. Optical highlighter molecules in neurobiology. (United States)

    Datta, Sandeep Robert; Patterson, George H


    The development of advanced optical methods has played a key role in propelling progress in neurobiology. Genetically-encoded fluorescent molecules found in nature have enabled labeling of individual neurons to study their physiology and anatomy. Here we discuss the recent use of both native and synthetic optical highlighter proteins to address key problems in neurobiology, including questions relevant to synaptic function, neuroanatomy, and the organization of neural circuits.

  14. Physics of Atoms and Molecules

    CERN Document Server

    Bransden, B H


    New edition of a well-established second and third year textbook for Physics degree students, covering the physical structure and behaviour of atoms and molecules. The aim of this new edition is to provide a unified account of the subject within an undergraduate framework, taking the opportunity to make improvements based on the teaching experience of users of the first edition, and cover important new developments in the subject.

  15. Water molecules orientation in surface layer (United States)

    Klingo, V. V.


    The water molecules orientation has been investigated theoretically in the water surface layer. The surface molecule orientation is determined by the direction of a molecule dipole moment in relation to outward normal to the water surface. Entropy expressions of the superficial molecules in statistical meaning and from thermodynamical approach to a liquid surface tension have been found. The molecules share directed opposite to the outward normal that is hydrogen protons inside is equal 51.6%. 48.4% water molecules are directed along to surface outward normal that is by oxygen inside. A potential jump at the water surface layer amounts about 0.2 volts.

  16. The neural cell adhesion molecule

    DEFF Research Database (Denmark)

    Berezin, V; Bock, E; Poulsen, F M


    During the past year, the understanding of the structure and function of neural cell adhesion has advanced considerably. The three-dimensional structures of several of the individual modules of the neural cell adhesion molecule (NCAM) have been determined, as well as the structure of the complex...... between two identical fragments of the NCAM. Also during the past year, a link between homophilic cell adhesion and several signal transduction pathways has been proposed, connecting the event of cell surface adhesion to cellular responses such as neurite outgrowth. Finally, the stimulation of neurite...

  17. Dissociation Energies of Diatomic Molecules

    Institute of Scientific and Technical Information of China (English)

    FAN Qun-Chao; SUN Wei-Guo


    Molecular dissociation energies of 10 electronic states of alkali molecules of KH, 7LID, 7LiH, 6LiH, NaK, NaLi and NaRb are studied using the highest three accurate vibrational energies of each electronic state, and an improved parameter-free analytical formula which is obtained starting from the LeRoy-Bernstein vibrational energy expression near the dissociation limit. The results show that as long as the highest three vibrational energies are accurate, the current analytical formula will give accurate theoretical dissociation energies Detheory, which are in excellent agreement with the experimental dissociation energies Dexpte.

  18. XUV ionization of aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)


    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  19. Small molecules for big tasks

    Institute of Scientific and Technical Information of China (English)

    Jiarui Wu


    @@ One of the most important achievements in the post-genome era is discovery of microRNAs (miRNAs), which widely exist from simple-genome organisms such as viruses and bacteria to complexgenome organisms such as plants and animals.miRNAs are single-stranded non-coding RNAs of 18-25 nucleotides in length, which are generated from larger precursors that are transcribed from noncoding genes.As a new type of regulatory molecules, miRNAs present unique features in regulating gene and its products, including rapidly turning off protein production, reversibly, and compartmentalized regulating gene expression.

  20. The molecule-metal interface

    CERN Document Server

    Koch, Norbert; Wee, Andrew Thye Shen


    Reviewing recent progress in the fundamental understanding of the molecule-metal interface, this useful addition to the literature focuses on experimental studies and introduces the latest analytical techniques as applied to this interface.The first part covers basic theory and initial principle studies, while the second part introduces readers to photoemission, STM, and synchrotron techniques to examine the atomic structure of the interfaces. The third part presents photoelectron spectroscopy, high-resolution UV photoelectron spectroscopy and electron spin resonance to study the electroni

  1. Molecules in Studio v. 1.0

    Energy Technology Data Exchange (ETDEWEB)


    A Powersim Studio implementation of the system dynamics’ ‘Molecules of Structure’. The original implementation was in Ventana’s Vensim language by James Hines. The molecules are fundamental constructs of the system dynamics simulation methodology.

  2. Proteins Are the Body's Worker Molecules (United States)

    ... PDF Chapter 1: Proteins are the Body's Worker Molecules You've probably heard that proteins are important ... are much more than that. Proteins are worker molecules that are necessary for virtually every activity in ...

  3. Characterization of Interstellar Organic Molecules (United States)

    Gençaǧa, Deniz; Carbon, Duane F.; Knuth, Kevin H.


    Understanding the origins of life has been one of the greatest dreams throughout history. It is now known that star-forming regions contain complex organic molecules, known as Polycyclic Aromatic Hydrocarbons (PAHs), each of which has particular infrared spectral characteristics. By understanding which PAH species are found in specific star-forming regions, we can better understand the biochemistry that takes place in interstellar clouds. Identifying and classifying PAHs is not an easy task: we can only observe a single superposition of PAH spectra at any given astrophysical site, with the PAH species perhaps numbering in the hundreds or even thousands. This is a challenging source separation problem since we have only one observation composed of numerous mixed sources. However, it is made easier with the help of a library of hundreds of PAH spectra. In order to separate PAH molecules from their mixture, we need to identify the specific species and their unique concentrations that would provide the given mixture. We develop a Bayesian approach for this problem where sources are separated from their mixture by Metropolis Hastings algorithm. Separated PAH concentrations are provided with their error bars, illustrating the uncertainties involved in the estimation process. The approach is demonstrated on synthetic spectral mixtures using spectral resolutions from the Infrared Space Observatory (ISO). Performance of the method is tested for different noise levels.

  4. Similarity of atoms in molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cioslowski, J.; Nanayakkara, A. (Florida State Univ., Tallahassee, FL (United States))


    Similarity of atoms in molecules is quantitatively assessed with a measure that employs electron densities within respective atomic basins. This atomic similarity measure does not rely on arbitrary assumptions concerning basis functions or 'atomic orbitals', is relatively inexpensive to compute, and has straightforward interpretation. Inspection of similarities between pairs of carbon, hydrogen, and fluorine atoms in the CH[sub 4], CH[sub 3]F, CH[sub 2]F[sub 2], CHF[sub 3], CF[sub 4], C[sub 2]H[sub 2], C[sub 2]H[sub 4], and C[sub 2]H[sub 6] molecules, calculated at the MP2/6-311G[sup **] level of theory, reveals that the atomic similarity is greatly reduced by a change in the number or the character of ligands (i.e. the atoms with nuclei linked through bond paths to the nucleus of the atom in question). On the other hand, atoms with formally identical (i.e. having the same nuclei and numbers of ligands) ligands resemble each other to a large degree, with the similarity indices greater than 0.95 for hydrogens and 0.99 for non-hydrogens. 19 refs., 6 tabs.

  5. Is JPC = 3-+ molecule possible? (United States)

    Zhu, Wei; Liu, Yan-Rui; Yao, Tao


    The confirmation of charged charmonium-like states indicates that heavy quark molecules should exist. Here we discuss the possibility of a molecule state with JPC = 3-+. In a one-boson-exchange model investigation for the S wave C = + D*D¯2* states, one finds that the strongest attraction is in the case J = 3 and I = 0 for both π and σ exchanges. Numerical analysis indicates that this hadronic bound state might exist if a phenomenological cutoff parameter around 2.3 GeV (1.5 GeV) is reasonable with a dipole (monopole) type form factor in the one-pion-exchange model. The cutoff for binding solutions may be reduced to a smaller value once the σ exchange contribution is included. If a state around the D*D¯2* threshold (≈4472 MeV) in the channel J/ψω (P wave) is observed, the heavy quark spin symmetry implies that it is not a cc¯ meson and the JPC are likely to be 3-+. Supported by National Natural Science Foundation of China (11275115), Shandong Province Natural Science Foundation (ZR2010AM023), SRF for ROCS, SEM, and Independent Innovation Foundation of Shandong University

  6. Time scales for molecule formation by ion-molecule reactions (United States)

    Langer, W. D.; Glassgold, A. E.


    Analytical solutions are obtained for nonlinear differential equations governing the time-dependence of molecular abundances in interstellar clouds. Three gas-phase reaction schemes are considered separately for the regions where each dominates. The particular case of CO, and closely related members of the Oh and CH families of molecules, is studied for given values of temperature, density, and the radiation field. Nonlinear effects and couplings with particular ions are found to be important. The time scales for CO formation range from 100,000 to a few million years, depending on the chemistry and regime. The time required for essentially complete conversion of C(+) to CO in the region where the H3(+) chemistry dominates is several million years. Because this time is longer than or comparable to dynamical time scales for dense interstellar clouds, steady-state abundances may not be observed in such clouds.

  7. How Is a Protein Molecule Nearsighted?

    Institute of Scientific and Technical Information of China (English)

    GAO De; JI Qing; L(U) Gang


    @@ The effect range of a local change of a protein molecule is calculated using a cluster method developed in this work based on the Gaussian software. This range is found to be about 8 A, which gives a concrete estimation on the "nearsightedness" by Kohn for protein molecules. The cluster method can be applied to calculation of the electronic density of a large molecule such as a motor protein and can provide a basis for the dynamical analysis of a single protein molecule.

  8. Hydrophobic Porous Material Adsorbs Small Organic Molecules (United States)

    Sharma, Pramod K.; Hickey, Gregory S.


    Composite molecular-sieve material has pore structure designed specifically for preferential adsorption of organic molecules for sizes ranging from 3 to 6 angstrom. Design based on principle that contaminant molecules become strongly bound to surface of adsorbent when size of contaminant molecules is nearly same as that of pores in adsorbent. Material used to remove small organic contaminant molecules from vacuum systems or from enclosed gaseous environments like closed-loop life-support systems.

  9. Visualization of large elongated DNA molecules. (United States)

    Lee, Jinyong; Kim, Yongkyun; Lee, Seonghyun; Jo, Kyubong


    Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.

  10. Anti-cancer Lead Molecule

    KAUST Repository

    Sagar, Sunil


    Derivatives of plumbagin can be selectively cytotoxic to breast cancer cells. Derivative `A` (Acetyl Plumbagin) has emerged as a lead molecule for testing against estrogen positive breast cancer and has shown low hepatotoxicity as well as overall lower toxicity in nude mice model. The toxicity of derivative `A` was determined to be even lower than vehicle control (ALT and AST markers). The possible mechanism of action identified based on the microarray experiments and pathway mapping shows that derivative `A` could be acting by altering the cholesterol-related mechanisms. The low toxicity profile of derivative `A` highlights its possible role\\'as future anti-cancer drug and/or as an adjuvant drug to reduce the toxicity of highly toxic chemotherapeutic\\'drugs

  11. Optoelectronics of Molecules and Polymers

    CERN Document Server

    Moliton, André


    Optoelectronic devices are being developed at an extraordinary rate. Organic light emitting diodes, photovoltaic devices and electro-optical modulators are pivotal to the future of displays, photosensors and solar cells, and communication technologies. This book details the theories underlying the relevant mechanisms in organic materials and covers, at a basic level, how the organic components are made. The first part of this book introduces the fundamental theories used to detail ordered solids and localised energy levels. The methods used to determine energy levels in perfectly ordered molecular and macromolecular systems are discussed, making sure that the effects of quasi-particles are not missed. The function of excitons and their transfer between two molecules are studied, and the problems associated with interfaces and charge injection into resistive media are presented. The second part details technological aspects such as the fabrication of devices based on organic materials by dry etching. The princ...

  12. Special Issue: "Molecules against Alzheimer". (United States)

    Decker, Michael; Muñoz-Torrero, Diego


    This Special Issue, entitled "Molecules against Alzheimer", gathers a number of original articles, short communications, and review articles on recent research efforts toward the development of novel drug candidates, diagnostic agents and therapeutic approaches for Alzheimer's disease (AD), the most prevalent neurodegenerative disorder and a leading cause of death worldwide. This Special Issue contains many interesting examples describing the design, synthesis, and pharmacological profiling of novel compounds that hit one or several key biological targets, such as cholinesterases, β-amyloid formation or aggregation, monoamine oxidase B, oxidative stress, biometal dyshomeostasis, mitochondrial dysfunction, serotonin and/or melatonin systems, the Wnt/β-catenin pathway, sigma receptors, nicotinamide phosphoribosyltransferase, or nuclear erythroid 2-related factor. The development of novel AD diagnostic agents based on tau protein imaging and the use of lithium or intranasal insulin for the prevention or the symptomatic treatment of AD is also covered in some articles of the Special Issue.

  13. Molecule Formation on Interstellar Grains (United States)

    Vidali, G.


    The first experiments that were expressively designed to be applicable to hydrogen formation reactions in the ISM measured the efficiency of formation of molecular hydrogen on a polycrystalline olivine (Pirronello et al. (1997a)). It soon turned out that more was needed, and research began on the mechanism of reaction, on the in uence of the surface morphology, and on the excitation of the just- ormed molecule. In this review, I summarize what we learned from these and other experiments, and where more work is needed: in the elementary steps of reaction, in the bridging of the laboratory-ISM gap (large ux/large surface - small ux/small grain) using simulations, and in using realistic samples of dust grains. Understanding what experiments can and cannot deliver will help in designing and targeting observations, and vice-versa.

  14. High-harmonic spectroscopy of aligned molecules (United States)

    Yun, Hyeok; Yun, Sang Jae; Lee, Gae Hwang; Nam, Chang Hee


    High harmonics emitted from aligned molecules driven by intense femtosecond laser pulses provide the opportunity to explore the structural information of molecules. The field-free molecular alignment technique is an expedient tool for investigating the structural characteristics of linear molecules. The underlying physics of field-free alignment, showing the characteristic revival structure specific to molecular species, is clearly explained from the quantum-phase analysis of molecular rotational states. The anisotropic nature of molecules is shown from the harmonic polarization measurement performed with spatial interferometry. The multi-orbital characteristics of molecules are investigated using high-harmonic spectroscopy, applied to molecules of N2 and CO2. In the latter case the two-dimensional high-harmonic spectroscopy, implemented using a two-color laser field, is applied to distinguish harmonics from different orbitals. Molecular high-harmonic spectroscopy will open a new route to investigate ultrafast dynamics of molecules.

  15. Observation of pendular butterfly Rydberg molecules. (United States)

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H; Ott, Herwig


    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron-perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance.

  16. Spin polarization effect for Cr2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying


    Density functional theory (DFT) (B3P86) of Ganssian 03 has been used to optimize the structure of the Cr2 molecule, a transition metal element molecule. The result shows that the ground state for the Cr2 molecule is a 13-multiple state, indicating that there exists a spin polarization effect in the Cr2 molecule. Meanwhile, we have not found any spin pollution because the wave function of the ground state does not mingle with wave functions of higher-energy states. So the ground state for Cr2 molecule being a 13-multiple state is indicative of spin polarization effect of the Cr2 molecule among transition metal elements, that is, there are 12 parallel spin electrons in the Cr2 molecule. The number of non-conjugated electrons is greatest. These electrons occupy different spatial orbitals so that the energy of the Cr2 molecule is minimized. It can be concluded that the effect of parallel spin in the Cr2 molecule is larger than the effect of the conjugated molecule, which is obviously related to the effect of electron d delocalization. In addition,the Murrell-Sorbie potential functions with the parameters for the ground state and other states of the Cr2 molecule are derived. The dissociation energy De for the ground state of the Cr2 molecule is 0.1034eV, equilibrium bond length Re is 0.3396nm, and vibration frequency ωe is 73.81cm-1. Its force constants f2, f3 and f4 are 0.0835, -0.2831 and 0.3535 aJ·nm-4 respectively. The other spectroscopic data for the ground state of the Cr2 molecule ωeχe, Be and αe are 1.2105, 0.0562 and 7.2938 × 10-4cm-1 respectively.

  17. Spin polarization effect of Ni2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying; Zhu Zheng-He


    The density functional theory (DFT) method (b3p86) of Gaussian 03 is used to optimize the structure of the Ni2 molecule. The result shows that the ground state for the Ni2 molecule is a 5-multiple state, symbolizing a spin polarization effect existing in the Ni2 molecule, a transition metal molecule, but no spin pollution is found because the wavefunction of the ground state does not mingle with wavefunctions of higher-energy states. So the ground state for Ni2 molecule, which is a 5-multiple state, is indicative of spin polarization effect of the Ni2 molecule, that is, there exist 4 parallel spin electrons in Ni2 molecule. The number of non-conjugated electrons is greatest. These electrons occupy different spatial orbitals so that the energy of the Ni2 molecule is minimized. It can be concluded that the effect of parallel spin in the Ni2 molecule is larger than that of the conjugated molecule, which is obviously related to the effect of electron d delocalization. In addition, the Murrell-Sorbie potential functions with the parameters of the ground state and other states of the Ni2 molecule are derived. The dissociation energy De for the ground state of the Ni2 molecule is 1.835 eV, equilibrium bond length Re is 0.2243 nm, vibration frequency ωe is 262.35 cm-1. Its force constants f2, f3 and f4 are 1.1901 aJ.nm-2, 5.8723 aJ.nm-3, and 21.2505 aJ.nm-4 respectively. The other spectroscopic data for the ground state of the Ni2 molecule ωexe, Be and αe are 1.6315cm-1, 0.1141 cm-1, and 8.0145×10-4 cm-1 respectively.

  18. Geochemical Origin of Biological Molecules (United States)

    Bassez, Marie-Paule


    A model for the geochemical origin of biological molecules is presented. Rocks such as peridotites and basalts, which contain ferromagnesian minerals, evolve in the presence of water. Their hydrolysis is an exothermic reaction which generates heat and a release of H2 and of minerals with modified structures. The hydrogen reacts with the CO2 embedded inside the rock or with the CO2 of the environment to form CO in an hydrothermal process. With the N2 of the environment, and with an activation source arising from cosmic radiation, ferromagnesian rocks might evolve towards the abiotic formation of biological molecules, such as peptide like macromolecules which produce amino acids after acid hydrolysis. The reactions concerned are described. The production of hydrothermal CO is discussed in geological sites containing ferromagnesian silicate minerals and the low intensity of the Earth's magnetic field during Paleoarchaean Era is also discussed. It is concluded that excitation sources arising from cosmic radiation were much more abundant during Paleoarchaean Era and that macromolecular structures of biological relevance might consequently form during Archaean Eon, as a product of the chemical evolution of the rocks and of their mineral contents. This synthesis of abiotically formed biological molecules is consecutively discussed for meteorites and other planets such as Mars. This model for the geochemical origin of biological molecules has first been proposed in 2008 in the context of reactions involving catalysers such as kaolinite [Bassez 2008a] and then presented in conferences and articles [Bassez 2008b, 2009, 2012; Bassez et al. 2009a to 2012b]. BASSEZ M.P. 2008a Synthèse prébiotique dans les conditions hydrothermales, CNRIUT'08, Lyon 29-30/05/2008, Conf. and open access article: 29 mai 11h-12h40. BASSEZ M.P. 2008b Prebiotic synthesis under hydrothermal conditions, ISSOL'08, P2-6, Firenze-Italy, 24-29/08/2008. Poster at the

  19. Cochleates bridged by drug molecules. (United States)

    Syed, Uwais M; Woo, Amy F; Plakogiannis, Fotios; Jin, Tuo; Zhu, Hua


    A new type of cochleate, able to microencapsulate water-soluble cationic drugs or peptides into its inter-lipid bi-layer space, was formed through interaction between negatively charged lipids and drugs or peptides acting as the inter-bi-layer bridges instead of multi-cationic metal ions. This new type of cochleate opened up to form large liposomes when treated with EDTA, suggesting that cationic organic molecules can be extracted from these cochleates in a way similar to multivalent metal ions from metal ion-bridged cochleates. Cochleates can be produced in sub-micron size using a method known as "hydrogel isolated cochleation" or simply by increasing the ratio of multivalent cationic peptides over negatively charged liposomes. When nanometer-sized cochleates and liposomes containing the same fluorescent labeled lipid component were incubated with human fibroblasts cells under identical conditions, cells exposed to cochleates showed bright fluorescent cell surfaces, whereas those incubated with liposomes did not. This result suggests that cochleates' edges made them fuse with the cell surfaces as compared to edge free liposomes. This mechanism of cochleates' fusion with cell membrane was supported by a bactericidal activity assay using tobramycin cochleates, which act by inhibiting intracellular ribosomes. Tobramycin bridged cochleates in nanometer size showed improved antibacterial activity than the drug's solution.

  20. Coordination programming of photofunctional molecules. (United States)

    Sakamoto, Ryota; Kusaka, Shinpei; Hayashi, Mikihiro; Nishikawa, Michihiro; Nishihara, Hiroshi


    Our recent achievements relating to photofunctional molecules are addressed. Section 1 discloses a new concept of photoisomerization. Pyridylpyrimidine-copper complexes undergo a ring inversion that can be modulated by the redox state of the copper center. In combination with an intermolecular photoelectron transfer (PET) initiated by the metal-to-ligand charge transfer (MLCT) transition of the Cu(I) state, we realize photonic regulation of the ring inversion. Section 2 reports on the first examples of heteroleptic bis(dipyrrinato)zinc(II) complexes. Conventional homoleptic bis(dipyrrinato)zinc(II) complexes suffered from low fluorescence quantum yields, whereas the heteroleptic ones feature bright fluorescence even in polar solvents. Section 3 describes our new findings on Pechmann dye, which was first synthesized in 1882. New synthetic procedures for Pechmann dye using dimethyl bis(arylethynyl)fumarate as a starting material gives rise to its new structural isomer. We also demonstrate potentiality of a donor-acceptor-donor type of Pechmann dye in organic electronics.

  1. Spin squeezing an ultracold molecule

    CERN Document Server

    Bhattacharya, M


    Most research on spin squeezing thus far has focused on realizations involving either atomic or nuclear degrees of freedom. In this article we discuss a concrete proposal for spin squeezing the ultracold ground state polar paramagnetic molecule OH, a system currently under fine control in the laboratory. Starting from an experimentally relevant effective Hamiltonian, we identify a parameter regime where different combinations of static electric and magnetic fields can be used to realize the single-axis twisting Hamiltonian of Kitagawa and Ueda [M. Kitagawa and M. Ueda, Phys. Rev. A 47, 5138 (1993)], the uniform field Hamiltonian proposed by Law et al. [C. K. Law, H. T Ng and P. T. Leung, Phys. Rev. A 63, 055601 (2001)], and a model of field propagation in a Kerr medium considered by Agarwal and Puri [G. S. Agarwal and R. R. Puri, Phys. Rev. A 39, 2969 (1989)]. To support our conclusions, we provide analytical expressions as well as numerical calculations, including optimization of field strengths and accounti...

  2. Coordination Programming of Photofunctional Molecules

    Directory of Open Access Journals (Sweden)

    Hiroshi Nishihara


    Full Text Available Our recent achievements relating to photofunctional molecules are addressed. Section 1 discloses a new concept of photoisomerization. Pyridylpyrimidine-copper complexes undergo a ring inversion that can be modulated by the redox state of the copper center. In combination with an intermolecular photoelectron transfer (PET initiated by the metal-to-ligand charge transfer (MLCT transition of the Cu(I state, we realize photonic regulation of the ring inversion. Section 2 reports on the first examples of heteroleptic bis(dipyrrinatozinc(II complexes. Conventional homoleptic bis(dipyrrinatozinc(II complexes suffered from low fluorescence quantum yields, whereas the heteroleptic ones feature bright fluorescence even in polar solvents. Section 3 describes our new findings on Pechmann dye, which was first synthesized in 1882. New synthetic procedures for Pechmann dye using dimethyl bis(arylethynylfumarate as a starting material gives rise to its new structural isomer. We also demonstrate potentiality of a donor-acceptor-donor type of Pechmann dye in organic electronics.

  3. Single Molecule Studies of Chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Jeans, C; Thelen, M P; Noy, A


    In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.

  4. Single-molecule stochastic resonance

    CERN Document Server

    Hayashi, K; Manosas, M; Huguet, J M; Ritort, F; 10.1103/PhysRevX.2.031012


    Stochastic resonance (SR) is a well known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic noise. Here we carry out the first experimental study of SR in single DNA hairpins which exhibit cooperatively folding/unfolding transitions under the action of an applied oscillating mechanical force with optical tweezers. By varying the frequency of the force oscillation, we investigated the folding/unfolding kinetics of DNA hairpins in a periodically driven bistable free-energy potential. We measured several SR quantifiers under varied conditions of the experimental setup such as trap stiffness and length of the molecular handles used for single-molecule manipulation. We find that the signal-to-noise ratio (SNR) of the spectral density of measured fluctuations in molecular extension of the DNA hairpins is a good quantifier of the SR. The frequency dependence of the SNR exhibits a peak at a frequency value given by the resonance match...

  5. Laser cooling of a diatomic molecule

    CERN Document Server

    Shuman, E S; DeMille, D


    It has been roughly three decades since laser cooling techniques produced ultracold atoms, leading to rapid advances in a vast array of fields. Unfortunately laser cooling has not yet been extended to molecules because of their complex internal structure. However, this complexity makes molecules potentially useful for many applications. For example, heteronuclear molecules possess permanent electric dipole moments which lead to long-range, tunable, anisotropic dipole-dipole interactions. The combination of the dipole-dipole interaction and the precise control over molecular degrees of freedom possible at ultracold temperatures make ultracold molecules attractive candidates for use in quantum simulation of condensed matter systems and quantum computation. Also ultracold molecules may provide unique opportunities for studying chemical dynamics and for tests of fundamental symmetries. Here we experimentally demonstrate laser cooling of the molecule strontium monofluoride (SrF). Using an optical cycling scheme re...

  6. Observation of pendular butterfly Rydberg molecules

    CERN Document Server

    Niederprüm, Thomas; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H; Ott, Herwig


    Obtaining full control over the internal and external quantum states of molecules is the central goal of ultracold chemistry and allows for the study of coherent molecular dynamics, collisions and tests of fundamental laws of physics. When the molecules additionally have a permanent electric dipole moment, the study of dipolar quantum gases and spin-systems with long-range interactions as well as applications in quantum information processing are possible. Rydberg molecules constitute a class of exotic molecules, which are bound by the interaction between the Rydberg electron and the ground state atom. They exhibit extreme bond lengths of hundreds of Bohr radii and giant permanent dipole moments in the kilo-Debye range. A special type with exceptional properties are the so-called butterfly molecules, whose electron density resembles the shape of a butterfly. Here, we report on the photoassociation of butterfly Rydberg molecules and their orientation in a weak electric field. Starting from a Bose-Einstein cond...

  7. Small-Molecule Carbohydrate-Based Immunostimulants. (United States)

    Marzabadi, Cecilia H; Franck, Richard W


    In this review, we discuss small-molecule, carbohydrate-based immunostimulants that target Toll-like receptor 4 (TLR-4) and cluster of differentiation 1D (CD1d) receptors. The design and use of these molecules in immunotherapy as well as results from their use in clinical trials are described. How these molecules work and their utilization as vaccine adjuvants are also discussed. Future applications and extensions for the use of these analogues as therapeutic agents will be outlined.

  8. Making "Operations" inside a Single Molecule

    Institute of Scientific and Technical Information of China (English)


    @@ Free and delicate manipulation of single molecules has long been expected by scientists so as to realize specific functions. In the 1990s, the laboratory led by Prof. Wison Ho from the University of California was successful in inducing chemical reactions at the single molecule level with scanning tunneling microscopy (STM), revealing the extensive potentials of "single molecule operation." However, until recently, researchers have failed to utilize the reaction to give rise to special physical properties.

  9. Negative refraction in Möbius molecules (United States)

    Fang, Y. N.; Shen, Yao; Ai, Qing; Sun, C. P.


    We theoretically show the negative refraction existing in Möbius molecules. The negative refractive index is induced by the nontrivial topology of the molecules. With the Möbius boundary condition, the effective electromagnetic fields felt by the electron in a Möbius ring is spatially inhomogeneous. In this regard, the DN symmetry is broken in Möbius molecules and thus the magnetic response is induced through the effective magnetic field. Our findings provide an alternative architecture for negative refractive index materials based on the nontrivial topology of Möbius molecules.

  10. Ultracold Molecules: Physics in the Quantum Regime

    Energy Technology Data Exchange (ETDEWEB)

    Doyle, John [Harvard Univ., Cambridge, MA (United States). Dept. of Physics


    Our research encompasses approaches to the trapping of diatomic molecules at low temperature plus the cooling and detection of polyatomic molecules in the kelvin temperature regime. We have cooled and trapped CaF and/or CaH molecules, loaded directly from a molecular beam. As part of this work, we are continuing to develop an important trapping technique, optical loading from a buffer-gas beam. This method was invented in our lab. We are also studying cold polyatomic molecules and their interactions with cold atoms.

  11. Electron-molecule interactions and their applications

    CERN Document Server

    Christophorou, L G


    Electron-Molecule Interactions and Their Applications, Volume 2 provides a balanced and comprehensive account of electron-molecule interactions in dilute and dense gases and liquid media. This book consists of six chapters. Chapter 1 deals with electron transfer reactions, while Chapter 2 discusses electron-molecular positive-ion recombination. The electron motion in high-pressure gases and electron-molecule interactions from single- to multiple-collision conditions is deliberated in Chapter 3. In Chapter 4, knowledge on electron-molecule interactions in gases is linked to that on similar proc

  12. Theoretical spectra of floppy molecules (United States)

    Chen, Hua


    Detailed studies of the vibrational dynamics of floppy molecules are presented. Six-D bound-state calculations of the vibrations of rigid water dimer based on several anisotropic site potentials (ASP) are presented. A new sequential diagonalization truncation approach was used to diagonalize the angular part of the Hamiltonian. Symmetrized angular basis and a potential optimized discrete variable representation for intermonomer distance coordinate were used in the calculations. The converged results differ significantly from the results presented by Leforestier et al. [J. Chem. Phys. 106 , 8527 (1997)]. It was demonstrated that ASP-S potential yields more accurate tunneling splittings than other ASP potentials used. Fully coupled 4D quantum mechanical calculations were performed for carbon dioxide dimer using the potential energy surface given by Bukowski et al [J. Chem. Phys., 110, 3785 (1999)]. The intermolecular vibrational frequencies and symmetry adapted force constants were estimated and compared with experiments. The inter-conversion tunneling dynamics was studied using the calculated virtual tunneling splittings. Symmetrized Radau coordinates and the sequential diagonalization truncation approach were formulated for acetylene. A 6D calculation was performed with 5 DVR points for each stretch coordinate, and an angular basis that is capable of converging the angular part of the Hamiltonian to 30 cm-1 for internal energies up to 14000 cm-1. The probability at vinylidene configuration were evaluated. It was found that the eigenstates begin to extend to vinylidene configuration from about 10000 cm-1, and the ra, coordinate is closely related to the vibrational dynamics at high energy. Finally, a direct product DVR was defined for coupled angular momentum operators, and the SDT approach were formulated. They were applied in solving the angular part of the Hamiltonian for carbon dioxide dimer problem. The results show the method is capable of giving very accurate

  13. Spin polarization effect for Tc2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying; Zhu Zheng-He


    Density functional method (DFT) (B3p86) of Gaussian98 has been used to optimize the structure of the Tc2 molecule. The result shows that the ground state for Tc2 molecule is an 11-multiple state and its electronic configuration is 11∑- g, which shows the spin polarization effect of Tc2 molecule of a transition metal element for the first time.Meanwhile, we have not found any spin pollution because the wavefunction of the ground state does not mingle with wavefunctions of higher energy states. So, that the ground state for Tc2 molecule is an 11-multiple state is indicative of the spin polarization effect of Tc2 molecule of a transition metal element: that is, there exist 10 parallel spin electrons. The non-conjugated electron is greatest in number. These electrons occupy different spacious tracks, so that the energy of Tc2 molecule is minimized. It can be concluded that the effect of parallel spin of the Tc2 molecule is larger than the effect of the conjugated molecule, which is obviously related to the effect of electron d delocalization.In addition, the Murrell-Sorbie potential functions with the parameters for the ground state 11∑- g and other states of Tc2 molecule are derived. Dissociation energy De for the ground state of Tc2 molecule is 2.266eV, equilibrium bond length Re is 0.2841nm, vibration frequency ωe is 178.52cm-1. Its force constants f2, f3, and f4 are 0.9200aJ.nm-2,-3.5700aJ.nm-3, 11.2748aJ.nm-4 respectively. The other spectroscopic data for the ground state of Tc2 molecule ωexe,Be, αe are 0.5523cm- 1, 0.0426cm- 1, 1.6331 × 10-4cm- 1 respectively.

  14. Spin polarization effect for Fe2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying; Zhu Zheng-He


    This paper uses the density functional theory (DFT)(B3p86) of Gaussian03 to optimize the structure of Fe2 molecule. The result shows that the ground state for Fe2 molecule is a 9-multiple state, which shows spin polarization effect of Fe2 molecule of transition metal elements for the first time. Meanwhile, we have not found any spin pollution because the wavefunction of the ground state does not mingle with wavefunctions with higher energy states. So, that the ground state for Fe2 molecule is a 9-multiple state is indicative of the spin polarization effect of Fe2 molecule of transition metal elements. That is, there exist 8 parallel spin electrons. The non-conjugated electron is greatest in number. These electrons occupy different spacious tracks, so that the energy of the Fe2 molecule is minimized. It can be concluded that the effect of parallel spin of the Fe2 molecule is larger than the effect of the conjugated molecule, which is obviously related to the effect of electron d delocalization. In addition, the Murrell-Sorbie potential functions with the parameters for the ground state and other states of Fe2 molecule are derived. Dissociation energy De for the ground state of Fe2 molecule is 2.8586ev, equilibrium bond length Re is 0.2124nm, vibration frequency ωe is 336.38 cm-1. Its force constants f2, f3, and f4 are 1.8615aJ·nm-2, -8.6704a J·nm-3, 29.1676aJ·nm-4 respectively. The other spectroscopic data for the ground state of Fe2 moleculeωeχe, Be, αe are 1.5461 cm-1, 0.1339 cm-1, 7.3428×10-4 cm-1 respectively.

  15. Single-molecule dynamics at variable temperatures

    NARCIS (Netherlands)

    Zondervan, Rob


    Single-molecule optics has evolved from a specialized variety of optical spectroscopy at low temperatures into a versatile tool to address questions in physics, chemistry, biology, and materials science. In this thesis, the potential of single-molecule (and ensemble) optical microscopy at variable t

  16. Molecule-oriented programming in Java

    NARCIS (Netherlands)

    Bergstra, J.A.


    Molecule-oriented programming is introduced as a programming style carrying some perspective for Java. A sequence of examples is provided. Supporting the development of the molecule-oriented programming style several matters are introduced and developed: profile classes allowing the representation o

  17. Matter-Wave Optics of Diatomic Molecules (United States)


    Lima , Peru (2010). S. Singh and P. Meystre, "Atomic probe Wigner tomography of a nanomechanical system," contributed paper, APS DAMOP Annual Meeting...Triangle Park , NC 27709-2211 15. SUBJECT TERMS matter-wave optics, ultracold molecules, polar molecules, quantum optomechanics, quantum-degenerate

  18. Spectrum Generating Algebra for X$_{3}$ Molecules

    CERN Document Server

    Bijker, R; Leviatan, A


    A new spectrum generating algebra for a unified description of rotations and vibrations in polyatomic molecules is introduced. An application to nonlinear X$_3$ molecules shows that this model (i) incorporates exactly the relevant point group, (ii) provides a complete classification of oblate top states, and (iii) treats properly both degenerate and nondegenerate vibrations.

  19. The MHC molecules of nonmammalian vertebrates

    DEFF Research Database (Denmark)

    Kaufman, J; Skjoedt, K; Salomonsen, J


    There is very little known about the long-term evolution of the MHC and MHC-like molecules. This is because both the theory (the evolutionary questions and models) and the practice (the animals systems, functional assays and reagents to identify and characterize these molecules) have been difficu...

  20. Near-field single molecule spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Xie, X.S.; Dunn, R.C.


    The high spatial resolution and sensitivity of near-field fluorescence microscopy allows one to study spectroscopic and dynamical properties of individual molecules at room temperature. Time-resolved experiments which probe the dynamical behavior of single molecules are discussed. Ground rules for applying near-field spectroscopy and the effect of the aluminum coated near-field probe on spectroscopic measurements are presented.

  1. Decelerating and Trapping Large Polar Molecules. (United States)

    Patterson, David


    Manipulating the motion of large polyatomic molecules, such as benzonitrile (C6 H5 CN), presents significant difficulties compared to the manipulation of diatomic molecules. Although recent impressive results have demonstrated manipulation, trapping, and cooling of molecules as large as CH3 F, no general technique for trapping such molecules has been demonstrated, and cold neutral molecules larger than 5 atoms have not been trapped (M. Zeppenfeld, B. G. U. Englert, R. Glöckner, A. Prehn, M. Mielenz, C. Sommer, L. D. van Buuren, M. Motsch, G. Rempe, Nature 2012, 491, 570-573). In particular, extending Stark deceleration and electrostatic trapping to such species remains challenging. Here, we propose to combine a novel "asymmetric doublet state" Stark decelerator with recently demonstrated slow, cold, buffer-gas-cooled beams of closed-shell volatile molecules to realize a general system for decelerating and trapping samples of a broad range of volatile neutral polar prolate asymmetric top molecules. The technique is applicable to most stable volatile molecules in the 100-500 AMU range, and would be capable of producing trapped samples in a single rotational state and at a motional temperature of hundreds of mK. Such samples would immediately allow for spectroscopy of unprecedented resolution, and extensions would allow for further cooling and direct observation of slow intramolecular processes such as vibrational relaxation and Hertz-level tunneling dynamics.

  2. Small Molecules in the Cone Snail Arsenal. (United States)

    Neves, Jorge L B; Lin, Zhenjian; Imperial, Julita S; Antunes, Agostinho; Vasconcelos, Vitor; Olivera, Baldomero M; Schmidt, Eric W


    Cone snails are renowned for producing peptide-based venom, containing conopeptides and conotoxins, to capture their prey. A novel small-molecule guanine derivative with unprecedented features, genuanine, was isolated from the venom of two cone snail species. Genuanine causes paralysis in mice, indicating that small molecules and not just polypeptides may contribute to the activity of cone snail venom.

  3. Controlled contact to a C-60 molecule

    DEFF Research Database (Denmark)

    Neel, N.; Kröger, J.; Limot, L.;


    The tip of a low-temperature scanning tunneling microscope is approached towards a C-60 molecule adsorbed at a pentagon-hexagon bond on Cu(100) to form a tip-molecule contact. The conductance rapidly increases to approximate to 0.25 conductance quanta in the transition region from tunneling...

  4. Nanoscience: Single-molecule instant replay (United States)

    Camillone, Nicholas


    A nanoscale imaging method that uses ultrashort light pulses to initiate and follow the motion of a single molecule adsorbed on a solid surface opens a window onto the physical and chemical dynamics of molecules on surfaces. See Letter p.263

  5. Spin polarization effect for Co2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying; Bao Wen-Sheng


    The density functional theory (DFT)(b3p86) of Gaussian 03 has been used to optimize the structure of the Co2molecule, a transition metal element molecule. The result shows that the ground state for the Co2 molecule is a 7-multiple state, indicating a spin polarization effect in the Co2 molecule. Meanwhile, we have not found any spin pollution because the wavefunction of the ground state is not mingled with wavefunctions of higher-energy states. So for the ground state of Co2 molecule to be a 7-multiple state is the indicative of spin polarization effect of the Co2molecule, that is, there exist 6 parallel spin electrons in a Co2 molecule. The number of non-conjugated electrons is the greatest. These electrons occupy different spacial orbitals so that the energy of the Co2 molecule is minimized. It can be concluded that the effect of parallel spin in the Co2 molecule is larger than the effect of the conjugated molecule,which is obviously related to the effect of electron d delocalization. In addition, the Murrell-Sorbie potential functions with the parameters for the ground state and the other states of the Co2 molecule are derived. The dissociation energy De for the ground state of Co2 molecule is 4.0489eV, equilibrium bond length Re is 0.2061 nm, and vibration frequency 11.2222 aJ.nm-4respectively(1 a.J=10-18 J). The other spectroscopic data for the ground state of Co2 molecule ωexe,Be, and αe are 0.7202 cm-1, 0.1347 cm-1, and 2.9120× 10-1 cm-1 respectively. And ωexe is the non-syntonic part of frequency, Be is the rotational constant, αe is revised constant of rotational constant for non-rigid part of Co2 molecule.

  6. The symmetry of single-molecule conduction. (United States)

    Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S


    We introduce the conductance point group which defines the symmetry of single-molecule conduction within the nonequilibrium Green's function formalism. It is shown, either rigorously or to within a very good approximation, to correspond to a molecular-conductance point group defined purely in terms of the properties of the conducting molecule. This enables single-molecule conductivity to be described in terms of key qualitative chemical descriptors that are independent of the nature of the molecule-conductor interfaces. We apply this to demonstrate how symmetry controls the conduction through 1,4-benzenedithiol chemisorbed to gold electrodes as an example system, listing also the molecular-conductance point groups for a range of molecules commonly used in molecular electronics research.

  7. Quantum transport of the single metallocene molecule (United States)

    Yu, Jing-Xin; Chang, Jing; Wei, Rong-Kai; Liu, Xiu-Ying; Li, Xiao-Dong


    The Quantum transport of three single metallocene molecule is investigated by performing theoretical calculations using the non-equilibrium Green's function method combined with density functional theory. We find that the three metallocen molecules structure become stretched along the transport direction, the distance between two Cp rings longer than the other theory and experiment results. The lager conductance is found in nickelocene molecule, the main transmission channel is the electron coupling between molecule and the electrodes is through the Ni dxz and dyz orbitals and the s, dxz, dyz of gold. This is also confirmed by the highest occupied molecular orbital resonance at Fermi level. In addition, negative differential resistance effect is found in the ferrocene, cobaltocene molecules, this is also closely related with the evolution of the transmission spectrum under applied bias.

  8. Electronic and thermal properties of Biphenyl molecules (United States)

    Medina, F. G.; Ojeda, J. H.; Duque, C. A.; Laroze, D.


    Transport properties of a single Biphenyl molecule coupled to two contacts are studied. We characterise this system by a tight-binding Hamiltonian. Based on the non-equilibrium Green's functions technique with a Landauer-Büttiker formalism the transmission probability, current and thermoelectrical power are obtained. We show that the Biphenyl molecule may have semiconductor behavior for certain values of the electrode-molecule-electrode junctions and different values of the angle between the two rings of the molecule. In addition, the density of states (DOS) is calculated to compare the bandwidths with the profile of the transmission probability. DOS allows us to explain the asymmetric shape with respect to the molecule's Fermi energy.

  9. Small azomethine molecules and their use in photovoltaic devices

    NARCIS (Netherlands)

    Dingemans, T.J.; Petrus, M.L.


    The present invention is in the field of a small azomethine molecule having photovoltaic characteristics, a method of synthesizing said molecule, use of said molecule in a photovoltaic device, a solar cell comprising said molecule, and a film comprising said molecule. The present molecules may find

  10. Novel Applications of Buffer-Gas Cooling to Cold Atoms, Diatomic Molecules, and Large Molecules


    Drayna, Garrett Korda


    Cold gases of atoms and molecules provide a system for the exploration of a diverse set of physical phenomena. For example, cold gasses of magnetically and electrically polar atoms and molecules are ideal systems for quantum simulation and quantum computation experiments, and cold gasses of large polar molecules allow for novel spectroscopic techniques. Buffer-gas cooling is a robust and widely applicable method for cooling atoms and molecules to temperatures of approximately 1 Kelvin. In thi...

  11. Search for complex organic molecules in space (United States)

    Ohishi, Masatoshi


    It was 1969 when the first organic molecule in space, H2CO, was discovered. Since then many organic molecules were discovered by using the NRAO 11 m (upgraded later to 12 m), Nobeyama 45 m, IRAM 30 m, and other highly sensitive radio telescopes as a result of close collaboration between radio astronomers and microwave spectroscopists. It is noteworthy that many famous organic molecules such as CH3OH, C2H5OH, (CH3)2O and CH3NH2 were detected by 1975. Organic molecules were found in so-called hot cores where molecules were thought to form on cold dust surfaces and then to evaporate by the UV photons emitted from the central star. These days organic molecules are known to exist not only in hot cores but in hot corinos (a warm, compact molecular clump found in the inner envelope of a class 0 protostar) and even protoplanetary disks. As was described above, major organic molecules were known since 1970s. It was very natural that astronomers considered a relationship between organic molecules in space and the origin of life. Several astronomers challenged to detect glycine and other prebiotic molecules without success. ALMA is expected to detect such important materials to further consider the gexogenous deliveryh hypothesis. In this paper I summarize the history in searching for complex organic molecules together with difficulties in observing very weak signals from larger species. The awfully long list of references at the end of this article may be the most useful part for readers who want to feel the exciting discovery stories.

  12. Spin polarization effect for Mn2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying; Xu Guo-Liang


    The density functional theory method (DFT) (b3p86) of Gaussian 03 has been used to optimize the structure of the Mn2 molecule.The result shows that the ground state of the Mn2 molecule is an 11-multiple state,indicating a spin polarization effect in the Mn2 molecule,a transition metal element molecule.Meanwhile,we have not found any spin pollution because the wavefunction of the ground state does not mingle with wavefunctions of higher-energy states.So the ground state for Mn2 molecule being of an 11-multiple state is the indicative of spin polarization effect of the Mn2 molecule among those in the transition metal elements:that is,there are 10 parallel spin electrons in a Mn2 molecule.The number of non-conjugated electrons is the greatest.These electrons occupy different spacious orbitals so that the energy of the Mn2 molecule is minimized.It can be concluded that the effect of parallel spin in the Mn2 molecule is larger than the effect of the conjugated molecule,which is obviously related to the effect of electron d delocalization.In addition,the Murrell-Sorbie potential functions with the parameters for the ground state and other states of the Mn2 molecule are derived.The dissociation energy De for the ground state of the Mn2 molecule is 1.4477eV,equilibrium bond length Re is 0.2506 nm,vibration frequency ωe is 211.51 cm-1.Its force constants,f2,f3,and f4 are 0.7240 aJ·nm-2,-3.35574 aJ·nm-3,11.4813 aJ·nm-4 respectively. The other spectroscopic data for the ground state of the Mn2 molecule ωeχe,Be,αe are 1.5301 cm-1,0.0978 cm-1,7.7825×10-4 cm-1 respectively.

  13. Optically active quantum-dot molecules. (United States)

    Shlykov, Alexander I; Baimuratov, Anvar S; Baranov, Alexander V; Fedorov, Anatoly V; Rukhlenko, Ivan D


    Chiral molecules made of coupled achiral semiconductor nanocrystals, also known as quantum dots, show great promise for photonic applications owing to their prospective uses as configurable building blocks for optically active structures, materials, and devices. Here we present a simple model of optically active quantum-dot molecules, in which each of the quantum dots is assigned a dipole moment associated with the fundamental interband transition between the size-quantized states of its confined charge carriers. This model is used to analytically calculate the rotatory strengths of optical transitions occurring upon the excitation of chiral dimers, trimers, and tetramers of general configurations. The rotatory strengths of such quantum-dot molecules are found to exceed the typical rotatory strengths of chiral molecules by five to six orders of magnitude. We also study how the optical activity of quantum-dot molecules shows up in their circular dichroism spectra when the energy gap between the molecular states is much smaller than the states' lifetime, and maximize the strengths of the circular dichroism peaks by optimizing orientations of the quantum dots in the molecules. Our analytical results provide clear design guidelines for quantum-dot molecules and can prove useful in engineering optically active quantum-dot supercrystals and photonic devices.

  14. Trapping and manipulating single molecules of DNA (United States)

    Shon, Min Ju

    This thesis presents the development and application of nanoscale techniques to trap and manipulate biomolecules, with a focus on DNA. These methods combine single-molecule microscopy and nano- and micro-fabrication to study biophysical properties of DNA and proteins. The Dimple Machine is a lab-on-a-chip device that can isolate and confine a small number of molecules from a bulk solution. It traps molecules in nanofabricated chambers, or "dimples", and the trapped molecules are then studied on a fluorescence microscope at the single-molecule level. The sampling of bulk solution by dimples is representative, reproducible, and automated, enabling highthroughput single-molecule experiments. The device was applied to study hybridization of oligonucleotides, particularly in the context of reaction thermodynamics and kinetics in nanoconfinement. The DNA Pulley is a system to study protein binding and the local mechanical properties of DNA. A molecule of DNA is tethered to a surface on one end, and a superparamagnetic bead is attached to the other. A magnet pulls the DNA taut, and a silicon nitride knife with a nanoscale blade scans the DNA along its contour. Information on the local properties of the DNA is extracted by tracking the bead with nanometer precision in a white-light microscope. The system can detect proteins bound to DNA and localize their recognition sites, as shown with a model protein, EcoRI restriction enzyme. Progress on the measurements of nano-mechanical properties of DNA is included.

  15. Single Molecule Biophysics Experiments and Theory

    CERN Document Server

    Komatsuzaki, Tamiki; Takahashi, Satoshi; Yang, Haw; Silbey, Robert J; Rice, Stuart A; Dinner, Aaron R


    Discover the experimental and theoretical developments in optical single-molecule spectroscopy that are changing the ways we think about molecules and atoms The Advances in Chemical Physics series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. This latest volume explores the advent of optical single-molecule spectroscopy, and how atomic force microscopy has empowered novel experiments on individual biomolecules, opening up new frontiers in molecular and cell biology and leading to new theoretical approaches

  16. Aligning molecules with intense nonresonant laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Safvan, C.P.; Sakai, H.;


    Molecules in a seeded supersonic beam are aligned by the interaction between an intense nonresonant linearly polarized laser field and the molecular polarizability. We demonstrate the general applicability of the scheme by aligning I2, ICl, CS2, CH3I, and C6H5I molecules. The alignment is probed...... by mass selective two dimensional imaging of the photofragment ions produced by femtosecond laser pulses. Calculations on the degree of alignment of I2 are in good agreement with the experiments. We discuss some future applications of laser aligned molecules....

  17. Formation of ultracold LiCs molecules

    CERN Document Server

    Kraft, S D; Lange, J; Vogel, L; Wester, R; Weidemüller, M; Kraft, Stephan D.; Staanum, Peter; Lange, Joerg; Vogel, Leif; Wester, Roland; Weidemueller, Matthias


    We present the first observation of ultracold LiCs molecules. The molecules are formed in a two-species magneto-optical trap and detected by two-photon ionization and time-of-flight mass spectrometry. The production rate coefficient is found to be in the range $10^{-18}\\unit{cm^3s^{-1}}$ to $10^{-16}\\unit{cm^3s^{-1}}$, at least an order of magnitude smaller than for other heteronuclear diatomic molecules directly formed in a magneto-optical trap.

  18. Imaging Cold Molecules on a Chip

    CERN Document Server

    Marx, S; Abel, M J; Zehentbauer, T; Meijer, G; Santambrogio, G


    We present the integrated imaging of cold molecules in a microchip environment. The on-chip de- tection is based on REMPI, which is quantum-state-selective and generally applicable. We demon- strate and characterize time-resolved spatial imaging and subsequently use it to analyze the effect of a phase-space manipulation sequence aimed at compressing the velocity distribution of a molec- ular ensemble with a view to future high-resolution spectroscopic studies. The realization of such on-chip measurements adds the final fundamental component to the molecule chip, offering a new and promising route for investigating cold molecules.

  19. Nano-manipulation of single DNA molecules

    Institute of Scientific and Technical Information of China (English)

    HU Jun; L(U) Jun-Hong; LI Hai-Kuo; AN Hong-Jie; WANG Guo-Hua; WANG Ying; LI Min-Qian; ZHANG Yi; LI Bin


    Nano-manipulation of single atoms and molecules is a critical technique in nanoscience and nanotechnology. This review paper will focus on the recent development of the manipulation of single DNA molecules based on atomic force microscopy (AFM). Precise manipulation has been realized including varied manipulating modes such as "cutting", "pushing", "folding", "kneading", "picking up", "dipping", etc. The cutting accuracy is dominated by the size of the AFM tip, which is usually 10nm or less. Single DNA fragments can be cut and picked up and then amplified by single molecule PCR. Thus positioning isolation and sequencing can be performed.

  20. Population redistribution in optically trapped polar molecules

    CERN Document Server

    Deiglmayr, J; Dulieu, O; Wester, R; Weidemüller, M


    We investigate the rovibrational population redistribution of polar molecules in the electronic ground state induced by spontaneous emission and blackbody radiation. As a model system we use optically trapped LiCs molecules formed by photoassociation in an ultracold two-species gas. The population dynamics of vibrational and rotational states is modeled using an ab-initio electric dipole moment function and experimental potential energy curves. Comparison with the evolution of the v"=3 electronic ground state yields good qualitative agreement. The analysis provides important input to assess applications of ultracold LiCs molecules in quantum simulation and ultracold chemistry.

  1. Kondo effect in molecules with strong correlations

    Energy Technology Data Exchange (ETDEWEB)

    Kuzmenko, Tetyana [Department of Physics, Ben-Gurion University, P.O. Box 653, Beer-Sheva 84105 (Israel)]. E-mail:; Kikoin, Konstantin [Department of Physics, Ben-Gurion University, P.O. Box 653, Beer-Sheva 84105 (Israel); Avishai, Yshai [Department of Physics, Ben-Gurion University, P.O. Box 653, Beer-Sheva 84105 (Israel)


    A theory of Kondo tunneling through molecules adsorbed on metallic substrate is constructed and the underlying physics is exposed. It is shown that in the case of weak chemisorption the sandwich-type molecules manifest a novel type of Kondo effect that has not been observed in magnetically doped bulk metals. The exchange Hamiltonian of these molecules unveils unusual dynamical SO(n) symmetries instead of conventional SU(2) symmetry. These symmetries can be experimentally realized and the specific value of n can be controlled by gate voltage.

  2. Nanopore analytics: sensing of single molecules. (United States)

    Howorka, Stefan; Siwy, Zuzanna


    In nanopore analytics, individual molecules pass through a single nanopore giving rise to detectable temporary blockades in ionic pore current. Reflecting its simplicity, nanopore analytics has gained popularity and can be conducted with natural protein as well as man-made polymeric and inorganic pores. The spectrum of detectable analytes ranges from nucleic acids, peptides, proteins, and biomolecular complexes to organic polymers and small molecules. Apart from being an analytical tool, nanopores have developed into a general platform technology to investigate the biophysics, physicochemistry, and chemistry of individual molecules (critical review, 310 references).

  3. Molecular Wring Resonances in Chain Molecules

    DEFF Research Database (Denmark)

    Bohr, Henrik; Brunak, Søren; Bohr, Jakob


    It is shown that the eigenfrequency of collective twist excitations in chain molecules can be in the megahertz and gigahertz range. Accordingly, resonance states can be obtained at specific frequencies, and phenomena that involve structural properties can take place. Chain molecules can alter...... their conformation and their ability to function, and a breaking of the chain can result. It is suggested that this phenomenon forms the basis for effects caused by the interaction of microwaves and biomolecules, e.g. microwave assisted hydrolysis of chain molecules....

  4. Tunable optical absorption in silicene molecules

    KAUST Repository

    Mokkath, Junais Habeeb


    Two-dimensional materials with a tunable band gap that covers a wide range of the solar spectrum hold great promise for sunlight harvesting. For this reason, we investigate the structural, electronic, and optical properties of silicene molecules using time dependent density functional theory. We address the influence of the molecular size, buckling, and charge state as well as that of a dielectric environment. Unlike planar graphene molecules, silicene molecules prefer to form low-buckled structures with strong visible to ultraviolet optical response. We also identify molecular plasmons.


    Perkel, Jeffrey


    More techniques aimed at probing the nature of single molecules are being developed and advanced in biophysics labs. Jeffrey Perkel takes a look at the scientists leading the charge into the micro-world.

  6. Single-Molecule Studies in Live Cells (United States)

    Yu, Ji


    Live-cell single-molecule experiments are now widely used to study complex biological processes such as signal transduction, self-assembly, active trafficking, and gene regulation. These experiments' increased popularity results in part from rapid methodological developments that have significantly lowered the technical barriers to performing them. Another important advance is the development of novel statistical algorithms, which, by modeling the stochastic behaviors of single molecules, can be used to extract systemic parameters describing the in vivo biochemistry or super-resolution localization of biological molecules within their physiological environment. This review discusses recent advances in experimental and computational strategies for live-cell single-molecule studies, as well as a selected subset of biological studies that have utilized these new technologies.

  7. The evolution of polymorphic compatibility molecules

    NARCIS (Netherlands)

    Boer, R.J. de


    Several primitive colonial organisms distinguish self from nonself by means of polymorphic compatibility molecules bearing similarity to the major histocompatibility complex (MHC). The evolution of such polymorphisms is generally explained in terms of resistance to parasites. Ignoring parasites, I d

  8. Stochastic Models of Molecule Formation on Dust (United States)

    Charnley, Steven; Wirstroem, Eva


    We will present new theoretical models for the formation of molecules on dust. The growth of ice mantles and their layered structure is accounted for and compared directly to observations through simulation of the expected ice absorption spectra

  9. Spin polarization effect for Os2 molecule

    Institute of Scientific and Technical Information of China (English)

    Xie An-Dong; Yan Shi-Ying; Zhu Zheng-He; Fu Yi-Bei


    Density functional Theory (DFT) (B3p86) of Gaussian03 has been used to optimize the structure of Os2 molecule.The result shows that the ground state for Os2 molecule is 9-multiple state and its electronic configuration is 9∑+g,which shows spin polarization effect of Os2 molecule of transition metal elements for the first time. Meanwhile, we have not found any spin pollution because the wavefunction of the ground state does not mingle with wavefunctions with higher energy states. So, the fact that the ground state for Os2 molecule is a 9-multiple state is indicative of spin polarization effect of Os2 molecule of transition metal elements. That is, there exist 8 parallel spin electrons.The non-conjugated electron is greatest in number. These electrons occupy different spacious tracks, so that the energy of Os2 molecule is minimized. It can be concluded that the effect of parallel spin of Os2 molecule is larger than the effect of the conjugated molecule, which is obviously related to the effect of electron d delocalization. In addition, the Murrell-Sorbie potential functions with the parameters for the ground state 9∑+g and other states of Os2 molecule are derived. Dissociation energy De for the ground state of Os2 molecule is 3.3971eV, equilibrium bond length Re is 0.2403nm, vibration frequency ωe is 235.32cm-1. Its force constants f2, f3, and f4 are 3.1032×102aJ.nm-2,-14.3425×103aJ.nm-3 and 50.5792×104aJ.nm-4 respectively. The other spectroscopic data for the ground state of Os2 molecule ωeχe, Be and αe are 0.4277cm-1, 0.0307cm-1 and 0.6491× 10-4cm-1 respectively.

  10. (pro)renin receptor: A stable molecule


    Wiwanitkit, Viroj


    Background: Basically, (pro)renin acts via a specific receptor, (pro)renin receptor (PRR) binding between renin and prorenin, its inactive proenzyme form. The study on the molecular level of PRR can give useful knowledge to help understand many renal disorders. Method: Here, the author focuses on the stability of the PRR molecule. The mutation prone positions within the PRR molecule was assessed using standard reference technique. Result: The study showed there is no identified mutation prone...

  11. Probing halo molecules with nonresonant light

    CERN Document Server

    Lemeshko, Mikhail


    We show that halo molecules can be probed by "shaking" in a pulsed nonresonant laser field. The field introduces a centrifugal term which expels the highest vibrational level from the potential that binds it. Our numerical simulations as well as an analytic model applied to the Rb$_2$ and KRb Feshbach molecules indicate that shaking by feasible laser pulses can be used to accurately recover the square of the vibrational wavefunction and, by inversion, also the molecular potential.

  12. On Chiral Space Groups and Chiral Molecules

    Institute of Scientific and Technical Information of China (English)


    This note explains the relationship (as well as the absence of a relationship) between chiral space groups and chiral molecules (which have absolute configurations). For a chiral molecule, which must crystallize in a chiral space group, the outcome of the absolute configuration determination must be linked to some other properties of the chiral crystal such as its optical activity for the observation to the relevant.

  13. On Chiral Space Groups and Chiral Molecules

    Institute of Scientific and Technical Information of China (English)

    NgSeikWng; HUSheng-Zhi


    This note explains the relationship (as well as the absence of a relationship) between chiral space groups and chiral molecules (which have absolute configurations).For a chiral molecule,which must crystallize in a chiral space group,the outcome of the absolute configuration determination must be linked to some other properties of the chiral crystal such as its optical activity for the observation to the relevant.

  14. New issues in zero dimensions: magnetic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Luban, M. E-mail:


    We discuss some major features of isolated magnetic molecules where intermolecular magnetic interactions are negligible and the magnetic properties are determined using a Heisenberg model of intramolecular exchange between a relatively small number of diverse paramagnetic ions. We survey some of the more challenging issues and results that have emerged to date, including the spectrum of excitations, effects of geometric frustration, and critical slowing down of the spin dynamics at low temperatures. Primary attention is given to realizable magnetic molecules.

  15. Hadronic molecules in the heavy baryon spectrum (United States)

    Entem, D. R.; Ortega, P. G.; Fernández, F.


    We study possible baryon molecules in the non-strange heavy baryon spectrum. We include configurations with a heavy-meson and a light baryon. We find several structures, in particular we can understand the Λc(2940) as a D*N molecule with JP = 3/2- quantum numbers. We also find D(*)Δ candidates for the recently discovered Xc(3250) resonance.

  16. Sol-gel method for encapsulating molecules (United States)

    Brinker, C. Jeffrey; Ashley, Carol S.; Bhatia, Rimple; Singh, Anup K.


    A method for encapsulating organic molecules, and in particular, biomolecules using sol-gel chemistry. A silica sol is prepared from an aqueous alkali metal silicate solution, such as a mixture of silicon dioxide and sodium or potassium oxide in water. The pH is adjusted to a suitably low value to stabilize the sol by minimizing the rate of siloxane condensation, thereby allowing storage stability of the sol prior to gelation. The organic molecules, generally in solution, is then added with the organic molecules being encapsulated in the sol matrix. After aging, either a thin film can be prepared or a gel can be formed with the encapsulated molecules. Depending upon the acid used, pH, and other processing conditions, the gelation time can be from one minute up to several days. In the method of the present invention, no alcohols are generated as by-products during the sol-gel and encapsulation steps. The organic molecules can be added at any desired pH value, where the pH value is generally chosen to achieve the desired reactivity of the organic molecules. The method of the present invention thereby presents a sufficiently mild encapsulation method to retain a significant portion of the activity of the biomolecules, compared with the activity of the biomolecules in free solution.

  17. Molecules on si: electronics with chemistry. (United States)

    Vilan, Ayelet; Yaffe, Omer; Biller, Ariel; Salomon, Adi; Kahn, Antoine; Cahen, David


    Basic scientific interest in using a semiconducting electrode in molecule-based electronics arises from the rich electrostatic landscape presented by semiconductor interfaces. Technological interest rests on the promise that combining existing semiconductor (primarily Si) electronics with (mostly organic) molecules will result in a whole that is larger than the sum of its parts. Such a hybrid approach appears presently particularly relevant for sensors and photovoltaics. Semiconductors, especially Si, present an important experimental test-bed for assessing electronic transport behavior of molecules, because they allow varying the critical interface energetics without, to a first approximation, altering the interfacial chemistry. To investigate semiconductor-molecule electronics we need reproducible, high-yield preparations of samples that allow reliable and reproducible data collection. Only in that way can we explore how the molecule/electrode interfaces affect or even dictate charge transport, which may then provide a basis for models with predictive power.To consider these issues and questions we will, in this Progress Report, review junctions based on direct bonding of molecules to oxide-free Si.describe the possible charge transport mechanisms across such interfaces and evaluate in how far they can be quantified.investigate to what extent imperfections in the monolayer are important for transport across the monolayer.revisit the concept of energy levels in such hybrid systems.

  18. Spin polarization effect for molecule Ta2

    Institute of Scientific and Technical Information of China (English)

    Xie An-Dong


    Density functional theory (DFT) (B3p86) has been used to optimize the structure of the molecule Taa- The result shows that the ground state of molecule Ta,2 is a 7- multiple state and its electronic configuration is 7∑+u which shows the spin polarization effect for molecule Ta2 of transition metal elements for the first time. Meanwhile, spin pollution has not been found because the wavefunction of the ground state does not mix with those of higher states. So, the fact that the ground state of molecule Ta2 is a 7-multiple state indicates a spin polarization effect of molecule Ta2 of the transition metal elements, i.e. there exist 6 parallel spin electrons and the non-conjugated electrons are greatest in number. These electrons occupy different space orbitals so that the energy of molecule Ta2 is minimized. It can be concluded that the effect of parallel spin of the molecule Ta2 is larger than the effect of the conjugated molecule, which is obviously related to the effect of d-electron delocalization. In addition, the Murrell-Sorbie potential functions with parameters for the ground state 7∑+u and other states of the molecule Ta2 are derived. The dissociation energy De, equilibrium bond length Re and vibration frequency ωe for the ground state of molecule Ta2 are 4.5513eV, 0.2433nm and 173.06cm-1, respectively. Its force constants f2,f3 and f4 are 1.5965×l02aJ·nm-2,-6.4722×l03aJ·nm-3 and 29.4851×04aJ·nm-4, respectively. Other spectroscopic data ωe χe, Be and αe for the ground state of Ta2 are 0.2078cm-1, 0.0315cm-1 and 0.7858×104 cm-1, respectively.

  19. Single-Molecule Electronics with Cross- Conjugated Molecules: Quantum Interference, IETS and Non-Equilibrium "Temperatures"

    DEFF Research Database (Denmark)

    Jørgensen, Jacob Lykkebo

    , which is characterised by destructive quantum interference. The molecules are cross-conjugated, which means that the two parts of the molecules are conjugated to a third part, but not to each other. This gives rise to an anti-resonance in the trans- mission. In the low bias and low temperature regime......, the electrons can tunnel in- elastically from the left to the right electrode. This is the process behind inelastic electron tunnelling spectroscopy (IETS), which is a single-molecule spectroscopic method, where the vibrational ngerprint of a molecule is di- rectly observed by the tunnelling current......-conjugated molecules. We nd that the vibrational modes that would be expected to dominate, following the propensity, rules are very weak. Instead, other modes are found to be the dominant ones. We study this phenomenon for a number of cross-conjugated molecules, and link these ndings to the anti...

  20. Quantum Computer Using Coupled Quantum Dot Molecules

    CERN Document Server

    Wu, N J; Natori, A; Yasunaga, H; Wu*, Nan-Jian


    We propose a method for implementation of a quantum computer using artificial molecules. The artificial molecule consists of two coupled quantum dots stacked along z direction and one single electron. One-qubit and two-qubit gates are constructed by one molecule and two coupled molecules, respectively.The ground state and the first excited state of the molecule are used to encode the |0> and |1> states of a qubit. The qubit is manipulated by a resonant electromagnetic wave that is applied directly to the qubit through a microstrip line. The coupling between two qubits in a quantum controlled NOT gate is switched on (off) by floating (grounding) the metal film electrodes. We study the operations of the gates by using a box-shaped quantum dot model and numerically solving a time-dependent Schridinger equation, and demonstrate that the quantum gates can perform the quantum computation. The operating speed of the gates is about one operation per 4ps. The reading operation of the output of the quantum computer can...

  1. Capillary condensation of short-chain molecules. (United States)

    Bryk, Paweł; Pizio, Orest; Sokolowski, Stefan


    A density-functional study of capillary condensation of fluids of short-chain molecules confined to slitlike pores is presented. The molecules are modeled as freely jointed tangent spherical segments with a hard core and with short-range attractive interaction between all the segments. We investigate how the critical parameters of capillary condensation of the fluid change when the pore width decreases and eventually becomes smaller than the nominal linear dimension of the single-chain molecule. We find that the dependence of critical parameters for a fluid of dimers and of tetramers on pore width is similar to that of the monomer fluid. On the other hand, for a fluid of chains consisting of a larger number of segments we observe an inversion effect. Namely, the critical temperature of capillary condensation decreases with increasing pore width for a certain interval of values of the pore width. This anomalous behavior is also influenced by the interaction between molecules and pore walls. We attribute this behavior to the effect of conformational changes of molecules upon confinement.

  2. Direct laser cooling of the BH molecule (United States)

    Holland, Darren; Truppe, Stefan; Hendricks, Richard; Sauer, Ben; Tarbutt, Michael


    Ultracold polar molecules are of interest for a variety of applications, including tests of fundamental physics, ultracold chemistry, and simulation of many-body quantum systems. The laser cooling techniques that have been so successful in producing ultracold atoms are difficult to apply to molecules. Recently however, laser cooling has been applied successfully to a few molecular species, and a magneto-optical trap of SrF molecules has now been demonstrated. We have investigated the BH molecule as a candidate for laser cooling. We have produced a molecular beam of BH and have measured the branching ratios for the excited electronic state, A1 Π (v' = 0) , to decay to the various vibrational states of the ground electronic state, X1 Σ . We verify that the branching ratio for the spin-forbidden transition to an intermediate triplet state is inconsequentially small. We measure the frequency of the lowest rotational transition of the X state, and the hyperfine structure in the relevant levels of both the X and A states, and determine the nuclear electric quadrupole and magnetic dipole coupling constants. Our results show that a relatively simple laser cooling scheme can be used to cool, slow and trap BH molecules.

  3. Classical interaction model for the water molecule. (United States)

    Baranyai, András; Bartók, Albert


    The authors propose a new classical model for the water molecule. The geometry of the molecule is built on the rigid TIP5P model and has the experimental gas phase dipole moment of water created by four equal point charges. The model preserves its rigidity but the size of the charges increases or decreases following the electric field created by the rest of the molecules. The polarization is expressed by an electric field dependent nonlinear polarization function. The increasing dipole of the molecule slightly increases the size of the water molecule expressed by the oxygen-centered sigma parameter of the Lennard-Jones interaction. After refining the adjustable parameters, the authors performed Monte Carlo simulations to check the ability of the new model in the ice, liquid, and gas phases. They determined the density and internal energy of several ice polymorphs, liquid water, and gaseous water and calculated the heat capacity, the isothermal compressibility, the isobar heat expansion coefficients, and the dielectric constant of ambient water. They also determined the pair-correlation functions of ambient water and calculated the energy of the water dimer. The accuracy of theirs results was satisfactory.

  4. Universal deceleration of highly polar molecules (United States)

    Hamamda, Mehdi; Pillet, Pierre; Lignier, Hans; Comparat, Daniel


    We propose a method to produce, in a pulsed or continuous way, cold samples of highly polar molecules. Using a pulsed or continuous standard (supersonic) beam of these molecules, our idea consists of transforming the molecules into their anionic counterparts, which are decelerated to a standstill by a well-controlled external electric field and ultimately neutralized. The neutral-to-anion transformation occurs through collisions with Rydberg atoms coming from an additional atomic beam. This Rydberg electron transfer process is possible provided that the molecular species has a sufficiently strong electric dipole (\\gt 2.5 D, i.e., \\gt 8.3× {{10}-30} cm). Whatever the mass of the species, the deceleration stage is realized by a temporally and spatially controlled electric field within a range of less than one centimeter, which is much shorter than in current deceleration experiments of neutral molecules. Once stopped, the molecular anions are neutralized by laser photodetachment or a pulsed electric field process. The resulting molecules might be held and accumulated, for instance, in a magnetic trap.

  5. Enlarged Molecules from Excited Atoms in Nanochannels

    CERN Document Server

    Boström, Mathias; Sernelius, Bo E; Dou, Maofeng; Persson, Clas; Ninham, Barry W


    The resonance interaction that takes place in planar nanochannels between pairs of excited state atoms is explored. We consider interactions in channels of silica, zinc oxide and gold. The nanosized channels induce a dramatically different interaction from that in free space. Illustrative calculations for two lithium and cesium atoms, demonstrate that there is a short range repulsion followed by long range attraction. The binding energy is strongest near the surfaces. The size of the enlarged molecule is biggest at the center of the cavity and increases with channel width. Since the interaction is generic, we predict that enlarged molecules are formed in porous structures, and that the molecule size depends on the size of the nanochannels

  6. Observational astrochemistry: The quest for interstellar molecules

    Directory of Open Access Journals (Sweden)

    Guélin M.


    Full Text Available Over 160 molecular species, not counting isotopologues, have been identified in circumstellar envelopes and interstellar clouds. These species have revealed a wealth of familiar, as much as exotic molecules and in complex organic (and silicon compounds, that was fully unexpected in view of the harshness of surrounding conditions: vanishingly low densities, extreme temperatures and intense embedding UV radiation. They illustrate the diversity of astrochemistry and show robust prebiotic molecules may be. In this lecture, we review the quest for interstellar molecules and show how tributary it is from theoretical ideas and technology developments. A. A. Penzias, who discovered interstellar CO and the 2.7 K Cosmic Background radiation, used to joke that astronomical research is easy: the great questions have largely been formulated; one only has to wait until technological progress makes it possible to answer.

  7. Complex Organic Molecules in Protoplanetary Disks (United States)

    Walsh, Catherine; Millar, T. J.; Nomura, H.; Herbst, E.; Widicus-Weaver, S.


    Protoplanetary disks are vital objects in star and planet formation. In addition to aiding mass accretion onto the central star and angular momentum dissipation, they also contain all material which may form an orbiting planetary system. Of great interest to the astrochemistry and astrobiology communities is the origin of prebiotic molecules, considered the "building blocks" of Life. Is it possible for complex molecules to form in protoplanetary disks and survive assimilation into planets and other planetary system objects, such as, comets? We explore the synthesis of large complex organic molecules (COMs) in protoplanetary disks which encompass young stars. We use a chemical network primarily developed for use in hot core models to calculate the abundance and distribution of gas-phase and grain-mantle (ice) COMs and discuss the potential of observing the gas-phase form of these species with new facilities, such as, ALMA.

  8. Prebiotically Important Molecules in Orion KL (United States)

    Kuan, Yi-Jehng; Chuang, Yo-Ling

    Many interstellar, complex organic molecules are known to be prebiotically important and have essential functions in terrestrial biochemistry. Observations of complex organic molecular species in molecular clouds can thus enable us to test the origin of the primitive organic material found in the Solar System. Interstellar pyrimidine and glycine, the building block of nucleic acid and the simplest amino acid, respectively, are key molecules for astrobiology and were both detected in meteorites and comets. Although the formation of prebiotic molecules in extraterrestrial environments and their contribution to prebiotic chemistry and the origin of life remains unsettled, the connection between interstellar organic chemistry, meteoritic pyrimidines and amino acids, and the emergence of life on the early Earth would be strengthened with the discovery of interstellar pyrimidine and glycine. We have therefore observed the Orion KL hot molecular core to search for interstellar pyrimidine and for the confirmation of interstellar glycine using the ALMA array. We will present some of the encouraging, positive results.

  9. Theoretical study on single-molecule spectroscopy

    Institute of Scientific and Technical Information of China (English)

    SHAN Guang-cun; HUANG Wei


    The photon-by-photon approach for single molecule spectroscopy experiments utilizes the information carried by each detected photon and allows the measurements of conformational fluctuation with time resolution on a vast range of time scales,where each photon represents a data point.Here,we theoretically simulate the photon emission dynamics of a single molecule spectroscopy using the kinetic Monte Carlo algorithm to understand the underlying complex photon dynamic process of a single molecule.In addition,by following the molecular process in real time,the mechanism of complex biochemical reactions can be revealed.We hope that this theoretical study will serve as an introduction and a guideline into this exciting new field.

  10. Single molecule transcription profiling with AFM

    Energy Technology Data Exchange (ETDEWEB)

    Reed, Jason [Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (United States); Mishra, Bud [Departments of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Pittenger, Bede [Veeco Instruments, Santa Barbara, CA 93117 (United States); Magonov, Sergei [Veeco Instruments, Santa Barbara, CA 93117 (United States); Troke, Joshua [Department of Pathology and Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095 (United States); Teitell, Michael A [Department of Pathology and Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095 (United States); Gimzewski, James K [Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (United States)


    Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.

  11. Diamond based single molecule magnetic resonance spectroscopy

    CERN Document Server

    Cai, J -M; Plenio, M B; Retzker, A


    The detection of a nuclear spin in an individual molecule represents a key challenge in physics and biology whose solution has been pursued for many years. The small magnetic moment of a single nucleus and the unavoidable environmental noise present the key obstacles for its realization. Here, we theoretically demonstrate that a single nitrogen-vacancy (NV) center in diamond can be used to construct a nano-scale single molecule spectrometer that is capable of detecting the position and spin state of a single nucleus and can determine the distance and alignment of a nuclear or electron spin pair. In combination with organic spin labels, this device will find applications in single molecule spectroscopy in chemistry and biology, such as in determining protein structure or monitoring macromolecular motions and can thus provide a tool to help unravelling the microscopic mechanisms underlying bio-molecular function.

  12. Single Molecule Sensitive FRET in Attoliter Droplets

    CERN Document Server

    Milas, Peker; Gamari, Ben D; Goldner, Lori S


    Single molecular-pair fluorescence resonance energy transfer (spFRET) has become an cross-disciplinary tool for understanding molecular folding and interactions. While providing detailed information about the individual members of a molecular ensemble, this technique is always limited by fluorophore brightness and stability. In the case of diffusing molecules, the experiment is further limited by the number of photons that can be collected during the time it takes for a molecule to diffuse across the detection volume. To maximize the number of photons it is common to either increase the detection volume at the expense of increased background, or increase the diffusion time by adding glycerol or sucrose to increase viscosity. Here we demonstrate that FRET from attoliter volume (100 nm radius) aqueous droplets in perfluorinated oil has significantly higher signal-to-noise and a much wider dynamic range than FRET from molecules diffusing in solution. However, our measurements also reveal a droplet environment th...

  13. Adhesion molecules in experimental phacoanaphylactic endophthalmitis. (United States)

    Till, G O; Lee, S; Mulligan, M S; Wolter, J R; Smith, C W; Ward, P A; Marak, G E


    Intraocular accumulation of inflammatory neutrophils is an important feature of experimental phacoanaphylactic endophthalmitis (EPE). Increasing evidence suggests that localization of neutrophils to the site of inflammation requires the participation of neutrophil and endothelial adhesion molecules. These studies were undertaken to determine if blocking of adhesion molecules on neutrophils (CD18) or endothelium (ELAM-1) could attenuate EPE in Lewis rats. Treatment of experimental animals with anti-CD18 or anti-ELAM-1 significantly suppressed intraocular neutrophil accumulation, retinal hemorrhage, and vasculitis, and attenuated retinal edema formation by 48% and 70%, respectively. These observations demonstrate that antibodies directed against adhesion molecules on the neutrophil (CD18) or the vascular endothelial cell (ELAM-1) exhibit potent anti-inflammatory effects, resulting in a striking amelioration of injury in EPE in rats.

  14. Protein Scaffolding for Small Molecule Catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Baker, David [Univ. of Washington, Seattle, WA (United States)


    We aim to design hybrid catalysts for energy production and storage that combine the high specificity, affinity, and tunability of proteins with the potent chemical reactivities of small organometallic molecules. The widely used Rosetta and RosettaDesign methodologies will be extended to model novel protein / small molecule catalysts in which one or many small molecule active centers are supported and coordinated by protein scaffolding. The promise of such hybrid molecular systems will be demonstrated with the nickel-phosphine hydrogenase of DuBois et. al.We will enhance the hydrogenase activity of the catalyst by designing protein scaffolds that incorporate proton relays and systematically modulate the local environment of the catalyticcenter. In collaboration with DuBois and Shaw, the designs will be experimentally synthesized and characterized.

  15. Chiral Molecules Revisited by Broadband Microwave Spectroscopy (United States)

    Schnell, Melanie


    Chiral molecules have fascinated chemists for more than 150 years. While their physical properties are to a very good approximation identical, the two enantiomers of a chiral molecule can have completely different (bio)chemical activities. For example, the right-handed enantiomer of carvone smells of spearmint while the left-handed one smells of caraway. In addition, the active components of many drugs are of one specific handedness, such as in the case of ibuprofen. However, in nature as well as in pharmaceutical applications, chiral molecules often exist in mixtures with other chiral molecules. The analysis of these complex mixtures to identify the molecular components, to determine which enantiomers are present, and to measure the enantiomeric excesses (ee) remains a challenging task for analytical chemistry, despite its importance for modern drug development. We present here a new method of differentiating enantiomers of chiral molecules in the gas phase based on broadband rotational spectroscopy. The phase of the acquired signal bares the signature of the enantiomer, as it depends upon the combined quantity, μ_a μ_b μ_c, which is of opposite sign between enantiomers. It thus also provides information on the absolute configuration of the particular enantiomer. Furthermore, the signal amplitude is proportional to the ee. A significant advantage of our technique is its inherent mixture compatibility due to the fingerprint-like character of rotational spectra. In this contribution, we will introduce the technique and present our latest results on chiral molecule spectroscopy and enantiomer differentiation. D. Patterson, M. Schnell, J.M. Doyle, Nature 497 (2013) 475-477 V.A. Shubert, D. Schmitz, D. Patterson, J.M. Doyle, M. Schnell, Angewandte Chemie International Edition 53 (2014) 1152-1155

  16. Simple and advanced ferromagnet/molecule spinterfaces (United States)

    Gruber, M.; Ibrahim, F.; Djedhloul, F.; Barraud, C.; Garreau, G.; Boukari, S.; Isshiki, H.; Joly, L.; Urbain, E.; Peter, M.; Studniarek, M.; Da Costa, V.; Jabbar, H.; Bulou, H.; Davesne, V.; Halisdemir, U.; Chen, J.; Xenioti, D.; Arabski, J.; Bouzehouane, K.; Deranlot, C.; Fusil, S.; Otero, E.; Choueikani, F.; Chen, K.; Ohresser, P.; Bertran, F.; Le Fèvre, P.; Taleb-Ibrahimi, A.; Wulfhekel, W.; Hajjar-Garreau, S.; Wetzel, P.; Seneor, P.; Mattana, R.; Petroff, F.; Scheurer, F.; Weber, W.; Alouani, M.; Beaurepaire, E.; Bowen, M.


    Spin-polarized charge transfer between a ferromagnet and a molecule can promote molecular ferromagnetism 1, 2 and hybridized interfacial states3, 4. Observations of high spin-polarization of Fermi level states at room temperature5 designate such interfaces as a very promising candidate toward achieving a highly spin-polarized, nanoscale current source at room temperature, when compared to other solutions such as half-metallic systems and solid-state tunnelling over the past decades. We will discuss three aspects of this research. 1) Does the ferromagnet/molecule interface, also called an organic spinterface, exhibit this high spin-polarization as a generic feature? Spin-polarized photoemission experiments reveal that a high spin-polarization of electronics states at the Fermi level also exist at the simple interface between ferromagnetic cobalt and amorphous carbon6. Furthermore, this effect is general to an array of ferromagnetic and molecular candidates7. 2) Integrating molecules with intrinsic properties (e.g. spin crossover molecules) into a spinterface toward enhanced functionality requires lowering the charge transfer onto the molecule8 while magnetizing it1,2. We propose to achieve this by utilizing interlayer exchange coupling within a more advanced organic spinterface architecture. We present results at room temperature across the fcc Co(001)/Cu/manganese phthalocyanine (MnPc) system9. 3) Finally, we discuss how the Co/MnPc spinterface's ferromagnetism stabilizes antiferromagnetic ordering at room temperature onto subsequent molecules away from the spinterface, which in turn can exchange bias the Co layer at low temperature10. Consequences include tunnelling anisotropic magnetoresistance across a CoPc tunnel barrier11. This augurs new possibilities to transmit spin information across organic semiconductors using spin flip excitations12.

  17. A toy model for a diatomic molecule (United States)

    Hecker Denschlag, Johannes


    We introduce a toy model for a diatomic molecule which is based on coupling electronic and nuclear spins to a rigid rotor. Despite its simplicity, the model can be used scientifically to analyze and understand complex molecular hyperfine spectra. In addition, the model has educational value as a number of fundamental symmetries and conservation laws of the molecule can be studied. Because of its simple structure, the model can be readily implemented as a computer program with comparatively short computing times on the order of a few seconds.

  18. Magneto-optical trap for polar molecules. (United States)

    Stuhl, Benjamin K; Sawyer, Brian C; Wang, Dajun; Ye, Jun


    We propose a method for laser cooling and trapping a substantial class of polar molecules and, in particular, titanium (II) oxide (TiO). This method uses pulsed electric fields to nonadiabatically remix the ground-state magnetic sublevels of the molecule, allowing one to build a magneto-optical trap based on a quasicycling J' = J'' -1 transition. Monte Carlo simulations of this electrostatically remixed magneto-optical trap demonstrate the feasibility of cooling TiO to a temperature of 10 micrpK and trapping it with a radiation-pumping-limited lifetime on the order of 80 ms.

  19. Extracellular Molecules Involved in Cancer Cell Invasion

    Energy Technology Data Exchange (ETDEWEB)

    Stivarou, Theodora; Patsavoudi, Evangelia, E-mail: [Department of Biochemistry, Hellenic Pasteur Institute, Athens 11521 (Greece); Technological Educational Institute of Athens, Egaleo, Athens 12210 (Greece)


    Nowadays it is perfectly clear that understanding and eradicating cancer cell invasion and metastasis represent the crucial, definitive points in cancer therapeutics. During the last two decades there has been a great interest in the understanding of the extracellular molecular mechanisms involved in cancer cell invasion. In this review, we highlight the findings concerning these processes, focusing in particular on extracellular molecules, including extracellular matrix proteins and their receptors, growth factors and their receptors, matrix metalloproteinases and extracellular chaperones. We report the molecular mechanisms underlying the important contribution of this pool of molecules to the complex, multi-step phenomenon of cancer cell invasion.

  20. Photoassociative production of ultracold heteronuclear ytterbium molecules

    Energy Technology Data Exchange (ETDEWEB)

    Borkowski, Mateusz; Ciurylo, Roman [Instytut Fizyki, Uniwersytet Mikolaja Kopernika, ul. Grudziadzka 5/7, PL-87-100 Torun (Poland); Julienne, Paul S. [Joint Quantum Institute, National Institute of Standards and Technology and the University of Maryland, 100 Bureau Drive, Stop 8423, Gaithersburg, Maryland 20899-8423 (United States); Yamazaki, Rekishu; Takahashi, Yoshiro [Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); CREST, JST, 4-1-8 Honcho Kawaguchi, Saitama 332-0012 (Japan); Hara, Hideaki; Taie, Shintaro; Sugawa, Seiji; Takasu, Yosuke [Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Enomoto, Katsunari [Department of Physics, University of Toyama, Toyama 930-8555 (Japan)


    We report observations of photoassociation (PA) spectra near the intercombination line in isotopic mixtures of ultracold ytterbium gases. Several heteronuclear bound states have been found for the excited {sup 170}Yb{sup 174}Yb and {sup 174}Yb{sup 176}Yb molecules. We develop a single-channel mass-scaled interaction model for the excited state molecule which well reproduces the measured bound state energies. This is an important step toward optical control of interactions in mixtures of ultracold ytterbium gases using heteronuclear optical Feshbach resonances. The model developed is applicable in collisions of other similar systems, such as cadmium and mercury.

  1. Extracellular Molecules Involved in Cancer Cell Invasion

    Directory of Open Access Journals (Sweden)

    Theodora Stivarou


    Full Text Available Nowadays it is perfectly clear that understanding and eradicating cancer cell invasion and metastasis represent the crucial, definitive points in cancer therapeutics. During the last two decades there has been a great interest in the understanding of the extracellular molecular mechanisms involved in cancer cell invasion. In this review, we highlight the findings concerning these processes, focusing in particular on extracellular molecules, including extracellular matrix proteins and their receptors, growth factors and their receptors, matrix metalloproteinases and extracellular chaperones. We report the molecular mechanisms underlying the important contribution of this pool of molecules to the complex, multi-step phenomenon of cancer cell invasion.

  2. Organic- and molecule-based magnets

    Indian Academy of Sciences (India)

    Joel S Miller


    The discovery of organic- and molecule-based magnets has led to design and synthesis of several families with magnetic ordering temperatures as high as ∼ 125° C. Examples of soft and hard magnets with coercivities as high as 27 kOe have also been reported. Examples from our laboratory of organic-based magnets using the tetracya- noethylene radical anion, [TCNE]$^{\\bullet -}$, are discussed. In addition, several molecule-based magnets based on Prussian Blue structured materials as well as dicyanamide are discussed.

  3. Hadronic molecules with hidden charm and bottom

    Directory of Open Access Journals (Sweden)

    Guo Feng-Kun


    Full Text Available Many of the new structures observed since 2003 in experiments in the heavy quarkonium mass region, such as the X(3872 and Zc (3900, are rather close to certain thresholds, and thus can be good candidates of hadronic molecules, which are loose bound systems of hadrons. We will discuss the consequences of heavy quark symmetry for hadronic molecules with heavy quarks. We will also emphasize that the hadronic molecular component of a given structure can be directly probed in long-distance processes, while the short-distance processes are not sensitive to it.

  4. Evidence of water molecules--a statistical evaluation of water molecules based on electron density. (United States)

    Nittinger, Eva; Schneider, Nadine; Lange, Gudrun; Rarey, Matthias


    Water molecules play important roles in many biological processes, especially when mediating protein-ligand interactions. Dehydration and the hydrophobic effect are of central importance for estimating binding affinities. Due to the specific geometric characteristics of hydrogen bond functions of water molecules, meaning two acceptor and two donor functions in a tetrahedral arrangement, they have to be modeled accurately. Despite many attempts in the past years, accurate prediction of water molecules-structurally as well as energetically-remains a grand challenge. One reason is certainly the lack of experimental data, since energetic contributions of water molecules can only be measured indirectly. However, on the structural side, the electron density clearly shows the positions of stable water molecules. This information has the potential to improve models on water structure and energy in proteins and protein interfaces. On the basis of a high-resolution subset of the Protein Data Bank, we have conducted an extensive statistical analysis of 2.3 million water molecules, discriminating those water molecules that are well resolved and those without much evidence of electron density. In order to perform this classification, we introduce a new measurement of electron density around an individual atom enabling the automatic quantification of experimental support. On the basis of this measurement, we present an analysis of water molecules with a detailed profile of geometric and structural features. This data, which is freely available, can be applied to not only modeling and validation of new water models in structural biology but also in molecular design.

  5. Evidence of disorder in biological molecules from single molecule pulling experiments

    CERN Document Server

    Hyeon, Changbong; Thirumalai, D


    Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an exactly solvable model in which the unfolding rate due to mechanical force depends parametrically on an auxiliary variable representing an entropy barrier arising from fluctuations in internal dynamics. When the rate of fluctuations, a measure of dynamical disorder, is comparable to or smaller than the rate of force-induced unbinding, we show that there are two experimentally observable consequences: non-exponential survival probability at constant force, and a heavy-tailed rupture force distribution at constant loading rate. By fitting our analytical expressions to data from single molecule pulling experiments on proteins and DNA, we quantify the extent of disorder. We show that only by analyzing data over a wide range of forces and loading rates can the role of disorder due...

  6. Strategy to discover diverse optimal molecules in the small molecule universe. (United States)

    Rupakheti, Chetan; Virshup, Aaron; Yang, Weitao; Beratan, David N


    The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 , 7296 - 7303 ) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10(5) molecules.

  7. Making More-Complex Molecules Using Superthermal Atom/Molecule Collisions (United States)

    Shortt, Brian; Chutjian, Ara; Orient, Otto


    A method of making more-complex molecules from simpler ones has emerged as a by-product of an experimental study in outer-space atom/surface collision physics. The subject of the study was the formation of CO2 molecules as a result of impingement of O atoms at controlled kinetic energies upon cold surfaces onto which CO molecules had been adsorbed. In this study, the O/CO system served as a laboratory model, not only for the formation of CO2 but also for the formation of other compounds through impingement of rapidly moving atoms upon molecules adsorbed on such cold interstellar surfaces as those of dust grains or comets. By contributing to the formation of increasingly complex molecules, including organic ones, this study and related other studies may eventually contribute to understanding of the origins of life.

  8. Large molecules in diffuse interstellar clouds

    NARCIS (Netherlands)

    Lepp, S.; Dalgarno, A.; Dishoeck, van E.F.; Black, J.H.


    The effects of the presence of a substantial component of large molecules on the chemistry of diffuse molecular clouds are explored, and detailed models of the zeta Persei and zeta Ophiuchi clouds are constructed. The major consequence is a reduction in the abundances of singly charged atomic specie

  9. Tunneling ionization of vibrationally excited nitrogen molecules (United States)

    Kornev, Aleksei S.; Zon, Boris A.


    Ionization of molecular nitrogen plays an important role in the process of light-filament formation in air. In the present paper we theoretically investigated tunneling ionization of the valence 3 σg and 1 πu shells in a N2 molecule using a strong near-infrared laser field. This research is based on our previously proposed theory of anti-Stokes-enhanced tunneling ionization with quantum accounting for the vibrationally excited states of the molecules [A. S. Kornev and B. A. Zon, Phys. Rev. A 86, 043401 (2012), 10.1103/PhysRevA.86.043401]. We demonstrated that if the N2 molecule is ionized from the ground vibrational state, then the contribution of the 1 πu orbital is 0.5%. In contrast, for vibrationally excited states with a certain angle between the light polarization vector and the molecule axis, both shells can compete and even reverse their contributions due to the anti-Stokes mechanism. The structure constants of molecular orbitals are extracted from numerical solutions to the Hartree-Fock equations. This approach correctly takes into account the exchange interaction. Quantum consideration of vibrational motion results in the occurrence of the critical vibrational state, the tunneling ionization from which has the maximum rate. The numbers of the critical vibrational states are different for different valence shells. In addition, quantum description of vibrations changes the rate of ionization from the ground vibrational state by 20%-40% in comparison with the quasiclassical results.

  10. The formation of molecules in protostellar winds (United States)

    Glassgold, A. E.; Mamon, G. A.; Huggins, P. J.


    The production and destruction processes for molecules in very fast protostellar winds are analyzed and modeled with a one-dimensional chemical kinetics code. Radial density and temperature distributions suggested by protostellar theory are explored as are a range of mass-loss rates. The efficiency of in situ formation of heavy molecules is found to be high if the wind temperature falls sufficiently rapidly, as indicated by theory. The degree of molecular conversion is a strong function of the mass-loss rate and of density gradients associated with the acceleration and collimation of the wind. Even in cases where essentially all of the heavy atoms are processed into molecules, a significant fraction of atomic hydrogen remains so that hghly molecular, protostellar winds are able to emit the 21-cm line. Although CO has a substantial abundance in most models relevant to very young protostars, high abundances of other molecules such as SiO and H2O signify more complete association characteristic of winds containing regions of very high density. Although the models apply only to regions close to the protostar, they are in qualitative accord with recent observations at much larger distances of both atomic and molecular emission from extremely high-velocity flow.

  11. Field-free orientation of molecules

    DEFF Research Database (Denmark)

    Machholm, Mette; Henriksen, Niels Engholm


    The excitation of angular motion, in particular, the creation of a wave packet in the angular degrees of freedom via short-pulse, off-resonant excitation with respect to rotational transitions, was examined. The key result was that field-free time-dependent orientation for a molecule like LiH can...

  12. Aging-From molecules to populations

    DEFF Research Database (Denmark)

    Sander, Miriam; Avlund, Kirsten; Lauritzen, Martin;


    -From Molecules to Populations. The following questions about human aging were discussed at the workshop: What is the limit of human life expectancy? What are the key indicators of human aging? What are the key drivers of human aging? Which genes have the greatest impact on human aging? How similar is aging...

  13. Comprehensive Map of Molecules Implicated in Obesity.

    Directory of Open Access Journals (Sweden)

    Jaisri Jagannadham

    Full Text Available Obesity is a global epidemic affecting over 1.5 billion people and is one of the risk factors for several diseases such as type 2 diabetes mellitus and hypertension. We have constructed a comprehensive map of the molecules reported to be implicated in obesity. A deep curation strategy was complemented by a novel semi-automated text mining system in order to screen 1,000 full-length research articles and over 90,000 abstracts that are relevant to obesity. We obtain a scale free network of 804 nodes and 971 edges, composed of 510 proteins, 115 genes, 62 complexes, 23 RNA molecules, 83 simple molecules, 3 phenotype and 3 drugs in "bow-tie" architecture. We classify this network into 5 modules and identify new links between the recently discovered fat mass and obesity associated FTO gene with well studied examples such as insulin and leptin. We further built an automated docking pipeline to dock orlistat as well as other drugs against the 24,000 proteins in the human structural proteome to explain the therapeutics and side effects at a network level. Based upon our experiments, we propose that therapeutic effect comes through the binding of one drug with several molecules in target network, and the binding propensity is both statistically significant and different in comparison with any other part of human structural proteome.

  14. Modified "DMC" technique for stretching DNA molecules

    Institute of Scientific and Technical Information of China (English)


    A modified "dynamic molecular combing"(DMC)technique used for stretching double-strandedDNA is reported. DNA molecules were stretched on the silanized mica surface by thistechnique, its speed being precisely controlled with a computer. This approachcombinedthe precise DNA stretching method with high resolution AFM imaging at nanometer scale,thusmaking it useful for DNA alignment manipulation and subsequent gene research.

  15. Molecules during stellar formation and death

    NARCIS (Netherlands)

    Li, Xiaohu


    This thesis explores the chemistry of interstellar and circumstellar molecules during star formation and death. From the perspective of chemical physics, the most important outcome of this thesis lies in that the rates for two important reactions are determined accurately for the first time: N2 phot

  16. Cluster ions and van der Waals molecules

    CERN Document Server

    Smirnov, Boris M


    This review discusses current ideas in the physics and chemistry of cluster ions and Van der Waals molecules as well as presenting numerical data on their parameters and the processes involving them. It is also a detailed reference on basic data relating to many species.

  17. Relativistic Scott correction for atoms and molecules

    DEFF Research Database (Denmark)

    Solovej, Jan Philip; Sørensen, Thomas Østergaard; Spitzer, Wolfgang Ludwig


    We prove the first correction to the leading Thomas-Fermi energy for the ground state energy of atoms and molecules in a model where the kinetic energy of the electrons is treated relativistically. The leading Thomas-Fermi energy, established in [25], as well as the correction given here, are of ...

  18. Photoelectron spectroscopy of heavy atoms and molecules

    Energy Technology Data Exchange (ETDEWEB)

    White, M.G.


    The importance of relativistic interactions in the photoionization of heavy atoms and molecules has been investigated by the technique of photoelectron spectroscopy. In particular, experiments are reported which illustrate the effects of the spin-orbit interaction in the neutral ground state, final ionic states and continuum states of the photoionization target.

  19. Mathematics and Molecules: Exploring Connections via Programming. (United States)

    Ploger, Don; Carlock, Margaret


    Examines the self-directed activity of two students who learned about molecular structure by writing computer programs. The programs displayed the solution of a mathematics problem, then the programs were extended to represent several classes of organic molecules. Different ways to enhance mathematical connections to chemistry education are…

  20. Polypetide signaling molecules in plant development (United States)

    Intercellular communication mediated by small signaling molecules is a key mechanism for coordinating plant growth and development. In the past few years, polypeptide signals have been shown to play prominent roles in processes as diverse as shoot and root meristem maintenance, vascular differentiat...

  1. Origin of organic molecules and biomolecular homochirality. (United States)

    Podlech, J


    Theories about the origin of biomolecular homochirality, which seems to be a prerequisite for the creation of life, are discussed. First, possible terrestrial and extraterrestrial sources of organic molecules are outlined. Then, mechanisms for the formation of enantiomerically enriched compounds and for the amplification of their chirality are described.

  2. Single Molecule Conductance of Oligothiophene Derivatives (United States)

    Dell, Emma J.

    This thesis studies the electronic properties of small organic molecules based on the thiophene motif. If we are to build next-generation devices, advanced materials must be designed which possess requisite electronic functionality. Molecules present attractive candidates for these ad- vanced materials since nanoscale devices are particularly sought after. However, selecting a molecule that is suited to a certain electronic function remains a challenge, and characterization of electronic behavior is therefore critical. Single molecule conductance measurements are a powerful tool to determine properties on the nanoscale and, as such, can be used to investigate novel building blocks that may fulfill the design requirements of next-generation devices. Combining these conductance results with strategic chemical synthesis allows for the development of new families of molecules that show attractive properties for future electronic devices. Since thiophene rings are the fruitflies of organic semiconductors on the bulk scale, they present an intriguing starting point for building functional materials on the nanoscale, and therefore form the structural basis of all molecules studied herein. First, the single-molecule conductance of a family of bithiophene derivatives was measured. A broad distribution in the single-molecule conductance of bithiophene was found compared with that of a biphenyl. This increased breadth in the conductance distribution was shown to be explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. By contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction

  3. Organic chemistry: Precision pruning of molecules (United States)

    Yang, Kin S.; Engle, Keary M.


    If organic molecules were trees, then the numerous carbon-hydrogen bonds within them would be leaves. A catalyst that targets one 'leaf' out of many similar other ones looks set to be a huge leap for synthetic chemistry. See Letter p.230

  4. The Molecules of the Cell Membrane. (United States)

    Bretscher, Mark S.


    Cell membrane molecules form a simple, two-dimensional liquid controlling what enters and leaves the cell. Discusses cell membrane molecular architecture, plasma membranes, epithelial cells, cycles of endocytosis and exocytosis, and other topics. Indicates that some cells internalize, then recycle, membrane area equivalent to their entire surface…

  5. The formation of molecules in protostellar winds

    Energy Technology Data Exchange (ETDEWEB)

    Glassgold, A.E.; Mamon, G.A.; Huggins, P.J. (New York University, NY (USA))


    The production and destruction processes for molecules in very fast protostellar winds are analyzed and modeled with a one-dimensional chemical kinetics code. Radial density and temperature distributions suggested by protostellar theory are explored as are a range of mass-loss rates. The efficiency of in situ formation of heavy molecules is found to be high if the wind temperature falls sufficiently rapidly, as indicated by theory. The degree of molecular conversion is a strong function of the mass-loss rate and of density gradients associated with the acceleration and collimation of the wind. Even in cases where essentially all of the heavy atoms are processed into molecules, a significant fraction of atomic hydrogen remains so that hghly molecular, protostellar winds are able to emit the 21-cm line. Although CO has a substantial abundance in most models relevant to very young protostars, high abundances of other molecules such as SiO and H2O signify more complete association characteristic of winds containing regions of very high density. Although the models apply only to regions close to the protostar, they are in qualitative accord with recent observations at much larger distances of both atomic and molecular emission from extremely high-velocity flow. 57 refs.

  6. The formation of molecules in protostellar winds (United States)

    Glassgold, A. E.; Mamon, G. A.; Huggins, P. J.


    The production and destruction processes for molecules in very fast protostellar winds are analyzed and modeled with a one-dimensional chemical kinetics code. Radial density and temperature distributions suggested by protostellar theory are explored as are a range of mass-loss rates. The efficiency of in situ formation of heavy molecules is found to be high if the wind temperature falls sufficiently rapidly, as indicated by theory. The degree of molecular conversion is a strong function of the mass-loss rate and of density gradients associated with the acceleration and collimation of the wind. Even in cases where essentially all of the heavy atoms are processed into molecules, a significant fraction of atomic hydrogen remains so that highly molecular, protostellar winds are able to emit the 21-cm line. Although CO has a substantial abundance in most models relevant to very young protostars, high abundances of other molecules such as SiO and H2O signify more complete association characteristic of winds containing regions of very high density. Although the models apply only to regions close to the protostar, they are in qualitative accord with recent observations at much larger distances of both atomic and molecular emission from extremely high-velocity flow.

  7. Chiral Sensitivity in Electron-Molecule Interactions (United States)

    Dreiling, Joan


    All molecular forms of life possess a chiral asymmetry, with amino acids and sugars found respectively in L- and D-enantiomers only. The primordial origin of this enantiomeric excess is unknown. One possible explanation is given by the Vester- Ulbricht hypothesis, which suggests that left-handed electrons present in beta-radiation, produced by parity-violating weak decays, interacted with biological precursors and preferentially destroyed one of the two enantiomers. Experimental tests of this idea have thus far yielded inconclusive results. We show direct evidence for chirally-dependent bond breaking through a dissociative electron attachment (DEA) reaction when spin-polarized electrons are incident on gas-phase chiral molecules. This provides unambiguous evidence for a well-defined, chirally-sensitive destructive molecular process and, as such, circumstantial evidence for the Vester-Ulbricht hypothesis. I will also present the results of our systematic study of the DEA asymmetry for different chiral halocamphor molecules. Three halocamphor molecules were investigated: 3-bromocamphor (C10H15BrO), 3-iodocamphor(C10H15IO), and 10-iodocamphor. The DEA asymmetries collected for bromocamphor and iodocamphor are qualitatively different, suggesting that the atomic number of the heaviest atom in the molecule plays a crucial role in the asymmetric interactions. The DEA asymmetry data for 3- and 10-iodocamphor have the same qualitative behavior, but the 10-iodocamphor asymmetry is about twice as large at the lowest energies investigated, so the location of the heavy atom in the camphor molecule also affects the asymmetries. This work was performed at the University of Nebraska-Lincoln. This project is funded by NSF Grant PHY-1206067.

  8. Single-molecule Michaelis-Menten equations. (United States)

    Kou, S C; Cherayil, Binny J; Min, Wei; English, Brian P; Xie, X Sunney


    This paper summarizes our present theoretical understanding of single-molecule kinetics associated with the Michaelis-Menten mechanism of enzymatic reactions. Single-molecule enzymatic turnover experiments typically measure the probability density f(t) of the stochastic waiting time t for individual turnovers. While f(t) can be reconciled with ensemble kinetics, it contains more information than the ensemble data; in particular, it provides crucial information on dynamic disorder, the apparent fluctuation of the catalytic rates due to the interconversion among the enzyme's conformers with different catalytic rate constants. In the presence of dynamic disorder, f(t) exhibits a highly stretched multiexponential decay at high substrate concentrations and a monoexponential decay at low substrate concentrations. We derive a single-molecule Michaelis-Menten equation for the reciprocal of the first moment of f(t), 1/, which shows a hyperbolic dependence on the substrate concentration [S], similar to the ensemble enzymatic velocity. We prove that this single-molecule Michaelis-Menten equation holds under many conditions, in particular when the intercoversion rates among different enzyme conformers are slower than the catalytic rate. However, unlike the conventional interpretation, the apparent catalytic rate constant and the apparent Michaelis constant in this single-molecule Michaelis-Menten equation are complicated functions of the catalytic rate constants of individual conformers. We also suggest that the randomness parameter r, defined as )2> / t2, can serve as an indicator for dynamic disorder in the catalytic step of the enzymatic reaction, as it becomes larger than unity at high substrate concentrations in the presence of dynamic disorder.

  9. Molecules for Fluorescence Detection of Specific Chemicals (United States)

    Fedor, Steve


    A family of fluorescent dye molecules has been developed for use in on-off fluorescence detection of specific chemicals. By themselves, these molecules do not fluoresce. However, when exposed to certain chemical analytes in liquid or vapor forms, they do fluoresce (see figure). These compounds are amenable to fixation on or in a variety of substrates for use in fluorescence-based detection devices: they can be chemically modified to anchor them to porous or non-porous solid supports or can be incorporated into polymer films. Potential applications for these compounds include detection of chemical warfare agents, sensing of acidity or alkalinity, and fluorescent tagging of proteins in pharmaceutical research and development. These molecules could also be exploited for use as two-photon materials for photodynamic therapy in the treatment of certain cancers and other diseases. A molecule in this family consists of a fluorescent core (such as an anthracene or pyrene) attached to two end groups that, when the dye is excited by absorption of light, transfer an electron to the core, thereby quenching the fluorescence. The end groups can be engineered so that they react chemically with certain analytes. Upon reaction, electrons on the end groups are no longer available for transfer to the core and, consequently, the fluorescence from the core is no longer quenched. The chemoselectivity of these molecules can be changed by changing the end groups. For example, aniline end groups afford a capability for sensing acids or acid halides (including those contained in chemical warfare agents). Pyridine or bipyridyl end groups would enable sensing of metal ions. Other chemicals that can be selectively detected through suitable choice of end groups include glucose and proteins. Moreover, the fluorescent cores can be changed to alter light-absorption and -emission characteristics: anthracene cores fluoresce at wavelengths around 500 nm, whereas perylene cores absorb and emit at

  10. Novel Applications of Buffer-gas Cooling to Cold Atoms, Diatomic Molecules, and Large Molecules (United States)

    Drayna, Garrett Korda

    Cold gases of atoms and molecules provide a system for the exploration of a diverse set of physical phenomena. For example, cold gasses of magnetically and electrically polar atoms and molecules are ideal systems for quantum simulation and quantum computation experiments, and cold gasses of large polar molecules allow for novel spectroscopic techniques. Buffer-gas cooling is a robust and widely applicable method for cooling atoms and molecules to temperatures of approximately 1 Kelvin. In this thesis, I present novel applications of buffer-gas cooling to obtaining gases of trapped, ultracold atoms and diatomic molecules, as well as the study of the cooling of large organic molecules. In the first experiment of this thesis, a buffer-gas beam source of atoms is used to directly load a magneto-optical trap. Due to the versatility of the buffer-gas beam source, we obtain trapped, sub-milliKelvin gases of four different lanthanide species using the same experimental apparatus. In the second experiment of this thesis, a buffer-gas beam is used as the initial stage of an experiment to directly laser cool and magneto-optically trap the diatomic molecule CaF. In the third experiment of this thesis, buffer-gas cooling is used to study the cooling of the conformational state of large organic molecules. We directly observe conformational relaxation of gas-phase 1,2-propanediol due to cold collisions with helium gas. Lastly, I present preliminary results on a variety of novel applications of buffer-gas cooling, such as mixture analysis, separation of chiral mixtures, the measurement of parity-violation in chiral molecules, and the cooling and spectroscopy of highly unstable reaction intermediates.

  11. Synthesis of single-molecule nanocars. (United States)

    Vives, Guillaume; Tour, James M


    The drive to miniaturize devices has led to a variety of molecular machines inspired by macroscopic counterparts such as molecular motors, switches, shuttles, turnstiles, barrows, elevators, and nanovehicles. Such nanomachines are designed for controlled mechanical motion and the transport of nanocargo. As researchers miniaturize devices, they can consider two complementary approaches: (1) the "top-down" approach, which reduces the size of macroscopic objects to reach an equivalent microscopic entity using photolithography and related techniques and (2) the "bottom-up" approach, which builds functional microscopic or nanoscopic entities from molecular building blocks. The top-down approach, extensively used by the semiconductor industry, is nearing its scaling limits. On the other hand, the bottom-up approach takes advantage of the self-assembly of smaller molecules into larger networks by exploiting typically weak molecular interactions. But self-assembly alone will not permit complex assembly. Using nanomachines, we hope to eventually consider complex, enzyme-like directed assembly. With that ultimate goal, we are currently exploring the control of nanomachines that would provide a basis for the future bottom-up construction of complex systems. This Account describes the synthesis of a class of molecular machines that resemble macroscopic vehicles. We designed these so-called nanocars for study at the single-molecule level by scanning probe microscopy (SPM). The vehicles have a chassis connected to wheel-terminated axles and convert energy inputs such as heat, electric fields, or light into controlled motion on a surface, ultimately leading to transport of nanocargo. At first, we used C(60) fullerenes as wheels, which allowed the demonstration of a directional rolling mechanism of a nanocar on a gold surface by STM. However, because of the low solubility of the fullerene nanocars and the incompatibility of fullerenes with photochemical processes, we developed new

  12. Adsorption. Cage molecules to pick up the pollutants; Adsorption. Des molecules cages pour capter les polluants

    Energy Technology Data Exchange (ETDEWEB)



    The cyclo-dextrins have the property to be cage molecules, that is to say they are able to shut up organic molecules in their structure. To use them in remedial action against pollution it is necessary to find a support on which they can be grafted. The Laboratory of organic chemistry and macromolecules from the University of Sciences and Technologies of Lilles is looking for this. The researchers have used a textile material in non weaved polypropylene, a support chemically steady that resists to aggressive media such polluted effluents. To graft the cage molecule, the technique of electrons bombing has been chosen. It produces a monomer (methacrylate of glycidyl) that allows to have a tissue bearer of epoxide functions susceptible to react with the cyclo-dextrin. The studies are continued in particular to valid the use of cage molecules on the dioxin and pesticides, and also to adapt the filter to gaseous media (volatile organic compounds, smells). (N.C.)

  13. Manifestation of the strong quadrupole light-molecule interaction in the SEHR spectra of symmetrical molecules

    CERN Document Server

    Polubotko, A M


    The paper demonstrates possibility of giant enhancement of Surface Enhanced Hyper Raman Scattering on the base of qualitative consideration of electromagnetic field near some models of rough metal surfaces and of some features of the dipole and quadrupole light-molecule interaction, such as it was made in the dipole-quadrupole SERS theory. Consideration of symmetrical molecules permits to obtain selection rules for their SEHR spectra and establish such regularity as appearance of the bands, caused by the totally symmetric vibrations, transforming after the unitary irreducible representation in molecules with C2h,D and higher symmetry groups, which are forbidden in usual HRS spectra. Analysis of literature data on trans-1,2-bis (4-pyridyle) ethylene and pyridine molecules demonstrates that their SEHR spectra can be explained by the SEHRS dipole-quadrupole theory, while analysis of the SEHR spectrum of pyrazine reveals appearance of the strong forbidden bands, caused by vibrations transforming after the unitary...

  14. Modelling proton transfer in water molecule chains

    CERN Document Server

    Korzhimanov, Artem; Shutova, Tatiana; Samuelsson, Goran


    The process of protons transport in molecular water chains is of fundamental interest for many biological systems. Although many features of such systems can be analyzed using large-scale computational modeling, other features are better understood in terms of simplified model problems. Here we have tested, analytically and numerically, a model describing the classical proton hopping process in molecular water chains. In order to capture the main features of the proton hopping process in such molecular chains, we use a simplified model for our analysis. In particular, our discrete model describes a 1D chain of water molecules situated in an external protein channel structure, and each water molecule is allowed to oscillate around its equilibrium point in this system, while the protons are allowed to move along the line of neighboring oxygen atoms. The occurrence and properties of nonlinear solitary transport structures, allowing for much faster proton transport, are discussed, and the possible implications of...

  15. Is the Focus on ``Molecules'' Obsolete? (United States)

    Whitesides, George M.


    The technologies developed in analytical chemistry have defined in spectacular detail the properties of molecules. The field now faces enormously important and interesting problems of which molecules are only a part: for example, understanding the nature of life; helping to manage megacities, oceans, and atmospheres; and making health care (especially diagnostics) affordable and relevant. The emergence of these problems involving molecular systems raises the issue of how (and what) analytical chemistry should teach. Historically, it has been essential to chemistry in teaching the science of measurement. As complicated analytical techniques proliferate, it must consider how to balance teaching the uses of sophisticated devices and the fundamentals of analysis and measurement. This review (by an admiring but nonanalytical chemist) sketches the essential role of analytical methods—especially simple ones made up on the spot—in guiding research in new fields, with examples from self-assembled monolayers, soft lithography, paper diagnostics, and self-assembly; and suggests issues in teaching.

  16. Multichannel quantum defect theory for polar molecules (United States)

    Elfimov, Sergei V.; Dorofeev, Dmitrii L.; Zon, Boris A.


    Our work is devoted to developing a general approach for nonpenetrating Rydberg states of polar molecules. We propose a method to estimate the accuracy of calculation of their wave functions and quantum defects. Basing on this method we estimate the accuracy of Born-Oppenheimer (BO) and inverse Born-Oppenheimer (IBO) approximations for these states. This estimation enables us to determine the space and energy regions where BO and IBO approximations are valid. It depends on the interplay between l coupling (due to dipole potential of the core) and l uncoupling (due to rotation the core). Next we consider the intermediate region where both BO and IBO are not valid. For this intermediate region we propose a modification of Fano's multichannel quantum defect theory to match BO and IBO wave functions and show that it gives more reliable results. They are demonstrated on the example of SO molecule.

  17. Rotational dynamics of simple asymmetric molecules (United States)

    Fragiadakis, D.; Roland, C. M.


    Molecular dynamic simulations were carried out on rigid diatomic molecules, which exhibit both α (structural) and β (secondary) dynamics. The relaxation scenarios range from onset behavior, in which a distinct α process emerges on cooling, to merging behavior, associated with two relaxation peaks that converge at higher temperature. These properties, as well as the manifestation of the β peak as an excess wing, depend not only on thermodynamic conditions, but also on both the symmetry of the molecule and the correlation function (odd or even) used to analyze its dynamics. These observations help to reconcile divergent results obtained from different experiments. For example, the β process is more intense and the α-relaxation peak is narrower in dielectric relaxation spectra than in dynamic light scattering or NMR measurements. In the simulations herein, this follows from the weaker contribution of the secondary relaxation to even-order correlation functions, related to the magnitude of the relevant angular jumps.

  18. Interstellar molecules - Formation in solar nebulae (United States)

    Anders, E.


    Herbig's (1970) hypothesis that solar nebulae might be the principal source of interstellar grains and molecules is investigated. The investigation includes the determination of physical and chemical conditions in the early solar system. The production of organic compounds in the solar nebula is studied, and the compounds in meteorites are compared with those obtained in Miller-Urey and Fischer-Tropsch-type (FTT) reactions, taking into consideration aliphatic hydrocarbons, aromatic hydrocarbons, purines, pyrimidines, amino acids, porphyrins, and aspects of carbon-isotope fractionation. It is found that FTT reactions account reasonably well for all well-established features of organic matter in meteorites investigated. The distribution of compounds produced by FTT reactions is compared with the distribution of interstellar molecules. Biological implications of the results are considered.

  19. Optical slowing of calcium monofluoride molecules (United States)

    Ravi, Aakash; Chae, Eunmi; Hemmerling, Boerge; Anderegg, Loic; Augenbraun, Benjamin; Drayna, Garrett; Hutzler, Nicholas; Collopy, Alejandra; Wu, Yewei; Ding, Shiqian; Ye, Jun; Ketterle, Wolfgang; Doyle, John


    We report white-light slowing of calcium monofluoride molecules. A single main laser (606 nm) plus two additional vibrational repump lasers (628 nm) are employed. The slowing lasers are spectrally broadened to address the molecules' velocity spread and hyperfine splittings. We use a background-free two-photon fluorescence detection scheme to make high signal-to-noise measurements of our molecular beam's longitudinal velocity distribution. This method is applied to slow CaF produced by a two-stage cryogenic buffer gas beam source by > 30 m/s to near the capture velocity of a molecular magneto-optical trap (MOT). Due to the presence of magnetic dark states which inhibit optical cycling, we will use an AC-MOT. We characterize the performance of this AC-MOT used in the trapping of Li and Yb.

  20. Atomic Rydberg Reservoirs for Polar Molecules

    CERN Document Server

    Zhao, Bo; Pupillo, Guido; Zoller, Peter


    We discuss laser dressed dipolar and Van der Waals interactions between atoms and polar molecules, so that a cold atomic gas with laser admixed Rydberg levels acts as a designed reservoir for both elastic and inelastic collisional processes. The elastic scattering channel is characterized by large elastic scattering cross sections and repulsive shields to protect from close encounter collisions. In addition, we discuss a dissipative (inelastic) collision where a spontaneously emitted photon carries away (kinetic) energy of the collision partners, thus providing a significant energy loss in a single collision. This leads to the scenario of rapid thermalization and cooling of a molecule in the mK down to the \\mu K regime by cold atoms.

  1. Atomic Rydberg Reservoirs for Polar Molecules (United States)

    Zhao, B.; Glaetzle, A. W.; Pupillo, G.; Zoller, P.


    We discuss laser-dressed dipolar and van der Waals interactions between atoms and polar molecules, so that a cold atomic gas with laser admixed Rydberg levels acts as a designed reservoir for both elastic and inelastic collisional processes. The elastic scattering channel is characterized by large elastic scattering cross sections and repulsive shields to protect from close encounter collisions. In addition, we discuss a dissipative (inelastic) collision where a spontaneously emitted photon carries away (kinetic) energy of the collision partners, thus providing a significant energy loss in a single collision. This leads to the scenario of rapid thermalization and cooling of a molecule in the mK down to the μK regime by cold atoms.

  2. Multiorbital tunneling ionization of the CO molecule

    CERN Document Server

    Wu, J; Kunitski, M; Meckel, M; Voss, S; Sann, H; Kim, H; Jahnke, T; Czasch, A; Dörner, R


    We coincidently measure the molecular frame photoelectron angular distribution and the ion sum-momentum distribution of single and double ionization of CO molecules by using circularly and elliptically polarized femtosecond laser pulses, respectively. The orientation dependent ionization rates for various kinetic energy releases allow us to individually identify the ionizations of multiple orbitals, ranging from the highest occupied to the next two lower-lying molecular orbitals for various channels observed in our experiments. Not only the emission of a single electron, but also the sequential tunneling dynamics of two electrons from multiple orbitals are traced step by step. Our results confirm that the shape of the ionizing orbitals determine the strong laser field tunneling ionization in the CO molecule, whereas the linear Stark effect plays a minor role.

  3. Handbook of Single-Molecule Biophysics

    CERN Document Server

    Hinterdorfer, Peter


    The last decade has seen the development of a number of novel biophysical methods that allow the manipulation and study of individual biomolecules. The ability to monitor biological processes at this fundamental level of sensitivity has given rise to an improved understanding of the underlying molecular mechanisms. Through the removal of ensemble averaging, distributions and fluctuations of molecular properties can be characterized, transient intermediates identified, and catalytic mechanisms elucidated. By applying forces on biomolecules while monitoring their activity, important information can be obtained on how proteins couple function to structure. The Handbook of Single-Molecule Biophysics provides an introduction to these techniques and presents an extensive discussion of the new biological insights obtained from them. Coverage includes: Experimental techniques to monitor and manipulate individual biomolecules The use of single-molecule techniques in super-resolution and functional imaging Single-molec...

  4. Trace Molecules in Giant Planet Atmospheres (United States)

    Huestis, D. L.; Smith, G. P.


    Chemical kinetics matters in the upper atmospheres of giant planets in our solar system and in extrasolar systems. The composition of a volume of gas depends not only on where it is, but also on how it got there. The giant planets in our own solar system still have much to teach us about what we will be observing on extrasolar giant planets and how to interpret what we observe. Some molecules, such as CO, C2H2, C2H6, PH3, and NH3, which we call tracer molecules, provide remotely observable signatures of vertical transport. PH3 and NH3 especially have complicated thermochemistry and chemical kinetics that, until recently, have been poorly understood. Based on analysis of recent literature, we have identified new chemical mechanisms for interconverting NH3 and N2 and for interconverting PH3 and NH4-H2PO4.

  5. Vibrational and coherence dynamics of molecules

    CERN Document Server

    Zhang, Zhedong


    We {\\it analytically} investigate the population and coherence dynamics and relaxations in the vibrational energy transport in molecules. The corresponding two time scales $t_1$ and $t_2$ are explored. Coherence-population entanglement is found to considerably promote the time scale $t_2$ for dephasing and the amplitude of coherence. This is attributed to the suppression of the environment-induced drift force by coherence. Moreover the population imbalance (magnetization) is shown to be significantly amplified with the coherence-population entanglement. Contrary to the previous studies, we exactly elucidate a coherent process by showing $t_1molecules dissolved in D$_2$O. Finally we explore the coherence effect on the heat current at the macroscopic level.

  6. Automated imaging system for single molecules (United States)

    Schwartz, David Charles; Runnheim, Rodney; Forrest, Daniel


    There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

  7. Effective interaction between helical bio-molecules

    CERN Document Server

    Allahyarov, E


    The effective interaction between two parallel strands of helicalbio-molecules, such as deoxyribose nucleic acids (DNA), is calculated usingcomputer simulations of the "primitive" model of electrolytes. In particular westudy a simple model for B-DNA incorporating explicitly its charge pattern as adouble-helix structure. The effective force and the effective torque exertedonto the molecules depend on the central distance and on the relativeorientation. The contributions of nonlinear screening by monovalent counterionsto these forces and torques are analyzed and calculated for different saltconcentrations. As a result, we find that the sign of the force dependssensitively on the relative orientation. For intermolecular distances smallerthan $6\\AA$ it can be both attractive and repulsive. Furthermore we report anonmonotonic behaviour of the effective force for increasing saltconcentration. Both features cannot be described within linear screeningtheories. For large distances, on the other hand, the results agree...

  8. Diiododurene: four centrosymmetric molecules in general positions. (United States)

    Britton, Doyle; Gleason, William B


    Diiododurene (1,4-diodo-2,3,5,6-tetramethylbenzene), C(10)H(12)I(2), packs with four molecules in the asymmetric unit. All four of these moleules violate Kitaigorodsky's suggestion that molecules with centers of symmetry will lie on crystallographic centers of symmetry. There is 5.6% disorder at one of the sites. Most of the I atoms are in contact with other I atoms, but only six of the I.I contacts are shorter than 4.2 A. Of these six contacts, one set of three contacts forms a triangular set in which all of the I.I distances are less than 3.9 A.

  9. Electron correlation in molecules and condensed phases

    CERN Document Server

    March, N H


    This reference describes the latest research on correlation effects in the multicenter problems of atoms, molecules, and solids The author utilizes first- and second-order matrices, including the important observable electron density rho(r), and the Green function for discussing quantum computer simulations With its focus on concepts and theories, this volume will benefit experimental physicists, materials scientists, and physical and inorganic chemists as well as graduate students

  10. Nuclear fusion in excited hydrogen molecules

    Energy Technology Data Exchange (ETDEWEB)

    Bellini, M.; Casetti, L.; Rosa-Clot, M. (Florence Univ. (Italy). Dipt. di Fisica Istituto Nazionale di Fisica Nucleare, Florence (Italy))


    We evaluate the nuclear fusion rates in the excited vibrational states of molecules of hydrogen isotopes. The ground state fusion rate is increased by about eight order of magnitude but even in the most favorable situation it is out of any possible experimental test. We discuss the effects due to the nuclear potential in different hyperfine states, and the improvements attainable using coherent states and a solid phase. (orig.).

  11. Soliton molecules for advanced optical telecommunications (United States)

    Mitschke, Fedor; Hause, Alexander; Mahnke, Christoph


    Recent developments in the technology of optical telecommunications are pushed forward by the rapidly growing demand for data-carrying capacity. Current approaches are discussed; most lines of investigation are limited to the linear (i.e. low power) regime. It is shown how this restriction poses a limit for further evolution. If, on the other hand, the nonlinear regime is entered, recent developments about soliton molecules offer a possibility to advance further.

  12. Molecules as tracers of galaxy evolution

    DEFF Research Database (Denmark)

    Costagliola, F.; Aalto, S.; I. Rodriguez, M.;


    We investigate the molecular gas properties of a sample of 23 galaxies in order to find and test chemical signatures of galaxy evolution and to compare them to IR evolutionary tracers. Observation at 3 mm wavelengths were obtained with the EMIR broadband receiver, mounted on the IRAM 30 m telesco...... detect the molecule in its vibrationally excited state.We find low HNC/HCN line ratios (...

  13. Potential energy landscapes of tetragonal pyramid molecules (United States)

    Yoshida, Yuichiro; Sato, Hirofumi; Morgan, John W. R.; Wales, David J.


    Hiraoka et al. have developed a self-assembling system referred to as a nanocube (Hiraoka et al., 2008). In the present contribution a coarse-grained model for this system is analysed, focusing on how the potential energy landscape for self-assembly is related to the geometry of the building blocks. We find that six molecules assemble to form various clusters, with cubic and sheet structures the most stable. The relative stability is determined by the geometry of the building blocks.

  14. Small Talk: Children's Everyday `Molecule' Ideas (United States)

    Jakab, Cheryl


    This paper reports on 6-11-year-old children's `sayings and doings' (Harré 2002) as they explore molecule artefacts in dialectical-interactive teaching interviews (Fleer, Cultural Studies of Science Education 3:781-786, 2008; Hedegaard et al. 2008). This sociocultural study was designed to explore children's everyday awareness of and meaning-making with cultural molecular artefacts. Our everyday world is populated with an ever increasing range of molecular or nanoworld words, symbols, images, and games. What do children today say about these artefacts that are used to represent molecular world entities? What are the material and social resources that can influence a child's everyday and developing scientific ideas about `molecules'? How do children interact with these cognitive tools when given expert assistance? What meaning-making is afforded when children are socially and materially assisted in using molecular tools in early chemical and nanoworld thinking? Tool-dependent discursive studies show that provision of cultural artefacts can assist and direct developmental thinking across many domains of science (Schoultz et al., Human Development 44:103-118, 2001; Siegal 2008). Young children's use of molecular artefacts as cognitive tools has not received much attention to date (Jakab 2009a, b). This study shows 6-11-year-old children expressing everyday ideas of molecular artefacts and raising their own questions about the artefacts. They are seen beginning to domesticate (Erneling 2010) the words, symbols, and images to their own purposes when given the opportunity to interact with such artefacts in supported activity. Discursive analysis supports the notion that using `molecules' as cultural tools can help young children to begin `putting on molecular spectacles' (Kind 2004). Playing with an interactive game (ICT) is shown to be particularly helpful in assisting children's early meaning-making with representations of molecules, atoms, and their chemical symbols.

  15. DNA, the central molecule of aging. (United States)

    Lenart, Peter; Krejci, Lumir


    Understanding the molecular mechanism of aging could have enormous medical implications. Despite a century of research, however, there is no universally accepted theory regarding the molecular basis of aging. On the other hand, there is plentiful evidence suggesting that DNA constitutes the central molecule in this process. Here, we review the roles of chromatin structure, DNA damage, and shortening of telomeres in aging and propose a hypothesis for how their interplay leads to aging phenotypes.

  16. Single Molecule Data Analysis: An Introduction

    CERN Document Server

    Tavakoli, Meysam; Li, Chun-Biu; Komatsuzaki, Tamiki; Pressé, Steve


    We review methods of data analysis for biophysical data with a special emphasis on single molecule applications. Our review is intended for anyone, from student to established researcher. For someone just getting started, we focus on exposing the logic, strength and limitations of each method and cite, as appropriate, the relevant literature for implementation details. We review traditional frequentist and Bayesian parametric approaches to data analysis and subsequently extend our discussion to recent non-parametric and information theoretic methods.

  17. Clinical review: Oxygen as a signaling molecule



    Molecular oxygen is obviously essential for conserving energy in a form useable for aerobic life; however, its utilization comes at a cost - the production of reactive oxygen species (ROS). ROS can be highly damaging to a range of biological macromolecules, and in the past the overproduction of these short-lived molecules in a variety of disease states was thought to be exclusively toxic to cells and tissues such as the lung. Recent basic research, however, has indicated that ROS production -...

  18. Circular Intensity Differential Scattering of chiral molecules

    Energy Technology Data Exchange (ETDEWEB)

    Bustamante, C.J.


    In this thesis a theory of the Circular Intensity Differential Scattering (CIDS) of chiral molecules as modelled by a helix oriented with respect to the direction of incidence of light is presented. It is shown that a necessary condition for the existence of CIDS is the presence of an asymmetric polarizability in the scatterer. The polarizability of the scatterer is assumed generally complex, so that both refractive and absorptive phenomena are taken into account.

  19. Isatin, a versatile molecule: studies in Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Barbara, E-mail: [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil)


    Isatin is a small, versatile and widely applicable pharmacological molecule. These characteristics make isatin and its derivatives attractive to many research groups as resources for chemical and pharmacological studies. Although it has a relatively simple structure, isatin is a useful chemical scaffold for a variety of chemical transformations. This article discusses several studies performed by Brazilian groups, including investigations of its structural changes, biological assay designs and new methods for the synthesis of isatin. (author)

  20. Origins of the handedness of biological molecules. (United States)

    Mason, S F


    Pasteur (1860) showed that many organic molecules form enantiomeric pairs with non-superposable mirror-image shapes, characterized by their oppositely signed optical rotation but otherwise apparently identical. Equal numbers of left-handed and right-handed molecules resulted from laboratory synthesis, whereas biosynthetic processes afforded only one of the two enantiomers, leading Pasteur to conclude that biosynthesis involves a chiral force. Fischer demonstrated (1890-1919) that functional biomolecules are composed specifically of the D-sugars and the L-amino acids and that the laboratory synthetic reactions of such molecules propagate with chiral stereoselectivity. Given a primordial enantiomer, biomolecular homochirality follows without the intervention of a chiral natural force, except prebiotically. Chiral forces known at the time were found to be even handed on a time and space average, exemplifying parity conservation (1927). The weak nuclear force, shown to violate parity (1956), was unified with electro-magnetism in the electroweak force (1970). Ab initio estimations including the chiral electroweak force indicate that the L-amino acids and the D-sugars are more stable than the corresponding enantiomers. The small energy difference between these enantiomeric pairs, with Darwinian reaction kinetics in a flow reactor, account for the choice of biomolecular handedness made when life began.

  1. Fixman compensating potential for general branched molecules

    Energy Technology Data Exchange (ETDEWEB)

    Jain, Abhinandan, E-mail: [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States); Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan, E-mail: [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States)


    The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

  2. Fluorescence Polarization Assays in Small Molecule Screening (United States)

    Lea, Wendy A.; Simeonov, Anton


    Importance of the field Fluorescence polarization (FP) is a homogeneous method that allows rapid and quantitative analysis of diverse molecular interactions and enzyme activities. This technique has been widely utilized in clinical and biomedical settings, including the diagnosis of certain diseases and monitoring therapeutic drug levels in body fluids. Recent developments in the field has been symbolized by the facile adoption of FP in high-throughput screening (HTS) and small molecule drug discovery of an increasing range of target classes. Areas covered in this review The article provides a brief overview on the theoretical foundation of FP, followed by updates on recent advancements in its application for various drug target classes, including G-protein coupled receptors (GPCRs), enzymes and protein-protein interactions (PPIs). The strengths and weaknesses of this method, practical considerations in assay design, novel applications, and future directions are also discussed. What the reader will gain The reader will be informed of the most recent advancements and future directions of FP application to small molecule screening. Take home message In addition to its continued utilization in high-throughput screening, FP has expanded into new disease and target areas and has been marked by increased use of labeled small molecule ligands for receptor binding studies. PMID:22328899

  3. Heavy Exotic Molecules with Charm and Bottom

    CERN Document Server

    Liu, Yizhuang


    We revisit the formation of pion-mediated heavy-light exotic molecules with both charm and bottom and their chiral partners under the general strictures of both heavy-quark and chiral symmetry. The chiral exotic partners with good parity formed using the $(0^+, 1^+)$ multiplet are about twice more bound than their primary exotic partners formed using the $(0^-,1^-)$ multiplet. The chiral couplings across the multiplets $(0^\\pm, 1^\\pm)$ cause the chiral exotic partners to unbind, and the primary exotic molecules to be about twice more bound, for $J\\leq 1$. Our multi-channel coupling results show that only the charm isosinglet exotic molecules with $J^{PC}=1^{++}$ binds, which we identify as the reported neutral $X(3872)$. Also, the bottom isotriplet exotic with $J^{PC}=1^{+-}$ binds, which we identify as a mixture of the reported charged exotics $Z^+_b(10610)$ and $Z^+_b(10650)$. The bound isosinglet with $J^{PC}=1^{++}$ is suggested as a possible neutral $X_b(10532)$ not yet reported.

  4. Sorption of small molecules in polymeric media (United States)

    Camboni, Federico; Sokolov, Igor M.


    We discuss the sorption of penetrant molecules from the gas phase by a polymeric medium within a model which is very close in spirit to the dual sorption mode model: the penetrant molecules are partly dissolved within the polymeric matrix, partly fill the preexisting voids. The only difference with the initial dual sorption mode situation is the assumption that the two populations of molecules are in equilibrium with each other. Applying basic thermodynamics principles we obtain the dependence of the penetrant concentration on the pressure in the gas phase and find that this is expressed via the Lambert W-function, a different functional form than the one proposed by dual sorption mode model. The Lambert-like isotherms appear universally at low and moderate pressures and originate from the assumption that the internal energy in a polymer-penetrant-void ternary mixture is (in the lowest order) a bilinear form in the concentrations of the three components. Fitting the existing data shows that in the domain of parameters where the dual sorption mode model is typically applied, the Lambert function, which describes the same behavior as the one proposed by the gas-polymer matrix model, fits the data equally well.

  5. Evaluating enzymatic synthesis of small molecule drugs. (United States)

    Moura, Matthew; Finkle, Justin; Stainbrook, Sarah; Greene, Jennifer; Broadbelt, Linda J; Tyo, Keith E J


    There have been many achievements in applying biochemical synthetic routes to the synthesis of commodity chemicals. However, most of these endeavors have focused on optimizing and increasing the yields of naturally existing pathways. We sought to evaluate the potential for biosynthesis beyond the limits of known biochemistry towards the production of small molecule drugs that do not exist in nature. Because of the potential for improved yields compared to total synthesis, and therefore lower manufacturing costs, we focused on drugs for diseases endemic to many resource poor regions, like tuberculosis and HIV. Using generalized biochemical reaction rules, we were able to design biochemical pathways for the production of eight small molecule drugs or drug precursors and identify potential enzyme-substrate pairs for nearly every predicted reaction. All pathways begin from native metabolites, abrogating the need for specialized precursors. The simulated pathways showed several trends with the sequential ordering of reactions as well as the types of chemistries used. For some compounds, the main obstacles to finding feasible biochemical pathways were the lack of appropriate, natural starting compounds and a low diversity of biochemical coupling reactions necessary to synthesize molecules with larger molecular size.

  6. Partially dark optical molecule via phase control (United States)

    Wang, Z. H.; Xu, Xun-Wei; Li, Yong


    We study the tunable photonic distribution in an optical molecule consisting of two linearly coupled single-mode cavities. With the intercavity coupling and two driving fields, the energy levels of the optical-molecule system form a closed cyclic energy-level diagram, and the phase difference between the driving fields serves as a sensitive controller on the dynamics of the system. Due to the quantum interference effect, we can realize a partially dark optical molecule, where the steady-state mean photon number in one of the cavities achieves zero even under the external driving. And the dark cavity can be changed from one of the cavities to the other by only adjusting the phase difference. We also show that our proposal is robust to the noise at zero temperature. Furthermore, we show that when one of the cavities couples with an atomic ensemble, it will be dark under the same condition as that in the case without atoms, but the condition for the other cavity to be dark is modified.

  7. Physiological roles of small RNA molecules. (United States)

    Michaux, Charlotte; Verneuil, Nicolas; Hartke, Axel; Giard, Jean-Christophe


    Unlike proteins, RNA molecules have emerged lately as key players in regulation in bacteria. Most reviews hitherto focused on the experimental and/or in silico methods used to identify genes encoding small RNAs (sRNAs) or on the diverse mechanisms of these RNA regulators to modulate expression of their targets. However, less is known about their biological functions and their implications in various physiological responses. This review aims to compile what is known presently about the diverse roles of sRNA transcripts in the regulation of metabolic processes, in different growth conditions, in adaptation to stress and in microbial pathogenesis. Several recent studies revealed that sRNA molecules are implicated in carbon metabolism and transport, amino acid metabolism or metal sensing. Moreover, regulatory RNAs participate in cellular adaptation to environmental changes, e.g. through quorum sensing systems or development of biofilms, and analyses of several sRNAs under various physiological stresses and culture conditions have already been performed. In addition, recent experiments performed with Gram-positive and Gram-negative pathogens showed that regulatory RNAs play important roles in microbial virulence and during infection. The combined results show the diversity of regulation mechanisms and physiological processes in which sRNA molecules are key actors.

  8. Self and directed assembly: people and molecules

    Directory of Open Access Journals (Sweden)

    Tony D. James


    Full Text Available Self-assembly and directed-assembly are two very important aspects of supramolecular chemistry. As a young postgraduate student working in Canada with Tom Fyles my introduction to Supramolecular Chemistry was through the self-assembly of phospholipid membranes to form vesicles for which we were developing unimolecular and self-assembling transporter molecules. The next stage of my development as a scientist was in Japan with Seiji Shinkai where in a “Eureka” moment, the boronic acid templating unit (directed-assembly of Wulff was combined with photoinduced electron transfer systems pioneered by De Silva. The result was a turn-on fluorescence sensor for saccharides; this simple result has continued to fuel my research to the present day. Throughout my career as well as assembling molecules, I have enjoyed bringing together researchers in order to develop collaborative networks. This is where molecules meet people resulting in assemblies worth more than the individual “molecule” or “researcher”. My role in developing networks with Japan was rewarded by the award of a Daiwa-Adrian Prize in 2013 and I was recently rewarded for developing networks with China with an Inaugural CASE Prize in 2015.

  9. Rydberg States of Atoms and Molecules (United States)

    Stebbings, R. F.; Dunning, F. B.


    List of contributors; Preface; 1. Rydberg atoms in astrophysics A. Dalgarno; 2. Theoretical studies of hydrogen Rydberg atoms in electric fields R. J. Damburg and V. V. Kolosov; 3. Rydberg atoms in strong fields D. Kleppner, Michael G. Littman and Myron L. Zimmerman; 4. Spectroscopy of one- and two-electron Rydberg atoms C. Fabre and S. Haroche; 5. Interaction of Rydberg atoms with blackbody radiation T. F. Gallagher; 6. Theoretical approaches to low-energy collisions of Rydberg atoms with atoms and ions A. P. Hickman, R. E. Olson and J. Pascale; 7. Experimental studies of the interaction of Rydberg atoms with atomic species at thermal energies F. Gounand and J. Berlande; 8. Theoretical studies of collisions of Rydberg atoms with molecules Michio Matsuzawa; 9. Experimental studies of thermal-energy collisions of Rydberg atoms with molecules F. B. Dunning and R. F. Stebbings; 10. High-Rydberg molecules Robert S. Freund; 11. Theory of Rydberg collisions with electrons, ions and neutrals M. R. Flannery; 12. Experimental studies of the interactions of Rydberg atoms with charged particles J. -F. Delpech; 13. Rydberg studies using fast beams Peter M. Koch; Index.

  10. Small molecule-guided thermoresponsive supramolecular assemblies

    KAUST Repository

    Rancatore, Benjamin J.


    Small organic molecules with strong intermolecular interactions have a wide range of desirable optical and electronic properties and rich phase behaviors. Incorporating them into block copolymer (BCP)-based supramolecules opens new routes to generate functional responsive materials. Using oligothiophene- containing supramolecules, we present systematic studies of critical thermodynamic parameters and kinetic pathway that govern the coassemblies of BCP and strongly interacting small molecules. A number of potentially useful morphologies for optoelectronic materials, including a nanoscopic network of oligothiophene and nanoscopic crystalline lamellae, were obtained by varying the assembly pathway. Hierarchical coassemblies of oligothiophene and BCP, rather than macrophase separation, can be obtained. Crystallization of the oligothiophene not only induces chain stretching of the BCP block the oligothiophene is hydrogen bonded to but also changes the conformation of the other BCP coil block. This leads to an over 70% change in the BCP periodicity (e.g., from 31 to 53 nm) as the oligothiophene changes from a melt to a crystalline state, which provides access to a large BCP periodicity using fairly low molecular weight BCP. The present studies have demonstrated the experimental feasibility of generating thermoresponsive materials that convert heat into mechanical energy. Incorporating strongly interacting small molecules into BCP supramolecules effectively increases the BCP periodicity and may also open new opportunities to tailor their optical properties without the need for high molecular weight BCP. © 2012 American Chemical Society.

  11. Heavy exotic molecules with charm and bottom (United States)

    Liu, Yizhuang; Zahed, Ismail


    We revisit the formation of pion-mediated heavy-light exotic molecules with both charm and bottom and their chiral partners under the general strictures of both heavy-quark and chiral symmetry. The chiral exotic partners with good parity formed using the (0+ ,1+) multiplet are about twice more bound than their primary exotic partners formed using the (0- ,1-) multiplet. The chiral couplings across the multiplets (0± ,1±) cause the chiral exotic partners to unbind, and the primary exotic molecules to be about twice more bound, for J ≤ 1. Our multi-channel coupling results show that only the charm isosinglet exotic molecules with JPC =1++ bind, which we identify as the reported neutral X (3872). Also, the bottom isotriplet exotic with JPC =1+- binds, which we identify as a mixture of the reported charged exotics Zb+ (10610) and Zb+ (10650). The bound isosinglet with JPC =1++ is suggested as a possible neutral Xb (10532) not yet reported.

  12. Electron attachment to the phthalide molecule

    Energy Technology Data Exchange (ETDEWEB)

    Asfandiarov, N. L. [Institute of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospect Oktyabrya 151, 450075 Ufa (Russian Federation); Bashkir State Pedagogical University, Oktyabrskoy Revolutsii St., 3a, 450000 Ufa (Russian Federation); Pshenichnyuk, S. A. [Institute of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospect Oktyabrya 151, 450075 Ufa (Russian Federation); St.-Petersburg State University, Uljanovskaja, 1, 198504 St.-Petersburg (Russian Federation); Vorob’ev, A. S.; Nafikova, E. P. [Institute of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospect Oktyabrya 151, 450075 Ufa (Russian Federation); Lachinov, A. N. [Bashkir State Pedagogical University, Oktyabrskoy Revolutsii St., 3a, 450000 Ufa (Russian Federation); Kraikin, V. A. [Institute of Organic Chemistry, Ufa Research Centre, Russian Academy of Sciences, Prospect Oktyabrya 59, 450075 Ufa (Russian Federation); Modelli, A. [Dipartimento di Chimica “G. Ciamician,” Universitá di Bologna, Via Selmi 2, 40126 Bologna (Italy); Centro Interdipartimentale di Ricerca in Scienze Ambientali (CIRSA), Universitá di Bologna, Via S. Alberto 163, 48123 Ravenna (Italy)


    Phthalide, the simplest chain of conductive polymer thin film, was investigated by means of Electron Transmission Spectroscopy, Negative Ion Mass Spectrometry, and density functional theory quantum chemistry. It has been found that formation of gas-phase long-lived molecular anions of phthalide around 0.7 eV takes place through cleavage of a C–O bond of the pentacyclic ring of the parent molecular anion to give a vibrationally excited (electronically more stable) open-ring molecular anion. The energy of the transition state for ring opening of the parent negative ion is calculated to be 0.65 eV above the neutral ground state of the molecule. The energy (2.64 eV) evaluated for the corresponding transition state in the neutral molecule is much higher, so that the process of electron detachment from the anion must lead to a neutral molecule with its initial pentacyclic structure. The average lifetime of the molecular negative ions formed at an electron energy of 0.75 eV and 80 °C is measured to be about 100 μs. The known switching effect of thin phthalide films could stem from the presence of a similar open/closed transition state also in the polymer.

  13. The origin of large molecules in primordial autocatalytic reaction networks

    CERN Document Server

    Giri, Varun


    Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we know that can accomplish this task consist of large molecules. Thus the origin of large molecules is a chicken and egg problem in chemistry. Here we present a mechanism, based on autocatalytic sets (ACSs), that is a possible solution to this problem. We discuss a mathematical model describing the population dynamics of molecules in a stylized but prebiotically plausible chemistry. Large molecules can be produced in this chemistry by the coalescing of smaller ones, with the smallest molecules, the `food set', being buffered. Some of the reactions can be catalyzed by molecules within the chemistry with varying catalytic strengths. Normally the concentrations of large molecules in such a scenario are very small, diminishing exponentially with their size. ACSs, if present in the c...

  14. Single Molecule Studies on Dynamics in Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Daniela Täuber


    Full Text Available Single molecule (SM methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC. Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization mechanisms within biological cells, where large molecules are found in nematic LC surroundings. This review gives a short overview related to the application of highly sensitive SM detection schemes in LC.

  15. Synthesis and characterization of lower generation broom molecules

    Institute of Scientific and Technical Information of China (English)

    Jun Wang; Cui Qin Li; Shu Yan Zhang; Fang Sun; Teng Jie Ge


    Dendritic molecules with dodecyl groups as the hyperbranchs were synthesized in methanol by Michael addition withdodecylamine and methyl acrylate as raw materials. This new-type dendritic molecules were called vividly "broom molecules" inthis report. The surface tension of the aqueous solution of broom molecule terminated amino group was measured by using the drop-volume method. The demulsification performance of the broom molecules for the oil/water (O/W) simulated crude oil emulsion wasexamined. The experimental results revealed that, as a new-type of surfactants, the broom molecules terminated amino groupsshowed demulsification for the O/W simulated crude oil emulsion.

  16. Oligomer Molecules for Efficient Organic Photovoltaics. (United States)

    Lin, Yuze; Zhan, Xiaowei


    Solar cells, a renewable, clean energy technology that efficiently converts sunlight into electricity, are a promising long-term solution for energy and environmental problems caused by a mass of production and the use of fossil fuels. Solution-processed organic solar cells (OSCs) have attracted much attention in the past few years because of several advantages, including easy fabrication, low cost, lightweight, and flexibility. Now, OSCs exhibit power conversion efficiencies (PCEs) of over 10%. In the early stage of OSCs, vapor-deposited organic dye materials were first used in bilayer heterojunction devices in the 1980s, and then, solution-processed polymers were introduced in bulk heterojunction (BHJ) devices. Relative to polymers, vapor-deposited small molecules offer potential advantages, such as a defined molecular structure, definite molecular weight, easy purification, mass-scale production, and good batch-to-batch reproducibility. However, the limited solubility and high crystallinity of vapor-deposited small molecules are unfavorable for use in solution-processed BHJ OSCs. Conversely, polymers have good solution-processing and film-forming properties and are easily processed into flexible devices, whereas their polydispersity of molecular weights and difficulty in purification results in batch to batch variation, which may hamper performance reproducibility and commercialization. Oligomer molecules (OMs) are monodisperse big molecules with intermediate molecular weights (generally in the thousands), and their sizes are between those of small molecules (generally with molecular weights 10000). OMs not only overcome shortcomings of both vapor-deposited small molecules and solution-processed polymers, but also combine their advantages, such as defined molecular structure, definite molecular weight, easy purification, mass-scale production, good batch-to-batch reproducibility, good solution processability, and film-forming properties. Therefore, OMs are a

  17. Contacting organic molecules by soft methods: towards molecule-based electronic devices. (United States)

    Haick, Hossam; Cahen, David


    Can we put organic molecules to use as electronic components? The answer to this question is to no small degree limited by the ability to contact them electrically without damaging the molecules. In this Account, we present some of the methods for contacting molecules that do not or minimally damage them and that allow formation of electronic junctions that can become compatible with electronics from the submicrometer to the macroscale. In "Linnaean" fashion, we have grouped contacting methods according to the following main criteria: (a) is a chemical bond is required between contact and molecule, and (b) is the contact "ready-made", that is, preformed, or prepared in situ? Contacting methods that, so far, seem to require a chemical bond include spin-coating a conductive polymer and transfer printing. In the latter, a metallic pattern on an elastomeric polymer is mechanically transferred to molecules with an exposed terminal group that can react chemically with the metal. These methods allow one to define structures from several tens of nanometers size upwards and to fabricate devices on flexible substrates, which is very difficult by conventional techniques. However, the requirement for bifunctionality severely restricts the type of molecules that can be used and can complicate their self-assembly into monolayers. Methods that rely on prior formation of the contact pad are represented by two approaches: (a) use of a liquid metal as electrode (e.g., Hg, Ga, various alloys), where molecules can be adsorbed on the liquid metal and the molecularly modified drop is brought into contact with the second electrode, the molecules can be adsorbed on the second electrode and then the liquid metal brought into contact with them, or bilayers are used, with a layer on both the metal and the second electrode and (b) use of preformed metal pads from a solid substrate and subsequent pad deposition on the molecules with the help of a liquid. These methods allow formation of

  18. Effect of lysosomotropic molecules on cellular homeostasis. (United States)

    Kuzu, Omer F; Toprak, Mesut; Noory, M Anwar; Robertson, Gavin P


    Weak bases that readily penetrate through the lipid bilayer and accumulate inside the acidic organelles are known as lysosomotropic molecules. Many lysosomotropic compounds exhibit therapeutic activity and are commonly used as antidepressant, antipsychotic, antihistamine, or antimalarial agents. Interestingly, studies also have shown increased sensitivity of cancer cells to certain lysosomotropic agents and suggested their mechanism of action as a promising approach for selective destruction of cancer cells. However, their chemotherapeutic utility may be limited due to various side effects. Hence, understanding the homeostatic alterations mediated by lysosomotropic compounds has significant importance for revealing their true therapeutic potential as well as toxicity. In this review, after briefly introducing the concept of lysosomotropism and classifying the lysosomotropic compounds into two major groups according to their cytotoxicity on cancer cells, we focused on the subcellular alterations mediated by class-II lysosomotropic compounds. Briefly, their effect on intracellular cholesterol homeostasis, autophagy and lysosomal sphingolipid metabolism was discussed. Accordingly, class-II lysosomotropic molecules inhibit intracellular cholesterol transport, leading to the accumulation of cholesterol inside the late endosomal-lysosomal cell compartments. However, the accumulated lysosomal cholesterol is invisible to the cellular homeostatic circuits, hence class-II lysosomotropic molecules also upregulate cholesterol synthesis pathway as a downstream event. Considering the fact that Niemann-Pick disease, a lysosomal cholesterol storage disorder, also triggers similar pathologic abnormalities, this review combines the knowledge obtained from the Niemann-Pick studies and lysosomotropic compounds. Taken together, this review is aimed at allowing readers a better understanding of subcellular alterations mediated by lysosomotropic drugs, as well as their potential

  19. Raman scattering mediated by neighboring molecules. (United States)

    Williams, Mathew D; Bradshaw, David S; Andrews, David L


    Raman scattering is most commonly associated with a change in vibrational state within individual molecules, the corresponding frequency shift in the scattered light affording a key way of identifying material structures. In theories where both matter and light are treated quantum mechanically, the fundamental scattering process is represented as the concurrent annihilation of a photon from one radiation mode and creation of another in a different mode. Developing this quantum electrodynamical formulation, the focus of the present work is on the spectroscopic consequences of electrodynamic coupling between neighboring molecules or other kinds of optical center. To encompass these nanoscale interactions, through which the molecular states evolve under the dual influence of the input light and local fields, this work identifies and determines two major mechanisms for each of which different selection rules apply. The constituent optical centers are considered to be chemically different and held in a fixed orientation with respect to each other, either as two components of a larger molecule or a molecular assembly that can undergo free rotation in a fluid medium or as parts of a larger, solid material. The two centers are considered to be separated beyond wavefunction overlap but close enough together to fall within an optical near-field limit, which leads to high inverse power dependences on their local separation. In this investigation, individual centers undergo a Stokes transition, whilst each neighbor of a different species remains in its original electronic and vibrational state. Analogous principles are applicable for the anti-Stokes case. The analysis concludes by considering the experimental consequences of applying this spectroscopic interpretation to fluid media; explicitly, the selection rules and the impact of pressure on the radiant intensity of this process.

  20. Spectral simulations of polar diatomic molecules immersed in He clusters: application to the ICl (X) molecule

    Energy Technology Data Exchange (ETDEWEB)

    Villarreal, P [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Lara-Castells, M P de [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Prosmiti, R [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Delgado-Barrio, G [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Lopez-Duran, D [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Gianturco, F A [Department of Chemistry and INFM, The University of Rome, Citta Universitaria, 00185, Rome (Italy); Jellinek, J [Chemistry Division, Argonne National Laboratory, Argonne, IL 60439 (United States)


    A recently developed quantum-chemistry-like methodology to study molecules solvated in atomic clusters is applied to the ICl (iodine chloride) polar diatomic molecule immersed in clusters of He atoms. The atoms of the solvent clusters are treated as the 'electrons' and the solvated molecule as a structured 'nucleus' of the combined solvent-solute system. The helium-helium and helium-dopant interactions are represented by parametrized two-body and ab initio three-body potentials, respectively. The ground-state wavefunctions are used to compute the infrared (IR) spectra of the solvated molecule. In agreement with the experimental observations, the computed spectra exhibit considerable differences depending on whether the solvent cluster is comprised of bosonic ({sup 4}He) or fermionic ({sup 3}He) atoms. The source of these differences is attributed to the different spin-statistics of the solvent clusters. The bosonic versus fermionic nature of the solvent is reflected in the IR absorption selection rules. Only P and R branches with single state transitions appear in the spectrum when the molecule is solvated in a bosonic cluster. On the other hand, when the solvent represents a fermionic environment, quasi-degenerate multiplets of spin states contribute to each branch and, in addition, the Q-branch becomes also allowed. Combined, these two factors explain the more congested nature of the spectrum in the fermionic case.

  1. Photonic molecules formed by coupled hybrid resonators

    CERN Document Server

    Peng, Bo; Zhu, Jiangang; Yang, Lan; 10.1364/OL.37.003435


    We describe a method that enables free-standing whispering-gallery-mode microresonators, and report spectral tuning of photonic molecules formed by coupled free and on-chip resonators with different geometries and materials. We study direct coupling via evanescent fields of free silica microtoroids and microspheres with on-chip polymer coated silica microtoroids. We demonstrate thermal tuning of resonance modes to achieve maximal spectral overlap, mode splitting induced by direct coupling, and the effects of distance between the resonators on the splitting spectra.

  2. Humidity Effects on Conductivity of DNA Molecules

    Institute of Scientific and Technical Information of China (English)

    YAN Xun-Ling; DONG Rui-Xin; LIN Qing-De


    We present a model related to the humidity to describe the conductivity of homogeneous DNA molecule,where the hydration of phosphate group and bases are taken into account. The calculated results show the oscillation feature of dⅠ/dⅤ-Ⅴ curves and the semiconductor behavior of DNA. With the relative humidity increasing, the voltage gap becomes narrow and the maximum of conductance increases nonlinearly. The conductivity of DNA approaches to stabilization when the relative humidity reaches a certain value. These results are in agreement with experimental measurements.

  3. Alignment of D-state Rydberg molecules

    CERN Document Server

    Krupp, Alexander T; Balewski, Jonathan B; Ilzhöfer, Philipp; Hofferberth, Sebastian; Löw, Robert; Pfau, Tilman; Kurz, Markus; Schmelcher, Peter


    We report on the formation of ultralong-range Rydberg D-state molecules via photoassociation in an ultracold cloud of rubidium atoms. By applying a magnetic offset field on the order of 10 G and high resolution spectroscopy, we are able to resolve individual rovibrational molecular states. A full theory, using the Born-Oppenheimer approximation including s- and p-wave scattering, reproduces the measured binding energies. The calculated molecular wavefunctions show that in the experiment we can selectively excite stationary molecular states with an extraordinary degree of alignment or anti-alignment with respect to the magnetic field axis.

  4. Inorganic Nanoparticles Conjugated with Biofunctional Molecules

    Institute of Scientific and Technical Information of China (English)



    1 Results We have attempted to conjugate inorganic nanoparticles with biofunctional molecules.Recently we were quite successful in demonstrating that a two-dimensional inorganic compound like layered double hydroxide (LDH),and natural and synthetic clays can be used as gene or drug delivery carriers1-4.To the best of our knowledge,such inorganic vectors are completely new and different from conventionally developed ones such as viruses and cationic liposomes,those which are limited in certain cases of ap...

  5. Structure of molecules and internal rotation

    CERN Document Server

    Mizushima, San-Ichiro


    Structure of Molecules and Internal Rotation reviews early studies on dihalogenoethanes. This book is organized into two parts encompassing 8 chapters that evaluate the Raman effect in ethane derivatives, the energy difference between rotational isomers, and the infrared absorption of ethane derivatives. Some of the topics covered in the book are the potential barrier to internal rotation; nature of the hindering potential; entropy difference between the rotational isomers; internal rotation in butane, pentane, and hexane; and internal rotation in long chain n-paraffins. Other chapters deal wi

  6. Nonrelativistic Lamb shift for muonic molecules (United States)

    Bukowski, Robert; Jeziorski, Bogumil


    A recently developed formula [R. Bukowski and B. Jeziorski, Phys. Rev. A46 (1992) 5437]. has been applied to estimate the soft-photon Lamb shift contribution to the energies of the muonic molecules ppμ, ddμ, ttμ, pdμ, ptμ and dtμ. The corresponding corrections to the dissociation energies for the excited P states of ddμ and dtμ have been found to be almost identical and equal to 0.048 meV. The magnitude of this stabilizing effect is too small to affect seriously the formation rates predictions.

  7. Plasmonic molecules via glass annealing in hydrogen (United States)

    Redkov, Alexey; Chervinskii, Semen; Baklanov, Alexander; Reduto, Igor; Zhurikhina, Valentina; Lipovskii, Andrey


    Growth of self-assembled metal nanoislands on the surface of silver ion-exchanged glasses via their thermal processing in hydrogen followed by out-diffusion of neutral silver is studied. The combination of thermal poling of the ion-exchanged glass with structured electrode and silver out-diffusion was used for simple formation of separated groups of several metal nanoislands presenting plasmonic molecules. The kinetics of nanoisland formation and temporal evolution of their size distribution on the surface of poled and unpoled glass are modeled.

  8. Bringing molecules back into molecular evolution.

    Directory of Open Access Journals (Sweden)

    Claus O Wilke

    Full Text Available Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events.

  9. Molecular-beam spectroscopy of interhalogen molecules

    Energy Technology Data Exchange (ETDEWEB)

    Sherrow, S.A.


    A molecular-beam electric-resonance spectrometer employing a supersonic nozzle source has been used to obtain hyperfine spectra of /sup 79/Br/sup 35/Cl. Analyses of these spectra and of microwave spectra published by other authors have yielded new values for the electric dipole moment and for the nuclear quadrupole coupling constants in this molecule. The new constants are significantly different from the currently accepted values. Van der Waals clusters containing chlorine monofluoride have been studied under various expansion conditions by the molecular-beam electric-deflection method. The structural possibilities indicated by the results are discussed, and cluster geometries are proposed.

  10. Spectra of Linear Polyene Molecule-canthaxanthin

    Institute of Scientific and Technical Information of China (English)

    OUYANG Shun-li; LI Zuo-wei; CHEN Yuan-zheng; MEN Zhi-wei; WU Nan-nan; SUN Cheng-lin


    Raman spectra and ultraviolet-visible(UV-Vis) absorption spectra of linear polyene molecule-canthaxanthin in n-hexane are measured and analyzed.In addition,the optimized structure of canthaxanthin was calculated via density functional theory(DFT) functional B3LYP.With decreasing the concentration,Raman scattering cross section (RSCS) of fundamental frequency is extremely high,and the UV-Vis absorption bands become narrower.The results of coherent weakly damped electron-Lattice vibration model were analyzed.

  11. Electron impact excitations of S2 molecules

    CERN Document Server

    Tashiro, Motomichi


    Low-energy electron impact excitations of S_2 molecules are studied using the fixed-bond R-matrix method based on state-averaged complete active space SCF orbitals. Integral cross sections are calculated for elastic electron collision as well as impact excitation of the 7 lowest excited electronic states. Also, differential cross sections are obtained for elastic collision and excitation of the a^1 Delta_g, b^1 Sigma_g^+ and B^3 Sigma_u^- states. The integrated cross section of optically allowed excitation of the B^3 Sigma_u^- state agrees reasonably well with the available theoretical result.

  12. Kondo tunneling through real and artificial molecules. (United States)

    Kikoin, K; Avishai, Y


    When an asymmetric double dot is hybridized with itinerant electrons, its singlet ground state and lowly excited triplet state cross, leading to a competition between the Zhang-Rice mechanism of singlet-triplet splitting in a confined cluster and the Kondo effect (which accompanies the tunneling through quantum dot under a Coulomb blockade restriction). The rich physics of an underscreened S = 1 Kondo impurity in the presence of low-lying triplet-singlet excitations is exposed and estimates of the magnetic susceptibility and the electric conductance are presented, together with applications for molecule chemisorption on metallic substrates.

  13. The calculation of thermodynamic properties of molecules

    DEFF Research Database (Denmark)

    van Speybroeck, Veronique; Gani, Rafiqul; Meier, Robert Johan


    such quantities by computation are quantum mechanical methods and group contribution methods. Although a lot of progress was made over the last decade, for the majority of chemical species we are still quite a bit away from what is often referred to as chemical accuracy, i.e.1 kcal mol-1. Currently, for larger...... molecules the combination of group contribution methods with group additive values that are determined with the best available computational ab initio methods seems to be a viable alternative to obtain thermodynamic properties near chemical accuracy. New developments and full use of existing tools may lead...

  14. Gaseous Electronics Tables, Atoms, and Molecules

    CERN Document Server

    Raju, Gorur Govinda


    With the constant emergence of new research and application possibilities, gaseous electronics is more important than ever in disciplines including engineering (electrical, power, mechanical, electronics, and environmental), physics, and electronics. The first resource of its kind, Gaseous Electronics: Tables, Atoms, and Molecules fulfills the author's vision of a stand-alone reference to condense 100 years of research on electron-neutral collision data into one easily searchable volume. It presents most--if not all--of the properly classified experimental results that scientists, researchers,

  15. Assembling molecular electronic junctions one molecule at a time. (United States)

    Bonifas, Andrew P; McCreery, Richard L


    Diffusion of metal atoms onto a molecular monolayer attached to a conducting surface permits electronic contact to the molecules with minimal heat transfer or structural disturbance. Surface-mediated metal deposition (SDMD) involves contact between "cold" diffusing metal atoms and molecules, due to shielding of the molecules from direct exposure to metal vapor. Measurement of the current through the molecular layer during metal diffusion permits observation of molecular conductance for junctions containing as few as one molecule. Discrete conductance steps were observed for 1-10 molecules within a monolayer during a single deposition run, corresponding to "recruitment" of additional molecules as the contact area between the diffusing Au layer and molecules increases. For alkane monolayers, the molecular conductance measured with SDMD exhibited an exponential dependence on molecular length with a decay constant (β) of 0.90 per CH(2) group, comparable to that observed by other techniques. Molecular conductance values were determined for three azobenzene molecules, and correlated with the offset between the molecular HOMO and the contact Fermi level, as expected for hole-mediated tunneling. Current-voltage curves were obtained during metal deposition showed no change in shape for junctions containing 1, 2, and 10 molecules, implying minimal intermolecular interactions as single molecule devices transitioned into several molecules devices. SDMD represents a "soft" metal deposition method capable of providing single molecule conductance values, then providing quantitative comparisons to molecular junctions containing 10(6) to 10(10) molecules.

  16. EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES (United States)

    Carr, Lincoln D.; Ye, Jun


    Cold and ultracold molecules are the next wave of ultracold physics, giving rise to an exciting array of scientific opportunities, including many body physics for novel quantum phase transitions, new states of matter, and quantum information processing. Precision tests of fundamental physical laws benefit from the existence of molecular internal structure with exquisite control. The study of novel collision and reaction dynamics will open a new chapter of quantum chemistry. Cold molecules bring together researchers from a variety of fields, including atomic, molecular, and optical physics, chemistry and chemical physics, quantum information science and quantum simulations, condensed matter physics, nuclear physics, and astrophysics, a truly remarkable synergy of scientific explorations. For the past decade there have been steady advances in direct cooling techniques, from buffer-gas cooling to cold molecular beams to electro- and magneto-molecular decelerators. These techniques have allowed a large variety of molecules to be cooled for pioneering studies. Recent amazing advances in experimental techniques combining the ultracold and the ultraprecise have furthermore brought molecules to the point of quantum degeneracy. These latter indirect cooling techniques magnetically associate atoms from a Bose-Einstein condensate and/or a quantum degenerate Fermi gas, transferring at 90% efficiency highly excited Fano-Feshbach molecules, which are on the order of 10 000 Bohr radii in size, to absolute ground state molecules just a few Bohr across. It was this latter advance, together with significant breakthroughs in internal state manipulations, which inspired us to coordinate this focus issue now, and is the reason why we say the next wave of ultracold physics has now arrived. Whether directly or indirectly cooled, heteronuclear polar molecules offer distinct new features in comparison to cold atoms, while sharing all of their advantages (purity, high coherence

  17. Nanodevices for generating power from molecules and batteryless sensing

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yinmin; Wang, Xianying; Hamza, Alex V.


    A nanoconverter or nanosensor is disclosed capable of directly generating electricity through physisorption interactions with molecules that are dipole containing organic species in a molecule interaction zone. High surface-to-volume ratio semiconductor nanowires or nanotubes (such as ZnO, silicon, carbon, etc.) are grown either aligned or randomly-aligned on a substrate. Epoxy or other nonconductive polymers are used to seal portions of the nanowires or nanotubes to create molecule noninteraction zones. By correlating certain molecule species to voltages generated, a nanosensor may quickly identify which species is detected. Nanoconverters in a series parallel arrangement may be constructed in planar, stacked, or rolled arrays to supply power to nano- and micro-devices without use of external batteries. In some cases breath, from human or other life forms, contain sufficient molecules to power a nanoconverter. A membrane permeable to certain molecules around the molecule interaction zone increases specific molecule nanosensor selectivity response.

  18. Formation of Ultracold NaRb Feshbach Molecules

    CERN Document Server

    Wang, Fudong; Li, Xiaoke; Zhu, Bing; Chen, Jun; Wang, Dajun


    We report the creation of ultracold bosonic $^{23}$Na$^{87}$Rb Feshbach molecules via magneto-association. By ramping the magnetic field across an interspecies Feshbach resonance, at least 4000 molecules can be produced out of the near degenerate ultracold mixture. Fast loss due to inelastic atom-molecule collisions is observed, which limits the pure molecule number, after residual atoms removal, to 1700. The pure molecule sample can live for 21.8(8) ms in the optical trap, long enough for future molecular spectroscopy studies toward coherently transferring to the singlet ro-vibrational ground state, where these molecules are stable against chemical reaction and have a permanent electric dipole moment of 3.3 Debye. We have also measured the Feshbach molecule's binding energy near the Feshbach resonance by the oscillating magnetic field method and found these molecules have a large closed-channel fraction.

  19. Nanodevices for generating power from molecules and batteryless sensing (United States)

    Wang, Yinmin; Wang, Xianying; Hamza, Alex V.


    A nanoconverter or nanosensor is disclosed capable of directly generating electricity through physisorption interactions with molecules that are dipole containing organic species in a molecule interaction zone. High surface-to-volume ratio semiconductor nanowires or nanotubes (such as ZnO, silicon, carbon, etc.) are grown either aligned or randomly-aligned on a substrate. Epoxy or other nonconductive polymers are used to seal portions of the nanowires or nanotubes to create molecule noninteraction zones. By correlating certain molecule species to voltages generated, a nanosensor may quickly identify which species is detected. Nanoconverters in a series parallel arrangement may be constructed in planar, stacked, or rolled arrays to supply power to nano- and micro-devices without use of external batteries. In some cases breath, from human or other life forms, contain sufficient molecules to power a nanoconverter. A membrane permeable to certain molecules around the molecule interaction zone increases specific molecule nanosensor selectivity response.

  20. Nonlinear optical absorption of photosynthetic pigment molecules in leaves. (United States)

    Ye, Zi-Piao


    A mathematical formulation of the relationship between optical absorption coefficient of photosynthetic pigment molecules and light intensity was developed. It showed that physical parameters of photosynthetic pigment molecule (i.e., light absorption cross-section of photosynthetic pigment molecule, its average lifetime in the excited state, total photosynthetic pigment molecules, the statistical weight, or degeneracy of energy level of photosynthetic pigment molecules in the ground state and in the excited state) influenced on both the light absorption coefficient and effective light absorption cross-section of photosynthetic pigment molecules. Moreover, it also showed that both the light absorption coefficient and effective light absorption cross-section of photosynthetic pigment molecules were not constant, they decreased nonlinearly with light intensity increasing. The occupation numbers of photosynthetic pigment molecules in the excited states increased nonlinearly with light intensity increasing.

  1. Proteinaceous molecules mediating Bifidobacterium-host interactions

    Directory of Open Access Journals (Sweden)

    Lorena Ruiz


    Full Text Available Bifidobacteria are commensal microoganisms found in the gastrointestinal tract.Several strains have been attributed beneficial traits at local and systemic levels, through pathogen exclusion or immune modulation, among other benefits. This has promoted a growing industrial and scientific interest in bifidobacteria as probiotic supplements. However, the molecular mechanisms mediating this cross-talk with the human host remain unknown. High-throughput technologies, from functional genomics to transcriptomics, proteomics and interactomics coupled to the development of both in vitro and in vivo models to study the dynamics of the intestinal microbiota and their effects on host cells, have eased the identification of key molecules in these interactions. Numerous secreted or surface-associated proteins or peptides have been identified as potential mediators of bifidobacteria-host interactions and molecular cross-talk, directly participating in sensing environmental factors, promoting intestinal colonization or mediating a dialogue with mucosa-associated immune cells. On the other hand, bifidobacteria induce the production of proteins in the intestine, by epithelial or immune cells, and other gut bacteria, which are key elements in orchestrating interactions among bifidobacteria, gut microbiota and host cells. This review aims to give a comprehensive overview on proteinaceous molecules described and characterized to date, as mediators of the dynamic interplay between bifidobacteria and the human host, providing a framework to identify knowledge gaps and future research needs.

  2. Floppy Molecules with Internal Rotation and Inversion (United States)

    Kreglewski, Marek


    There are different ways to analyze rovibrational structure of molecules having several large amplitude motions of different type, like internal rotation and inversion or ring-puckering. In my research group we have developed and used methods starting from potential surfaces for large amplitude motions but also applied purely effective Hamiltonians, where tunneling splittings were key parameters. Whatever is the method the following problems must be solved when addressing a rovibrational problem with large amplitude vibrations: 1) a definition of the permutation-inversion molecular symmetry group, 2) a choice of the internal coordinates and their transformation in the symmetry group, 3) derivation of the Hamiltonian in chosen coordinates, 4) calculation of the Hamiltonian matrix elements in a symmetrized basis set. These points will be discussed. The advantage of methods which start from the geometry and potential surface for large amplitude vibrations give much clearer picture of internal dynamics of molecules but generally the fit to experimental data is much poorer. The fitting procedure is strongly non-linear and the iteration procedure much longer. The effective Hamiltonians the fit is generally much better since almost all optimized parameters are linear but the parameters have no clear physical meaning. This method is very useful in the assignment of experimental spectra. Results of the application of both method to methylamine and hydrazine will be presented.

  3. Size selective hydrophobic adsorbent for organic molecules (United States)

    Sharma, Pramod K. (Inventor); Hickey, Gregory S. (Inventor)


    The present invention relates to an adsorbent formed by the pyrolysis of a hydrophobic silica with a pore size greater than 5 .ANG., such as SILICALITE.TM., with a molecular sieving polymer precursor such as polyfurfuryl alcohol, polyacrylonitrile, polyvinylidene chloride, phenol-formaldehyde resin, polyvinylidene difluoride and mixtures thereof. Polyfurfuryl alcohol is the most preferred. The adsorbent produced by the pyrolysis has a silicon to carbon mole ratio of between about 10:1 and 1:3, and preferably about 2:1 to 1:2, most preferably 1:1. The pyrolysis is performed as a ramped temperature program between about and C., and preferably between about and C. The present invention also relates to a method for selectively adsorbing organic molecules having a molecular size (mean molecular diameter) of between about 3 and 6 .ANG. comprising contacting a vapor containing the small organic molecules to be adsorbed with the adsorbent composition of the present invention.

  4. Filovirus tropism: Cellular molecules for viral entry

    Directory of Open Access Journals (Sweden)

    Ayato eTakada


    Full Text Available In human and nonhuman primates, filoviruses (Ebola and Marburg viruses cause severe hemorrhagic fever.Recently, other animals such as pigs and some species of fruit bats have also been shown to be susceptible to these viruses. While having a preference for some cell types such as hepatocytes, endothelial cells, dendritic cells, monocytes, and macrophages, filoviruses are known to be pantropic in infection of primates. The envelope glycoprotein (GP is responsible for both receptor binding and fusion of the virus envelope with the host cell membrane. It has been demonstrated that filovirus GP interacts with multiple molecules for entry into host cells, whereas none of the cellular molecules so far identified as a receptor/coreceptor fully explains filovirus tissue tropism and host range. Available data suggest that the mucin-like region (MLR on GP plays an important role in attachment to the preferred target cells, whose infection is likely involved in filovirus pathogenesis, whereas the MLR is not essential for the fundamental function of the GP in viral entry into cells in vitro. Further studies elucidating the mechanisms of cellular entry of filoviruses may shed light on the development of strategies for prophylaxis and treatment of Ebola and Marburg hemorrhagic fevers.

  5. Conformational elasticity theory of chain molecules

    Institute of Scientific and Technical Information of China (English)

    YANG; Xiaozhen


    This paper develops a conformational elasticity theory of chain molecules, which is based on three key points: (ⅰ) the molecular model is the rotational isomeric state (RIS) model; (ⅱ) the conformational distribution function of a chain molecule is described by a function of two variables, the end-to-end distance of a chain conformation and the energy of the conformation; (ⅲ) the rule of changes in the chain conformational states during deformation is that a number of chain conformations would vanish. The ideal deformation behavior calculated by the theory shows that the change in chain conformations is physically able to make the upward curvature of the stress-strain curve at the large-scale deformation of natural rubber. With the theory, different deformation behaviors between polymers with different chemical structures can be described, the energy term of the stress in the deformations can be predicted, and for natural rubber the fraction of the energy term is around 13%, coinciding with the experimental results.

  6. Sisyphus Laser Cooling of a Polyatomic Molecule

    CERN Document Server

    Kozyryev, Ivan; Matsuda, Kyle; Augenbraun, Benjamin L; Anderegg, Loic; Sedlack, Alexander P; Doyle, John M


    We perform magnetically-assisted Sisyphus laser cooling of the triatomic free radical strontium monohydroxide (SrOH). This is achieved with principal optical cycling in the rotationally closed $P\\left(N"=1\\right)$ branch of either the $\\tilde{X}^{2}\\Sigma^{+}\\left(000\\right)\\leftrightarrow\\tilde{A}^{2}\\Pi_{1/2}\\left(000\\right)$ or the $\\tilde{X}^{2}\\Sigma^{+}\\left(000\\right)\\leftrightarrow\\tilde{B}^{2}\\Sigma^{+}\\left(000\\right)$ vibronic transitions. Molecules lost into the excited vibrational states during the cooling process are repumped back through the $\\tilde{B}\\left(000\\right)$ state for both the $\\left(100\\right)$ level of the Sr-O stretching mode and the $\\left(02^{0}0\\right)$ level of the bending mode. The transverse temperature of a SrOH molecular beam is reduced in one dimension by two orders of magnitude to $\\sim700\\ {\\rm \\mu K}$. This approach opens a path towards creating a variety of ultracold polyatomic molecules, including much larger ones, by means of direct laser cooling.

  7. Complex molecules in W51 North region

    CERN Document Server

    Rong, Jialei; Zapata, Luis A; Wu, Yuefang; Liu, Tie; Zhang, Chengpeng; Peng, Yaping; Zhang, Li; Liu, Ying


    We present Submillimeter Array (SMA) molecular line observations in two 2 GHz-wide bands centered at 217.5 and 227.5 GHz, toward the massive star forming region W51 North. We identified 84 molecular line transitions from 17 species and their isotopologues. The molecular gas distribution of these lines mainly peaks in the continuum position of W51 North, and has a small tail extending to the west, probably associated with W51 d2. In addition to the commonly detected nitrogen and oxygen-bearing species, we detected a large amount of transitions of the Acetone (CH$_3$COCH$_3$) and Methyl Formate (CH$_3$OCHO), which may suggest that these molecules are present in an early evolutionary stage of the massive stars. We also found that W51 North is an ethanol-rich source. There is no obvious difference in the molecular gas distributions between the oxygen-bearing and nitrogen-bearing molecules. Under the assumption of Local Thermodynamic Equilibrium (LTE), with the XCLASS tool, the molecular column densities, and rota...

  8. Small molecule phagocytosis inhibitors for immune cytopenias. (United States)

    Neschadim, Anton; Kotra, Lakshmi P; Branch, Donald R


    Immune cytopenias are conditions characterized by low blood cell counts, such as platelets in immune thrombocytopenia (ITP) and red blood cells in autoimmune hemolytic anemia (AIHA). Chronic ITP affects approximately 4 in 100,000 adults annually while AIHA is much less common. Extravascular phagocytosis and massive destruction of autoantibody-opsonized blood cells by macrophages in the spleen and liver are the hallmark of these conditions. Current treatment modalities for ITP and AIHA include the first-line use of corticosteroids; whereas, IVIg shows efficacy in ITP but not AIHA. One main mechanism of action by which IVIg treatment leads to the reduction in platelet destruction rates in ITP is thought to involve Fcγ receptor (FcγR) blockade, ultimately leading to the inhibition of extravascular platelet phagocytosis. IVIg, which is manufactured from the human plasma of thousands of donors, is a limited resource, and alternative treatments, particularly those based on bioavailable small molecules, are needed. In this review, we overview the pathophysiology of ITP, the role of Fcγ receptors, and the mechanisms of action of IVIg in treating ITP, and outline the efforts and progress towards developing novel, first-in-class inhibitors of phagocytosis as synthetic, small molecule substitutes for IVIg in ITP and other conditions where the pathobiology of the disease involves phagocytosis.

  9. Laser Spectroscopy of bi-alkali molecules (United States)

    Dutta, Sourav; Altaf, A.; Lorenz, J.; Elliott, D.; Chen, Yong


    We report a study of laser spectroscopy of bi-alkali molecules, such as Li2, Rb2 and LiRb (work is in progress). We have constructed a dual-species (Li/Rb) heat pipe oven with a side viewport. The molecular fluorescence is excited by a dye laser with Rh6G dye (operating between 564 nm and 610 nm) and various home-made diode lasers (operating near 635 nm and 665 nm). The fluorescence is recorded using a .5ex1 -.1em/ -.15em.25ex4 m monochromator with a 0.1 nm (˜ 3 cm-1) spectral resolution. Transitions to the X^1σg^+ in Li2 and Rb2 have been measured and studies on LiRb are in progress. Molecular parameters, such as force constant, may be obtained from the analysis of the data (which agree with previously known values to within ˜ 3%). Using the known values of dissociation energy De and harmonic frequency φe for the alkali dimers, we also demonstrate that simple calculations with Morse potential approximation can be used to estimate the molecular transition wavelengths to within a few (1-3) nanometers from the experimentally measured values. Such information will aid in creating cold molecules via photoassociation in a dual species magneto-optical trap (LiRb in our case).

  10. Half collision resonance phenomena in molecules

    Energy Technology Data Exchange (ETDEWEB)

    Maximo Garcia-Sucre (Universidad Central de Venezuela, Caracas (Venezuela)); Raseev, G. (Paris-11 Univ., 91 - Orsay (France)); Ross, S.C. (New Brunswick Univ., Fredericton, NB (Canada)) (eds.)


    The Escuela Latinoamericana de Fisica (ELAF) is a series of meeting s that for 28 years has played an important role in research-level teaching of physics in Latin America. This book contains the proceedings of ELAF 90 which was held at the Instituto Venezolano de Investigaciones Cientificas (IVIC) in Caracas, Venezuela from July 23 to August 3, 1990, as part of the commemoration of the 30th anniversary of IVIC. In contrast to previous ELAF's that were of general scope, ELAF 90 centered on a particular subject matter: Half Collisional Resonance Phenomena in Molecules, Experimental and Theoretical Approaches. The term Half Collision'' refers to the fragmentation of a molecular system following is excitation by light. The lack of an incident fragmentation of a molecular system following is excitation by light. The lack of an incident particle (other than the photon) in the fragmentation process is what leads to the term. The purpose of this volume is to present current results in the experimental and theoretical study of half collisions and also to include pedagogical papers at an introductory or intermediate level. The contributions are grouped into several sections; light sources; ionization; dissociation-experimental; dissociation-theory; competition between ionization and dissociation; and particle-molecule collisions.

  11. Interstellar grain chemistry and organic molecules (United States)

    Allamandola, L. J.; Sandford, S. A.


    The detection of prominant infrared absorption bands at 3250, 2170, 2138, 1670 and 1470 cm(-1) (3.08, 4.61, 4.677, 5.99 and 6.80 micron m) associated with molecular clouds show that mixed molecular (icy) grain mantles are an important component of the interstellar dust in the dense interstellar medium. These ices, which contain many organic molecules, may also be the production site of the more complex organic grain mantles detected in the diffuse interstellar medium. Theoretical calculations employing gas phase as well as grain surface reactions predict that the ices should be dominated only by the simple molecules H2O, H2CO, N2, CO, O2, NH3, CH4, possibly CH3OH, and their deuterated counterparts. However, spectroscopic observations in the 2500 to 1250 cm(-1)(4 to 8 micron m) range show substantial variation from source reactions alone. By comparing these astronomical spectra with the spectra of laboratory-produced analogs of interstellar ices, one can determine the composition and abundance of the materials frozen on the grains in dense clouds. Experiments are described in which the chemical evolution of an interstellar ice analog is determined during irradiation and subsequent warm-up. Particular attention is paid to the types of moderately complex organic materials produced during these experiments which are likely to be present in interstellar grains and cometary ices.

  12. Chemokines: Small Molecules Participate in Diabetes

    Directory of Open Access Journals (Sweden)

    S. Mostafa Hosseini-Zijoud


    Full Text Available Background: Chemokines are small protein molecules involved in cell signaling processes. They play a crucial role in many physiological and pathological processes. Chemokines are functionally classified into two categories; inflammatory/inducible and constitutive. Their biologic functional differences are the result of their receptors structural differences. Recently some studies were performed about the chemokines changes in diabetes. Inflammatory mechanisms have an important role in diabetes.Materials and Methods: In this review article we searched the keywords chemokines, diabetes, diabetes pathogenesis, and type 1 and 2 diabetes in Persian resources, PubMed and famous English-language websites through advanced search engines and found the newest studies about the role of chemokines in the pathogenesis of diabetes.Results: The results of the studies showed that diabetes and its disorders enhance the activation of immune cells and the expression of cytokines such as IL-1, IL-6, IL-8, IL-10, SDF-1, INF-γ, TGF-β, MCP-1, IP-10, TNF-α, and RANTES; most of them have impact on the pathogenesis of diabetes.Conclusion: Comparison and analysis of the results obtained from our research and the results of performed studies in the world and Iran shows that chemokines, like other protein molecules involved in the pathogenesis and etiology of diabetes, play a role in this process.

  13. Organic- and molecule-based magnets

    Directory of Open Access Journals (Sweden)

    Joel S. Miller


    Full Text Available Magnets have been known for millennia and are strongly associated with metals (e.g. Fe, Co, Ni, Gd, intermetallics (e.g. Co17Sm2, Nd2Fe14B, or their oxides (e.g. CrO2, Fe3O4. The development of new magnetic materials has led to ubiquitous uses for electricity generation, memory storage media, and devices such as electric motors, microphones, telephones and computers. These magnets are fabricated via energy demanding metallurgical methods and are frequently brittle, chemically reactive, and possess elements in limited supply. The end of the last millennium has seen a surge in using organic, molecular, and polymeric materials as substitutes for metal and ceramic materials in many applications. Also, in the past few decades organic and molecule-based materials have been shown to magnetically order with examples having ordering temperatures exceeding room temperature, higher-than-iron saturation magnetizations, large coercive fields, etc. An overview of organic-based, and more generally molecule-based magnetic materials that exhibit unusual magnetic properties ranging from ferromagnets to synthetic antiferromagnets with emphasis on magnetic ordering using examples possessing organic nitriles (—CN or inorganic cyanide (CN− is described.

  14. Spin-crossover molecule based thermoelectric junction

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Dibyajyoti [Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064 (India); Parida, Prakash [Institute for Theoretical Physics, University of Regensburg, D-93040 Regensburg (Germany); Pati, Swapan K. [Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064 (India)


    Using ab-initio numerical methods, we explore the spin-dependent transport and thermoelectric properties of a spin-crossover molecule (i.e., iron complex of 2-(1H-pyrazol-1-yl)-6-(1H-tetrazole-5-yl)pyridine) based nano-junction. We demonstrate a large magnetoresistance, efficient conductance-switching, and spin-filter activity in this molecule-based two-terminal device. The spin-crossover process also modulates the thermoelectric entities. It can efficiently switch the magnitude as well as spin-polarization of the thermocurrent. We find that thermocurrent is changed by ∼4 orders of magnitude upon spin-crossover. Moreover, it also substantially affects the thermopower and consequently, the device shows extremely efficient spin-crossover magnetothermopower generation. Furthermore, by tuning the chemical potential of electrodes into a certain range, a pure spin-thermopower can be achieved for the high-spin state. Finally, the reasonably large values of figure-of-merit in the presence and absence of phonon demonstrate a large heat-to-voltage conversion efficiency of the device. We believe that our study will pave an alternative way of tuning the transport and thermoelectric properties through the spin-crossover process and can have potential applications in generation of spin-dependent current, information storage, and processing.

  15. Axion Dark Matter Detection with Cold Molecules

    CERN Document Server

    Graham, Peter W


    Current techniques cannot detect axion dark matter over much of its parameter space, particularly in the theoretically well-motivated region where the axion decay constant f_a lies near the GUT and Planck scales. We suggest a novel experimental method to search for QCD axion dark matter in this region. The axion field oscillates at a frequency equal to its mass when it is a component of dark matter. These oscillations induce time varying CP-odd nuclear moments, such as electric dipole and Schiff moments. The coupling between internal atomic fields and these nuclear moments gives rise to time varying shifts to atomic energy levels. These effects can be enhanced by using elements with large Schiff moments such as the light Actinides, and states with large spontaneous parity violation, such as molecules in a background electric field. The energy level shift in such a molecule can be ~ 10^-24 eV or larger. While challenging, this energy shift may be observable in a molecular clock configuration with technology pr...

  16. Atomic-Scale Control of Electron Transport through Single Molecules

    DEFF Research Database (Denmark)

    Wang, Y. F.; Kroger, J.; Berndt, R.;


    Tin-phthalocyanine molecules adsorbed on Ag(111) were contacted with the tip of a cryogenic scanning tunneling microscope. Orders-of-magnitude variations of the single-molecule junction conductance were achieved by controllably dehydrogenating the molecule and by modifying the atomic structure...... of the surface electrode. Nonequilibrium Green's function calculations reproduce the trend of the conductance and visualize the current flow through the junction, which is guided through molecule-electrode chemical bonds....

  17. Theory of long-range ultracold atom-molecule photoassociation


    Pérez-Ríos, Jesús; Lepers, Maxence; Dulieu, Olivier


    The creation of ultracold molecules is currently limited to diatomic species. In this letter we present a theoretical description of the photoassociation of ultracold atoms and molecules to create ultracold excited triatomic molecules, thus being a novel example of light-assisted ultracold chemical reaction. The calculation of the photoassociation rate of ultracold Cs atoms with ultracold Cs2 molecules in their rovibrational ground state is reported, based on the solution of the quantum dynam...

  18. The Stereochemistry of Biochemical Molecules: A Subject to Revisit (United States)

    Centelles, Josep J.; Imperial, Santiago


    Although Fischer's convention for stereoisomers is useful for simple molecules, the stereochemistry of complex biochemical molecules is often poorly indicated in textbooks. This article reports on errors in stereochemistry of complex hydrosoluble vitamin B12 molecule. Twenty-five popular biochemistry textbooks were examined for their treatment of…

  19. New frontiers for quantum gases of polar molecules (United States)

    Moses, Steven A.; Covey, Jacob P.; Miecnikowski, Matthew T.; Jin, Deborah S.; Ye, Jun


    Compared to atoms, molecules possess additional degrees of freedom that can be exploited in fundamental tests, ultracold chemistry, and engineering new quantum phases in many-body systems. Here, we review the recent progress in creating and manipulating ultracold bialkali molecules to study quantum gases of polar molecules.

  20. Molecular electronics with single molecules in solid-state devices

    DEFF Research Database (Denmark)

    Moth-Poulsen, Kasper; Bjørnholm, Thomas


    The ultimate aim of molecular electronics is to understand and master single-molecule devices. Based on the latest results on electron transport in single molecules in solid-state devices, we focus here on new insights into the influence of metal electrodes on the energy spectrum of the molecule...

  1. Interstellar molecules in the Large Magellanic Cloud (United States)

    Johansson, L. E. B.; Olofsson, H.; Hjalmarson, A.; Gredel, R.; Black, J. H.


    We present the results of a mm-wave molecular line search in the Large Magellanic Cloud (LMC) obtained with the Swedish-ESO Submillimeter Telescope (SEST) in the area of the N 159 complex of HII regions. Isotopomers of CO, CS, SO, CN, HCN, HNC, HCO(+) and H2CO have been detected. Some of these molecules have been observed in two transitions allowing excitation temperature estimates, For (13)CO and (12)CO we find temperatures close to, or in excess of 10 K, while C(18)O, CS and HCO(+) show temperatures between 5 and 10 K. All observed isotopomer intensity ratios suggest small optical depths provided that Galactic isoptopic abundances ratios apply. From the C-12 and C-13-isotopomer data of CS and HCO(+), combined with the C(34)S line emission we estimate the gas phase C-12/C-13 abundance ratio to be 50+25, sub-20 in N 159. The 0-18/0-17 abundance ratio is observed to be a factor of about 2 lower than in the Galaxy, and another factor of 2 lower than in starburst galaxies. Using the OSO 20m telescope, we have mapped the Galactic molecular cloud associated with the H II region S 138 in the 3 mm transitions of most of the molecules detected in the LMC. These data have been used to investigate the effects of linear resolution on line ratios and fractional abundances. Based upon cloud luminosities, normalized to that of the CO(1-0) line, the detected lines in the LMC are weaker by a factor of 1.5 to 3 relative to those of the S 138 cloud. The exception is HCO(+), which shows stronger normalized emission in N 159. The normalized luminosities of the S 138 cloud are similar to those observed in a sample of strong CO galaxies. Fractional abundances of the detected molecules have been estimated using the conversion factor from CO emission to H2 column density. While the derived fractional abundances of S 138 generally agree to within a factor of 3 with those reported for Orion KL and TMC-1, all molecular concentrations observed in the LMC are typically a factor of 10 lower.

  2. Excitonic Coupling in Linear and Trefoil Trimer Perylenediimide Molecules Probed by Single-Molecule Spectroscopy

    KAUST Repository

    Yoo, Hyejin


    Perylenediimide (PDI) molecules are promising building blocks for photophysical studies of electronic interactions within multichromophore arrays. Such PDI arrays are important materials for fabrication of molecular nanodevices such as organic light-emitting diodes, organic semiconductors, and biosensors because of their high photostability, chemical and physical inertness, electron affinity, and high tinctorial strength over the entire visible spectrum. In this work, PDIs have been organized into linear (L3) and trefoil (T3) trimer molecules and investigated by single-molecule fluorescence microscopy to probe the relationship between molecular structures and interchromophoric electronic interactions. We found a broad distribution of coupling strengths in both L3 and T3 and hence strong/weak coupling between PDI units by monitoring spectral peak shifts in single-molecule fluorescence spectra upon sequential photobleaching of each constituent chromophore. In addition, we used a wide-field defocused imaging technique to resolve heterogeneities in molecular structures of L3 and T3 embedded in a PMMA polymer matrix. A systematic comparison between the two sets of experimental results allowed us to infer the correlation between intermolecular interactions and molecular structures. Our results show control of the PDI intermolecular interactions using suitable multichromophoric structures. © 2012 American Chemical Society.

  3. Discrete energy transport in collagen molecules (United States)

    Alain, Mvogo; Germain, H. Ben-Bolie; Timoléon, C. Kofané


    The modulational instability in the three coupled α-polypeptide chains of a collagen molecule is investigated. Choosing symmetric and asymmetric solutions, and applying the so-called rotating-wave approximation, we describe the dynamics of the system by the discrete nonlinear Schrödinger (DNLS) equation. The linear stability analysis of the continuous wave solution is performed. The numerical simulations show the generation of trains of solitonic structures in the lattice with increasing amplitude as time progresses. The effect of damping and noise forces of the physiological temperature (T = 300 K) introduces an erratic behavior to the formed patterns, reinforcing the idea that the energy used in metabolic processes is confined to specific regions for efficiency.

  4. CO-releasing molecule (CORM) conjugate systems. (United States)

    Kautz, Anna Christin; Kunz, Peter C; Janiak, Christoph


    The development of CORMs (CO-releasing molecules) as a prodrug for CO administration in living organisms has attracted significant attention. CORMs offer the promising possibility of a safe and controllable release of CO in low amounts triggered by light, ligands, enzymes, etc. For the targeting of specific tissues or diseases and to prevent possible side effects from metals and other residues after CO release, these CORMs are attached to biocompatible systems, like peptides, polymers, nanoparticles, dendrimers, protein cages, non-wovens, tablets, and metal-organic frameworks. We discuss in this review the known CORM carrier conjugates, in short CORM conjugates, with covalently-bound or incorporated CORMs for medicinal and therapeutic applications. Most conjugates are nontoxic, show increasing half-lives of CO release, and make use of the EPR-effect, but still show problems because of a continuous background of CO release and the absence of an on/off-switch for the CO release.

  5. Carotenoids as signaling molecules in cardiovascular biology

    Directory of Open Access Journals (Sweden)

    Abolfazl Barzegari


    Full Text Available Oxidative stress and inflammation play important roles in the etiology of cardiovascular disease (CVD. Thus, natural antioxidant carotenoids existing in fruits and vegetables could have a significant role in the prevention of CVD. Nevertheless,clinical data are conflicting about the positive effect of some antioxidant carotenoids in reducing cardiovascular morbidity and mortality. Many biological actions of carotenoids have been attributed to their antioxidant effect; however, the precise mechanism by which carotenoids produce their beneficial effects is still under discussion. They might modulate molecular pathways involved in cell proliferation, acting at Akt, tyrosine kinases, mitogen activated protein kinase (MAP kinase and growth factor signaling cascades. Screening for a promising cardiovascular protective carotenoids therefore might be performed in vitro and in vivo with caution in cross-interaction with other molecules involved in signaling pathways especially those affecting microRNAs, performing a role in molecular modulation of cardiovascular cells.

  6. [Ants: a chemical library of anticancer molecules]. (United States)

    Vétillard, Angélique; Bouzid, Wafa


    Animal venoms are complex mixtures containing simple organic molecules, proteins, peptides, and other bioactive elements with extraordinary biological properties associated with their ability to act on a number of molecular receptors in the process of incapacitating their target organisms. In such a context, arthropod venoms are invaluable sources of bioactive substances, with therapeutic interest but the limited availability of some venom such as those from ants, has restricted the potential that these biomolecules could represent. We investigated for the first time transcriptomic expression from the ant species Tetramorium bicarinatum. Four hundred randomly selected clones from cDNA libraries were sequenced and a total of 374 expressed sequence tags (ESTs) were generated. Based on the results of BLAST searches, these sequences were clustered and assembled into 269 contigs. About 72% (269) of these matched BLASTx hits with an interesting diversity and unusual abundance of cellular transcripts (48%) related to gene and protein expression reflecting the specialization of this tissue. In addition, transcripts encoding transposases were relatively highly expressed (14%). It may be that transposable elements are present and that their presence accounts for some of the variation in venom toxins. About twenty per cent of the ESTs were categorized as putative toxins, the major part represented by allergens (48% of the total venom toxins) such as pilosulin 5, sol i 3 and Myp p I and II. Several contigs encoding enzymes, including zinc-metalloproteases (17%) that are likely involved in the processing and activation of venom proteins/peptides, were also identified from the library. In addition, a number of sequences (8%) had no significant similarity to any known sequence which indicates a potential source of for the discovery of new toxins. In order to provide a global insight on the transcripts expressed in the venom gland of the Brazilian ant species Tetramorium

  7. Extracellular Matrix Molecules Facilitating Vascular Biointegration

    Directory of Open Access Journals (Sweden)

    Martin K.C. Ng


    Full Text Available All vascular implants, including stents, heart valves and graft materials exhibit suboptimal biocompatibility that significantly reduces their clinical efficacy. A range of biomolecules in the subendothelial space have been shown to play critical roles in local regulation of thrombosis, endothelial growth and smooth muscle cell proliferation, making these attractive candidates for modulation of vascular device biointegration. However, classically used biomaterial coatings, such as fibronectin and laminin, modulate only one of these components; enhancing endothelial cell attachment, but also activating platelets and triggering thrombosis. This review examines a subset of extracellular matrix molecules that have demonstrated multi-faceted vascular compatibility and accordingly are promising candidates to improve the biointegration of vascular biomaterials.

  8. Hard molecule-based magnet of Fe (United States)

    Vaz, M. G. F.; Ardisson, J. D.; Stumpf, H. O.; Macedo, W. A. A.


    A new molecule-based magnet containing Fe 2+, Fe 3+, Cu(opba) 2- and Bu 4N +, with opba=ortho-phenylenebis(oxamato) and Bu 4N +=tetra-n-butylammonium, was synthesized. The samples were characterized by infrared spectroscopy, elemental analysis, atomic absorption, vibrating sample magnetometry and 57Fe Mössbauer spectroscopy. The magnetic measurements show that the compound presents a magnetic transition around 25 K and a high coercivity, around 1.3 T. Above the transition temperature, the Mössbauer spectrum is dominated by a broad doublet characteristic of Fe 2+. At 20 K, the spectrum shows clear magnetic splitting and at least two non-equivalent Fe sites can be identified. To the best of our knowledge, this compound presents the highest coercive field observed for an iron-based molecular magnetic system.

  9. Hard molecule-based magnet of Fe

    Energy Technology Data Exchange (ETDEWEB)

    Vaz, M.G.F. E-mail:; Ardisson, J.D.; Stumpf, H.O.; Macedo, W.A.A


    A new molecule-based magnet containing Fe{sup 2+}, Fe{sup 3+}, Cu(opba){sup 2-} and Bu{sub 4}N{sup +}, with opba=ortho-phenylenebis(oxamato) and Bu{sub 4}N{sup +}=tetra-n-butylammonium, was synthesized. The samples were characterized by infrared spectroscopy, elemental analysis, atomic absorption, vibrating sample magnetometry and {sup 57}Fe Moessbauer spectroscopy. The magnetic measurements show that the compound presents a magnetic transition around 25 K and a high coercivity, around 1.3 T. Above the transition temperature, the Moessbauer spectrum is dominated by a broad doublet characteristic of Fe{sup 2+}. At 20 K, the spectrum shows clear magnetic splitting and at least two non-equivalent Fe sites can be identified. To the best of our knowledge, this compound presents the highest coercive field observed for an iron-based molecular magnetic system.

  10. [Action of antibiotics as signalling molecules]. (United States)

    Bulgakova, V G; Vinogradova, K A; Orlova, T I; Kozhevin, P A; Polin, A N


    It was thought that antibiotics should be produced by soil microorganisms to inhibit the growth of competitors in natural habitats. Yet it has been shown that antibiotics at subinhibitory concentrations may have a role as signalling molecules providing cell-to-cell communication in bacteria in the environment. Antibiotics modulate gene transcription and regulate gene expression in microbial populations. Subinhibitory concentrations of antibiotics may cause a number of phenotypic and genotypic changes in microorganisms. These transcription changes are dependent on the interaction of antibiotics with macromolecular receptors such as ribosome or RNA-polymerase. Antibiotic signalling and quorum-sensing system are important regulatory mechanisms in bacteria. It was demonstrated that antibiotics interfered with quorum-sensing system.

  11. Special Issue: “Molecules against Alzheimer”

    Directory of Open Access Journals (Sweden)

    Michael Decker


    Full Text Available This Special Issue, entitled “Molecules against Alzheimer”, gathers a number of original articles, short communications, and review articles on recent research efforts toward the development of novel drug candidates, diagnostic agents and therapeutic approaches for Alzheimer’s disease (AD, the most prevalent neurodegenerative disorder and a leading cause of death worldwide. This Special Issue contains many interesting examples describing the design, synthesis, and pharmacological profiling of novel compounds that hit one or several key biological targets, such as cholinesterases, β-amyloid formation or aggregation, monoamine oxidase B, oxidative stress, biometal dyshomeostasis, mitochondrial dysfunction, serotonin and/or melatonin systems, the Wnt/β-catenin pathway, sigma receptors, nicotinamide phosphoribosyltransferase, or nuclear erythroid 2-related factor. The development of novel AD diagnostic agents based on tau protein imaging and the use of lithium or intranasal insulin for the prevention or the symptomatic treatment of AD is also covered in some articles of the Special Issue.

  12. Simulated single molecule microscopy with SMeagol

    CERN Document Server

    Lindén, Martin; Boucharin, Alexis; Fange, David; Elf, Johan


    Recent advances in single particle tracking (SPT) microscopy 1 make it possible to obtain tens of thousands macromolecular trajectories from within a living cell in just a few minutes. Since molecules typically change their movement properties upon interactions, these trajectories contain information about both locations and rates of intracellular reactions. This information is unfortunately obscured by physical limitations of the optical microscope and noise in detection systems, making statistical methods development for SPT analysis a very active research field. Unbiased testing and comparison of such methods are however difficult given the absence of in vivo data of intracellular dynamics where the true states of interaction are known, a.k.a. the ground truth. A common resort is to instead use simulated, synthetic, data. However, tests using such data give unrealistically optimistic results if the simplifying assumptions underlying the analysis method are satisfied in the synthetic data, a practice known ...

  13. Evolutionary game theory: molecules as players. (United States)

    Bohl, Katrin; Hummert, Sabine; Werner, Sarah; Basanta, David; Deutsch, Andreas; Schuster, Stefan; Theissen, Günter; Schroeter, Anja


    In this and an accompanying paper we review the use of game theoretical concepts in cell biology and molecular biology. This review focuses on the subcellular level by considering viruses, genes, and molecules as players. We discuss in which way catalytic RNA can be treated by game theory. Moreover, genes can compete for success in replication and can have different strategies in interactions with other genetic elements. Also transposable elements, or "jumping genes", can act as players because they usually bear different traits or strategies. Viruses compete in the case of co-infecting a host cell. Proteins interact in a game theoretical sense when forming heterodimers. Finally, we describe how the Shapley value can be applied to enzymes in metabolic pathways. We show that game theory can be successfully applied to describe and analyse scenarios at the molecular level resulting in counterintuitive conclusions.

  14. Magneto-optical trapping of diatomic molecules

    CERN Document Server

    Hummon, Matthew T; Stuhl, Benjamin K; Collopy, Alejandra L; Xia, Yong; Ye, Jun


    The development of the magneto-optical trap revolutionized the fields of atomic and quantum physics by providing a simple method for the rapid production of ultracold, trapped atoms. A similar technique for producing a diverse set of dense, ultracold diatomic molecular species will likewise transform the study of strongly interacting quantum systems, precision measurement, and physical chemistry. We demonstrate one- and two-dimensional transverse laser cooling and magneto-optical trapping of the polar molecule yttrium (II) oxide (YO). Using a quasicycling optical transition we observe transverse Doppler cooling of a YO molecular beam to a temperature of 5 mK, limited by interaction time. With the addition of an oscillating magnetic quadrupole field we demonstrate a transverse magneto-optical trap and achieve temperatures of 2 mK.

  15. Coupled Cluster Theory for Large Molecules

    DEFF Research Database (Denmark)

    Baudin, Pablo


    This thesis describes the development of local approximations to coupled cluster (CC) theory for large molecules. Two different methods are presented, the divide–expand–consolidate scheme (DEC), for the calculation of ground state energies, and a local framework denoted LoFEx, for the calculation...... of electronic excitation energies and oscillator strengths. After an introduction to the relevant notions of electronic-structure theory, the principal aspects of DEC and LoFEx are summarized. For comparison, a selected review of the state-of-the-art is presented for each domain. This thesis should serve...... as an introduction to the work developed and presented in the scientific articles collected as appendices. The DEC scheme has been applied successfully to the calculation of MP2, CCSD and CCSD(T) ground state energies. The intrinsic structure of DEC allows for a linear-scaling (with system size) and massively...

  16. Small Molecule Library Synthesis Using Segmented Flow

    Directory of Open Access Journals (Sweden)

    Christina M. Thompson


    Full Text Available Flow chemistry has gained considerable recognition as a simple, efficient, and safe technology for the synthesis of many types of organic and inorganic molecules ranging in scope from large complex natural products to silicon nanoparticles. In this paper we describe a method that adapts flow chemistry to the synthesis of libraries of compounds using a fluorous immiscible solvent as a spacer between reactions. The methodology was validated in the synthesis of two small heterocycle containing libraries. The reactions were performed on a 0.2 mmol scale, enabling tens of milligrams of material to be generated in a single 200 mL reaction plug. The methodology allowed library synthesis in half the time of conventional microwave synthesis while maintaining similar yields. The ability to perform multiple, potentially unrelated reactions in a single run is ideal for making small quantities of many different compounds quickly and efficiently.

  17. Spin doping using transition metal phthalocyanine molecules (United States)

    Atxabal, A.; Ribeiro, M.; Parui, S.; Urreta, L.; Sagasta, E.; Sun, X.; Llopis, R.; Casanova, F.; Hueso, L. E.


    Molecular spins have become key enablers for exploring magnetic interactions, quantum information processes and many-body effects in metals. Metal-organic molecules, in particular, let the spin state of the core metal ion to be modified according to its organic environment, allowing localized magnetic moments to emerge as functional entities with radically different properties from its simple atomic counterparts. Here, using and preserving the integrity of transition metal phthalocyanine high-spin complexes, we demonstrate the magnetic doping of gold thin films, effectively creating a new ground state. We demonstrate it by electrical transport measurements that are sensitive to the scattering of itinerant electrons with magnetic impurities, such as Kondo effect and weak antilocalization. Our work expands in a simple and powerful way the classes of materials that can be used as magnetic dopants, opening a new channel to couple the wide range of molecular properties with spin phenomena at a functional scale.

  18. Fragmentation of methane molecules by antiproton impact (United States)

    Salehzadeh, Arash; Kirchner, Tom


    Extending previous work for proton impact, we have investigated the fragmentation of methane molecules due to collisions with antiprotons in the 25 keV to 5 MeV impact energy range. The multi-center nature of the problem is addressed by using a spectral representation of the molecular Hartree-Fock-level Hamiltonian and a single-center expansion of the initially populated molecular orbitals. The two-center basis generator method (TC-BGM) is used for orbital propagation. Electron-removal cross sections obtained from the TC-BGM solutions are complemented with a dynamical decay-route fragmentation model to calculate cross sections for the production of fragment ions. Good agreement with the available experimental data is observed for CH4+,CH3+,CH2+and CH+. Work supported by NSERC, Canada.

  19. Low energy ion-molecule reactions

    Energy Technology Data Exchange (ETDEWEB)

    Farrar, J.M. [Univ. of Rochester, NY (United States)


    This project is concerned with elucidating the dynamics of elementary ion-molecule reactions at collision energies near and below 1 eV. From measurements of the angular and energy distributions of the reaction products, one can infer intimathe details about the nature of collisions leading to chemical reaction, the geometries and lifetimes of intermediate complexes that govern the reaction dynamics, and the collision energy dependence of these dynamical features. The author employs crossed-beam low energy mass spectrometry technology developed over the last several years, with the focus of current research on proton transfer and hydrogen atom transfer reactions of te O{sup {minus}} ion with species such as HF, H{sub 2}O, and NH{sub 3}.

  20. Combinatorial analysis of interacting RNA molecules

    CERN Document Server

    Li, Thomas J X


    Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with two backbones drawn horizontally on top of each other such that (1) intramolecular and intermolecular bonds are noncrossing and (2) there is no "zig-zag" configuration. This paper studies joint structures with arc-length at least four in which both, interior and exterior stack-lengths are at least two (no isolated arcs). The key idea in this paper is to consider a new type of shape, based on which joint structures can be derived via symbolic enumeration. Our results imply simple asymptotic formulas for the number of joint structures with surprisingly small exponential growth rates. They are of interest in the context of designing prediction algorithms for RNA-RNA interactions.

  1. Full Alignment of Molecules Using Elliptically Polarized Light

    DEFF Research Database (Denmark)

    Larsen, Jakob Juul; Hald, Kasper; Seideman, Tamar

    When a molecule with an anisotropic polarizability is placed in a strong nonresonant laser field the interaction occurs through the induced dipole moment. The outcome is that the molecule experiences an angular dependent potential energy. It is now well established that a linearly polarized laser...... of the molecule the third axis is also aligned. Experimentally, we investigate the effect by aligning 3,4-dibromothiophene molecules with a strong, nonresonant, nanosecond laser pulse. The alignment is probed by Coulomb exploding the molecules with an intense 20 femtosecond laser pulse. Detection of the emerging...

  2. Theoretical investigation on single-molecule chiroptical spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Wakabayashi, M. [Tokyo Institute of Technology, School and Graduate School of Bioscience and Biotechnology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa (Japan); Yokojima, S. [Tokyo University of Pharmacy and Life Sciences, 1423-1 Horinouchi, Hachiouji-shi, Tokyo (Japan); Fukaminato, T. [Research Institute for Electronic Science, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020 (Japan); Ogata, K.; Nakamura, S. [Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)


    Some experimental results of chiroptical response of single molecule have already reported. In those experiments, dissymmetry parameter, g was used as an indicator of the relative circular dichroism intensity. The parameter for individual molecules was measured. For the purpose of giving an interpretation or explanation to the experimental result, the dissymmetry parameter is formulated on the basis of Fermi’s golden rule. Subsequently, the value of individual molecules is evaluated as a function of the direction of light propagation to the orientationary fixed molecules. The ground and excited wavefunction of electrons in the molecule and transition moments needed are culculated using the density functional theory.

  3. Nondestructive Detection of Polar Molecules via Rydberg Atoms

    CERN Document Server

    Zeppenfeld, Martin


    A highly sensitive, general, and preferably nondestructive technique to detect polar molecules would greatly advance a number of fields, in particular quantum science with cold and ultracold molecules. Here, we propose using resonant energy transfer between molecules and Rydberg atoms to detect molecules. Based on an energy transfer cross section of $>10^{-6}\\,$cm$^2$ for sufficiently low collision energies, a near unit efficiency non-destructive detection of basically any polar molecule species in a well defined internal state should be possible.

  4. Small Organic Molecules for Direct Aldol Reaction

    Institute of Scientific and Technical Information of China (English)

    TANG Zhuo; GONG Liu-Zhu; MI Ai-Qiao; JIANG Yao-Zhong


    Since the pioneering finding by List and Barbas Ⅲ and their coworkers that L-proline could work as a catalyst in the intermolecular direct aldol reaction, the concept of small organic molecules as catalysts has received great attention. However, new organic molecule which have better catalysis ability are reported scarcely.Our groups1 found L-Prolinamides 1 to be active catalysts for the direct aldol reaction of 4-nitrobenaldehyde with neat acetone at room temperature. The enantioselectivity increases as the amide N-H becomes more acidic and thus a better hydrogen bond donor. Introducing another proton donor, hydroxyl, in the catalyst lead to a further improvement in the catalytic enantioselectivity.The calculations reveal that the amide N-H and the terminal hydroxyl groups form hydrogen bonds with the benzaldehyde substrate. These hydrogen bonds reduce the activation energy and cause high enantioselectivity.Catalyst 2, prepared from L-proline and (1S, 2S)-diphenyl-2-aminoethanol, exhibits high enantioselectivities of up to 93% ee for aromatic aldehydes and up to >99% ee for aliphatic aldehydes. It is noteworthy that our results refuted the conventional wisdom that the carboxylic acid group of proline is a reqirement for high enatioselectivity and provide a powerful strategy in the molecular design of new organic catalyst because plentiful chiral resource containing multi-hydrogen bonding donor, for example, peptides.Very recently, we found that L-proline-based peptides 3-7 can catalyze the aldol reactions of hydroxyacetone with aldehydes 8 in aqueous media, to give 1,4-diols 9, the disfavored products with either aldolase or L-proline. Both peptides 5 and 6 give good results.The abilities of peptides 5 and 6 to catalyze the direct aldol reactions of hydroxyacetone with avariety of aldehydes were examined under optimal conditions. The results are shown in table. Highyields and entioselectivities of up to 96% ee were observed for aromatic aldehydes

  5. Molecules in Laboratory and in Interstellar Space? (United States)

    Thimmakondu, Venkatesan S.


    In this talk, the quantum chemistry of astronomically relevant molecules will be outlined with an emphasis on the structures and energetics of C_7H_2 isomers, which are yet to be identified in space. Although more than 100's of isomers are possible for C_7H_2, to date only 6 isomers had been identified in the laboratory. The equilibrium geometries of heptatriynylidene (1), cyclohepta-1,2,3,4-tetraen-6-yne (2), and heptahexaenylidene (3), which we had investigated theoretically will be discussed briefly. While 1 and 3 are observed in the laboratory, 2 is a hypothetical molecule. The theoretical data may be useful for the laboratory detection of 2 and astronomical detection of 2 and 3. THIS WORK IS SUPPORTED BY A RESEARCH GRANT (YSS/2015/00099) FROM SERB, DST, GOVERNMENT OF INDIA. Apponi, A. P.; McCarthy, M. C.; Gottlieb, C. A.; Thaddeus, P. Laboratory Detection of Four New Cumulene Carbenes: H_2C_7, H_2C_8, H_2C_9, and D_2C10, Astrophys. J. 2000, 530, 357-361 Ball, C. D; McCarthy, M. C.; Thaddeus, P. Cavity Ringdown Spectroscopy of the Linear Carbon Chains HC_7H, HC_9H, HC11H, and HC13H. J. Chem. Phys. 2000, 112, 10149-10155 Dua, S.; Blanksby, S. J.; Bowie, J. H. Formation of Neutral C_7H_2 Isomers from Four Isomeric C_7H_2 Radical Anion Precursors in the Gas Phase. J. Phys. Chem. A, 2000, 104, 77-85. Thimmakondu, V. S. The equilibrium geometries of heptatriynylidene, cyclohepta-1,2,3,4-tetraen-6-yne, and heptahexaenylidene, Comput. Theoret. Chem. 2016, 1079, 1-10

  6. Photophysics of thermally activated delayed fluorescence molecules (United States)

    Dias, Fernando B.; Penfold, Thomas J.; Monkman, Andrew P.


    Thermally activated delayed fluorescence (TADF) has recently emerged as one of the most attractive methods for harvesting triplet states in metal-free organic materials for application in organic light emitting diodes (OLEDs). A large number of TADF molecules have been reported in the literature with the purpose of enhancing the efficiency of OLEDs by converting non-emissive triplet states into emissive singlet states. TADF emitters are able to harvest both singlets and triplet states through fluorescence (prompt and delayed), the latter due to the thermally activated reverse intersystem crossing mechanism that allows up-conversion of low energy triplet states to the emissive singlet level. This allows otherwise pure fluorescent OLEDs to overcome their intrinsic limit of 25% internal quantum efficiency (IQE), which is imposed by the 1:3 singlet–triplet ratio arising from the recombination of charges (electrons and holes). TADF based OLEDS with IQEs close to 100% are now routinely fabricated in the green spectral region. There is also significant progress for blue emitters. However, red emitters still show relatively low efficiencies. Despite the significant progress that has been made in recent years, still significant challenges persist to achieve full understanding of the TADF mechanism and improve the stability of these materials. These questions need to be solved in order to fully implement TADF in OLEDs and expand their application to other areas. To date, TADF has been exploited mainly in the field of OLEDs, but applications in other areas, such as sensing and fluorescence microscopies, are envisaged. In this review, the photophysics of TADF molecules is discussed, summarising current methods to characterise these materials and the current understanding of the TADF mechanism in various molecular systems.

  7. Decomposition of Chemical Chain Molecules with Atmospheric Pressure Plasma (United States)

    Tansli, Murat; Tasal, Erol


    Chemical chain molecules' decomposition is an interesting subject area for the atmospheric pressure plasma applications. The effects of the atmospheric pressure argon plasma on 4-((2-methoxyphenyl)Diazenyl)Benzene-1,3,-Diol molecule at room temperature are investigated. This molecule is one of the industrial dye molecules used widely. When considering the ecological life, this molecule will be very harmful and danger. We suggest a different, easy and useful decomposing method for such molecules. Atmospheric pressure plasma jet was principally treated for this decomposing of the molecule. Fourier transform infrared spectrometry (FT-IR) was used to characterization of the molecule after the plasma application to molecule in liquid phase with ethanol and methanol solvents. The atmospheric-pressure plasma jet of argon (Ar) as non-equilibrium has been formed by ac-power generator with frequency - 24 kHz and voltage - 12 kV. Characterizations for solutions prepared with ethanol and methanol solvents of molecule have been examined after applying (duration: 3 minutes) the atmospheric pressure plasma jet. The molecule was broken at 6C-7N =8N-9C stretching peak after the plasma treatment. The new plasma photo-products for ethanol and methanol solutions were produced as 6C-7N-8N =9C (strong, varying) and 12C =17O (strong, wide) stretching peaks.

  8. Long-range effects in electron scattering by polar molecules (United States)

    Fabrikant, Ilya I.


    We review long-range effects in electron collisions with polar molecules, starting with elastic scattering. We then go to rotationally and vibrationally inelastic processes and dissociative electron attachment. The last two are strongly affected by vibrational Feshbach resonances which have been observed and described theoretically in many systems from simple diatomic molecules to more complex polyatomics, biologically relevant molecules, and van der Waals clusters. We then review environmental effects which include electron interaction with molecules adsorbed on surfaces and molecules in cluster environments. We concentrate on physics rather than on listing results of ab initio calculations. With increasing complexity of targets and processes model approaches become more relevant. We demonstrate their success in the theoretical description of electron attachment to polyatomic molecules and to molecules in complex environments.

  9. Formation of ultracold NaRb Feshbach molecules (United States)

    Wang, Fudong; He, Xiaodong; Li, Xiaoke; Zhu, Bing; Chen, Jun; Wang, Dajun


    We report the creation of ultracold bosonic 23Na87Rb Feshbach molecules via magneto-association. By ramping the magnetic field across an interspecies Feshbach resonance (FR), at least 4000 molecules can be produced out of the near degenerate ultracold mixture. Fast loss due to inelastic atom-molecule collisions is observed, which limits the pure molecule number, after residual atoms removal, to 1700. The pure molecule sample can live for 21.8(8) ms in the optical trap, long enough for future molecular spectroscopy studies toward coherently transferring to the singlet ro-vibrational ground state, where these molecules are stable against chemical reaction and have a permanent electric dipole moment of 3.3 Debye. We have also measured the Feshbach molecule’s binding energy near the FR by the oscillating magnetic field method and found these molecules have a large closed-channel fraction.

  10. Single-molecule electronics: from chemical design to functional devices. (United States)

    Sun, Lanlan; Diaz-Fernandez, Yuri A; Gschneidtner, Tina A; Westerlund, Fredrik; Lara-Avila, Samuel; Moth-Poulsen, Kasper


    The use of single molecules in electronics represents the next limit of miniaturisation of electronic devices, which would enable us to continue the trend of aggressive downscaling of silicon-based electronic devices. More significantly, the fabrication, understanding and control of fully functional circuits at the single-molecule level could also open up the possibility of using molecules as devices with novel, not-foreseen functionalities beyond complementary metal-oxide semiconductor technology (CMOS). This review aims at highlighting the chemical design and synthesis of single molecule devices as well as their electrical and structural characterization, including a historical overview and the developments during the last 5 years. We discuss experimental techniques for fabrication of single-molecule junctions, the potential application of single-molecule junctions as molecular switches, and general physical phenomena in single-molecule electronic devices.

  11. Atoms and Molecules Interacting with Light (United States)

    van der Straten, Peter; Metcalf, Harold


    ; 15. The periodic system of the elements; Appendix 15. A paramagnetism; Appendix 15.B. The color of gold; 16. Molecules; Appendix 16.A. Morse potential; 17. Binding in the hydrogen molecule; Appendix 17.A. Confocal elliptical coordinates; Appendix 17.B. One-electron two-center integrals; Appendix 17.C. Electron-electron interaction in molecular hydrogen; 18. Ultra-cold chemistry; Part III. Applications: 19. Optical forces and laser cooling; 20. Confinement of neutral atoms; 21. Bose-Einstein condensation; Appendix 21.A. Distribution functions; Appendix 21.B. Density of states; 22. Cold molecules; 23. Three level systems; Appendix 23.A. General Case for _1 , _2; 24. Fundamental physics; Part IV. Appendices: Appendix A. Notation and definitions; Appendix B. Units and notation; Appendix C. Angular momentum in quantum mechanics; Appendix D. Transition strengths; References; Index.

  12. Searching for line active molecules on biphasic lipid monolayers. (United States)

    Bischof, Andrea Alejandra; Mangiarotti, Agustín; Wilke, Natalia


    In membranes with phase coexistence, line tension appears as an important parameter for the determination of the amount of domains, as well as their size and their shape, thus defining the membrane texture. Different molecules have been proposed as "linactants" (i.e. molecules that reduce the line tension, thereby modulating the membrane texture). In this work, we explore the efficiency of different molecules as linactants in monolayers with two coexisting phases of different thicknesses. We tested the linactant ability of a molecule with chains of different saturation degrees, another molecule with different chain lengths and a bulky molecule. In this way, we show in the same system the effect of molecules with chains of different rigidities, with an intrinsic thickness mismatch and with a bulky moiety, thereby analyzing different hypotheses of how a molecule may change the line tension in a monolayer system. Both lipids with different hydrocarbon chains did not act as linactants, while only one of the bulky molecules tested decreased the line tension in the monolayer studied. We conclude that there are no universal rules for the structure of a molecule that enable us to predict that it will behave as a linactant and thus, designing linactants appears to be a difficult task and a challenge for future studies. Furthermore, in regard to the membrane texture, there was no direct influence of the line tension in the distribution of domain sizes.

  13. Small molecule screening at Helmholtz Zentrum München - from biology to molecules. (United States)

    Schorpp, Kenji; Hadian, Kamyar


    Within the last few years the Helmholtz Zentrum München has established several initiatives enabling the translation of basic research results into discovery of novel small molecules that affect pathomechanisms of chronic and complex diseases. Here, one of the main operations is the Assay Development and Screening Platform (ADSP) that has state-of-the-art equipment for compound screening and provides knowledge in a variety of biochemical or cell-based phenotypic assays. In particular, ADSP has a strong focus on complex assays such as high-content screening in stem cells that are likely to provide an innovative approach complementary to biochemical assays for the discovery of novel small molecules modulating key biological processes.

  14. Molecules in strong laser fields. In depth study of H{sub 2} molecule

    Energy Technology Data Exchange (ETDEWEB)

    Awasthi, Manohar


    A method for solving the time-dependent Schroedinger equation (TDSE) describing the electronic motion of the molecules exposed to very short intense laser pulses has been developed. The time-dependent electronic wavefunction is expanded in terms of a superposition of field-free eigenstates. The field-free eigenstates are calculated in two ways. In the first approach, which is applicable to two electron systems like H{sub 2}, fully correlated field-free eigenstates are obtained in complete dimensionality using configuration-interaction calculation where the one-electron basis functions are built from B splines. In the second approach, which is even applicable to larger molecules, the field-free eigenstates are calculated within the single-active-electron (SAE) approximation using density functional theory. In general, the method can be divided into two parts, in the first part the field-free eigenstates are calculated and then in the second part a time propagation for the laser pulse parameters is performed. The H{sub 2} molecule is the testing ground for the implementation of both the methods. The reliability of the configuration interaction (CI) based method for the solution of TDSE (CI-TDSE) is tested by comparing results in the low-intensity regime to the prediction of lowest-order perturbation theory. Another test for the CI-TDSE method is in the united atom limit for the H{sub 2} molecule. By selecting a very small value of the internuclear distance close to zero for the H{sub 2} molecule, Helium atom is obtained. Once the functionality and the reliability of the method is established, it is used for obtaining accurate results for molecular hydrogen exposed to intense laser fields. The results for the standard 800 nm Titanium-Sapphire laser and its harmonics at 400 nm and 266 nm are shown. The results for a scan over a wide range of incident photon energies as well as dependence on the internuclear distance are presented. The photoelectron spectra including

  15. Two-dimensional, phenanthroline-based, extended {pi}-conjugated molecules for single-molecule conduction

    Energy Technology Data Exchange (ETDEWEB)

    Wohlthat, Soeren; Reimers, Jeffrey R [School of Chemistry, The University of Sydney, Sydney, NSW 2006 (Australia); Pauly, Fabian [Institut fuer Theoretische Festkoerperphysik and DFG-Center for Functional Nanostructures, Universitaet Karlsruhe, 76128 Karlsruhe (Germany)], E-mail:


    The conduction properties of phenanthroline-terminated, polycyclic extended {pi}-conjugated molecular wires are investigated using density functional theory (DFT) in combination with Green's function techniques and group theory. While these molecules could possibly be thought of as accessible graphene-like fragments, they are calculated to conduct poorly. The decay constant for their exponential decrease of conductance with length is in excess of 0.6 A{sup -1} for the addition of internal fused quinoxaline groups and in excess of 0.9 A{sup -1} for the addition of internal pyrazine-fused pyrene groups. Furthermore, while the bidentate phenanthroline connectors adhere strongly to gold, they are sometimes predicted to be less conductive than related monodentate connectors. Careful design is thus required for any graphene-like extended {pi}-system intended for single-molecule conduction applications.

  16. Killer bee molecules: antimicrobial peptides as effector molecules to target sporogonic stages of Plasmodium.

    Directory of Open Access Journals (Sweden)

    Victoria Carter

    Full Text Available A new generation of strategies is evolving that aim to block malaria transmission by employing genetically modified vectors or mosquito pathogens or symbionts that express anti-parasite molecules. Whilst transgenic technologies have advanced rapidly, there is still a paucity of effector molecules with potent anti-malaria activity whose expression does not cause detrimental effects on mosquito fitness. Our objective was to examine a wide range of antimicrobial peptides (AMPs for their toxic effects on Plasmodium and anopheline mosquitoes. Specifically targeting early sporogonic stages, we initially screened AMPs for toxicity against a mosquito cell line and P. berghei ookinetes. Promising candidate AMPs were fed to mosquitoes to monitor adverse fitness effects, and their efficacy in blocking rodent malaria infection in Anopheles stephensi was assessed. This was followed by tests to determine their activity against P. falciparum in An. gambiae, initially using laboratory cultures to infect mosquitoes, then culminating in preliminary assays in the field using gametocytes and mosquitoes collected from the same area in Mali, West Africa. From a range of 33 molecules, six AMPs able to block Plasmodium development were identified: Anoplin, Duramycin, Mastoparan X, Melittin, TP10 and Vida3. With the exception of Anoplin and Mastoparan X, these AMPs were also toxic to an An. gambiae cell line at a concentration of 25 µM. However, when tested in mosquito blood feeds, they did not reduce mosquito longevity or egg production at concentrations of 50 µM. Peptides effective against cultured ookinetes were less effective when tested in vivo and differences in efficacy against P. berghei and P. falciparum were seen. From the range of molecules tested, the majority of effective AMPs were derived from bee/wasp venoms.

  17. Compactness Aromaticity of Atoms in Molecules

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz


    Full Text Available A new aromaticity definition is advanced as the compactness formulation through the ratio between atoms-in-molecule and orbital molecular facets of the same chemical reactivity property around the pre- and post-bonding stabilization limit, respectively. Geometrical reactivity index of polarizability was assumed as providing the benchmark aromaticity scale, since due to its observable character; with this occasion new Hydrogenic polarizability quantum formula that recovers the exact value of 4.5 a03 for Hydrogen is provided, where a0 is the Bohr radius; a polarizability based–aromaticity scale enables the introduction of five referential aromatic rules (Aroma 1 to 5 Rules. With the help of these aromatic rules, the aromaticity scales based on energetic reactivity indices of electronegativity and chemical hardness were computed and analyzed within the major semi-empirical and ab initio quantum chemical methods. Results show that chemical hardness based-aromaticity is in better agreement with polarizability based-aromaticity than the electronegativity-based aromaticity scale, while the most favorable computational environment appears to be the quantum semi-empirical for the first and quantum ab initio for the last of them, respectively.

  18. Artificial nanomachines based on interlocked molecules

    Energy Technology Data Exchange (ETDEWEB)

    Credi, Alberto [Dipartimento di Chimica ' G Ciamician' , Universita di Bologna, via Selmi 2, 40126 Bologna (Italy)


    The extension of the concept of machine to the molecular level is of great interest for the growth of nanoscience and the development of nanotechnology. A molecular machine can be defined as an assembly of a discrete number of molecular components (that is, a supramolecular structure) designed to perform a function through the mechanical movements of its components, which occur under appropriate external stimulation. Hence, molecular machines contain a motor part, that is a device capable of converting energy into mechanical work. Molecular motors and machines operate via nuclear rearrangements and, like their macroscopic counterparts, are characterized by the kind of energy input supplied to make them work, the manner in which their operation can be monitored, the possibility to repeat the operation at will, i.e., establishing a cyclic process, the timescale needed to complete a cycle of operation, and the performed function. Owing to the progresses made in several branches of chemistry, and to the better understanding of the operation mechanisms of molecular machines of the biological world, it has become possible to design and construct simple prototypes of artificial molecular motors and machines. Some examples based on rotaxanes, catenanes, and related interlocked molecules will be described.

  19. Hidden charm molecules in finite volume

    CERN Document Server

    Albaladejo, Miguel; Nieves, Juan; Oset, Eulogio


    In the present paper we address the interaction of pairs of charmed mesons with hidden charm in a finite box. We use the interaction from a recent model based on heavy quark spin symmetry that predicts molecules of hidden charm in the infinite volume. The energy levels in the box are generated within this model, and from them some synthetic data are generated. These data are then employed to study the inverse problem of getting the energies of the bound states and phase shifts for $D \\bar D$ or $D^* {\\bar D}^*$. Different strategies are investigated using the lowest two levels for different values of the box size, carrying a study of the errors produced. Starting from the upper level, fits to the synthetic data are carried out to determine the scattering length and effective range plus the binding energy of the ground state. A similar strategy using the effective range formula is considered with a simultaneous fit to the two levels, one above and the other one below threshold. This method turns out to be more...

  20. Selection of Prebiotic Molecules in Amphiphilic Environments

    Directory of Open Access Journals (Sweden)

    Christian Mayer


    Full Text Available A basic problem in all postulated pathways of prebiotic chemistry is the low concentration which generally is expected for interesting reactants in fluid environments. Even though compounds, like nucleobases, sugars or peptides, principally may form spontaneously under environmental conditions, they will always be rapidly diluted in an aqueous environment. In addition, any such reaction leads to side products which often exceed the desired compound and generally hamper the first steps of a subsequent molecular evolution. Therefore, a mechanism of selection and accumulation of relevant prebiotic compounds seems to be crucial for molecular evolution. A very efficient environment for selection and accumulation can be found in the fluid continuum circulating in tectonic fault zones. Vesicles which form spontaneously at a depth of approximately 1 km present a selective trap for amphiphilic molecules, especially for peptides composed of hydrophilic and hydrophobic amino acids in a suitable sequence. The accumulation effect is shown in a numeric simulation on a simplified model. Further, possible mechanisms of a molecular evolution in vesicle membranes are discussed. Altogether, the proposed scenario can be seen as an ideal environment for constant, undisturbed molecular evolution in and on cell-like compartments.

  1. Perspective: Mechanochemistry of biological and synthetic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Makarov, Dmitrii E., E-mail: [Department of Chemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712 (United States)


    Coupling of mechanical forces and chemical transformations is central to the biophysics of molecular machines, polymer chemistry, fracture mechanics, tribology, and other disciplines. As a consequence, the same physical principles and theoretical models should be applicable in all of those fields; in fact, similar models have been invoked (and often repeatedly reinvented) to describe, for example, cell adhesion, dry and wet friction, propagation of cracks, and action of molecular motors. This perspective offers a unified view of these phenomena, described in terms of chemical kinetics with rates of elementary steps that are force dependent. The central question is then to describe how the rate of a chemical transformation (and its other measurable properties such as the transition path) depends on the applied force. I will describe physical models used to answer this question and compare them with experimental measurements, which employ single-molecule force spectroscopy and which become increasingly common. Multidimensionality of the underlying molecular energy landscapes and the ensuing frequent misalignment between chemical and mechanical coordinates result in a number of distinct scenarios, each showing a nontrivial force dependence of the reaction rate. I will discuss these scenarios, their commonness (or its lack), and the prospects for their experimental validation. Finally, I will discuss open issues in the field.

  2. Partitioned R-matrix theory for molecules

    Energy Technology Data Exchange (ETDEWEB)

    Tennyson, Jonathan [Department of Physics and Astronomy, University College London, Gower St., London WC1E 6BT (United Kingdom)


    R-matrix calculations usually require all the eigenvalues and eigenvectors of the inner region Hamiltonian matrix. For molecular problems, particularly when large configuration interaction expansions are used for the target, the Hamiltonian matrix is often too large to be completely diagonalized. Berrington and Ballance (2002 J. Phys. B: At. Mol. Opt. Phys. 35 2275) proposed a partitioned R-matrix theory which only required a proportion of the solutions of the Hamiltonian matrix. This theory was implemented and tested in the atomic R-matrix code. The theory is adapted to the needs of R-matrix calculations on low-energy electron-molecule collisions. A number of alternative procedures are tested. The best is shown to give reliable results with explicit inclusion of only a fraction of the solutions. It is shown that with this revised theory the number of solutions required does not depend on the complexity of the target wavefunction even though this strongly influences the size of the final Hamiltonian matrix. This method will be implemented as part of the UK molecular R-matrix program suite.

  3. Indexing molecules with chemical graph identifiers. (United States)

    Gregori-Puigjané, Elisabet; Garriga-Sust, Rut; Mestres, Jordi


    Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used.

  4. Single molecule DNA compaction by purified histones

    Institute of Scientific and Technical Information of China (English)

    RAN ShiYong; WANG XiaoLing; FU WenBo; WANG WeiChi; LI Ming


    The compaction of single DNA molecules by purified histones is studied using magnetic tweezers, The compaction rate increases rapidly when the histone concentration is increased from 0.002 to 0.2 mmol/L, and saturates when the concentration is beyond 0.2 mmol/L, The time course of compaction is exponential at low histone concentrations. It becomes sigmoidal at high concentrations. Cooperativity between the histones bound to DNA is proposed to be responsible for the transition. The histones are loaded onto DNA randomly at low concentrations. They tend to bind DNA cooperatively at high con-centrations because the structural torsions of DNA induced by the bound histones become overlapping so that the binding of one histone facilitates the binding of others. Under very large forces, the com-pacted histone-DNA complex can be disrupted in a discrete manner with a step size of ~60 nm. But the histones cannot be completely stripped off DNA, as is revealed by the lowered B-S transition plateau of the histone-bound DNA.

  5. Organization of 'nanocrystal molecules' using DNA (United States)

    Alivisatos, A. Paul; Johnsson, Kai P.; Peng, Xiaogang; Wilson, Troy E.; Loweth, Colin J.; Bruchez, Marcel P.; Schultz, Peter G.


    PATTERNING matter on the nanometre scale is an important objective of current materials chemistry and physics. It is driven by both the need to further miniaturize electronic components and the fact that at the nanometre scale, materials properties are strongly size-dependent and thus can be tuned sensitively1. In nanoscale crystals, quantum size effects and the large number of surface atoms influence the, chemical, electronic, magnetic and optical behaviour2-4. 'Top-down' (for example, lithographic) methods for nanoscale manipulation reach only to the upper end of the nanometre regime5; but whereas 'bottom-up' wet chemical techniques allow for the preparation of mono-disperse, defect-free crystallites just 1-10 nm in size6-10, ways to control the structure of nanocrystal assemblies are scarce. Here we describe a strategy for the synthesis of'nanocrystal molecules', in which discrete numbers of gold nanocrystals are organized into spatially defined structures based on Watson-Crick base-pairing interactions. We attach single-stranded DNA oligonucleotides of defined length and sequence to individual nanocrystals, and these assemble into dimers and trimers on addition of a complementary single-stranded DNA template. We anticipate that this approach should allow the construction of more complex two-and three-dimensional assemblies.

  6. Transition paths in molecules at finite temperature (United States)

    Pinski, F. J.; Stuart, A. M.


    In the zero temperature limit, it is well known that in systems evolving via Brownian dynamics, the most likely transition path between reactant and product may be found as a minimizer of the Freidlin-Wentzell action functional. An analog for finite temperature transitions is given by the Onsager-Machlup functional. The purpose of this work is to investigate properties of Onsager-Machlup minimizers. We study transition paths for thermally activated molecules governed by the Langevin equation in the overdamped limit of Brownian dynamics. Using gradient descent in pathspace, we minimize the Onsager-Machlup functional for a range of model problems in one and two dimensions and then for some simple atomic models including Lennard-Jones seven-atom and 38-atom clusters, as well as for a model of vacancy diffusion in a planar crystal. Our results demonstrate interesting effects, which can occur at nonzero temperature, showing transition paths that could not be predicted on the basis of the zero temperature limit. However the results also demonstrate unphysical features associated with such Onsager-Machlup minimizers. As there is a growing literature that addresses transition path sampling by related techniques, these insights add a potentially useful perspective into the interpretation of this body of work.

  7. Neutrino Spectroscopy with Atoms and Molecules

    CERN Document Server

    Fukumi, Atsushi; Miyamoto, Yuki; Nakajima, Kyo; Nakano, Itsuo; Nanjo, Hajime; Ohae, Chiaki; Sasao, Noboru; Tanaka, Minoru; Taniguchi, Takashi; Uetake, Satoshi; Wakabayashi, Tomonari; Yamaguchi, Takuya; Yoshimi, Akihiro; Yoshimura, Motohiko


    We give a comprehensive account of our proposed experimental method of using atoms or molecules in order to measure parameters of neutrinos still undetermined; the absolute mass scale, the mass hierarchy pattern (normal or inverted), the neutrino mass type (Majorana or Dirac), and the CP violating phases including Majorana phases. There are advantages of atomic targets, due to the closeness of available atomic energies to anticipated neutrino masses, over nuclear target experiments. Disadvantage of using atomic targets, the smallness of rates, is overcome by the macro-coherent amplification mechanism. The atomic or molecular process we use is a cooperative deexcitation of a collective body of atoms in a metastable level |e> emitting a neutrino pair and a photon; |e> -> |g> + gamma + nu_i nu_j where nu_i's are neutrino mass eigenstates. The macro-coherence is developed by trigger laser irradiation. We discuss aspects of the macro-coherence development by setting up the master equation for the target quantum st...

  8. Complex organic molecules in protoplanetary disks

    CERN Document Server

    Walsh, Catherine; Nomura, Hideko; Herbst, Eric; Weaver, Susanna L Widicus; Aikawa, Yuri; Laas, Jake C; Vasyunin, Anton I


    (Abridged) Protoplanetary disks are vital objects in star and planet formation, possessing all the material which may form a planetary system orbiting the new star. We investigate the synthesis of complex organic molecules (COMs) in disks to constrain the achievable chemical complexity and predict species and transitions which may be observable with ALMA. We have coupled a 2D model of a protoplanetary disk around a T Tauri star with a gas-grain chemical network including COMs. We compare compare synthesised line intensities and calculated column densities with observations and determine those COMs which may be observable in future. COMs are efficiently formed in the disk midplane via grain-surface chemical reactions, reaching peak grain-surface fractional abundances 1e-6 - 1e-4 that of the H nuclei number density. COMs formed on grain surfaces are returned to the gas phase via non-thermal desorption; however, gas-phase species reach lower fractional abundances than their grain-surface equivalents, 1e-12 - 1e-...

  9. Dynamics of molecules and clusters at surfaces

    CERN Document Server

    Goldby, I M


    and aggregate into round particles with a 'universal' diameter of approx 14 nm. This preferred diameter is attributed to the strain between the silver and graphite lattices. The deposition rate and the cluster impact angle are also shown to be important parameters, which strongly influence the morphology of the islands. Computer simulation results indicate that, to produce the observed island size distributions, the mobility of the particles must fall off rapidly as their size increases. In chapter five, I present results from angular resolved electron stimulated desorption studies of 0 sup - , 0 sub 2 sup - , and 0 sub 3 sup - , produced from ordered films of 0 sub 2 on HOPG. Resonances in the yields of all products as a function of electron impact energy are attributed to dissociative electron attachment, generating 0 sup - ions, which can react with neighbouring O sub 2 molecules in the film. Characteristic differences in the ion yield profiles from one product to another are explained in terms of a binary...

  10. Database of Small Molecule Thermochemistry for Combustion

    KAUST Repository

    Goldsmith, C. Franklin


    High-accuracy ab initio thermochemistry is presented for 219 small molecules relevant in combustion chemistry, including many radical, biradical, and triplet species. These values are critical for accurate kinetic modeling. The RQCISD(T)/cc-PV∞QZ//B3LYP/6-311++G(d,p) method was used to compute the electronic energies. A bond additivity correction for this method has been developed to remove systematic errors in the enthalpy calculations, using the Active Thermochemical Tables as reference values. On the basis of comparison with the benchmark data, the 3σ uncertainty in the standard-state heat of formation is 0.9 kcal/mol, or within chemical accuracy. An uncertainty analysis is presented for the entropy and heat capacity. In many cases, the present values are the most accurate and comprehensive numbers available. The present work is compared to several published databases. In some cases, there are large discrepancies and errors in published databases; the present work helps to resolve these problems. © 2012 American Chemical Society.

  11. Proteoglycans: from structural compounds to signaling molecules. (United States)

    Schaefer, Liliana; Schaefer, Roland M


    Our knowledge of proteoglycan biology has significantly expanded over the past decade with the discovery of a host of new members of this multifunctional family leading to their present classification into three major categories: (1) small leucine-rich proteoglycans, 2) modular proteoglycans, and 3) cell-surface proteoglycans. In addition to being structural proteins, proteoglycans play a major role in signal transduction with regulatory functions in various cellular processes. Being mostly extracellular, they are upstream of many signaling cascades and are capable of affecting intracellular phosphorylation events and modulating distinct pathways, including those driven by bone morphogenetic protein/transforming growth factor superfamily members, receptor tyrosine kinases, the insulin-like growth factor-I receptor, and Toll-like receptors. Mechanistic insights into the molecular and cellular functions of proteoglycans have revealed both the sophistication of these regulatory proteins and the challenges that remain in uncovering the entirety of their biological functions. This review aims to summarize the multiple functions of proteoglycans with special emphasis on their intricate composition and the newly described signaling events in which these molecules play a key role.

  12. Tripartite entanglement dynamics of vibrations in triatomic molecules. (United States)

    Zhai, Liangjun; Zheng, Yujun


    In the present study, the dynamical behaviors of tripartite entanglement of vibrations in triatomic molecules are studied based on the Lie algebraic models of molecules. The dynamical behaviors of tripartite entanglement of the local mode molecule H2O and normal mode molecule NO2 are comparatively studied for different initial states by employing the general concurrence. Our results show that the dynamics of tripartite entanglement are relied on the dynamics of intramolecular energy distribution. The local mode molecule is more suitable to construct the tripartite entangled states. Also, the greater degree of tripartite entanglement can be obtained if the stretching vibration is first excited. These results shed new light on the understanding of quantum multipartite entanglement of vibrations in the polyatomic molecules.

  13. Mapping molecules in scanning far-field fluorescence nanoscopy (United States)

    Ta, Haisen; Keller, Jan; Haltmeier, Markus; Saka, Sinem K.; Schmied, Jürgen; Opazo, Felipe; Tinnefeld, Philip; Munk, Axel; Hell, Stefan W.


    In fluorescence microscopy, the distribution of the emitting molecule number in space is usually obtained by dividing the measured fluorescence by that of a single emitter. However, the brightness of individual emitters may vary strongly in the sample or be inaccessible. Moreover, with increasing (super-) resolution, fewer molecules are found per pixel, making this approach unreliable. Here we map the distribution of molecules by exploiting the fact that a single molecule emits only a single photon at a time. Thus, by analysing the simultaneous arrival of multiple photons during confocal imaging, we can establish the number and local brightness of typically up to 20 molecules per confocal (diffraction sized) recording volume. Subsequent recording by stimulated emission depletion microscopy provides the distribution of the number of molecules with subdiffraction resolution. The method is applied to mapping the three-dimensional nanoscale organization of internalized transferrin receptors on human HEK293 cells.

  14. Filming the Birth of Molecules and Accompanying Solvent Rearrangement

    DEFF Research Database (Denmark)

    Lee, Jae Hyuk; Wulff, Michael; Bratos, Savo;


    Molecules are often born with high energy and large-amplitude vibrations. In solution, a newly formed molecule cools down by transferring energy to the surrounding solvent molecules. The progression of the molecular and solute−solvent cage structure during this fundamental process has been elusive......, and spectroscopic data generally do not provide such structural information. Here, we use picosecond X-ray liquidography (solution scattering) to visualize timedependent structural changes associated with the vibrational relaxation of I2 molecules in two different solvents, CCl4 and cyclohexane. The birth...... and vibrational relaxation of I2 molecules and the associated rearrangement of solvent molecules are mapped out in the form of a temporally varying interatomic distance distribution. The I−I distance increases up to ∼4 Å and returns to the equilibrium distance (2.67 Å) in the ground state, and the first solvation...

  15. Theory of long-range ultracold atom-molecule photoassociation

    CERN Document Server

    Pérez-Ríos, Jesús; Dulieu, Olivier


    The creation of ultracold molecules is currently limited to diatomic species. In this letter we present a theoretical description of the photoassociation of ultracold atoms and molecules to create ultracold excited triatomic molecules, thus being a novel example of light-assisted ultracold chemical reaction. The calculation of the photoassociation rate of ultracold Cs atoms with ultracold Cs$_2$ molecules in their rovibrational ground state is reported, based on the solution of the quantum dynamics involving the atom-molecule long-range interactions, and assuming a model potential for the short-range physics. The rate for the formation of excited Cs$_3$ molecules is predicted to be comparable with currently observed atom-atom photoassociation rates. We formulate an experimental proposal to observe this process relying on the available techniques of optical lattices and standard photoassociation spectroscopy.

  16. Fullerene molecule strain in RbC 60 (United States)

    Aksenov, V. L.; Ossipyan, Yu. À.; Forro, L.; Khasanov, S.; Chernyshev, V. V.; Shakhmatov, V. S.


    Strain displacements of carbon atoms in a Ñ 60 molecule in the Pnnm phase of the RbC 60 fulleride are first determined by X-ray diffraction. The measurements show that the polymeric bond length between carbon atoms of two nearest molecules C 60 is equal to 1.69(1) Å, the rotation angle of the molecule about the polymeric direction is 47.0(3)°.

  17. Fullerene Molecule Strain in $RbC_{60}$

    CERN Document Server

    Aksenov, V L; Forró, L; Khasanov, S S; Chernyshev, V V; Shakhmatov, V S


    Strain displacements of carbon atoms in a C$_60$ molecule in the $Pnnm$ phase of the RbC$_60$ fulleride are first determined by X-ray diffraction. The measurements show that the polymeric bond length between carbon atoms of two nearest molecules C$_60$ is equal to 1.69(1) $\\AA$, the rotation angle of the molecule about the polymeric direction is 47.0(3)$^0$.

  18. Quantum Transport in a Biphenyl Molecule: Effects of Magnetic Flux


    Maiti, Santanu K.


    Electron transport properties of a biphenyl molecule are studied based on the Green's function formalism. The molecule is sandwiched between two metallic electrodes, where each benzene ring is threaded by a magnetic flux $\\phi$. The results are focused on the effects of the molecule to electrode coupling strength and the magnetic flux $\\phi$. Our numerical study shows that, for a fixed molecular coupling, the current amplitude across the bridge can be {\\em regulated} significantly just by tun...

  19. Probing molecular choreography through single-molecule biochemistry. (United States)

    van Oijen, Antoine M; Dixon, Nicholas E


    Single-molecule approaches are having a dramatic impact on views of how proteins work. The ability to observe molecular properties at the single-molecule level allows characterization of subpopulations and acquisition of detailed kinetic information that would otherwise be hidden in the averaging over an ensemble of molecules. In this Perspective, we discuss how such approaches have successfully been applied to in vitro-reconstituted systems of increasing complexity.

  20. Signal molecule-mediated hepatic cell communication during liver regeneration

    Institute of Scientific and Technical Information of China (English)

    Zhen-Yu Zheng; Shun-Yan Weng; Yan Yu


    Liver regeneration is a complex and well-orchestrated process, during which hepatic cells are activated to produce large signal molecules in response to liver injury or mass reduction. These signal molecules, in turn, set up the connections and cross-talk among liver cells to promote hepatic recovery. In this review, we endeavor to summarize the network of signal molecules that mediates hepatic cell communication in the regulation of liver regeneration.

  1. Transitional Description of Diatomic Molecules in U(4) Vibron Model

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xin; PAN Feng


    U(3)-O(4) transitional description of diatomic molecules in the U(4) vibron model is studied by using the algebraic Bethe ansatz, in which the O(4) limit is a special case of the theory. Vibrational band-heads of some typical diatornic molecules are fitted by both transitional theory and the O(4) limit within the same framework. The results show that there are evident deviations from the O(4) limit in description of vibrational spectra of some diatomic molecules.

  2. Ultrafast Imaging of Electronic Motion in Atoms and Molecules (United States)


    AFRL-AFOSR-VA-TR-2016-0045 Ultrafast Imaging of Electronic Motion in Atoms and Molecules Martin Centurion UNIVERSITY OF NEBRSKA Final Report 01/12...Ultrafast Imaging of Electronic Motion in Atoms and Molecules 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550-12-1-0149 5c. PROGRAM ELEMENT NUMBER 6...a gaseous target of atoms or molecules . An optical setup was designed and constructed to compensate for the blurring of the temporal resolution due

  3. Imaging and manipulation of a polar molecule on Ag(111)

    DEFF Research Database (Denmark)

    Lin, R.; Braun, K.F.; Tang, H.;


    A scanning tunneling microscope (STM) was applied to image and laterally manipulate isolated phosphangulene molecules on Ag(111) at 6 K. Atomic-resolution images clearly revealed three characteristic types of appearances (three-lobed, fish and bump shape) for the adsorbed molecules, which could c......! their manipulating processes can be much more complex in comparison with atoms and small molecules. Such information can shed light on the involved mechanisms on a molecular seals. (C) 2001 Published by Elsevier Science B.V....

  4. Nanostructure sensor of presence and concentration of a target molecule (United States)

    Schipper, John F. (Inventor)


    Method and system (i) to determine when a selected target molecule is present or absent in a fluid, (2) to estimate concentration of the target molecule in the fluid and (3) estimate possible presence of a second (different) target molecule in the fluid, by analyzing differences in resonant frequencies of vibration of a thin beam suspended in the fluid, after the fluid has moved across the beam.

  5. Single Molecule Raman Detection of Enkephalin on Silver Colloidal Particles

    DEFF Research Database (Denmark)

    Kneipp, Katrin; Kneipp, Holger; Abdali, Salim;


    the Raman signal the enkephalin molecules have been attached to silver colloidal cluster structures. The experiments demonstrate that the SERS signal of the strongly enhanced ring breathing vibration of phenylalanine at 1000 cm-1 can be used as “intrinsic marker” for detecting a single enkephalin molecule...... and for monitoring its diffusion on the surface of the silver colloidal cluster without using a specific label molecule....

  6. The role of the ion-molecule and molecule-molecule interactions in the formation of the two-ion average force interaction potential

    CERN Document Server

    Ajrian, E A; Sidorenko, S N


    The effect of the ion-molecule and intermolecular interactions on the formation of inter-ion average force potentials is investigated within the framework of a classical ion-dipole model of electrolyte solutions. These potentials are shown to possess the Coulomb asymptotics at large distances while in the region of mean distances they reveal creation and disintegration of solvent-shared ion pairs. The calculation results provide a qualitatively authentic physical picture which is experimentally observed in strong electrolytes solutions. In particular, an increased interaction between an ion and a molecule enhances formation of ion pairs in which the ions are separated by one solvent molecule

  7. Novel approaches for single molecule activation and detection

    CERN Document Server

    Benfenati, Fabio; Torre, Vincent


    How can we obtain tools able to process and exchange information at the molecular scale In order to do this, it is necessary to activate and detect single molecules under controlled conditions. This book focuses on the generation of biologically-inspired molecular devices. These devices are based on the developments of new photonic tools able to activate and stimulate single molecule machines. Additionally, new light sensitive molecules can be selectively activated by photonic tools. These technological innovations will provide a way to control activation of single light-sensitive molecules, a

  8. Enantiomer-Specific State Transfer of Chiral Molecules

    CERN Document Server

    Eibenberger, Sandra; Patterson, David


    State-selective enantiomeric excess is realized using microwave-driven coherent population transfer. The method selectively promotes either R- or S- molecules to a higher rotational state by phase-controlled microwave pulses that drive electric-dipole allowed rotational transitions. We demonstrate the method using a racemic mixture of 1,2-propanediol. This method of chiral enrichment can be applied to nearly any chiral molecule that can be vaporized and cooled to the point where rotationally resolved spectroscopy is possible, including molecules that rapidly racemize. The rapid chiral switching demonstrated here allows for new applications in high-precision spectroscopic searches for parity violation in chiral molecules.

  9. Observation of individual molecules trapped on a nanostructured insulator

    CERN Document Server

    Nony, L; Baratoff, A; Alkauskas, A; Bennewitz, R P; Pfeiffer, O; Maier, S; Wezel, A; Meyer, E; Gerber, C E; Nony, Laurent; Gnecco, Enrico Dr.; Baratoff, Alexis; Alkauskas, Audrius; Bennewitz, Roland; Pfeiffer, Oliver; Maier, Sabine; Wezel, Adrian; Meyer, Ernst; Gerber, Christophe


    For the first time, ordered polar molecules confined in monolayer-deep rectangular pits produced on an alkali halide surface by electron irradiation have been resolved at room temperature by non-contact atomic force microscopy. Molecules self-assemble in a specific fashion inside pits of width smaller than 15 nm. By contrast no ordered aggregates of molecules are observed on flat terraces. Conclusions regarding nucleation and ordering mechanisms are drawn. Trapping in pits as small as 2 nm opens a route to address single molecules.

  10. Facilities for small-molecule crystallography at synchrotron sources. (United States)

    Barnett, Sarah A; Nowell, Harriott; Warren, Mark R; Wilcox, Andrian; Allan, David R


    Although macromolecular crystallography is a widely supported technique at synchrotron radiation facilities throughout the world, there are, in comparison, only very few beamlines dedicated to small-molecule crystallography. This limited provision is despite the increasing demand for beamtime from the chemical crystallography community and the ever greater overlap between systems that can be classed as either small macromolecules or large small molecules. In this article, a very brief overview of beamlines that support small-molecule single-crystal diffraction techniques will be given along with a more detailed description of beamline I19, a dedicated facility for small-molecule crystallography at Diamond Light Source.

  11. An optical nanofiber-based interface for single molecules

    CERN Document Server

    Skoff, Sarah M; Schauffert, Hardy; Rauschenbeutel, Arno


    Optical interfaces for quantum emitters are a prerequisite for implementing quantum networks. Here, we couple single molecules to the guided modes of an optical nanofiber. The molecules are embedded within a crystal that provides photostability and due to its inhomogeneous environment, a means to spectrally address single molecules. Single molecules are excited and detected solely via the nanofiber interface without the requirement of additional optical access. In this way, we realize a fully fiber-integrated system that is scalable and may become a versatile constituent for quantum hybrid systems.

  12. Domain-based small molecule binding site annotation

    Directory of Open Access Journals (Sweden)

    Dumontier Michel


    Full Text Available Abstract Background Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and function prediction, but small molecule binding site protein sequence annotation is sparse. The Small Molecule Interaction Database (SMID, a database of protein domain-small molecule interactions, was created using structural data from the Protein Data Bank (PDB. More importantly it provides a means to predict small molecule binding sites on proteins with a known or unknown structure and unlike prior approaches, removes large numbers of false positive hits arising from transitive alignment errors, non-biologically significant small molecules and crystallographic conditions that overpredict ion binding sites. Description Using a set of co-crystallized protein-small molecule structures as a starting point, SMID interactions were generated by identifying protein domains that bind to small molecules, using NCBI's Reverse Position Specific BLAST (RPS-BLAST algorithm. SMID records are available for viewing at The SMID-BLAST tool provides accurate transitive annotation of small-molecule binding sites for proteins not found in the PDB. Given a protein sequence, SMID-BLAST identifies domains using RPS-BLAST and then lists potential small molecule ligands based on SMID records, as well as their aligned binding sites. A heuristic ligand score is calculated based on E-value, ligand residue identity and domain entropy to assign a level of confidence to hits found. SMID-BLAST predictions were validated against a set of 793 experimental small molecule interactions from the PDB, of which 472 (60% of predicted interactions identically matched the experimental small molecule and of these, 344 had greater than 80% of the binding site residues correctly identified. Further, we estimate that 45% of predictions which were not observed in the PDB validation set may be true positives. Conclusion By

  13. Detection and Imaging of He_2 Molecules in Superfluid Helium

    CERN Document Server

    Rellergert, W G; Garvan, A; Hanson, J C; Lippincott, W H; Nikkel, J A; McKinsey, D N


    We present data supporting our previous proposal [1] for using cycling transitions to detect and image metastable He_2 triplet molecules in superfluid helium. We demonstrate that limitations on the cycling efficiency due to the vibrational structure of the molecule can be mitigated by the use of repumping lasers. Images of the molecules obtained using the method are also shown. This technique gives rise to a new kind of ionizing radiation detector. The use of He_2 triplet molecules as tracer particles in the superfluid promises to be a powerful tool for visualization of both quantum [2-4] and classical [5] turbulence in liquid helium.

  14. Atom-Specific Identification of Adsorbed Chiral Molecules by Photoemission (United States)

    Kim, J. W.; Carbone, M.; Dil, J. H.; Tallarida, M.; Flammini, R.; Casaletto, M. P.; Horn, K.; Piancastelli, M. N.


    The study of chiral adsorbed molecules is important for an analysis of enantioselectivity in heterogeneous catalysis. Here we show that such molecules can be identified through circular dichroism in core-level photoemission arising from the chiral carbon atoms in stereoisomers of 2,3-butanediol molecules adsorbed on Si(100), using circularly polarized x rays. The asymmetry in the carbon 1s intensity excited by right and left circularly polarized light is readily observed, and changes sign with the helicity of the radiation or handedness of the enantiomers; it is absent in the achiral form of the molecule. This observation demonstrates the possibility of determining molecular chirality in the adsorbed phase.

  15. Quantum effects at low-energy atom–molecule interface

    Indian Academy of Sciences (India)

    B Deb; A Rakshit; J Hazra; D Chakraborty


    The effects of quantum interference in inter-conversion between cold atoms and diatomic molecules are analysed in this study. Within the framework of Fano’s theory, continuum bound anisotropic dressed state formalism of atom–molecule quantum dynamics is presented. This formalism is applicable in photo- and magneto-associative strong-coupling regimes. The significance of Fano effect in ultracold atom–molecule transitions is discussed. Quantum effects at low-energy atom–molecule interface are important for exploring coherent phenomena in hitherto unexplored parameter regimes.

  16. Nuclear magnetic shieldings of stacked aromatic and antiaromatic molecules. (United States)

    Sundholm, Dage; Rauhalahti, Markus; Özcan, Nergiz; Mera-Adasme, Raul; Kussmann, Jörg; Luenser, Arne; Ochsenfeld, Christian


    Nuclear magnetic shieldings have been calculated at the density functional theory (DFT) level for stacks of benzene, hexadehydro[12]annulene, dodecadehydro[18]annulene and hexabenzocoronene. The magnetic shieldings due to the ring currents in the adjacent molecules have been estimated by calculating nucleus independent molecular shieldings for the monomer in the atomic positions of neighbor molecules. The calculations show that the independent shielding model works reasonable well for the (1)H NMR shieldings of benzene and hexadehydro[12]annulene, whereas for the larger molecules and for the (13)C NMR shieldings the interaction between the molecules leads to shielding effects that are at least of the same size as the ring current contributions from the adjacent molecules. A better agreement is obtained when the nearest neighbors are also considered at full quantum mechanical (QM) level. The calculations suggest that the nearest solvent molecules must be included in the quantum mechanical system, at least when estimating solvent shifts at the molecular mechanics (MM) level. Current density calculations show that the stacking does not significantly affect the ring current strengths of the individual molecules, whereas the shape of the ring current for a single molecule differs from that of the stacked molecules.

  17. Charge transport in nitro substituted oligo(phenylene-ethynylene) molecules (United States)

    Cabassi, Marco Alberto


    This thesis presents research aimed at tackling two issues in the field of molecular electronics. The first issue is the large range of molecular conductance values reported by various research groups for identical molecules. This is addressed by studying the same molecule in dissimilar environments. The second issue is experimental uncertainty---whether the observed effects are inherent to the molecule or due to external causes. This is addressed by performing in-situ spectroscopy of the molecule as part of its electrical characterization. Oligo(phenylene-ethynylene)s are a well studied class of molecules in the field of molecular electronics, and this work focuses on charge transport through nitro substituted oligo(phenylene-ethynylene) molecules. The electrical characterization of these molecules was performed utilizing two testbeds. An electromigrated break-junction testbed was used to probe individual molecules, while a nanowire molecular junction testbed was used to probe self-assembled monolayers of the molecule. Experiments performed on individual molecules revealed a temperature dependent transition in the dominant charge transport mechanism. Above 50K, hopping is the dominant charge transport mechanism, while below 50K direct tunneling is the dominant charge transport mechanism. Experiments performed on self-assembled monolayers did not reveal any temperature dependent transitions. The dominant charge transport mechanism appears to be direct tunneling throughout the temperature range investigated. The results also indicate that molecules embedded in a self-assembled monolayer have significantly lower conductance than individual molecules. This is primarily due to a second charge transport mechanism (hopping) that opens up above 50K that is available only to individual molecules, and secondarily due to better potential screening properties of the self-assembled monolayers. Inelastic electron tunneling spectra obtained for the molecules in a self

  18. The photodissociation and reaction dynamics of vibrationally excited molecules

    Energy Technology Data Exchange (ETDEWEB)

    Crim, F.F. [Univ. of Wisconsin, Madison (United States)


    This research determines the nature of highly vibrationally excited molecules, their unimolecular reactions, and their photodissociation dynamics. The goal is to characterize vibrationally excited molecules and to exploit that understanding to discover and control their chemical pathways. Most recently the author has used a combination of vibrational overtone excitation and laser induced fluorescence both to characterize vibrationally excited molecules and to study their photodissociation dynamics. The author has also begun laser induced grating spectroscopy experiments designed to obtain the electronic absorption spectra of highly vibrationally excited molecules.

  19. Systematic Theoretical Study on the Interstellar Carbon Chain Molecules (United States)

    Etim, Emmanuel E.; Gorai, Prasanta; Das, Ankan; Chakrabarti, Sandip K.; Arunan, Elangannan


    In an effort to further our interest in understanding the basic chemistry of interstellar molecules, here we carry out an extensive investigation of the stabilities of interstellar carbon chains; C n , H2C n , HC n N and C n X (X = N, O, Si, S, H, P, H-, N-). These sets of molecules account for about 20% of all the known interstellar and circumstellar molecules. Their high abundances, therefore, demand serious attention. High-level ab initio quantum chemical calculations are employed to accurately estimate the enthalpy of formation, chemical reactivity indices, global hardness and softness, and other chemical parameters of these molecules. Chemical modeling of the abundances of these molecular species has also been performed. Of the 89 molecules considered from these groups, 47 have been astronomically observed, and these observed molecules are found to be more stable with respect to other members of the group. Of the 47 observed molecules, 60% are odd-numbered carbon chains. Interstellar chemistry is not actually driven by thermodynamics, but it is primarily dependent on various kinetic parameters. However, we found that the detectability of the odd-numbered carbon chains could be correlated due to the fact that they are more stable than the corresponding even-numbered carbon chains. Based on this aspect, the next possible carbon chain molecule for astronomical observation in each group is proposed. The effect of kinetics in the formation of some of these carbon chain molecules is also discussed.

  20. Rotation of a single molecule within a supramolecular bearing

    DEFF Research Database (Denmark)

    Gimzewski, J.K.; Joachim, C.; Schlittler, R.R.;


    Experimental visualization and verification of a single-molecule rotor operating within a supramolecular bearing is reported. Using a scanning tunneling microscope, single molecules were observed to exist in one of two spatially defined states Laterally separated by 0.26 nanometers. One was ident......Experimental visualization and verification of a single-molecule rotor operating within a supramolecular bearing is reported. Using a scanning tunneling microscope, single molecules were observed to exist in one of two spatially defined states Laterally separated by 0.26 nanometers. One...

  1. Visualization of DNA molecules in time during electrophoresis (United States)

    Lubega, Seth


    For several years individual DNA molecules have been observed and photographed during agarose gel electrophoresis. The DNA molecule is clearly the largest molecule known. Nevertheless, the largest molecule is still too small to be seen using a microscope. A technique developed by Morikawa and Yanagida has made it possible to visualize individual DNA molecules. When these long molecules are labeled with appropriate fluorescence dyes and observed under a fluorescence microscope, although it is not possible to directly visualize the local ultrastructure of the molecules, yet because they are long light emitting chains, their microscopic dynamical behavior can be observed. This visualization works in the same principle that enables one to observe a star through a telescope because it emits light against a dark background. The dynamics of individual DNA molecules migrating through agarose matrix during electrophoresis have been described by Smith et al. (1989), Schwartz and Koval (1989), and Bustamante et al. (1990). DNA molecules during agarose gel electrophoresis advance lengthwise thorough the gel in an extended configuration. They display an extension-contraction motion and tend to bunch up in their leading ends as the 'heads' find new pores through the gel. From time to time they get hooked on obstacles in the gel to form U-shaped configurations before they resume their linear configuration.

  2. DNA entropic elasticity for short molecules attached to beads

    CERN Document Server

    Li, J; Nelson, P C; Li, Jinyu; Nelson, Philip C.


    Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer force-extension behavior to calibrate the experiments; typically the experiments use the worm-like chain (WLC) theory for double-stranded DNA and RNA. This theory agrees well with experiments for long molecules. Recent single-molecule experiments have used shorter molecules, with contour lengths in the range of 1-10 persistence lengths. Most WLC theory calculations to date have assumed infinite molecule lengths, and do not agree well with experiments on shorter chains. Key physical effects that become important when shorter molecules are used include (i) boundary conditions which constrain the allowed fluctuations at the ends of the molecule and (ii) rotational fluctuations of the bead to which the polymer is attached, which change the apparent extension of the molecule. We describe the...

  3. Electron attachment to indole and related molecules

    Energy Technology Data Exchange (ETDEWEB)

    Modelli, Alberto, E-mail: [Dipartimento di Chimica “G. Ciamician”, Universitá di Bologna, via Selmi 2, 40126 Bologna (Italy); Centro Interdipartimentale di Ricerca in Scienze Ambientali (CIRSA), Universitá di Bologna, via S. Alberto 163, 48123 Ravenna (Italy); Jones, Derek, E-mail: [ISOF, Istituto per la Sintesi Organica e la Fotoreattività, C.N.R., via Gobetti 101, 40129 Bologna (Italy); Pshenichnyuk, Stanislav A., E-mail: [Institute of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya 151, 450075 Ufa (Russian Federation)


    Gas-phase formation of temporary negative ion states via resonance attachment of low-energy (0–6 eV) electrons into vacant molecular orbitals of indoline (I), indene (II), indole (III), 2-methylen-1,3,3-trimethylindoline (IV), and 2,3,3-trimethyl-indolenine (V) was investigated for the first time by electron transmission spectroscopy (ETS). The description of their empty-level structures was supported by density functional theory and Hartree-Fock calculations, using empirically calibrated linear equations to scale the calculated virtual orbital energies. Dissociative electron attachment spectroscopy (DEAS) was used to measure the fragment anion yields generated through dissociative decay channels of the parent molecular anions of compounds I-V, detected with a mass filter as a function of the incident electron energy in the 0–14 eV energy range. The vertical and adiabatic electron affinities were evaluated at the B3LYP/6-31+G(d) level as the anion/neutral total energy difference. The same theoretical method is also used for evaluation of the thermodynamic energy thresholds for production of the negative fragments observed in the DEA spectra. The loss of a hydrogen atom from the parent molecular anion ([M-H]{sup −}) provides the most intense signal in compounds I-IV. The gas-phase DEAS data can provide support for biochemical reaction mechanisms in vivo involving initial hydrogen abstraction from the nitrogen atom of the indole moiety, present in a variety of biologically important molecules.

  4. Application of a small molecule radiopharmaceutical concept to improve kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Jae Min [Dept. of Nuclear Medicine, Seoul National University College of Medicine, Seoul (Korea, Republic of)


    Recently, large molecules or nanoparticles are actively studied as radiopharmaceuticals. However, their kinetics is problematic because of a slow penetration through the capillaries and slow distribution to the target. To improve the kinetics, a two-step targeting method can be applied by using small molecules and very rapid copper-free click reaction. Although this method might have limitations such as internalization of the first targeted conjugate, it will provide high target-to-non-target ratio imaging of radiopharmaceuticals. The majority of radiopharmaceuticals belong to small molecules of which the molecular weight is less than 2000 Da, and the molecular size is smaller than 2 nm generally. The outstanding feature of the small molecule radiopharmaceuticals compared to large molecules is with their kinetics. Their distribution to target and clearance from non-target tissues are very rapid, which is the essential requirement of radiopharmaceuticals. In conclusion, the small molecule radiopharmaceuticals generally show excellent biodistribution properties; however, they show poor efficiency of radioisotope delivery. Large molecule or nanoparticle radiopharmaceuticals have advantages of multimodal and efficient delivery, but lower target-to-non-target ratio. Two-step targeting using a bio-orthogonal copper-free click reaction can be a solution of the problem of large molecule or nanoparticle radiopharmaceuticals. The majority of radiopharmaceuticals belong to small molecules of which the molecular weight is less than 2000 Da, and the molecular size is smaller than 2 nm generally. The outstanding feature of the small molecule radiopharmaceuticals compared to large molecules is with their kinetics. Their distribution to target and clearance from non-target tissues are very rapid, which is the essential requirement of radiopharmaceuticals.

  5. Role of Adhesion Molecules in Eosinophil Activation: A Comparative Study on the Effect of Adhesion Molecules on Eosinophil Survival

    Directory of Open Access Journals (Sweden)

    Kazutoshi Yamaguchi


    Conclusions: The regulation of adhesion molecules, by not only preventing eosinophil adhesion but also eosinophil activation, may be a potential target in the treatment of allergic inflammatory disorders.

  6. Targeting Mycobacterium tuberculosis topoisomerase I by small-molecule inhibitors. (United States)

    Godbole, Adwait Anand; Ahmed, Wareed; Bhat, Rajeshwari Subray; Bradley, Erin K; Ekins, Sean; Nagaraja, Valakunja


    We describe inhibition of Mycobacterium tuberculosis topoisomerase I (MttopoI), an essential mycobacterial enzyme, by two related compounds, imipramine and norclomipramine, of which imipramine is clinically used as an antidepressant. These molecules showed growth inhibition of both Mycobacterium smegmatis and M. tuberculosis cells. The mechanism of action of these two molecules was investigated by analyzing the individual steps of the topoisomerase I (topoI) reaction cycle. The compounds stimulated cleavage, thereby perturbing the cleavage-religation equilibrium. Consequently, these molecules inhibited the growth of the cells overexpressing topoI at a low MIC. Docking of the molecules on the MttopoI model suggested that they bind near the metal binding site of the enzyme. The DNA relaxation activity of the metal binding mutants harboring mutations in the DxDxE motif was differentially affected by the molecules, suggesting that the metal coordinating residues contribute to the interaction of the enzyme with the drug. Taken together, the results highlight the potential of these small molecules, which poison the M. tuberculosis and M. smegmatis topoisomerase I, as leads for the development of improved molecules to combat mycobacterial infections. Moreover, targeting metal coordination in topoisomerases might be a general strategy to develop new lead molecules.

  7. Soluble adhesion molecules in human cancers: sources and fates.

    NARCIS (Netherlands)

    Kilsdonk, J.W.J. van; Kempen, L.C.L.T. van; Muijen, G.N.P. van; Ruiter, D.J.; Swart, G.W.


    Adhesion molecules endow tumor cells with the necessary cell-cell contacts and cell-matrix interactions. As such, adhesion molecules are involved in cell signalling, proliferation and tumor growth. Rearrangements in the adhesion repertoire allow tumor cells to migrate, invade and form metastases. Be

  8. Single-Molecule FRET Study of DNA G-Quadruplex

    Institute of Scientific and Technical Information of China (English)


    The DNA G-quadruplex formed by the human telomeric sequence is a potential target for novel anticancer drugs. We have investigated an intramolecular DNA G-quadruplex using single-molecule fluorescence resonance energy transfer and shown that individual folded quadruplexes can be identified. The mean proximity ratio measured at the single-molecule level was consistent with ensemble measurement.


    Institute of Scientific and Technical Information of China (English)

    Zhu Jun; Cheng Yan; Chen Xiang-rong; Gou Qing-quan


    A four-parameter nonlinear model is introduced to the description of theX - Y stretching modes of XY6 octahedral molecules in the electronicground state. We here only apply it to the calculations of S--Fstretches of SF6 molecule. The model calculations appear to describethe observed data well, and predict some new vibrational bands ataccurate energies not yet observed.

  10. Formation of Prebiotic Molecules in Interstellar and Cometary Ices (United States)

    Bernstein, Max P.; Sandford, Scott A.; Allamandola, Louis J.; Dworkin, Jason; Gilette, J. Seb; Zare, Richard N.; DeVincenzi, D. (Technical Monitor)


    We report here on our lab studies of ice photochemistry of large organic molecules under cometary conditions. We focus on polycyclic aromatic hydrocarbons (PAHs), their photoproducts, and their similarities to molecules seen in living systems today. We note that these kinds of compounds are seen in meteorites and we propose an explanation for both their formation and their observed deuterium enrichments.

  11. Searches for interstellar molecules of potential prebiotic importance

    NARCIS (Netherlands)

    Kuan, Y.-J.; Charnley, S.B.; Huang, H.-C.; Kisiel, Z.; Ehrenfreund, P.; Tseng, W.-L.; Yan, C.-H.


    Interstellar chemistry leads to the formation of many prebiologically important molecules and is therefore of the fundamental interest to Astrobiology. Many organics can be produced in the gas phase where they can be detected. Molecules formed by reactions on the surfaces of dust grains are also bes

  12. Large negative differential conductance in single-molecule break junctions

    NARCIS (Netherlands)

    Perrin, Mickael L.; Frisenda, Riccardo; Koole, Max; Seldenthuis, Johannes S.; Gil, Jose A. Celis; Valkenier, Hennie; Hummelen, Jan C.; Renaud, Nicolas; Grozema, Ferdinand C.; Thijssen, Joseph M.; Dulic, Diana; van der Zant, Herre S. J.


    Molecular electronics aims at exploiting the internal structure and electronic orbitals of molecules to construct functional building blocks(1). To date, however, the overwhelming majority of experimentally realized single-molecule junctions can be described as single quantum dots, where transport i

  13. Investigating single molecule adhesion by atomic force spectroscopy. (United States)

    Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten


    Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.

  14. Electrochemical Single-Molecule Transistors with Optimized Gate Coupling

    DEFF Research Database (Denmark)

    Osorio, Henrry M.; Catarelli, Samantha; Cea, Pilar


    Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids....

  15. A Prospective Method to Guide Small Molecule Drug Design (United States)

    Johnson, Alan T.


    At present, small molecule drug design follows a retrospective path when considering what analogs are to be made around a current hit or lead molecule with the focus often on identifying a compound with higher intrinsic potency. What this approach overlooks is the simultaneous need to also improve the physicochemical (PC) and pharmacokinetic (PK)…


    NARCIS (Netherlands)



    A spectrum-generating algebra for a unified description of rotations and vibrations in polyatomic molecules is introduced. An application to nonlinear X(3) molecules shows that this model (i) incorporates exactly the relevant point group, (ii) provides a complete classification of oblate top states,

  17. Highly parallel translation of DNA sequences into small molecules.

    Directory of Open Access Journals (Sweden)

    Rebecca M Weisinger

    Full Text Available A large body of in vitro evolution work establishes the utility of biopolymer libraries comprising 10(10 to 10(15 distinct molecules for the discovery of nanomolar-affinity ligands to proteins. Small-molecule libraries of comparable complexity will likely provide nanomolar-affinity small-molecule ligands. Unlike biopolymers, small molecules can offer the advantages of cell permeability, low immunogenicity, metabolic stability, rapid diffusion and inexpensive mass production. It is thought that such desirable in vivo behavior is correlated with the physical properties of small molecules, specifically a limited number of hydrogen bond donors and acceptors, a defined range of hydrophobicity, and most importantly, molecular weights less than 500 Daltons. Creating a collection of 10(10 to 10(15 small molecules that meet these criteria requires the use of hundreds to thousands of diversity elements per step in a combinatorial synthesis of three to five steps. With this goal in mind, we have reported a set of mesofluidic devices that enable DNA-programmed combinatorial chemistry in a highly parallel 384-well plate format. Here, we demonstrate that these devices can translate DNA genes encoding 384 diversity elements per coding position into corresponding small-molecule gene products. This robust and efficient procedure yields small molecule-DNA conjugates suitable for in vitro evolution experiments.

  18. Electronic structure of Fe- vs. Ru-based dye molecules

    DEFF Research Database (Denmark)

    Johnson, Phillip S.; Cook, Peter L.; Zegkinoglou, Ioannis;


    In order to explore whether Ru can be replaced by inexpensive Fe in dye molecules for solar cells, the differences in the electronic structure of Fe- and Ru-based dyes are investigated by X-ray absorption spectroscopy and first-principles calculations. Molecules with the metal in a sixfold...

  19. Imaging and manipulation of a polar molecule oil Ag(111)

    DEFF Research Database (Denmark)

    Lin, Rong; Braun, K.F.; Tang, H.;


    on the surface. Accompanying with the reposition, molecular rotation and/or changing of binding configurations can also be induced. It is found that the dipole moment of the molecule has minor effects on its lateral movement. The results demonstrate that due to many degrees of freedom for large molecules...

  20. Time-Varying Triplet State Lifetimes of Single Molecules

    NARCIS (Netherlands)

    Veerman, J.A.; Garcia-Parajo, M.F.; Kuipers, L.; Hulst, van N.F.


    It is found that triplet state lifetimes and intersystem crossing yields of individual molecules embedded in a polymer host at room temperature are not constant in time. The range over which the triplet lifetime of a single molecule varies during long observation times shows a strong similarity with

  1. Structure and dynamics of water molecules confined in triglyceride oils. (United States)

    Groot, Carien C M; Velikov, Krassimir P; Bakker, Huib J


    Though it is commonly known that a small amount of water can be present in triglyceride oil, a molecular picture of how water molecules organize in the oil phase is lacking. We investigate the hydrogen-bond configuration and dynamics of water in triacetin, tributyrin and trioctanoin using linear infrared and time-resolved two-dimensional infrared (2DIR) spectroscopy of the water hydroxyl stretch vibration. We identify water molecules with a single strong hydrogen bond to the triglyceride, water molecules with two weaker hydrogen bonds to the triglycerides, and water clusters. These species do not interconvert on the 20 ps timescale of the experiment, as evidenced by the absence of cross-peaks in the 2DIR spectrum. The vibrational response of water molecules with a single strong hydrogen bond to the triglyceride depends strongly on the excitation frequency, revealing the presence of different subspecies of singly-bound water molecules that correspond to different hydrogen-bond locations. In contrast, the water molecules with two weaker hydrogen bonds to the triglyceride correspond to a single, specific hydrogen-bond configuration; these molecules likely bridge the carbonyl groups of adjacent triglyceride molecules, which can have considerable influence on liquid triglyceride properties.

  2. AC trapping and high-resolution spectroscopy of ammonia molecules

    NARCIS (Netherlands)

    Veldhoven, Jacqueline van


    Cold molecules are potentially beneficial for several areas of research. They have applications in spectroscopy, collision studies and, for instance, the study of the effects of dipole-dipole interactions in BECs. One method to decelerate and thereby cool down neutral dipolar molecules is to use a S

  3. Synchrotron radiation VUV double photoionization of some small molecules

    Institute of Scientific and Technical Information of China (English)

    Zhao Yu-Jie; Shan Xiao-Bin; Sheng Liu-Si; Wang Zhen-Ya; Zhang Jie; Yu Chun-Ri


    The VUV double photoionizations of small molecules(NO, CO, CO2, CS2, OSC and NH3)were investigated with photoionization mass spectroscopy using synchrotron radiation. The double ionization energies of molecules were determined with photoionization efficiency spectroscopy. The total energies of these molecules and their parent dications (NO2+, CO2+, CO2+2,CS2+2,OS2+C and NH2+3)were calculated using the Gaussian 03 program and Gaussian 2calculations. Then, the adiabatic double ionization energies of the molecules were predicated by using high accuracy energy mode. The experimental double ionization energies of these small molecules were all in reasonable agreement with their respective calculated adiabatic double ionization energies. The mechanisms of double photoionization of these molecules were discussed based on a comparison of our experimental results with those predicted theoretically. The equilibrium geometries and harmonic vibrational frequencies of molecules and their parent dications were calculated by using the MP2(full)method. The differences in configurations between these molecules and their parent dications were also discussed on the basis of theoretical calculations.

  4. MARTINI Model for Physisorption of Organic Molecules on Graphite

    NARCIS (Netherlands)

    Gobbo, Cristian; Beurroies, Isabelle; de Ridder, David; Eelkema, Rienk; Marrink, Siewert J.; De Feyter, Steven; van Esch, Jan H.; de Vries, Alex H.


    An extension to the MARTINI coarse-grained model is presented to describe the adsorption of organic molecules on graphite surfaces. The model allows the study of the dynamics of the preferential adsorption of long-chain organic molecules from solvent and the formation of ordered structures on the su

  5. Reversible switching of ultrastrong light-molecule coupling

    DEFF Research Database (Denmark)

    Schwartz, T; Hutchison, J A; Genet, C


    We demonstrate that photochromic molecules enable switching from the weak- to ultrastrong-coupling regime reversibly, by using all-optical control. This switch is achieved by photochemically inducing conformational changes in the molecule. Remarkably, a Rabi splitting of 700 meV is measured at room...

  6. Impulsive Laser Induced Alignment of Molecules Dissolved in Helium Nanodroplets

    DEFF Research Database (Denmark)

    Pentlehner, Dominik; H. Nielsen, Jens; Slenczka, Alkwin


    We show that a 450 fs nonresonant, moderately intense, linearly polarized laser pulse can induce field-free molecular axis alignment of methyliodide (CH3I) molecules dissolved in a helium nanodroplet. Time-resolved measurements reveal rotational dynamics much slower than that of isolated molecule...

  7. Fluorescence Emission from Small Molecules Containing Amino Group

    Institute of Scientific and Technical Information of China (English)


    After the treatment of oxygen gas, the small molecules containing amine group could emit fluorescence. Oxidation was believed to play an important role in the formation of fluorescence centers. Compared to previous results, both small molecules and macromolecules might have the same fluorescence centers.

  8. Spectroscopic probes of vibrationally excited molecules at chemically significant energies

    Energy Technology Data Exchange (ETDEWEB)

    Rizzo, T.R. [Univ. of Rochester, NY (United States)


    This project involves the application of multiple-resonance spectroscopic techniques for investigating energy transfer and dissociation dynamics of highly vibrationally excited molecules. Two major goals of this work are: (1) to provide information on potential energy surfaces of combustion related molecules at chemically significant energies, and (2) to test theoretical modes of unimolecular dissociation rates critically via quantum-state resolved measurements.

  9. RGM is a repulsive guidance molecule for retinal axons

    DEFF Research Database (Denmark)

    Monnier, Philippe P; Sierra, Ana; Macchi, Paolo;


    the temporal half, is guided by repulsive cues expressed in a graded fashion in the optic tectum, part of the midbrain. Here we report the cloning and functional characterization of a membrane-associated glycoprotein, which we call RGM (repulsive guidance molecule). This molecule shares no sequence homology...

  10. Bioinspired assembly of small molecules in cell milieu. (United States)

    Wang, Huaimin; Feng, Zhaoqianqi; Xu, Bing


    Self-assembly, the autonomous organization of components to form patterns or structures, is a prevalent process in nature at all scales. Particularly, biological systems offer remarkable examples of diverse structures (as well as building blocks) and processes resulting from self-assembly. The exploration of bioinspired assemblies not only allows for mimicking the structures of living systems, but it also leads to functions for applications in different fields that benefit humans. In the last several decades, efforts on understanding and controlling self-assembly of small molecules have produced a large library of candidates for developing the biomedical applications of assemblies of small molecules. Moreover, recent findings in biology have provided new insights on the assemblies of small molecules to modulate essential cellular processes (such as apoptosis). These observations indicate that the self-assembly of small molecules, as multifaceted entities and processes to interact with multiple proteins, can have profound biological impacts on cells. In this review, we illustrate that the generation of assemblies of small molecules in cell milieu with their interactions with multiple cellular proteins for regulating cellular processes can result in primary phenotypes, thus providing a fundamentally new molecular approach for controlling cell behavior. By discussing the correlation between molecular assemblies in nature and the assemblies of small molecules in cell milieu, illustrating the functions of the assemblies of small molecules, and summarizing some guiding principles, we hope this review will stimulate more molecular scientists to explore the bioinspired self-assembly of small molecules in cell milieu.

  11. STM CONTROL OF CHEMICAL REACTIONS: Single-Molecule Synthesis (United States)

    Hla, Saw-Wai; Rieder, Karl-Heinz


    The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.


    Institute of Scientific and Technical Information of China (English)


    Objective: To investigate the expression of immune- related molecules in glioblastoma multiform(GBM) cells. Methods: The expression of major histocompatibility complex (MHC), β2-microglobulin, Fas, CD80 and CD86 molecules on the surface of GBM cells were evaluated by flow cytometry. The expression of TAP-1, TAP-2 and Tapasin in the GBM cells were evaluated by RT-PCR method. Results: MHC class Ⅰ, β2 microglobulin, TAP-1, TAP-2 and tapasin were expressed in most GBM cell lines. Except U87, there was no MHC class Ⅱ molecule expression on any of the other GBM cell lines. Fas was expressed on all the GBM cell lines examined. Conclusion: The mechanism by which GBM escapes immune surveillance may involve down regulation of expression of MHC class Ⅰ molecules and MHC class Ⅱ molecules. MHC class Ⅰpositive GBM may be the suitable target of immunotherapy.

  13. Small-Molecule Binding Aptamers: Selection Strategies, Characterization, and Applications (United States)

    Ruscito, Annamaria; DeRosa, Maria


    Aptamers are single-stranded, synthetic oligonucleotides that fold into 3-dimensional shapes capable of binding non-covalently with high affinity and specificity to a target molecule. They are generated via an in vitro process known as the Systematic Evolution of Ligands by EXponential enrichment, from which candidates are screened and characterized, and then applied in aptamer-based biosensors for target detection. Aptamers for small molecule targets such as toxins, antibiotics, molecular markers, drugs, and heavy metals will be the focus of this review. Their accurate detection is ultimately needed for the protection and wellbeing of humans and animals. However, issues such as the drastic difference in size of the aptamer and small molecule make it challenging to select, characterize, and apply aptamers for the detection of small molecules. Thus, recent (since 2012) notable advances in small molecule aptamers, which have overcome some of these challenges, are presented here, while defining challenges that still exist are discussed

  14. Computer systems for annotation of single molecule fragments (United States)

    Schwartz, David Charles; Severin, Jessica


    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  15. Single Molecule Junctions: Probing Contact Chemistry and Fundamental Circuit Laws

    Energy Technology Data Exchange (ETDEWEB)

    Hybertsen M. S.


    By exploiting selective link chemistry, formation of single molecule junctions with reproducible conductance has become established. Systematic studies reveal the structure-conductance relationships for diverse molecules. I will draw on experiments from my collaborators at Columbia University, atomic-scale calculations and theory to describe progress in two areas. First, I will describe a novel route to form single molecule junctions, based on SnMe3 terminated molecules, in which gold directly bonds to carbon in the molecule backbone resulting in near ideal contact resistance [1]. Second, comparison of the conductance of junctions formed with molecular species containing either one backbone or two backbones in parallel allows demonstration of the role of quantum interference in the conductance superposition law at the molecular scale [2].

  16. Superexciplex of Coumarin Molecules using Tunable Ti-Sapphire Laser (United States)

    Al-Ghamdi, Attieh Ali; Al-Dwayyan, Abdullah S.; Masilamani, Vadivel; Al-Saud, Turki Saud M.; Al-Salhi, Mohammed Saleh


    Certain highly polar dye molecules exhibit an additional optical gain band under pulsed laser excitation, while there is no such band under steady-state continuous wave (CW) lamp excitation. This new band is not due to an excimer, an exciplex or a two-photon fluorescence band but stems from the formation of a new molecular complex in which two excited molecules remain associated with a solvent molecule acting as a bridge. In this paper, the characteristics of superexciplexes of four related coumarin molecules are presented. All molecules were excited using a tunable Ti-sapphire laser pulse 10 ns in width. The distinct difference between the amplified spontaneous emission (ASE) spectra obtained with tunable laser and tunable lamp excitation demonstrated that twisted intramolecular charge transfer (TICT) conformations might also assist in the formation of these superexciplexes.

  17. Positron-molecule interactions: resonant attachment, annihilation, and bound states

    CERN Document Server

    Gribakin, G F; Surko, C M; 10.1103/RevModPhys.82.2557


    This article presents an overview of current understanding of the interaction of low-energy positrons with molecules with emphasis on resonances, positron attachment and annihilation. Annihilation rates measured as a function of positron energy reveal the presence of vibrational Feshbach resonances (VFR) for many polyatomic molecules. These resonances lead to strong enhancement of the annihilation rates. They also provide evidence that positrons bind to many molecular species. A quantitative theory of VFR-mediated attachment to small molecules is presented. It is tested successfully for selected molecules (e.g., methyl halides and methanol) where all modes couple to the positron continuum. Combination and overtone resonances are observed and their role is elucidated. In larger molecules, annihilation rates from VFR far exceed those explicable on the basis of single-mode resonances. These enhancements increase rapidly with the number of vibrational degrees of freedom. While the details are as yet unclear, intr...

  18. Entanglement Dynamics in Typical Local- and Normal-Mode Molecules

    Institute of Scientific and Technical Information of China (English)

    HOU Xi-Wen; WAN Ming-Fang; MA Zhong-Qi


    The entanglement dynamics of two stretching vibrations in theoretically typical local- and normal-mode molecules and realistic molecules H2O and SO2 in an algebraic model is studied in terms of the reduced-density linear entropy with initial entangled states taken to be two-mode squeezed vacuum states. It is shown that the behaviour of the entropy in theoretically typical molecules appears to be more regular than that in realistic ones, and that the entropy becomes irregular as the amplitude of two-mode squeezed vacuum states increases. For initial states with a small amplitude, it is demonstrated that the periodicity and the "classical" beat phenomenon of the entropy occur with the beat in theoretically typical molecules being more regular than that in realistic molecules H2O and SO2.

  19. Assembly of MHC class I molecules within the endoplasmic reticulum. (United States)

    Zhang, Yinan; Williams, David B


    MHC class I molecules bind cytosolically derived peptides within the endoplasmic reticulum (ER) and present them at the cell surface to cytotoxic T cells. A major focus of our laboratory has been to understand the functions of the diverse proteins involved in the intracellular assembly of MHC class I molecules. These include the molecular chaperones calnexin and calreticulin, which enhance the proper folding and subunit assembly of class I molecules and also retain assembly intermediates within the ER; ERp57, a thiol oxidoreductase that promotes heavy chain disulfide formation and proper assembly of the peptide loading complex; tapasin, which recruits class I molecules to the TAP peptide transporter and enhances the loading of high affinity peptide ligands; and Bap31, which is involved in clustering assembled class I molecules at ER exit sites for export along the secretory pathway. This review describes our contributions to elucidating the functions of these proteins; the combined effort of many dedicated students and postdoctoral fellows.

  20. A proposal for sympathetically cooling neutral molecules using cold ions

    CERN Document Server

    Robicheaux, F


    We describe a method for cooling neutral molecules that have magnetic and electric dipole moments using collisions with cold ions. An external magnetic field is used to split the ground rovibrational energy levels of the molecule. The highest energy state within the ground rovibrational manifold increases in energy as the distance to the ion decreases leading to a repelling potential. At low energy, inelastic collisions are strongly suppressed due to the large distance of closest approach. Thus, a collision between a neutral molecule and a cold ion will lead to a decrease in the molecule's kinetic energy with no change in internal energy. We present results for the specific case of OH molecules cooled by Be$^+$, Mg$^+$, or Ca$^+$ ions.

  1. Gold Nanoparticle-Biological Molecule Interactions and Catalysis

    Directory of Open Access Journals (Sweden)

    Jonathan G. Heddle


    Full Text Available This review gives a brief summary of the field of gold nanoparticle interactions with biological molecules, particularly those with possible catalytic relevance. Gold nanoparticles are well known as catalysts in organic chemistry but much is unknown regarding their potential as catalysts of reactions involving biological molecules such as protein and nucleic acids. Biological molecules may be the substrate for catalysis or, if they are the ligand coating the gold particle, may be the catalyst itself. In other cases biological molecules may form a template upon which gold nanoparticles can be precisely arrayed. As relatively little is currently known about the catalytic capabilities of gold nanoparticles in this area, this review will consider templating in general (including, but not restricted to, those which result in structures having potential as catalysts before going on to consider firstly catalysis by the gold nanoparticle itself followed by catalysis by ligands attached to gold nanoparticles, all considered with a focus on biological molecules.

  2. Single-Molecule Electronics: Chemical and Analytical Perspectives. (United States)

    Nichols, Richard J; Higgins, Simon J


    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.

  3. Massively parallel single-molecule manipulation using centrifugal force

    CERN Document Server

    Halvorsen, Ken


    Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues with a new approach: massively parallel single-molecule force measurements using centrifugal force. This approach is realized in a novel instrument that we call the Centrifuge Force Microscope (CFM), in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force-field while their micro-to-nanoscopic motions are observed. We demonstrate high-throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Additionally, we verify the force accuracy of the instrument by measuring the well-est...

  4. Synthesis of interlocked molecules by olefin metathesis (United States)

    Clark, Paul Gregory

    A large body of work in the Grubbs group has focused on the development of functional-group tolerant ruthenium alkylidene catalysts that perform a number of olefin metathesis reactions. These catalysts have seen application in a wide range of fields, including classic total synthesis as well as polymer and materials chemistry. One particular family of compounds, interlocked molecules, has benefitted greatly from these advances in catalyst stability and activity. This thesis describes several elusive and challenging interlocked architectures whose syntheses have been realized through the utilization of different types of ruthenium-catalyzed olefin metathesis reactions. Ring-closing olefin metathesis has enabled the synthesis of a [c2]daisy-chain dimer with the ammonium binding site near the cap of the dimer. A deprotonated DCD possessing such a structural attribute will more forcefully seek to restore coordinating interactions upon reprotonation, enhancing its utility as a synthetic molecular actuator. Dimer functionalization facilitated incorporation into linear polymers, with a 48% size increase of an unbound, extended analogue of the polymer demonstrating slippage of the dimer units. Ongoing work is directed at further materials studies, in particular, exploring the synthesis of macroscopic networks containing the DCD units and analyzing the correlation between molecular-scale extension-contraction manipulations and resulting macro-scale changes. A "clipping" approach to a polycatenated cyclic polymer, a structure that resembles a molecular "charm bracelet", has been described. The use of ring-opening metathesis polymerization of a carbamate monomer in the presence of a chain transfer agent allowed for the synthesis of a linear polymer that was subsequently functionalized and cyclized to the corresponding cyclic analogue. This cyclic polymer was characterized through a variety of techniques, and subjected to further functionalization reactions, affording a cyclic

  5. Angiogenic Effect of Intercellular Adhesion Molecule-1

    Institute of Scientific and Technical Information of China (English)

    DENG Chenguo; ZHANG Duanlian; SHAN Shengguo; WU Jingwen; YANG Hong; YU Ying


    In order to investigate the angiogenic effect of intercellular adhesion molecule-1 (ICAM-1), two parts of experiment were performed. Chick embryo chorioallantoic membrane (CAM) assay was used for in vivo angiogenic research. The chick embryos were divided into 4 groups: ICAM-1 group (divided into 3 subgroups, Ⅰ, Ⅱ and Ⅲ) for screening the angiogenic effect of ICAM-1 by adding different concentrations of ICAM-1 (0.1, 0.2 and 0.3 μg/μL) 5 μL into the chick embryo CAMs on the day 10 after incubation for every subgroup; Anti-ICAM-1 group A (divided into 2 subgroups, Ⅰ and Ⅱ) by adding different concentrations of Anti-ICAM-1 (1:100, 1:50) 5 μL into the chick embryo CAMs on the day 10 after incubation for every subgroup to evaluate the effect of ICAM-1 on the survival of microvessels through observing whether Anti-ICAM-1 could induce involution of the microvessels on CAMs; Anti-ICAM-1 group B (divided into 2 subgroups, Ⅰ and Ⅱ ) by adding different concentrations of Anti-ICAM-1 (1:100, 1:50) 5 μL into the chick embryo CAMs on the day 6 after incubation for every subgroup to evaluate whether ICAM-1 involved in embryonic angiogenesis through observing the growth of microvessels on CAMs; Control group: ICAM-1 or Anti-ICAM-1 was substituted by PBS 5 μL on the day 10 or day 6 after incubation. Three days later, the CAMs were photographed in vivo, excised, sectioned and the number of microvessels was counted. In ICAM-1 group, there was increased number of microvessels arranged radially with "spoked-wheel" pattern around the gelatin sponges. The new microvessels growing perpendicularly to gelatin sponges were observed. The number of the microvessels growing in the CAM mesenchymes around the sponges in 3 subgroups was higher than that in control group (P<0.01), however, there was no significant difference among the 3 subgroups (P>0.05). In anti-ICAM-1 group A, the radially arranged microvessels were very unclear around the sponges contrast to that of ICAM

  6. Electronic transport in benzodifuran single-molecule transistors (United States)

    Xiang, An; Li, Hui; Chen, Songjie; Liu, Shi-Xia; Decurtins, Silvio; Bai, Meilin; Hou, Shimin; Liao, Jianhui


    Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices.Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices. Electronic supplementary information (ESI) available: The fabrication procedure for BDF single-molecule

  7. Electron impact cross sections of vibrationally and electronically excited molecules

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Jung-Sik, E-mail: [Plasma Technology Research Center, National Fusion Research Institute, 814-2, Osikdo-Dong, Gunsan, Jeollabuk-Do, 573-540 (Korea, Republic of); Song, Mi-Young; Kwon, Deuk-Chul; Choi, Heechol [Plasma Technology Research Center, National Fusion Research Institute, 814-2, Osikdo-Dong, Gunsan, Jeollabuk-Do, 573-540 (Korea, Republic of); Kim, Chang-Geun [National Center for Standard Reference Data, Korea Research Institute of Standards and Science, Doryong-Dong, Yuseong-Gu, Daejeon 305-340 (Korea, Republic of); Kumar, Vijay [B-82, Aarohi Twin Bungalows, Near Govt. Tubewell, Bopal, Ahmedabad-380058 (India)


    It is well known that the electron impact cross sections for elastic and inelastic processes for the vibrationally and electronically excited molecules are predominantly different than those for molecules in the ground state. Collisions of low energy electrons with excited molecules play an important role in explaining the behavior of gas discharges in laser and plasma physics, in planetary atmospheres, stars, and interstellar medium and in plasmas widely used in the fabrication of microelectronics. This explains as to why there is a need for having validated sets of electron impact cross sections for different processes. This work reviews the subject of electron collisions with vibrationally and electronically excited molecules in a comprehensive way. The survey has been carried out for a few excited molecules such as H{sub 2}, D{sub 2}, T{sub 2}, HD, HT, DT, N{sub 2}, O{sub 2}, and CO{sub 2}. This review includes the discussion on the methods to produce and detect vibrationally and electronically excited molecules. We will take up the cross section data available in the literature for such molecules on electron scattering, dissociation, ionization and attachment processes and will discuss, evaluate and well-validate the same wherever and whenever possible.

  8. Statistical analysis of unlabeled point sets: comparing molecules in chemoinformatics. (United States)

    Dryden, Ian L; Hirst, Jonathan D; Melville, James L


    We consider Bayesian methodology for comparing two or more unlabeled point sets. Application of the technique to a set of steroid molecules illustrates its potential utility involving the comparison of molecules in chemoinformatics and bioinformatics. We initially match a pair of molecules, where one molecule is regarded as random and the other fixed. A type of mixture model is proposed for the point set coordinates, and the parameters of the distribution are a labeling matrix (indicating which pairs of points match) and a concentration parameter. An important property of the likelihood is that it is invariant under rotations and translations of the data. Bayesian inference for the parameters is carried out using Markov chain Monte Carlo simulation, and it is demonstrated that the procedure works well on the steroid data. The posterior distribution is difficult to simulate from, due to multiple local modes, and we also use additional data (partial charges on atoms) to help with this task. An approximation is considered for speeding up the simulation algorithm, and the approximating fast algorithm leads to essentially identical inference to that under the exact method for our data. Extensions to multiple molecule alignment are also introduced, and an algorithm is described which also works well on the steroid data set. After all the steroid molecules have been matched, exploratory data analysis is carried out to examine which molecules are similar. Also, further Bayesian inference for the multiple alignment problem is considered.

  9. Comets as a possible source of prebiotic molecules (United States)

    Huebner, W. F.; Boice, D. C.


    Prebiotic molecules derive from abiotic organic molecules, radicals, and ions that pervade the universe at temperatures as high as several 1000 K. Here we review the role of organic molecules that condensed at low temperatures before or during comet formation in the early history of the Solar System. Recent spacecraft encounters and ground-based observations of carbon-rich volatile and dust components of comet comae provide a broad database for the investigation of these organic molecules. New laboratory data for some potential cometary organics are presented. Probable icy organic constituents of the nucleus and CHON particles as likely candidates for the distributed sources of gas-phase organic species in the coma are discussed. There is broad agreement that many organic molecules observed in the coma originate from the dust that must have existed in the solar nebula at the time and place of comet formation. We conclude that complex organic molecules found in comets may be a source of prebiotic molecules that led to the origins of life.

  10. Kinetics of Hydrogen Molecules in MAGNUM-PSI

    Institute of Scientific and Technical Information of China (English)



    Results from simulations of plasma and neutrals under conditions predictively characterizing the detached plasma regime in the linear machine MAGNUM-PSI are presented. The relaxation of the vibrationally excited hydrogen molecules is investigated in order to establish a relation between their relaxation and dwell times, and the role of the various mechanisms of the molecular vibrational kinetics. The results obtained show that the individual vibrational states have to be included in the transport code for neutrals as distinct species, since the relaxation time of the vibrational states is sufficiently longer than the typical dwell time of hydrogen molecules in the detached plasma region. The parameters of plasma and neutrals are affected by the transport of the vibrationally excited hydrogen molecules. Furthermore, the rate of molecular recombination is overestimated by a factor of~5 provided that the transport of hydrogen molecules only in their ground vibrational state is considered. The role of the various processes of vibrational kinetics is studied. The vibrational excitation through singlet electronic states has a strong influence on the molecular densities for levels with vibrational quantum numbers v≥ 5. Vibration-vibration (V-V) collisions between vibrationally excited hydrogen molecules and vibration-translation (V-T) collisions between vibrationally excited hydrogen molecules and ground state molecules and atoms are of minor importance in MAGNUM-PSI.

  11. Sympathetic cooling of molecules with laser-cooled atoms (United States)

    Hudson, Eric


    Cooling molecules through collisions with laser-cooled atoms is an attractive route to ultracold, ground state molecules. The technique is simple, applicable to a wide class of molecules, and does not require molecule specific laser systems. Particularly suited to this technique are charged molecules, which can be trapped indefinitely, even at room temperature, and undergo strong, short-ranged collisions with ultracold atoms. In this talk, I will focus on recent efforts to use the combination of a magneto-optical trap (MOT) and an ion trap, dubbed the MOTion trap, to produce cold, ground state diatomic charged molecules. The low-energy internal structure of these diatomic molecules, e.g. the electric dipole moment and vibrational, rotational, and Ω-doublet levels, presents a host of opportunities for advances in quantum simulation, precision measurement, cold chemistry, and quantum information. Excitingly, recent proof-of-principle experiments have demonstrated that the MOTion trap is extremely efficient at cooling the vibrational motion of molecular ions. Supported by the ARO and NSF.

  12. Spectroscopy of ultracold LiRb molecules using ionization detection (United States)

    Altaf, Adeel

    We present spectroscopic studies of ultracold LiRb molecules using ionization detection. The molecules are created by cooling and trapping Li and Rb atoms in overlapping magneto-optical traps (MOTs) and using light resonant with a free-bound transition to create weakly bound excited state molecules in a process known as photoassociation (PA). We explore weakly bound vibrational levels of LiRb with PA spectroscopy using ionization detection and, where possible, compare our results with earlier measurements performed in our lab using trap-loss spectroscopy. In addition, we also probe vibrational levels of the ground triplet electronic state and excited electronic states using resonantly enhanced multiphoton ionization (REMPI) spectroscopy. We identify several vibrational levels of the alpha3Sigma+, (3)3piO and (4)3Sigma + states and compare our observations with theoretical calculations. As LiRb is one of the least studied heteronuclear diatomic molecules, these studies are aimed towards exploring the molecular structure. The spectroscopic work is also in line with the long-term project goals of transferring ultracold LiRb molecules into the lowest rotational and vibrational levels of the ground singlet electronic state. Molecules in this rovibronic ground state possess a large electric dipole moment, which is essential for application of ultracold molecules in various quantum computation schemes. The rovibronic ground state will also be an ideal starting point for investigating molecular entangled states.


    Institute of Scientific and Technical Information of China (English)

    吴成印; 龚旗煌


    In order to predict the field ionization probabilities, the accurate ab initio electrostatic potential of molecules has to be calculated. However, the calculation of the full ab initio electrostatic potential of molecules is complicated,even impossible for some larger molecules with low symmetry. Here, we present a semi-empirical model to treat the field ionization of molecules in an intense laser field. In this model, a modified Coulomb potential is used to take the place of the complicated ab initio electrostatic potential of molecules. The analytic equations of the Keldysh adiabatic parameter using the Coulomb potential and the modified Coulomb potential have first been given. Using our semiempirical model, we have calculated the field ionization probabilities and the Keldysh adiabatic parameters of O2,N2, SO2, C2H4, CH3CN and C6H6 in an intense laser field. The results agree excellently with the calculations using the ab initio electrostatic potential of molecules. As the modified parameter for the Coulomb potential can be found from experimental measurements, the field ionization mechanism of molecules can be immediately predicted with our semi-empirical model.

  14. Circulating adhesion molecules in obstructive sleep apnea and cardiovascular disease. (United States)

    Pak, Victoria M; Grandner, Michael A; Pack, Allan I


    Over 20 years of evidence indicates a strong association between obstructive sleep apnea (OSA) and cardiovascular disease. Although inflammatory processes have been heavily implicated as an important link between the two, the mechanism for this has not been conclusively established. Atherosclerosis may be one of the mechanisms linking OSA to cardiovascular morbidity. This review addresses the role of circulating adhesion molecules in patients with OSA, and how these may be part of the link between cardiovascular disease and OSA. There is evidence for the role of adhesion molecules in cardiovascular disease risk. Some studies, albeit with small sample sizes, also show higher levels of adhesion molecules in patients with OSA compared to controls. There are also studies that show that levels of adhesion molecules diminish with continuous positive airway pressure therapy. Limitations of these studies include small sample sizes, cross-sectional sampling, and inconsistent control for confounding variables known to influence adhesion molecule levels. There are potential novel therapies to reduce circulating adhesion molecules in patients with OSA to diminish cardiovascular disease. Understanding the role of cell adhesion molecules generated in OSA will help elucidate one mechanistic link to cardiovascular disease in patients with OSA.

  15. Electrospray deposition of organic molecules on bulk insulator surfaces. (United States)

    Hinaut, Antoine; Pawlak, Rémy; Meyer, Ernst; Glatzel, Thilo


    Large organic molecules are of important interest for organic-based devices such as hybrid photovoltaics or molecular electronics. Knowing their adsorption geometries and electronic structures allows to design and predict macroscopic device properties. Fundamental investigations in ultra-high vacuum (UHV) are thus mandatory to analyze and engineer processes in this prospects. With increasing size, complexity or chemical reactivity, depositing molecules by thermal evaporation becomes challenging. A recent way to deposit molecules in clean conditions is Electrospray Ionization (ESI). ESI keeps the possibility to work with large molecules, to introduce them in vacuum, and to deposit them on a large variety of surfaces. Here, ESI has been successfully applied to deposit triply fused porphyrin molecules on an insulating KBr(001) surface in UHV environment. Different deposition coverages have been obtained and characterization of the surface by in-situ atomic force microscopy working in the non-contact mode shows details of the molecular structures adsorbed on the surface. We show that UHV-ESI, can be performed on insulating surfaces in the sub-monolayer regime and to single molecules which opens the possibility to study a variety of complex molecules.

  16. Formation of Complex Molecules via radiative association reactions (United States)

    Acharyya, Kinsuk; Herbst, Eric


    The detection of increasing numbers of complex organic molecules in the various phases of star formation plays a key role since they follow the same chemical rules of carbon-based chemistry that are observed in our planet Earth. Many of these molecules are believed to be formed on the surfaces of grains, and can then be released to the gas phase when these grains are heated. This is evident when we observe a rich chemistry in hot core regions. However, recently complex organic molecules have also been observed in cold clouds. Therefore, it is necessary to re-examine various pathways for the formation of these molecules in the gas phase. In this presentation, I will discuss role of radiative association reactions in the formation of complex molecules in the gas phase and at low temperature. We will compare abundance of assorted molecules with and without new radiative association reactions and will show that the abundance of a few complex molecules such as HCOOCH3, CH3OCH3 etc. can go up due to introduction of these reactions, which can help to explain their observed abundances.

  17. Laser cooling and slowing of CaF molecules (United States)

    Truppe, Stefan; Williams, Hannah; Hambach, Moritz; Sauer, Ben; Hinds, Ed; Tarbutt, Mike


    We have developed a cold and bright source for CaF molecules and use laser radiation pressure to slow the molecules to within the capture velocity of a magneto-optical trap (MOT). Using laser ablation of Ca into a continuous flow of cryogenic Helium buffer gas mixed with SF6 we produce up to 1011 molecules per steradian per pulse in a single rotational state. The molecules move with a mean forward velocity of 160m/s and have a velocity spread of 80m/s. We then apply laser radiation pressure to the molecular beam to slow and cool the molecules. We form a quasi-closed laser-cooling cycle by using a main cooling laser to drive the B2Σ+ (v' = 0) - X2Σ+ (v'' = 0) transition and a single repump laser to address the A2Π1 / 2 (v' = 0) -X2Σ+ (v'' = 1) transition. Radio-frequency sidebands applied to both lasers address the hyperfine structure. By chirping the frequencies of both lasers to keep the decelerating molecules resonant with the light, we scatter more than 10000 photons and reduce the speed to below 50 m/s. We achieve a similar effect by broadening the linewidth of the laser to several hundred MHz. This ``white-light'' slowing is compared to the chirped slowing technique. We also present progress towards a MOT of CaF molecules.

  18. Systematic Theoretical Study on the Interstellar Carbon Chain Molecules

    CERN Document Server

    Etim, Emmanuel E; Das, Ankan; Chakrabarti, Sandip K; Arunan, Elangannan


    In an effort to further our interest in understanding basic chemistry of interstellar molecules, we carry out here an extensive investigation of the stabilities of interstellar carbon chains; Cn, H2Cn, HCnN and CnX (X=N, O, Si, S, H, P, H-, N-). These sets of molecules accounts for about 20% of all the known interstellar and circumstellar molecules, their high abundances therefore demand a serious attention. High level ab initio quantum chemical calculations are employed to accurately estimate enthalpy of formation, chemical reactivity indices; global hardness and softness; and other chemical parameters of these molecules. Chemical modeling of the abundances of these molecular species has also been performed. Of the 89 molecules considered from these groups, 47 have been astronomically observed, these observed molecules are found to be more stable with respect to other members of the group. Of the 47 observed molecules, 60% are odd number carbon chains. Interstellar chemistry is not actually driven by the the...

  19. Free enthalpies of replacing water molecules in protein binding pockets (United States)

    Riniker, Sereina; Barandun, Luzi J.; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F.


    Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH3 group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH3 at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.

  20. Evaluation of genotoxicity testing of FDA approved large molecule therapeutics. (United States)

    Sawant, Satin G; Fielden, Mark R; Black, Kurt A


    Large molecule therapeutics (MW>1000daltons) are not expected to enter the cell and thus have reduced potential to interact directly with DNA or related physiological processes. Genotoxicity studies are therefore not relevant and typically not required for large molecule therapeutic candidates. Regulatory guidance supports this approach; however there are examples of marketed large molecule therapeutics where sponsors have conducted genotoxicity studies. A retrospective analysis was performed on genotoxicity studies of United States FDA approved large molecule therapeutics since 1998 identified through the Drugs@FDA website. This information was used to provide a data-driven rationale for genotoxicity evaluations of large molecule therapeutics. Fifty-three of the 99 therapeutics identified were tested for genotoxic potential. None of the therapeutics tested showed a positive outcome in any study except the peptide glucagon (GlucaGen®) showing equivocal in vitro results, as stated in the product labeling. Scientific rationale and data from this review indicate that testing of a majority of large molecule modalities do not add value to risk assessment and support current regulatory guidance. Similarly, the data do not support testing of peptides containing only natural amino acids. Peptides containing non-natural amino acids and small molecules in conjugated products may need to be tested.

  1. Atoms, molecules and optical physics 2. Molecules and photons - Spectroscopy and collisions

    Energy Technology Data Exchange (ETDEWEB)

    Hertel, Ingolf V.; Schulz, Claus-Peter [Max-Born-Institut fuer Nichtlineare Optik und Kurzzeitspektroskopie im Forschungsverbund Berlin e.V. (Germany)


    This is the second volume of textbooks on atomic, molecular and optical physics, aiming at a comprehensive presentation of this highly productive branch of modern physics as an indispensable basis for many areas in physics and chemistry as well as in state of the art bio- and material-sciences. It primarily addresses advanced students (including PhD students), but in a number of selected subject areas the reader is lead up to the frontiers of present research. Thus even the active scientist is addressed. This volume 2 introduces lasers and quantum optics, while the main focus is on the structure of molecules and their spectroscopy, as well as on collision physics as the continuum counterpart to bound molecular states. The emphasis is always on the experiment and its interpretation, while the necessary theory is introduced from this perspective in a compact and occasionally somewhat heuristic manner, easy to follow even for beginners.

  2. Platelet Endothelial Cell Adhesion Molecule 1 (PECAM-1/CD31): A Multifunctional Vascular Cell Adhesion Molecule. (United States)

    Delisser, H M; Baldwin, H S; Albelda, S M


    PECAM-1/CD31 is a member of the immunoglobulin gene superfamily found on platelets, leukocytes, and endothelial cells, where it concentrates at cell-cell borders. It has been shown to both mediate cell-cell adhesion through homophilic and heterophilic interactions and to transduce intracellular signals that upregulate the function of integrins on leukocytes. Its cellular distribution and ability to mediate adhesive and signaling phenomena suggested that PECAM-1 was a multifunctional vascular cell adhesion molecule involved in leukocyte-endothelial and endothelial-endothelial interactions. These initial suggestions have been largely confirmed as recent studies have implicated PECAM-1 in the inflammatory process and in the formation of blood vessels. As our understanding of the molecular and functional properties of PECAM-1 grows, new insights will be gained that may have therapeutic implications for cardiovascular development and disease. (Trends Cardiovasc Med 1997;7:203-210). © 1997, Elsevier Science Inc.

  3. Resonant propagation of femtosecond laser pulse in DBASVP molecule:one-dimensional asymmetric organic molecule

    Institute of Scientific and Technical Information of China (English)

    Zhao Ke; Liu Ji-Cai; Wang Chuan-Kui; Luo Yi


    We have investigated the resonant propagation of femtosecond laser pulse in 4-trans-[p-(N, N-Di-n-butylamino)-p-stilbenyl vinyl] pyridine medium with permanent dipole moments. The electronic structures and parameters for the compound have been calculated by using density functional theory. In the optical regime, there is one charge-transfer state, and the molecule can thus be simplified as a two-level system. Both the one- and two-photon transitions occur between the ground and charge-transfer states. The numerical results show that the permanent dipole moments have an obvious effect on the propagation of the ultrashort pulse laser. The ideal self-induced transparency disappears for 2π pulse, and second harmonic spectral components occur significantly due to the two-photon absorption process. For the 6π pulse, continuum frequency generation is produced and a shorter duration pulse in time domain with 465 as is obtained.

  4. Mechanical response of collagen molecule under hydrostatic compression

    Energy Technology Data Exchange (ETDEWEB)

    Saini, Karanvir, E-mail:; Kumar, Navin


    Proteins like collagen are the basic building blocks of various body tissues (soft and hard). Collagen molecules find their presence in the skeletal system of the body where they bear mechanical loads from different directions, either individually or along with hydroxy-apatite crystals. Therefore, it is very important to understand the mechanical behavior of the collagen molecule which is subjected to multi-axial state of loading. The estimation of strains of collagen molecule along different directions resulting from the changes in hydrostatic pressure magnitude, can provide us new insights into its mechanical behavior. In the present work, full atomistic simulations have been used to study global (volumetric) as well as local (along different directions) mechanical properties of the hydrated collagen molecule which is subjected to different hydrostatic pressure magnitudes. To estimate the local mechanical properties, the strains of collagen molecule along its longitudinal and transverse directions have been acquired at different hydrostatic pressure magnitudes. In spite of non-homogeneous distribution of atoms within the collagen molecule, the calculated values of local mechanical properties have been found to carry the same order of magnitude along the longitudinal and transverse directions. It has been demonstrated that the values of global mechanical properties like compressibility, bulk modulus, etc. as well as local mechanical properties like linear compressibility, linear elastic modulus, etc. are functions of magnitudes of applied hydrostatic pressures. The mechanical characteristics of collagen molecule based on the atomistic model have also been compared with that of the continuum model in the present work. The comparison showed up orthotropic material behavior for the collagen molecule. The information on collagen molecule provided in the present study can be very helpful in designing the future bio-materials.

  5. Electron transmission through a class of anthracene aldehyde molecules (United States)

    Petreska, Irina; Ohanesjan, Vladimir; Pejov, Ljupco; Kocarev, Ljupco


    Transmission of electrons via metal-molecule-metal junctions, involving rotor-stator anthracene aldehyde molecules is investigated. Two model barriers having input parameters evaluated from accurate ab initio calculations are proposed and the transmission coefficients are obtained by using the quasiclassical approximation. Transmission coefficients further enter in the integral for the net current, utilizing Simmons' method. Conformational dependence of the tunneling processes is evident and the presence of the side groups enhances the functionality of the future single-molecule based electronic devices.

  6. Multiple Ionic-Covalent Couplings in Molecules and Clusters

    Institute of Scientific and Technical Information of China (English)

    GwangHi Jeung


    The electronic states of molecules made of electropositive and electronegative components result from the interfcrence between the covalent configurations and the ionic configurations.This work shows complex aspects of these ionic-covalent couplings in small molecules such as Li2H, Li2F, and Li4F. The extension of this type of analysis to the adsorption of the electrophilic molecules on the metal clusters or on the metal surfaces is supposed to lead to a radically new interpretation of the observed physical and chemical properties.

  7. Screening in resonant X-ray emission of molecules

    DEFF Research Database (Denmark)

    Ågren, Hans; Luo, Yi; Gelmukhanov, Faris;


    We explore the effects of screening in resonant X-ray emission from molecules by means of unconstrained multi-configurational self-consistent field optimizations of each state involved in the resonant and nonresonant X-ray processes. It is found that, although screening can produce shifts...... in transition energies of a few eV, its effect on the transition intensities is relatively minor. Using results from the investigated molecules, we find that the screening is quite dependent on the type of molecule - saturated versus unsaturated - and on the core site, but depends little on the particular core...

  8. Recording Intramolecular Mechanics during the Manipulation of a Large Molecule (United States)

    Moresco, Francesca; Meyer, Gerhard; Rieder, Karl-Heinz; Tang, Hao; Gourdon, André; Joachim, Christian


    The technique of single atom manipulation by means of the scanning tunneling microscope (STM) applies to the controlled displacement of large molecules. By a combined experimental and theoretical work, we show that in a constant height mode of manipulation the STM current intensity carries detailed information on the internal mechanics of the molecule when guided by the STM tip. Controlling and time following the intramolecular behavior of a large molecule on a surface is the first step towards the design of molecular tunnel-wired nanorobots.

  9. Stochastic single-molecule dynamics of synaptic membrane protein domains

    CERN Document Server

    Kahraman, Osman; Haselwandter, Christoph A


    Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic proteins provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the single-molecule trajectories observed for synaptic proteins, and spatially inhomogeneous protein lifetimes at the cell membrane. Our results suggest that central aspects of the single-molecule and collective dynamics observed for membrane protein domains can be understood in terms of stochastic reaction-diffusion processes at the cell membrane.

  10. Photoassociative Production and Trapping of Ultracold KRb Molecules

    CERN Document Server

    Wang, D; Stone, M F; Nikolayeva, O; Wang, H; Hattaway, B; Gensemer, S D; Gould, P L; Eyler, E E; Stwalley, W C


    We have produced ultracold heteronuclear KRb molecules by the process of photoassociation in a two-species magneto-optical trap. Following decay of the photoassociated KRb*, the molecules are detected using two-photon ionization and time-of-flight mass spectroscopy of KRb$^+$. A portion of the metastable triplet molecules thus formed are magnetically trapped. Photoassociative spectra down to 91 cm$^{-1}$ below the K(4$s$) + Rb (5$p_{1/2}$) asymptote have been obtained. We have made assignments to all eight of the attractive Hund's case (c) KRb* potential curves in this spectral region.

  11. Electrochemical proton relay at the single-molecule level

    DEFF Research Database (Denmark)

    Kuznetsov, A. M.; Medvedev, I. G.; Ulstrup, Jens


    A scheme for the experimental study of single-proton transfer events, based on proton-coupled two-electron transfer between a proton donor and a proton acceptor molecule confined in the tunneling gap between two metal leads in electrolyte solution is suggested. Expressions for the electric current...... are derived and compared with formalism for electron tunneling through redox molecules. The scheme allows studying the kinetics of proton and hydrogen atom transfer as well as kinetic isotope effects at the single-molecule level under electrochemical potential control....

  12. Recent progress in electron scattering from atoms and molecules

    Energy Technology Data Exchange (ETDEWEB)

    Brunger, M. J. [Centre for Antimatter-Matter Studies, CAPS, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia and Institute of Mathematical Sciences, University of Malaya, Kuala Lumpur (Malaysia); Buckman, S. J. [Institute of Mathematical Sciences, University of Malaya, Kuala Lumpur, Malaysia and Centre for Antimatter-Matter Studies, AMPL, Australian National University, Canberra, ACT 0200 (Australia); Sullivan, J. P.; Palihawadana, P. [Centre for Antimatter-Matter Studies, AMPL, Australian National University, Canberra, ACT 0200 (Australia); Jones, D. B. [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001 (Australia); Chiari, L.; Pettifer, Z. [Centre for Antimatter-Matter Studies, CAPS, Flinders University, GPO Box 2100, Adelaide, SA 5001 (Australia); Silva, G. B. da [Centre for Antimatter-Matter Studies, CAPS, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia and Universidade Federal de Mato Grosso, Barra do Garças, Mato Grosso (Brazil); Lopes, M. C. A. [Centre for Antimatter-Matter Studies, CAPS, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia and Departamento de Fisica, Universidade Federal de Juiz de Fora, Juiz de Fora, MG (Brazil); Duque, H. V. [Departamento de Fisica, Universidade Federal de Juiz de Fora, Juiz de Fora, MG (Brazil); Masin, Z.; Gorfinkiel, J. D. [Department of Physical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA (United Kingdom); Garcia, G. [Instituto de Fisica Fundamental, CSIC, Madrid E-28006 (Spain); Hoshino, M.; Tanaka, H. [Department of Physics, Sophia University, Tokyo, 102-8554 (Japan); Limão-Vieira, P. [Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal)


    We present and discuss recent results, both experimental and theoretical (where possible), for electron impact excitation of the 3s[3/2 ]{sub 1} and 3s′[1/2 ]{sub 1} electronic states in neon, elastic electron scattering from the structurally similar molecules benzene, pyrazine, and 1,4-dioxane and excitation of the electronic states of the important bio-molecule analogue α-tetrahydrofurfuryl alcohol. While comparison between theoretical and experimental results suggests that benchmarked cross sections for electron scattering from atoms is feasible in the near-term, significant further theoretical development for electron-molecule collisions, particularly in respect to discrete excitation processes, is still required.

  13. Recent progress in molecule modification with heavy ion beam irradiation

    Institute of Scientific and Technical Information of China (English)


    The research into heavy ion beam biology started in the 1960s, and so far it has become an important interdisciplinary study. Heavy ion beam is more suitable for molecule modification than other sorts of radiation, for it has many superiorities such as the energy transfer effect and the mass deposition effect. Molecule modification with heavy ion beam irradiation can be applied to developing new medicines and their precursors, genetic engineering, protein engi neering, outer space radiobiology, etc. Retrospect and prospect of the research and development of molecule modifica tion with heavy ion beam irradiation are given.

  14. Detection of Ordered Molecules Adsorbed on Graphene: a Theoretical Study (United States)

    Wang, Yong; Zhang, Xue-Qing; Li, Hui


    Graphene has been demonstrated to be able to detect individual gas molecules [Schedin et al. Nat. Mater. 6 (2007) 652], which has attracted a lot of sensor research activities. Here we report for the first time that graphene is capable of detecting the ordering degree of absorbed water molecules. The efficiency of doping varies from the degrees of molecular ordering. The simulated results show that the highly ordered water molecules contribute more to the doping effect, which reduces the conductance of the water/graphene system.

  15. Self-assembly patterning of organic molecules on a surface

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Minghu; Fuentes-Cabrera, Miguel; Maksymovych, Petro; Sumpter, Bobby G.; Li, Qing


    The embodiments disclosed herein include all-electron control over a chemical attachment and the subsequent self-assembly of an organic molecule into a well-ordered three-dimensional monolayer on a metal surface. The ordering or assembly of the organic molecule may be through electron excitation. Hot-electron and hot-hole excitation enables tethering of the organic molecule to a metal substrate, such as an alkyne group to a gold surface. All-electron reactions may allow a direct control over the size and shape of the self-assembly, defect structures and the reverse process of molecular disassembly from single molecular level to mesoscopic scale.

  16. Laser-coolable polyatomic molecules with heavy nuclei

    CERN Document Server

    Isaev, T A; Eliav, E


    Recently a number of diatomic and polyatomics molecules has been identified as a prospective systems for Doppler cooling. Polyatomic molecules with heavy nuclei present great interest for search for new physics outside of Standard Model and a large variety of other applications including cold chemistry, quantum informatics etc. Herein we propose radium monohydroxide molecule (RaOH) which is on the one hand amenable for Doppler cooling and on the other hand has considerable potential for searching for $\\cal P$-odd and $\\cal P,T$-odd effects.

  17. Stability of the Hydrogen and Hydrogen-like Molecules


    Richard, Jean-Marc


    We present a simple proof of the stability of the hydrogen molecule $(M^+M^+m^-m^-)$. It does not rely on the proton-to-electron mass ratio $M/m$ being very large, and actually holds for arbitrary values of $M/m$. Some asymmetric molecules of the type $(m_1^+m_2^+m_3^-m_4^-)$ are also stable. Possible applications to molecules containing antiparticles and to exotic hadrons in the quark model are briefly outlined. Revtex Version 3.0, 4 Figures available on request by Fax or Mail.

  18. Phase Transition Induced by Small Molecules in Confined Copolymer Films

    Institute of Scientific and Technical Information of China (English)

    ZHOU Ling


    We investigate the phase transition induced by small molecules in confined copolymer films by using density functional theory.It is found that the addition of small molecules can effectively promote the phase separation of copolymers.In a symmetric diblock copolymer film,the affinity and concentration of small molecules play an important role in the structure transjtions.The disordered-lamellar transitions lamellar-lamellar transitions and the re-entrant transitions of the same structures are observed.Our results have potential applications in the fabrication of new functional materials.

  19. Dust-forming molecules in VY Canis Majoris (and Betelgeuse)

    CERN Document Server

    Kaminski, T; Schmidt, M R; Patel, N A; Young, K H; Menten, K M; Brunken, S; Muller, H S P; Winters, J M; McCarthy, M C


    The formation of inorganic dust in circumstellar environments of evolved stars is poorly understood. Spectra of molecules thought to be most important for the nucleation, i.e. AlO, TiO, and TiO2, have been recently detected in the red supergiant VY CMa. These molecules are effectively formed in VY CMa and the observations suggest that non-equilibrium chemistry must be involved in their formation and nucleation into dust. In addition to exploring the recent observations of VY CMa, we briefly discuss the possibility of detecting these molecules in the dust-poor circumstellar environment of Betelgeuse.

  20. The art of catching and probing single molecules


    Kumar, Avijit


    This thesis presents several studies performed in the field of “molecular electronics” using scanning tunneling microscopy (STM) and spectroscopy. We have investigated electronic (transport) properties of a single octanethiol, a single CuPc molecule and molecular assemblies of ß–cyclodextrin (ß-CD) molecules immobilized on Pt/Ge(001), Au/Ge(001), and Au(111) substrates, respectively. A single octanethiol molecule is trapped between an STM tip and Pt/Ge(001) substrate, and the transport proper...

  1. Proposal for Laser Cooling of Complex Polyatomic Molecules. (United States)

    Kozyryev, Ivan; Baum, Louis; Matsuda, Kyle; Doyle, John M


    An experimentally feasible strategy for direct laser cooling of polyatomic molecules with six or more atoms is presented. Our approach relies on the attachment of a metal atom to a complex molecule, where it acts as an active photon cycling site. We describe a laser cooling scheme for alkaline earth monoalkoxide free radicals taking advantage of the phase space compression of a cryogenic buffer-gas beam. Possible applications are presented including laser cooling of chiral molecules and slowing of molecular beams using coherent photon processes.

  2. Laser cooling of internal degrees of freedom of molecules (United States)

    Horchani, R.


    Optical pumping techniques using laser fields combined with photo-association of ultracold atoms leads to control of the vibrational and/or rotational population of molecules. In this study, we review the basic concepts and main steps that should be followed, including the excitation schemes and detection techniques used to achieve ro-vibrational cooling of Cs2 molecules. We also discuss the extension of this technique to other molecules. In addition, we present a theoretical model used to support the experiment. These simulations can be widely used for the preparation of various experiments because they allow the optimization of several important experimental parameters.

  3. Human thymic epithelial cells express functional HLA-DP molecules

    DEFF Research Database (Denmark)

    Jørgensen, A; Röpke, C; Nielsen, M


    T lymphocytes, we examined whether human thymic epithelial cells (TEC) expressed HLA-DP molecules. We present evidence that TEC obtained from short time culture express low but significant levels of HLA-DP molecules. The expression of HLA-DP molecules was comparable to or higher than the expression...... of HLA-DP allospecific primed lymphocyte typing (PLT) CD4 T cell lines. IFN-gamma treatment strongly upregulated the HLA-DP allospecific PLT responses whereas other PLT responses remained largely unchanged. In conclusion, these data indicate that human thymus epithelial cells express significant levels...

  4. Recording Intramolecular Mechanics during the Manipulation of a Large Molecule

    Energy Technology Data Exchange (ETDEWEB)

    Moresco, Francesca; Meyer, Gerhard; Rieder, Karl-Heinz; Tang, Hao; Gourdon, Andre; Joachim, Christian


    The technique of single atom manipulation by means of the scanning tunneling microscope (STM) applies to the controlled displacement of large molecules. By a combined experimental and theoretical work, we show that in a constant height mode of manipulation the STM current intensity carries detailed information on the internal mechanics of the molecule when guided by the STM tip. Controlling and time following the intramolecular behavior of a large molecule on a surface is the first step towards the design of molecular tunnel-wired nanorobots.

  5. Recording intramolecular mechanics during the manipulation of a large molecule. (United States)

    Moresco, F; Meyer, G; Rieder, K H; Tang, H; Gourdon, A; Joachim, C


    The technique of single atom manipulation by means of the scanning tunneling microscope (STM) applies to the controlled displacement of large molecules. By a combined experimental and theoretical work, we show that in a constant height mode of manipulation the STM current intensity carries detailed information on the internal mechanics of the molecule when guided by the STM tip. Controlling and time following the intramolecular behavior of a large molecule on a surface is the first step towards the design of molecular tunnel-wired nanorobots.

  6. Microcanonical distribution for one-electron triatomic molecules

    CERN Document Server

    Lazarou, C; Emmanouilidou, A


    We formulate a microcanonical distribution for an arbitrary one-electron triatomic molecule. This distribution can be used to describe the initial state in strongly-driven two-electron triatomic molecules. Namely, in many semiclassical models that describe ionization of two-electron molecules driven by intense infrared laser fields in the tunneling regime initially one electron tunnels while the other electron is bound. The microcanonical distribution presented in this work can be used to describe the initial state of this bound electron.

  7. Electron Scattering From Atoms, Molecules, Nuclei, and Bulk Matter

    CERN Document Server

    Whelan, Colm T


    Topics that are covered include electron scattering in the scanning TEM; basic theory of inelastic electron imaging; study of confined atoms by electron excitation; helium bubbles created in extreme pressure with application to nuclear safety; lithium ion implantation; electron and positron scattering from clusters; electron scattering from physi- and chemi-absorbed molecules on surfaces; coincidence studies; electron scattering from biological molecules; electron spectroscopy as a tool for environmental science; electron scattering in the presence of intense fields; electron scattering from astrophysical molecules; electon interatctions an detection of x-ray radiation.

  8. The Magnetic Shielding Polarizabilities of Some Tetrahedral Molecules

    Directory of Open Access Journals (Sweden)

    Paul Chittenden


    Full Text Available TMS is the commonest standard reference for both protons and 13C NMR spectroscopy. The Magnetic Shielding and its Polarizabilities, plus the static polarizability have been calculated for TMS, tetramethyl ammonium cation and 2,2-dimethylpropane. An investigation of continuum solvation effects on these highly symmetrical molecules, whose first surviving electric moment is the octopole, showed interaction with solvent makes little change to these magnetic properties. This small change is however consistent with both the high symmetry of the molecules and the available extensive experimental data for TMS. A rationalization of the signs and magnitudes of A in a sequence of related molecules has been suggested.

  9. Large scale study of multiple-molecule queries

    Directory of Open Access Journals (Sweden)

    Nasr Ramzi J


    Full Text Available Abstract Background In ligand-based screening, as well as in other chemoinformatics applications, one seeks to effectively search large repositories of molecules in order to retrieve molecules that are similar typically to a single molecule lead. However, in some case, multiple molecules from the same family are available to seed the query and search for other members of the same family. Multiple-molecule query methods have been less studied than single-molecule query methods. Furthermore, the previous studies have relied on proprietary data and sometimes have not used proper cross-validation methods to assess the results. In contrast, here we develop and compare multiple-molecule query methods using several large publicly available data sets and background. We also create a framework based on a strict cross-validation protocol to allow unbiased benchmarking for direct comparison in future studies across several performance metrics. Results Fourteen different multiple-molecule query methods were defined and benchmarked using: (1 41 publicly available data sets of related molecules with similar biological activity; and (2 publicly available background data sets consisting of up to 175,000 molecules randomly extracted from the ChemDB database and other sources. Eight of the fourteen methods were parameter free, and six of them fit one or two free parameters to the data using a careful cross-validation protocol. All the methods were assessed and compared for their ability to retrieve members of the same family against the background data set by using several performance metrics including the Area Under the Accumulation Curve (AUAC, Area Under the Curve (AUC, F1-measure, and BEDROC metrics. Consistent with the previous literature, the best parameter-free methods are the MAX-SIM and MIN-RANK methods, which score a molecule to a family by the maximum similarity, or minimum ranking, obtained across the family. One new parameterized method introduced in

  10. Supramolecular Photochemistry in Solution and on Surfaces: Encapsulation and Dynamics of Guest Molecules and Communication between Encapsulated and Free Molecules. (United States)

    Ramamurthy, V; Jockusch, Steffen; Porel, Mintu


    Supramolecular assemblies that help to preorganize reactant molecules have played an important role in the development of concepts related to the control of excited-state processes. This has led to a persistent search for newer supramolecular systems (hosts), and this review briefly presents our work with octa acid (OA) to a host to control excited-state processes of organic molecules. Octa acid, a water-soluble host, forms 1:1, 2:1, and 2:2 (host-guest) complexes with various organic molecules. A majority of the guest molecules are enclosed within a capsule made up of two molecules of OA whereas OA by itself remains as a monomer or aggregates. Luminescence and (1)H NMR spectroscopy help to characterize the structure and dynamics of these host-guest complexes. The guest molecule as well as the host-guest complex as a whole undergoes various types of motion, suggesting that the guests possess freedom inside the confined space of the octa acid capsule. In addition, the confined guests are not isolated but are able to communicate (energy, electron, and spin) with molecules present closer to the capsule. The host-guest complexes are stable even on solid surfaces such as silica, clay, α-Zr phosphate, TiO2, and gold nanoparticles. This opens up new opportunities to explore the interaction between confined guests and active surfaces of TiO2 and gold nanoparticles. In addition, this allows the possibility of performing energy and electron transfer between organic molecules that do not adsorb on inert surfaces of silica, clay, or α-Zr phosphate. The results summarized here, in addition to providing a fundamental understanding of the behavior of molecules in a confined space provided by the host OA, are likely to have a long-range effect on the capture and release of solar energy.

  11. PREFACE: Nanoelectronics, sensors and single molecule biophysics Nanoelectronics, sensors and single molecule biophysics (United States)

    Tao, Nongjian


    This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar

  12. Coherent spectroscopy in the single molecule limit (Conference Presentation) (United States)

    Potma, Eric O.; Crampton, Kevin; Fast, Alex; Alfonso García, Alba; Apkarian, Vartkess A.


    Surface enhanced Raman scattering (SERS) is a popular technique for detecting and analyzing molecules at very low concentrations. The sensitivity of SERS is high enough to detect single molecules. It has proven difficult, however, to perform similar measurements in the so-called nonlinear optical regime, a regime in which the molecule is responding to multiple light pulses. Nonetheless, recent experiments indicate that after careful optimization, it is possible to generate signals derived from nonlinear analogs of SERS. Such measurements make it possible to view molecular vibrations in real time, which amounts to the femto- to pico-second range. In this contribution, we discuss in detail under which conditions detectable surface-enhanced coherent Raman signals can be expected, provide experimental evidence of coherent Raman scattering of single molecules, and highlight the unique information that can be attained from such measurements.

  13. Forces and conductances in a single-molecule bipyridine junction

    DEFF Research Database (Denmark)

    Stadler, Robert; Thygesen, Kristian Sommer; Jacobsen, Karsten Wedel


    Inspired by recent measurements of forces and conductances of bipyridine nanojunctions, we have performed density functional theory calculations of structure and electron transport in a bipyridine molecule attached between gold electrodes for seven different contact geometries. The calculations...

  14. Single Molecule Scanning of DNA Radiation Oxidative Damage Project (United States)

    National Aeronautics and Space Administration — This proposal will develop an assay to map genomic DNA, at the single molecule level and in a nanodevice, for oxidative DNA damage arising from radiation exposure;...

  15. Single Molecule Spectroscopy of Monomeric LHCII: Experiment and Theory

    CERN Document Server

    Malý, Pavel; van Grondelle, Rienk; Mančal, Tomáš


    We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlo...

  16. Trajectory Dynamics of Gas Molecules and Galaxy Formation

    CERN Document Server

    Llanos, Pedro J; Hintz, Gerald R


    The probability distribution of the velocity of gas molecules in a closed container is described by the kinetic theory of gases. When molecules collide or impact the walls of a container, they exchange energy and momentum in accordance with Newton's laws of motion. Between collisions, the trajectory of individual molecules is a straight line, neglecting gravity. During the formation of a galaxy, the stars are constrained to a region of space and exchange energy and momentum in a manner similar to molecules. In this paper, an exact model of an ideal gas is derived and analyzed to determine the probability distribution of the molecular velocities, which are then compared with the probability distribution of velocities associated with stars during galaxy formation.

  17. Orientation of KRb molecules in a switched electrostatic field

    Institute of Scientific and Technical Information of China (English)

    Huang Yun-Xia; Xu Shu-Wu; Yang Xiao-Hua


    We theoretically investigate the orientation of the cold KRb molecules induced in a switched electrostatic field by numerically solving the full time-dependent Schr(o)dinger equation.The results show that the periodic field-free molecular orientation can be realized for the KRb molecules by rapidly switching off the electrostatic field.Meanwhile,by varying the switching times of the electrostatic field,the adiabatic and nonadiabatic interactions of the molecules with the applied field can be realized.Moreover,the influences of the electrostatic field strength and the rotational temperature to the degree of the molecular orientation are studied.The investigations show that increasing the electrostatic field will increase the degree of the molecular orientation,both in the constant-field regime and in the field-free regime,while the increasing of the rotational temperature of the cold molecules will greatly decrease the degree of the molecular orientation.

  18. Optical Stark decelerator for molecules with a traveling potential well (United States)

    Deng, Lianzhong; Hou, Shunyong; Yin, Jianping


    We propose a versatile scheme to slow supersonically cooled molecules using a decelerating potential well, obtained by steering a focusing laser beam onto a pair of spinning reflective mirrors under a high-speed brake. The longitudinal motion of molecules in the moving red-detuned light field is analyzed and their corresponding phase-space stability is investigated. Trajectories of C H4 molecules under the influence of the potential well are simulated using the Monte Carlo method. For instance, with a laser beam of power 20 kW focused onto a spot of waist radius 40-100 μm, corresponding to a peak laser intensity on the order of ˜108W /c m2 , a C H4 molecule of ˜250 m /s can be decelerated to ˜10 m /s over a distance of a few centimeters on a time scale of hundreds of microseconds.

  19. Asymptotic behavior of subradiant states in homonuclear diatomic molecules

    CERN Document Server

    McGuyer, Bart H; Iwata, Geoffrey Z; Tarallo, Marco G; Skomorowski, Wojciech; Moszynski, Robert; Zelevinsky, Tanya


    Weakly bound molecules have physical properties without atomic analogues, even as the bond length approaches dissociation. In particular, the internal symmetries of homonuclear diatomic molecules result in the formation of two-body superradiant and subradiant excited states. While superradiance has been demonstrated in a variety of systems, subradiance is more elusive due to the inherently weak interaction with the environment. Transition mechanisms that are strictly forbidden for atoms become allowed just below the dissociation asymptote due to new selection rules associated with the subradiant states. Here we directly probe deeply subradiant states in ultracold diatomic strontium molecules and characterize their properties near the intercombination atomic asymptote via optical spectroscopy of doubly-forbidden transitions with intrinsic quality factors exceeding 10^(13). This precision measurement of subradiance is made possible by tightly trapping the molecules in a state-insensitive optical lattice and ach...

  20. Bioactive molecules: current trends in discovery, synthesis, delivery and testing

    Directory of Open Access Journals (Sweden)

    Yew Beng Kang


    Full Text Available Important bioactive molecules are moleculesthat are pharmacologically active derived from naturalsources and through chemical synthesis. Over the yearsmany of such molecules have been discovered throughbioprospective endeavours. The discovery of taxol fromthe pacific yew tree bark that has the ability in stabilisingcellular microtubules represents one of the hallmarks ofsuccess of such endeavours. In recent years, the discoveryprocess has been aided by the rapid developmentof techniques and technologies in chemistry andbiotechnology. The progress in advanced genetics andcomputational biology has also transformed the wayhypotheses are formulated as well as the strategies for drugdiscovery. Of equal importance is the use of advanceddrug delivery vehicles in enhancing the efficacy andbioavailability of bioactive molecules. The availability ofsuitable animal models for testing and validation is yetanother major determinant in increasing the prospect forclinical trials of bioactive molecules.

  1. Preparation of cold molecules for high-precision measurements (United States)

    Wall, T. E.


    Molecules can be used to test fundamental physics. Such tests often require cold molecules for detailed spectroscopic analysis. Cooling internal degrees of freedom provides a high level of state-selectivity, with large populations in the molecular states of interest. Cold translational motion allows slow, bright beams to be created, allowing long interaction times. In this tutorial article we describe the common techniques for producing cold molecules for high-precision spectroscopy experiments. For each technique we give examples of its application in experiments that use molecular structure to probe fundamental physics, choosing one experiment in particular as a case study. We then discuss a number of new techniques, some currently under development, others proposed, that promise high flux sources of cold molecules applicable to precise spectroscopic tests of fundamental physics.

  2. Exohedral and skeletal rearrangements in the molecules of fullerene derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Ignat' eva, Daria V; Ioffe, I N; Troyanov, Sergey I; Sidorov, Lev N [Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow (Russian Federation)


    The data on the migration of monoatomic addends, perfluoroalkyl and more complex organic groups in the molecules of fullerene derivatives published mainly in the last decade are analyzed. Skeletal rearrangements of the carbon cage occurring during chemical reactions are considered.

  3. Differentiating Alzheimer disease-associated aggregates with small molecules. (United States)

    Honson, Nicolette S; Johnson, Ronald L; Huang, Wenwei; Inglese, James; Austin, Christopher P; Kuret, Jeff


    Alzheimer disease is diagnosed postmortem by the density and spatial distribution of beta-amyloid plaques and tau-bearing neurofibrillary tangles. The major protein component of each lesion adopts cross-beta-sheet conformation capable of binding small molecules with submicromolar affinity. In many cases, however, Alzheimer pathology overlaps with Lewy body disease, characterized by the accumulation of a third cross-beta-sheet forming protein, alpha-synuclein. To determine the feasibility of distinguishing tau aggregates from beta-amyloid and alpha-synuclein aggregates with small molecule probes, a library containing 72,455 small molecules was screened for antagonists of tau-aggregate-mediated changes in Thioflavin S fluorescence, followed by secondary screens to distinguish the relative affinity for each substrate protein. Results showed that >10-fold binding selectivity among substrates could be achieved, with molecules selective for tau aggregates containing at least three aromatic or rigid moieties connected by two rotatable bonds.

  4. Deflection of Rotating Symmetric Molecules by Inhomogeneous Fields

    CERN Document Server

    Gershnabel, Erez


    We consider deflection of rotating symmetric molecules by inhomogeneous optical and static electric fields, compare results with the case of linear molecules, and find new singularities in the distribution of the scattering angle. Scattering of the prolate/oblate molecules is analyzed in detail, and it is shown that the process can be efficiently controlled by means of short and strong femtosecond laser pulses. In particular, the angular dispersion of the deflected molecules may be dramatically reduced by laser-induced molecular pre-alignment. We first study the problem by using a simple classical model, and then find similar results by means of more sophisticated methods, including the formalism of adiabatic invariants and direct numerical simulation of the Euler-Lagrange equations of motion. The suggested control scheme opens new ways for many applications involving molecular focusing, guiding, and trapping by optical and static fields.

  5. Quantum-State Controlled Chemical Reactions of Ultracold KRb Molecules

    CERN Document Server

    Ospelkaus, S; Wang, D; de Miranda, M H G; Neyenhuis, B; Quéméner, G; Julienne, P S; Bohn, J L; Jin, D S; Ye, J


    How does a chemical reaction proceed at ultralow temperatures? Can simple quantum mechanical rules such as quantum statistics, single scattering partial waves, and quantum threshold laws provide a clear understanding for the molecular reactivity under a vanishing collision energy? Starting with an optically trapped near quantum degenerate gas of polar $^{40}$K$^{87}$Rb molecules prepared in their absolute ground state, we report experimental evidence for exothermic atom-exchange chemical reactions. When these fermionic molecules are prepared in a single quantum state at a temperature of a few hundreds of nanoKelvins, we observe p-wave-dominated quantum threshold collisions arising from tunneling through an angular momentum barrier followed by a near-unity probability short-range chemical reaction. When these molecules are prepared in two different internal states or when molecules and atoms are brought together, the reaction rates are enhanced by a factor of 10 to 100 due to s-wave scattering, which does not ...

  6. Non-destructive Imaging of Individual Bio-Molecules

    CERN Document Server

    Germann, Matthias; Escher, Conrad; Fink, Hans-Werner


    Radiation damage is considered to be the major problem that still prevents imaging an individual biological molecule for structural analysis. So far, all known mapping techniques using sufficient short wave-length radiation, be it X-rays or high energy electrons, circumvent this problem by averaging over many molecules. Averaging, however, leaves conformational details uncovered. Even the anticipated use of ultra-short but extremely bright X-ray bursts of a Free Electron Laser shall afford averaging over 10^6 molecules to arrive at atomic resolution. Here we present direct experimental evidence for non-destructive imaging of individual DNA molecules. In fact, we show that DNA withstands coherent low energy electron radiation with deBroglie wavelength in the Angstrom regime despite a vast dose of 10^8 electrons/nm^2 accumulated over more than one hour.

  7. Formation and dissociation of dust molecules in dusty plasma (United States)

    Yan, Jia; Feng, Fan; Liu, Fucheng; Dong, Lifang; He, Yafeng


    Dust molecules are observed in a dusty plasma experiment. By using measurements with high spatial resolution, the formation and dissociation of the dust molecules are studied. The ion cloud in the wake of an upper dust grain attracts the lower dust grain nearby. When the interparticle distance between the upper dust grain and the lower one is less than a critical value, the two dust grains would form a dust molecule. The upper dust grain always leads the lower one as they travel. When the interparticle distance between them is larger than the critical value, the dust molecule would dissociate. Project supported by the National Natural Science Foundation of China (Grant Nos. 11205044 and 11405042), the Natural Science Foundation of Hebei Province, China (Grant Nos. A2011201006 and A2012201015), the Research Foundation of Education Bureau of Hebei Province, China (Grant No. Y2012009), the Program for Young Principal Investigators of Hebei Province, China, and the Midwest Universities Comprehensive Strength Promotion Project, China.

  8. Coupling of Photonic and Electronic Spin Catalyzed by Diatomic Molecules (United States)

    Gay, Timothy


    Recent experiments involving the collisions of polarized photons or polarized electrons with simple diatomic molecules have shown novel ways in which the net spin of electrons can be converted into the net spin of photons following the collisions, or vice versa. I will discuss three recent experiments that illustrate such transformations: the production of nuclear rotational spin in nitrogen molecules excited by polarized electrons with the subsequent emission of polarized photons, the excitation by polarized electrons of rotational eigenstates of hydrogen molecules and the subsequent emission of circularly-polarized light, and the photolysis of hydrogen molecules by circularly-polarized light yielding photofragments that ``spin the wrong way.'' To our knowledge, these latter measurements represent the first observation of photofragment orientation by direct observation of the polarization of the photofragment fluoresence. Work supported by the NSF through grant PHY-0821385, the DOE through the use of the ALS at LBL, and ANSTO (Access to Major Research Facilities Programme).

  9. Rotational state detection of electrically trapped polyatomic molecules

    CERN Document Server

    Glöckner, Rosa; Rempe, Gerhard; Zeppenfeld, Martin


    Detecting the internal state of polar molecules is a substantial challenge when standard techniques such as resonance-enhanced multi photon ionization (REMPI) or laser-induced fluorescense (LIF) do not work. As this is the case for most polyatomic molecule species, we here investigate an alternative based on state selective removal of molecules from an electrically trapped ensemble. Specifically, we deplete molecules by driving rotational and/or vibrational transitions to untrapped states. Fully resolving the rotational state with this method can be a considerable challenge as the frequency differences between various transitions is easily substantially less than the Stark broadening in an electric trap. However, making use of a unique trap design providing homogeneous fields in a large fraction of the trap volume, we successfully discriminate all rotational quantum numbers, including the rotational M-substate.

  10. Single-molecule emulsion PCR in microfluidic droplets. (United States)

    Zhu, Zhi; Jenkins, Gareth; Zhang, Wenhua; Zhang, Mingxia; Guan, Zhichao; Yang, Chaoyong James


    The application of microfluidic droplet PCR for single-molecule amplification and analysis has recently been extensively studied. Microfluidic droplet technology has the advantages of compartmentalizing reactions into discrete volumes, performing highly parallel reactions in monodisperse droplets, reducing cross-contamination between droplets, eliminating PCR bias and nonspecific amplification, as well as enabling fast amplification with rapid thermocycling. Here, we have reviewed the important technical breakthroughs of microfluidic droplet PCR in the past five years and their applications to single-molecule amplification and analysis, such as high-throughput screening, next generation DNA sequencing, and quantitative detection of rare mutations. Although the utilization of microfluidic droplet single-molecule PCR is still in the early stages, its great potential has already been demonstrated and will provide novel solutions to today's biomedical engineering challenges in single-molecule amplification and analysis.

  11. Single Molecule Imaging in Living Cell with Optical Method

    Institute of Scientific and Technical Information of China (English)


    Significance, difficult, international developing actuality and our completed works for single molecules imaging in living cell with optical method are described respectively. Additionally we give out some suggestions for the technology development further.

  12. Isolated menthone reductase and nucleic acid molecules encoding same (United States)

    Croteau, Rodney B; Davis, Edward M; Ringer, Kerry L


    The present invention provides isolated menthone reductase proteins, isolated nucleic acid molecules encoding menthone reductase proteins, methods for expressing and isolating menthone reductase proteins, and transgenic plants expressing elevated levels of menthone reductase protein.

  13. Probing the Conformations of Single Molecule via Photon Counting Statistics

    CERN Document Server

    Peng, Yonggang; Yang, Chuanlu; Zheng, Yujun


    We suggest an approach to detect the conformation of single molecule by using the photon counting statistics. The generalized Smoluchoswki equation is employed to describe the dynamical process of conformational change of single molecule. The resonant trajectories of the emission photon numbers $$ and the Mandel's $Q$ parameter, in the space of conformational coordinates $\\bm{\\mathcal{X}}$ and frequency $\\omega_L$ of external field ($\\bm{\\mathcal{X}}-\\omega_L$ space), can be used to rebuild the conformation of the single molecule. As an example, we consider Thioflavin T molecule. It demonstrates that the results of conformations extracted by employing the photon counting statistics is excellent agreement with the results of {\\it ab initio} computation.

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

    CERN Document Server

    Gräslund, Astrid; Widengren, Jerker


    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.

  15. Ultracold Molecules in Lattices for Metrology and Precision Measurements (United States)

    Reinaudi, Gael; Osborn, Chris; McDonald, Mickey; Wang, Dili; Zelevinsky, Tanya


    Ultracold diatomic molecules offer exciting possibilities for studies of novel states of matter, quantum information, and metrology. Two-electron-atom based molecules are particularly promising for precision measurements, such as molecular time metrology and variations of the proton-electron mass ratio. We present an experimental setup that allows for the photoassociation, in an optical lattice, of strontium atoms into molecules using the narrow singlet-triplet transitions. We feature newly observed two-photon photoassociation to deeply bound molecular levels, as well as the study of the lifetime of such molecules in lattices, which is a determining factor concerning the practical use of this system. Other characteristics of our setup are presented, such as a computer controlled permanent-magnet Zeeman slower optimized with a genetic algorithm.

  16. Single-molecule mechanochemical sensing using DNA origami nanostructures. (United States)

    Koirala, Deepak; Shrestha, Prakash; Emura, Tomoko; Hidaka, Kumi; Mandal, Shankar; Endo, Masayuki; Sugiyama, Hiroshi; Mao, Hanbin


    While single-molecule sensing offers the ultimate detection limit, its throughput is often restricted as sensing events are carried out one at a time in most cases. 2D and 3D DNA origami nanostructures are used as expanded single-molecule platforms in a new mechanochemical sensing strategy. As a proof of concept, six sensing probes are incorporated in a 7-tile DNA origami nanoassembly, wherein binding of a target molecule to any of these probes leads to mechanochemical rearrangement of the origami nanostructure, which is monitored in real time by optical tweezers. Using these platforms, 10 pM platelet-derived growth factor (PDGF) are detected within 10 minutes, while demonstrating multiplex sensing of the PDGF and a target DNA in the same solution. By tapping into the rapid development of versatile DNA origami nanostructures, this mechanochemical platform is anticipated to offer a long sought solution for single-molecule sensing with improved throughput.

  17. Optical manipulation of single molecules in the living cell

    DEFF Research Database (Denmark)

    Norregaard, Kamilla; Jauffred, Liselotte; Berg-Sørensen, Kirstine;


    Optical tweezers are the only nano-tools capable of manipulating and performing force-measurements on individual molecules and organelles within the living cell without performing destructive penetration through the cell wall and without the need for inserting a non-endogenous probe. Here, we...... describe how optical tweezers are used to manipulate individual molecules and perform accurate force and distance measurements within the complex cytoplasm of the living cell. Optical tweezers can grab individual molecules or organelles, if their optical contrast to the medium is large enough......, as is the case, e. g., for lipid granules or chromosomes. However, often the molecule of interest is specifically attached to a handle manipulated by the optical trap. The most commonly used handles, their insertion into the cytoplasm, and the relevant micro-rheology of the cell are discussed here and we also...

  18. Extending single-molecule microscopy using optical Fourier processing. (United States)

    Backer, Adam S; Moerner, W E


    This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules.

  19. The Single-Molecule Approach to Membrane Protein Stoichiometry. (United States)

    Nichols, Michael G; Hallworth, Richard


    The advent of techniques for imaging solitary fluorescent molecules has made possible many new kinds of biological experiments. Here, we describe the application of single-molecule imaging to the problem of subunit stoichiometry in membrane proteins. A membrane protein of unknown stoichiometry, prestin, is coupled to the fluorescent enhanced green fluorescent protein (eGFP) and synthesized in the human embryonic kidney (HEK) cell line. We prepare adherent membrane fragments containing prestin-eGFP by osmotic lysis. The molecules are then exposed to continuous low-level excitation until their fluorescence reaches background levels. Their fluorescence decreases in discrete equal-amplitude steps, consistent with the photobleaching of single fluorophores. We count the number of steps required to photobleach each molecule. The molecular stoichiometry is then deduced using a binomial model.

  20. Alignment of symmetric top molecules by short laser pulses

    DEFF Research Database (Denmark)

    Hamilton, Edward; Seideman, Tamar; Ejdrup, Tine


    Nonadiabatic alignment of symmetric top molecules induced by a linearly polarized, moderately intense picosecond laser pulse is studied theoretically and experimentally. Our studies are based on the combination of a nonperturbative solution of the Schrodinger equation with femtosecond time...