Numerical optimization of conical flow waveriders including detailed viscous effects

Science.gov (United States)

Bowcutt, Kevin G.; Anderson, John D., Jr.; Capriotti, Diego

1987-01-01

A family of optimized hypersonic waveriders is generated and studied wherein detailed viscous effects are included within the optimization process itself. This is in contrast to previous optimized waverider work, wherein purely inviscid flow is used to obtain the waverider shapes. For the present waveriders, the undersurface is a streamsurface of an inviscid conical flowfield, the upper surface is a streamsurface of the inviscid flow over a tapered cylinder (calculated by the axisymmetric method of characteristics), and the viscous effects are treated by integral solutions of the boundary layer equations. Transition from laminar to turbulent flow is included within the viscous calculations. The optimization is carried out using a nonlinear simplex method. The resulting family of viscous hypersonic waveriders yields predicted high values of lift/drag, high enough to break the L/D barrier based on experience with other hypersonic configurations. Moreover, the numerical optimization process for the viscous waveriders results in distinctly different shapes compared to previous work with inviscid-designed waveriders. Also, the fine details of the viscous solution, such as how the shear stress is distributed over the surface, and the location of transition, are crucial to the details of the resulting waverider geometry. Finally, the moment coefficient variations and heat transfer distributions associated with the viscous optimized waveriders are studied.

Atkins' molecules

CERN Document Server

Atkins, Peters

2003-01-01

Originally published in 2003, this is the second edition of a title that was called 'the most beautiful chemistry book ever written'. In it, we see the molecules responsible for the experiences of our everyday life - including fabrics, drugs, plastics, explosives, detergents, fragrances, tastes, and sex. With engaging prose Peter Atkins gives a non-technical account of an incredible range of aspects of the world around us, showing unexpected connections, and giving an insight into how this amazing world can be understood in terms of the atoms and molecules from which it is built. The second edition includes dozens of extra molecules, graphical presentation, and an even more accessible and enthralling account of the molecules themselves.

Molecule nanoweaver

Science.gov (United States)

Gerald, II; Rex, E [Brookfield, IL; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL; Diaz, Rocio [Chicago, IL; Vukovic, Lela [Westchester, IL

2009-03-10

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.

Cold Rydberg molecules

Science.gov (United States)

Raithel, Georg; Zhao, Jianming

2017-04-01

Cold atomic systems have opened new frontiers at the interface of atomic and molecular physics. These include research on novel types of Rydberg molecules. Three types of molecules will be reviewed. Long-range, homonuclear Rydberg molecules, first predicted in [1] and observed in [2], are formed via low-energy electron scattering of the Rydberg electron from a ground-state atom within the Rydberg atom's volume. The binding mostly arises from S- and P-wave triplet scattering. We use a Fermi model that includes S-wave and P-wave singlet and triplet scattering, the fine structure coupling of the Rydberg atom and the hyperfine structure coupling of the 5S1/2 atom (in rubidium [3]). The hyperfine structure gives rise to mixed singlet-triplet potentials for both low-L and high-L Rydberg molecules [3]. A classification into Hund's cases [3, 4, 5] will be discussed. The talk further includes results on adiabatic potentials and adiabatic states of Rydberg-Rydberg molecules in Rb and Cs. These molecules, which have even larger bonding length than Rydberg-ground molecules, are formed via electrostatic multipole interactions. The leading interaction term of neutral Rydberg-Rydberg molecules is between two dipoles, while for ionic Rydberg molecules it is between a dipole and a monopole. NSF (PHY-1506093), NNSF of China (61475123).

Theory of tunneling ionization of molecules: Weak-field asymptotics including dipole effects

DEFF Research Database (Denmark)

Tolstikhin, Oleg I.; Morishita, Toru; Madsen, Lars Bojer

2011-01-01

The formulation of the parabolic adiabatic expansion approach to the problem of ionization of atomic systems in a static electric field, originally developed for the axially symmetric case [ Phys. Rev. A 82 023416 (2010)], is generalized to arbitrary potentials. This approach is used to rederive...... the asymptotic theory of tunneling ionization in the weak-field limit. In the atomic case, the resulting formulas for the ionization rate coincide with previously known results. In addition, the present theory accounts for the possible existence of a permanent dipole moment of the unperturbed system and, hence......, applies to polar molecules. Accounting for dipole effects constitutes an important difference of the present theory from the so-called molecular Ammosov-Delone-Krainov theory. The theory is illustrated by comparing exact and asymptotic results for a set of model polar molecules and a realistic molecular...

Muon cycling rate in D/T mixture including doubly muonic molecule formation

Directory of Open Access Journals (Sweden)

M. R. Eskandari

2002-06-01

Full Text Available   In the present work, the fundamental behavior of four body molecule formations of pt μμ , pd μμ , dt μμ , tt μμ , and pp μμ in a D/T fusion are considered. Their higher fusion rate, specially the available data for dt μμ , encouraged us to study the muon cycling rate in D/T fusion in the temperature range of (100-1400 K, density and deuterium-tritium concentration ratio. For this purpose, various values for the doubly muonic molecule formation are chosen and with the comparison to the experimental results, the doubly muonic formation rate of 109 s-1 is predicted theoretically. Our calculated cycling rate has shown that having not considered the doubly muonic formation in previous calculations had made no serious changes in the previously calculated values.

Chondroitin sulfates and their binding molecules in the central nervous system.

Science.gov (United States)

Djerbal, L; Lortat-Jacob, H; Kwok, Jcf

2017-06-01

Chondroitin sulfate (CS) is the most abundant glycosaminoglycan (GAG) in the central nervous system (CNS) matrix. Its sulfation and epimerization patterns give rise to different forms of CS, which enables it to interact specifically and with a significant affinity with various signalling molecules in the matrix including growth factors, receptors and guidance molecules. These interactions control numerous biological and pathological processes, during development and in adulthood. In this review, we describe the specific interactions of different families of proteins involved in various physiological and cognitive mechanisms with CSs in CNS matrix. A better understanding of these interactions could promote a development of inhibitors to treat neurodegenerative diseases.

Fluorescent scattering by molecules embedded in small particles. Progress report, May 1, 1977--October 31, 1978

International Nuclear Information System (INIS)

Chew, H.; McNulty, P.J.

1978-01-01

A model for the fluorescence and Raman scattering by molecules that comprise or are embedded in small particles was developed and numerical calculations performed. The emphasis during this first year of the contract was on writing and testing the computer programs necessary for numerical calculations and on demonstrating the extent of the potential effects that the geometrical and optical properties of the particle would have on the Raman and fluorescent emissions. For the purpose of demonstrating effects emphasis was focused upon the case of isotropically polarizable molecules that fluoresce or Raman scatter through electric dipole transitions. Some preliminary results are described. One result of these investigations that is of particular significance for remote sensing of pollutants is that it would be a serious mistake to use inelastic scattering techniques such as Raman and fluorescent scattering for quantitative assay of specific molecules in aerosols containing particulates without taking into account the size, structure and refractive index of the particles. A list of publications is included

Inelastic collisions between an atom and a diatomic molecule. I. Theoretical and numerical considerations for the close coupling approximation

International Nuclear Information System (INIS)

Choi, B.H.; Tang, K.T.

1975-01-01

The close coupled differential equations for rotational excitation in collisions between an atom and a diatomic molecule are reformulated. Although it is equivalent to other formulations, it is computationally more convenient and gives a simpler expression for differential cross sections. Questions concerning real boundary conditions and the unitarity of the S matrix are discussed. Stormer's algorithm for solving coupled differential equations is introduced for molecular scatterings. This numerical procedure, which is known to be very useful in nuclear scattering problems, has to be modified for molecular systems. It is capable of treating the case where all channels are open as well as the case where some of the channels are closed. This algorithm is compared with other typical procedures of solving coupled differential equations

Fully self-consistent GW calculations for molecules

DEFF Research Database (Denmark)

Rostgaard, Carsten; Jacobsen, Karsten Wedel; Thygesen, Kristian Sommer

2010-01-01

We calculate single-particle excitation energies for a series of 34 molecules using fully self-consistent GW, one-shot G0W0, Hartree-Fock (HF), and hybrid density-functional theory (DFT). All calculations are performed within the projector-augmented wave method using a basis set of Wannier...... functions augmented by numerical atomic orbitals. The GW self-energy is calculated on the real frequency axis including its full frequency dependence and off-diagonal matrix elements. The mean absolute error of the ionization potential (IP) with respect to experiment is found to be 4.4, 2.6, 0.8, 0.4, and 0...

Flexible single molecule simulation of reaction-diffusion processes

International Nuclear Information System (INIS)

Hellander, Stefan; Loetstedt, Per

2011-01-01

An algorithm is developed for simulation of the motion and reactions of single molecules at a microscopic level. The molecules diffuse in a solvent and react with each other or a polymer and molecules can dissociate. Such simulations are of interest e.g. in molecular biology. The algorithm is similar to the Green's function reaction dynamics (GFRD) algorithm by van Zon and ten Wolde where longer time steps can be taken by computing the probability density functions (PDFs) and then sample from the distribution functions. Our computation of the PDFs is much less complicated than GFRD and more flexible. The solution of the partial differential equation for the PDF is split into two steps to simplify the calculations. The sampling is without splitting error in two of the coordinate directions for a pair of molecules and a molecule-polymer interaction and is approximate in the third direction. The PDF is obtained either from an analytical solution or a numerical discretization. The errors due to the operator splitting, the partitioning of the system, and the numerical approximations are analyzed. The method is applied to three different systems involving up to four reactions. Comparisons with other mesoscopic and macroscopic models show excellent agreement.

Real-Time Observation of Internal Motion within Ultrafast Dissipative Optical Soliton Molecules

Science.gov (United States)

Krupa, Katarzyna; Nithyanandan, K.; Andral, Ugo; Tchofo-Dinda, Patrice; Grelu, Philippe

2017-06-01

Real-time access to the internal ultrafast dynamics of complex dissipative optical systems opens new explorations of pulse-pulse interactions and dynamic patterns. We present the first direct experimental evidence of the internal motion of a dissipative optical soliton molecule generated in a passively mode-locked erbium-doped fiber laser. We map the internal motion of a soliton pair molecule by using a dispersive Fourier-transform imaging technique, revealing different categories of internal pulsations, including vibrationlike and phase drifting dynamics. Our experiments agree well with numerical predictions and bring insights to the analogy between self-organized states of lights and states of the matter.

Final Report: Cooling Molecules with Laser Light

International Nuclear Information System (INIS)

Di Rosa, Michael D.

2012-01-01

Certain diatomic molecules are disposed to laser cooling in the way successfully applied to certain atoms and that ushered in a revolution in ultracold atomic physics, an identification first made at Los Alamos and which took root during this program. Despite their manipulation into numerous achievements, atoms are nonetheless mundane denizens of the quantum world. Molecules, on the other hand, with their internal degrees of freedom and rich dynamical interplay, provide considerably more complexity. Two main goals of this program were to demonstrate the feasibility of laser-cooling molecules to the same temperatures as laser-cooled atoms and introduce a means for collecting laser-cooled molecules into dense ensembles, a foundational start of studies and applications of ultracold matter without equivalence in atomic systems.

Linear-algebraic approach to electron-molecule collisions: General formulation

International Nuclear Information System (INIS)

Collins, L.A.; Schneider, B.I.

1981-01-01

We present a linear-algebraic approach to electron-molecule collisions based on an integral equations form with either logarithmic or asymptotic boundary conditions. The introduction of exchange effects does not alter the basic form or order of the linear-algebraic equations for a local potential. In addition to the standard procedure of directly evaluating the exchange integrals by numerical quadrature, we also incorporate exchange effects through a separable-potential approximation. Efficient schemes are developed for reducing the number of points and channels that must be included. The method is applied at the static-exchange level to a number of molecular systems including H 2 , N 2 , LiH, and CO 2

New directions in low energy electron molecule collision calculations

International Nuclear Information System (INIS)

Burke, P.G.; Noble, C.J.

1982-01-01

New theoretical and computational methods for studying low energy electron molecule collisions are discussed. Having considered the fixed-nuclei approximation and the form of the expansion of the total collision wavefunction, the various approximations which have been made are examined, including the static plus model exchange approximation, the static exchange approximation and the close coupling approximation, particular attention being paid to methods of including the molecular charge polarisation. Various ways which have been developed to solve the resultant equations are discussed and it is found that there is increasing emphasis being given to methods which combine the advantages of discrete multi-centre analytic bases with single centre numerical bases. (U.K.)

Raman and fluorescent scattering by molecules embedded in small particles

International Nuclear Information System (INIS)

Chew, H.W.; McNulty, P.J.

1983-01-01

We have formulated a model for fluorescent and Raman scattering by molecules embedded in or in the vicinity of small particles. The model takes into account the size, shape, refractive index, and morphology of the host particles. Analytic and numerical results have been obtained for spherical (one and more layers, including magnetic dipole transitions) cylindrical and spheroidal particles. Particular attention has been given to the spherical case with fluorescent/Raman scatterers uniformly distributed in the particles radiating both coherently and incohorently. Depolarization effects have been studied with suitable averaging process, and good agreement with experiment has been obtained. Analytic and numerical results have been obtained for the elastic scattering of evanescent waves; these results are useful for the study of fluorescent under excitation by evanescent waves

Experimental studies of processes with vibrationally excited hydrogen molecules that are important for tokamak edge plasma

International Nuclear Information System (INIS)

Cadez, I.; Markelj, S.; Rupnik, Z.; Pelicon, P.

2006-01-01

We are currently conducting a series of different laboratory experimental studies of processes involving vibrationally excited hydrogen molecules that are relevant to fusion edge plasma. A general overview of our activities is presented together with results of studies of hydrogen recombination on surfaces. This includes vibrational spectroscopy of molecules formed by recombination on metal surfaces exposed to the partially dissociated hydrogen gas and recombination after hydrogen permeation through metal membrane. The goal of these studies is to provide numerical parameters needed for edge plasma modelling and better understanding of plasma wall interaction processes. (author)

Quantum chemical approach for positron annihilation spectra of atoms and molecules beyond plane-wave approximation

Science.gov (United States)

Ikabata, Yasuhiro; Aiba, Risa; Iwanade, Toru; Nishizawa, Hiroaki; Wang, Feng; Nakai, Hiromi

2018-05-01

We report theoretical calculations of positron-electron annihilation spectra of noble gas atoms and small molecules using the nuclear orbital plus molecular orbital method. Instead of a nuclear wavefunction, the positronic wavefunction is obtained as the solution of the coupled Hartree-Fock or Kohn-Sham equation for a positron and the electrons. The molecular field is included in the positronic Fock operator, which allows an appropriate treatment of the positron-molecule repulsion. The present treatment succeeds in reproducing the Doppler shift, i.e., full width at half maximum (FWHM) of experimentally measured annihilation (γ-ray) spectra for molecules with a mean absolute error less than 10%. The numerical results indicate that the interpretation of the FWHM in terms of a specific molecular orbital is not appropriate.

Cluster ions and van der Waals molecules

CERN Document Server

Smirnov, Boris M

1992-01-01

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.

Stabilizing photoassociated Cs2 molecules by optimal control

International Nuclear Information System (INIS)

Zhang Wei; Xie Ting; Huang Yin; Wang Gao-Ren; Cong Shu-Lin

2013-01-01

We demonstrate theoretically that photoassociated molecules can be stabilized to deeply bound states. This process is achieved by transferring the population from the outer well to the inner well using the optimal control theory, the Cs 2 molecule is taken as an example. Numerical calculations show that weakly bound molecules formed in the outer well by a pump pulse can be compressed to the inner well via a vibrational level of the ground electronic state as an intermediary by an additionally optimized laser pulse. The positively chirped pulse can enhance the population of the target state. With a transform-limited dump pulse, nearly all the photoassociated molecules in the inner well of the excited electronic state can be transferred to the deeply vibrational level of the ground electronic state. (atomic and molecular physics)

Stabilizing photoassociated Cs2 molecules by optimal control

Science.gov (United States)

Zhang, Wei; Xie, Ting; Huang, Yin; Wang, Gao-Ren; Cong, Shu-Lin

2013-01-01

We demonstrate theoretically that photoassociated molecules can be stabilized to deeply bound states. This process is achieved by transferring the population from the outer well to the inner well using the optimal control theory, the Cs2 molecule is taken as an example. Numerical calculations show that weakly bound molecules formed in the outer well by a pump pulse can be compressed to the inner well via a vibrational level of the ground electronic state as an intermediary by an additionally optimized laser pulse. The positively chirped pulse can enhance the population of the target state. With a transform-limited dump pulse, nearly all the photoassociated molecules in the inner well of the excited electronic state can be transferred to the deeply vibrational level of the ground electronic state.

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

Energy Technology Data Exchange (ETDEWEB)

Fidiani, Elok [Department of Physics, Parahyangan Catholic University, Bandung-Jawa Barat (Indonesia)

2016-03-11

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H{sub 2} and O{sub 2}. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction between the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

International Nuclear Information System (INIS)

Fidiani, Elok

2016-01-01

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H_2 and O_2. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction between the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.

Dielectric response of molecules in empirical tight-binding theory

Science.gov (United States)

Boykin, Timothy B.; Vogl, P.

2002-01-01

In this paper we generalize our previous approach to electromagnetic interactions within empirical tight-binding theory to encompass molecular solids and isolated molecules. In order to guarantee physically meaningful results, we rederive the expressions for relevant observables using commutation relations appropriate to the finite tight-binding Hilbert space. In carrying out this generalization, we examine in detail the consequences of various prescriptions for the position and momentum operators in tight binding. We show that attempting to fit parameters of the momentum matrix directly generally results in a momentum operator which is incompatible with the underlying tight-binding model, while adding extra position parameters results in numerous difficulties, including the loss of gauge invariance. We have applied our scheme, which we term the Peierls-coupling tight-binding method, to the optical dielectric function of the molecular solid PPP, showing that this approach successfully predicts its known optical properties even in the limit of isolated molecules.

Experimental investigation and numerical modelling of positive corona discharge: ozone generation

Energy Technology Data Exchange (ETDEWEB)

Yanallah, K; Castellanos, A [Departamento de Electronica y Electromagnetismo, Universidad de Sevilla (Spain); Pontiga, F; Fernandez-Rueda, A [Departamento de FIsica Aplicada II, Universidad de Sevilla (Spain)

2009-03-21

The spatial distribution of the species generated in a wire-cylinder positive corona discharge in pure oxygen has been computed using a plasma chemistry model that includes the most significant reactions between electrons, ions, atoms and molecules. The plasma chemistry model is included in the continuity equations of each species, which are coupled with Poisson's equation for the electric field and the energy conservation equation for the gas temperature. The current-voltage characteristic measured in the experiments has been used as an input data to the numerical simulation. The numerical model is able to reproduce the basic structure of the positive corona discharge and highlights the importance of Joule heating on ozone generation. The average ozone density has been computed as a function of current intensity and compared with the experimental measurements of ozone concentration determined by UV absorption spectroscopy.

Experimental investigation and numerical modelling of positive corona discharge: ozone generation

International Nuclear Information System (INIS)

Yanallah, K; Castellanos, A; Pontiga, F; Fernandez-Rueda, A

2009-01-01

The spatial distribution of the species generated in a wire-cylinder positive corona discharge in pure oxygen has been computed using a plasma chemistry model that includes the most significant reactions between electrons, ions, atoms and molecules. The plasma chemistry model is included in the continuity equations of each species, which are coupled with Poisson's equation for the electric field and the energy conservation equation for the gas temperature. The current-voltage characteristic measured in the experiments has been used as an input data to the numerical simulation. The numerical model is able to reproduce the basic structure of the positive corona discharge and highlights the importance of Joule heating on ozone generation. The average ozone density has been computed as a function of current intensity and compared with the experimental measurements of ozone concentration determined by UV absorption spectroscopy.

Experimental investigation and numerical modelling of positive corona discharge: ozone generation

Science.gov (United States)

Yanallah, K; Pontiga, F; Fernández-Rueda, A; Castellanos, A

2009-03-01

The spatial distribution of the species generated in a wire-cylinder positive corona discharge in pure oxygen has been computed using a plasma chemistry model that includes the most significant reactions between electrons, ions, atoms and molecules. The plasma chemistry model is included in the continuity equations of each species, which are coupled with Poisson's equation for the electric field and the energy conservation equation for the gas temperature. The current-voltage characteristic measured in the experiments has been used as an input data to the numerical simulation. The numerical model is able to reproduce the basic structure of the positive corona discharge and highlights the importance of Joule heating on ozone generation. The average ozone density has been computed as a function of current intensity and compared with the experimental measurements of ozone concentration determined by UV absorption spectroscopy.

Angle and Spin Resolved Auger Emission Theory and Applications to Atoms and Molecules

CERN Document Server

Lohmann, Bernd

2009-01-01

The Auger effect must be interpreted as the radiationless counterpart of photoionization and is usually described within a two-step model. Angle and spin resolved Auger emission physics deals with the theoretical and numerical description, analysis and interpretation of such types of experiments on free atoms and molecules. This monograph derives the general theory applying the density matrix formalism and, in terms of irreducible tensorial sets, so called state multipoles and order parameters, for parameterizing the atomic and molecular systems, respectively. Propensity rules and non-linear dependencies between the angular distribution and spin polarization parameters are included in the discussion. The numerical approaches utilizing relativistic distorted wave (RDWA), multiconfigurational Dirac-Fock (MCDF), and Greens operator methods are described. These methods are discussed and applied to theoretical predictions, numerical results and experimental data for a variety of atomic systems, especially the rare...

Impact of Dendrimers on Solubility of Hydrophobic Drug Molecules

Directory of Open Access Journals (Sweden)

Sonam Choudhary

2017-05-01

Full Text Available Adequate aqueous solubility has been one of the desired properties while selecting drug molecules and other bio-actives for product development. Often solubility of a drug determines its pharmaceutical and therapeutic performance. Majority of newly synthesized drug molecules fail or are rejected during the early phases of drug discovery and development due to their limited solubility. Sufficient permeability, aqueous solubility and physicochemical stability of the drug are important for achieving adequate bioavailability and therapeutic outcome. A number of different approaches including co-solvency, micellar solubilization, micronization, pH adjustment, chemical modification, and solid dispersion have been explored toward improving the solubility of various poorly aqueous-soluble drugs. Dendrimers, a new class of polymers, possess great potential for drug solubility improvement, by virtue of their unique properties. These hyper-branched, mono-dispersed molecules have the distinct ability to bind the drug molecules on periphery as well as to encapsulate these molecules within the dendritic structure. There are numerous reported studies which have successfully used dendrimers to enhance the solubilization of poorly soluble drugs. These promising outcomes have encouraged the researchers to design, synthesize, and evaluate various dendritic polymers for their use in drug delivery and product development. This review will discuss the aspects and role of dendrimers in the solubility enhancement of poorly soluble drugs. The review will also highlight the important and relevant properties of dendrimers which contribute toward drug solubilization. Finally, hydrophobic drugs which have been explored for dendrimer assisted solubilization, and the current marketing status of dendrimers will be discussed.

Low energy cross section data for ion-molecule reactions in hydrogen systems and for charge transfer of multiply charged ions with atoms and molecules

International Nuclear Information System (INIS)

Okuno, Kazuhiko

2007-04-01

Systematic cross section measurements for ion-molecule reactions in hydrogen systems and for charge transfer of multiply charged ions in low energy collisions with atoms and molecules have been performed continuously by the identical apparatus installed with an octo-pole ion beam guide (OPIG) since 1980 till 2004. Recently, all of accumulated cross section data for a hundred collision systems has been entered into CMOL and CHART of the NIFS atomic and molecular numerical database together with some related cross section data. In this present paper, complicated ion-molecule reactions in hydrogen systems are revealed and the brief outlines of specific properties in low energy charge transfer collisions of multiply charged ions with atoms and molecules are introduced. (author)

Symmetry Adaptation of the Rotation-Vibration Theory for Linear Molecules

Directory of Open Access Journals (Sweden)

Katy L. Chubb

2018-04-01

Full Text Available A numerical application of linear-molecule symmetry properties, described by the D ∞ h point group, is formulated in terms of lower-order symmetry groups D n h with finite n. Character tables and irreducible representation transformation matrices are presented for D n h groups with arbitrary n-values. These groups can subsequently be used in the construction of symmetry-adapted ro-vibrational basis functions for solving the Schrödinger equations of linear molecules. Their implementation into the symmetrisation procedure based on a set of “reduced” vibrational eigenvalue problems with simplified Hamiltonians is used as a practical example. It is shown how the solutions of these eigenvalue problems can also be extended to include the classification of basis-set functions using ℓ, the eigenvalue (in units of ℏ of the vibrational angular momentum operator L ^ z . This facilitates the symmetry adaptation of the basis set functions in terms of the irreducible representations of D n h . 12 C 2 H 2 is used as an example of a linear molecule of D ∞ h point group symmetry to illustrate the symmetrisation procedure of the variational nuclear motion program Theoretical ROVibrational Energies (TROVE.

On the role of hydrogel structure and degradation in controlling the transport of cell-secreted matrix molecules for engineered cartilage.

Science.gov (United States)

Dhote, Valentin; Skaalure, Stacey; Akalp, Umut; Roberts, Justine; Bryant, Stephanie J; Vernerey, Franck J

2013-03-01

Damage to cartilage caused by injury or disease can lead to pain and loss of mobility, diminishing one's quality of life. Because cartilage has a limited capacity for self-repair, tissue engineering strategies, such as cells encapsulated in synthetic hydrogels, are being investigated as a means to restore the damaged cartilage. However, strategies to date are suboptimal in part because designing degradable hydrogels is complicated by structural and temporal complexities of the gel and evolving tissue along multiple length scales. To address this problem, this study proposes a multi-scale mechanical model using a triphasic formulation (solid, fluid, unbound matrix molecules) based on a single chondrocyte releasing extracellular matrix molecules within a degrading hydrogel. This model describes the key players (cells, proteoglycans, collagen) of the biological system within the hydrogel encompassing different length scales. Two mechanisms are included: temporal changes of bulk properties due to hydrogel degradation, and matrix transport. Numerical results demonstrate that the temporal change of bulk properties is a decisive factor in the diffusion of unbound matrix molecules through the hydrogel. Transport of matrix molecules in the hydrogel contributes both to the development of the pericellular matrix and the extracellular matrix and is dependent on the relative size of matrix molecules and the hydrogel mesh. The numerical results also demonstrate that osmotic pressure, which leads to changes in mesh size, is a key parameter for achieving a larger diffusivity for matrix molecules in the hydrogel. The numerical model is confirmed with experimental results of matrix synthesis by chondrocytes in biodegradable poly(ethylene glycol)-based hydrogels. This model may ultimately be used to predict key hydrogel design parameters towards achieving optimal cartilage growth. Copyright © 2012 Elsevier Ltd. All rights reserved.

Rotation-vibrational spectra of diatomic molecules and nuclei with Davidson interactions

CERN Document Server

Rowe, D J

1998-01-01

Complete rotation-vibrational spectra and electromagnetic transition rates are obtained for Hamiltonians of diatomic molecules and nuclei with Davidson interactions. Analytical results are derived by dynamical symmetry methods for diatomic molecules and a liquid-drop model of the nucleus. Numerical solutions are obtained for a many-particle nucleus with quadrupole Davidson interactions within the framework of the microscopic symplectic model. (author)

Pharmacology of cell adhesion molecules of the nervous system

DEFF Research Database (Denmark)

Kiryushko, Darya; Bock, Elisabeth; Berezin, Vladimir

2007-01-01

Cell adhesion molecules (CAMs) play a pivotal role in the development and maintenance of the nervous system under normal conditions. They also are involved in numerous pathological processes such as inflammation, degenerative disorders, and cancer, making them attractive targets for drug...

The effect of gold nanoparticles on exchange processes in collision complexes of triplet and singlet oxygen molecules with excited eosin molecules

Science.gov (United States)

Bryukhanov, V. V.; Minaev, B. M.; Tsibul'nikova, A. V.; Slezhkin, V. A.

2015-07-01

We have studied exchange processes in contact complexes of triplet eosin molecules with oxygen molecules in the triplet (3Σ{/g -}) and singlet (1Δ g ) states in thin polyvinylbutyral films in the presence of gold nanoparticles. Upon resonant excitation of surface plasmons in gold nanoparticles into the absorption band of eosin molecules-singlet oxygen sensitizers-we have obtained an increase in the intensity of the delayed fluorescence and an increase in the lifetime of the dye with simultaneous quenching of the luminescence of singlet oxygen. The kinetics of the delayed fluorescence of the dye as a result of singlet-triplet annihilation of triplet eosin molecules with singlet oxygen molecules has been investigated. To compare theoretical and experimental data, we have numerically simulated energy transfer processes. Rate constants of energy transfer and of singlet-triplet annihilation, as well as quenching constants of triplet states of the dye by molecular oxygen, have been calculated. Luminescence quantum yield 1Δ g of polyvinylbutyral has been estimated. We have analyzed quantum-chemically electronic mechanisms of singlet-triplet annihilation of oxygen and eosin.

The Molecule Cloud - compact visualization of large collections of molecules

Directory of Open Access Journals (Sweden)

Ertl Peter

2012-07-01

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

Tunneling Ionization of Diatomic Molecules

DEFF Research Database (Denmark)

Svensmark, Jens Søren Sieg

2016-01-01

When a molecule is subject to a strong laser field, there is a probability that an electron can escape, even though the electrons are bound by a large potential barrier. This is possible because electrons are quantum mechanical in nature, and they are therefore able to tunnel through potential...... barriers, an ability classical particles do not possess. Tunnelling is a fundamental quantum mechanical process, a process that is distinctly non-classical, so solving this tunnelling problem is not only relevant for molecular physics, but also for quantum theory in general. In this dissertation the theory...... of tunneling ionizaion of molecules is presented and the results of numerical calculations are shown. One perhaps surprising result is, that the frequently used Born-Oppenheimer approximation breaks down for weak fields when describing tunneling ionization. An analytic theory applicable in the weak-field limit...

EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES

Science.gov (United States)

Carr, Lincoln D.; Ye, Jun

2009-05-01

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

Chemical Principles and Interference in the Electrical Conductance of Single Molecules

DEFF Research Database (Denmark)

Borges, Anders Christian

, the conductance of molecules can vary orders of magnitude and the concept of interference is believed to play a major role in this. This thesis investigates the links between single molecule conductance, chemistry and interference effects in short organic molecules. It is investigated to which extent...... the conductance can be understood in terms of separate contributions and when the effects of interference are important. Links between chemical principles and constructive- and destructive interference effects are demonstrated using a combination of simple models, atomistic calculations and Scanning......-Tunneling Microscope Break-Junction experiments (STM-BJ). It is demonstrated that these links can be used to design molecules exhibiting surprising interference effects and to interpret and predict the trends in the characteristic conductance of single molecules without resorting to numerical computational methods...

An experimental and numerical study of endwall heat transfer in a turbine blade cascade including tangential heat conduction analysis

Science.gov (United States)

Ratto, Luca; Satta, Francesca; Tanda, Giovanni

2018-06-01

This paper presents an experimental and numerical investigation of heat transfer in the endwall region of a large scale turbine cascade. The steady-state liquid crystal technique has been used to obtain the map of the heat transfer coefficient for a constant heat flux boundary condition. In the presence of two- and three-dimensional flows with significant spatial variations of the heat transfer coefficient, tangential heat conduction could lead to error in the heat transfer coefficient determination, since local heat fluxes at the wall-to-fluid interface tend to differ from point to point and surface temperatures to be smoothed out, thus making the uniform-heat-flux boundary condition difficult to be perfectly achieved. For this reason, numerical simulations of flow and heat transfer in the cascade including the effect of tangential heat conduction inside the endwall have been performed. The major objective of numerical simulations was to investigate the influence of wall heat conduction on the convective heat transfer coefficient determined during a nominal iso-flux heat transfer experiment and to interpret possible differences between numerical and experimental heat transfer results. Results were presented and discussed in terms of local Nusselt number and a convenient wall heat flux function for two values of the Reynolds number (270,000 and 960,000).

Influence of excited molecules on electron swarm transport coefficients and gas discharge kinetics

International Nuclear Information System (INIS)

Petrovic, Z.L.; Jovanovic, J.V.; Raspopovic, Z.M.; Bzenic, S.A.; Vrhovac, S.B.

1997-01-01

In this paper we study different effects of excited molecules on swarm parameters, electron energy distribution functions and gas discharge modeling. First we discuss a possible experiment in parahydrogen to resolve the discrepancy in hydrogen vibrational excitation cross section data. Negative differential conductivity (NDC) is a kinetic phenomenon which manifests itself in a particular dependence of the drift velocity on E=N and it is affected by superelastic collisions with excited states. A complete kinetic scheme for argon required to model excited state densities in gas discharges is also described. These results are used to explain experiments in capacitively and inductively coupled RF plasmas used for processing. The paper illustrates the application of atomic and molecular collision data, swarm data and the theoretical techniques in modeling of gas discharges with large abundances of excited molecules. It is pointed out that swarm experiments with excited molecules are lacking and that there is a shortage of reliable data, while the numerical procedures are sufficiently developed to include all the important effects. (authors). 59 refs., 12 figs

Pumping vortex into a Bose-Einstein condensate of heteronuclear molecules

International Nuclear Information System (INIS)

Xu, Z F; Wang, R Q; You, L

2009-01-01

Heteronuclear molecules have attracted wide attention due to their permanent electric dipole moments. Analogous to atoms with magnetic dipoles, the existence of nonzero electric dipoles significantly enhances the possibilities and mechanisms for the control and design of quantum degenerate molecule systems with electric (E) fields. This work proposes a vortex creation mechanism inside a condensate of heteronuclear molecules through the adiabatic flipping of the axial bias of an analogous E-field Ioffe-Pritchard trap (IPT), extending the original protocol of Isoshima et al (2000 Phys. Rev. A 61 063610) for an atomic spinor condensate inside a magnetic (B)-field IPT. We provide both analytic proof and numerical simulations to illustrate the high fidelity operation of this vortex pump protocol. We hope our work provides stimulating experimental possibilities for active investigations in quantum degenerate molecule systems.

Mechanism of pulse discharge production of iodine atoms from CF3I molecules for a chemical oxygen-iodine laser

International Nuclear Information System (INIS)

Kochetov, I V; Napartovich, A P; Vagin, N P; Yuryshev, N N

2009-01-01

The pulsed chemical oxygen-iodine laser (COIL) development is aimed at many new applications. Pulsed electric discharge is most effective in turning COIL operation into the pulse mode by instant production of iodine atoms. A numerical model is developed for simulations of the pulsed COIL initiated by an electric discharge. The model comprises a system of kinetic equations for neutral and charged species, electric circuit equation, gas thermal balance equation and the photon balance equation. Reaction rate coefficients for processes involving electrons are found by solving the electron Boltzmann equation, which is re-calculated in a course of computations when plasma parameters changed. The processes accounted for in the Boltzmann equation include excitation and ionization of atoms and molecules, dissociation of molecules, electron attachment processes, electron-ion recombination, electron-electron collisions, second-kind collisions and stepwise excitation of molecules. The last processes are particularly important because of a high singlet oxygen concentration in gas flow from the singlet oxygen chemical generator. Results of numerical simulations are compared with experimental laser pulse waveforms. It is concluded that there is satisfactory agreement between theory and the experiment. The prevailing mechanism of iodine atom formation from the CF 3 I donor in a very complex kinetic system of the COIL medium under pulse discharge conditions, based on their detailed numerical modelling and by comparing these results both with experimental results of other authors and their own experiments, is established. The dominant iodine atom production mechanism for conditions under study is the electron-impact dissociation of CF 3 I molecules. It was proved that in the conditions of the experiment the secondary chemical reactions with O atoms play an insignificant role.

[Fluorescent and Raman scattering by molecules embedded in small particles]: Annual report, 1983

International Nuclear Information System (INIS)

Chew, H.; McNulty, P.J.

1983-01-01

An overview is given of the model formulated for fluorescent and Raman scattering by molecules embedded in or in the vicinity of small particles. The model takes into account the size, shape, refractive index, and morphology of the host particles. Analytic and numerical results have been obtained for spherical (one and more layers, including magnetic dipole transitions), cylindrical, and spheroidal particles. Particular attention has been given to the spherical case with fluorescent/Raman scatterers uniformly distributed in the particles radiating both coherently and incoherently. Depolarization effects have been studied with suitable averaging process, and good agreement with experiment has been obtained. Analytic and numerical results have been obtained for the elastic scattering of evanescent waves; these results are useful for the study of fluorescence under excitation by evanescent waves

Orientation of KRb molecules in a switched electrostatic field

International Nuclear Information System (INIS)

Huang Yun-Xia; Xu Shu-Wu; Yang Xiao-Hua

2013-01-01

We theoretically investigate the orientation of the cold KRb molecules induced in a switched electrostatic field by numerically solving the full time-dependent Schrödinger 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. (atomic and molecular physics)

Numerical-analytic implementation of the higher-order canonical Van Vleck perturbation theory for the interpretation of medium-sized molecule vibrational spectra.

Science.gov (United States)

Krasnoshchekov, Sergey V; Isayeva, Elena V; Stepanov, Nikolay F

2012-04-12

Anharmonic vibrational states of semirigid polyatomic molecules are often studied using the second-order vibrational perturbation theory (VPT2). For efficient higher-order analysis, an approach based on the canonical Van Vleck perturbation theory (CVPT), the Watson Hamiltonian and operators of creation and annihilation of vibrational quanta is employed. This method allows analysis of the convergence of perturbation theory and solves a number of theoretical problems of VPT2, e.g., yields anharmonic constants y(ijk), z(ijkl), and allows the reliable evaluation of vibrational IR and Raman anharmonic intensities in the presence of resonances. Darling-Dennison and higher-order resonance coupling coefficients can be reliably evaluated as well. The method is illustrated on classic molecules: water and formaldehyde. A number of theoretical conclusions results, including the necessity of using sextic force field in the fourth order (CVPT4) and the nearly vanishing CVPT4 contributions for bending and wagging modes. The coefficients of perturbative Dunham-type Hamiltonians in high-orders of CVPT are found to conform to the rules of equality at different orders as earlier proven analytically for diatomic molecules. The method can serve as a good substitution of the more traditional VPT2.

A numerical model including PID control of a multizone crystal growth furnace

Science.gov (United States)

Panzarella, Charles H.; Kassemi, Mohammad

1992-01-01

This paper presents a 2D axisymmetric combined conduction and radiation model of a multizone crystal growth furnace. The model is based on a programmable multizone furnace (PMZF) designed and built at NASA Lewis Research Center for growing high quality semiconductor crystals. A novel feature of this model is a control algorithm which automatically adjusts the power in any number of independently controlled heaters to establish the desired crystal temperatures in the furnace model. The control algorithm eliminates the need for numerous trial and error runs previously required to obtain the same results. The finite element code, FIDAP, used to develop the furnace model, was modified to directly incorporate the control algorithm. This algorithm, which presently uses PID control, and the associated heat transfer model are briefly discussed. Together, they have been used to predict the heater power distributions for a variety of furnace configurations and desired temperature profiles. Examples are included to demonstrate the effectiveness of the PID controlled model in establishing isothermal, Bridgman, and other complicated temperature profies in the sample. Finally, an example is given to show how the algorithm can be used to change the desired profile with time according to a prescribed temperature-time evolution.

Recent advances in the discovery of small molecule c-Met Kinase inhibitors.

Science.gov (United States)

Parikh, Palak K; Ghate, Manjunath D

2018-01-01

c-Met is a prototype member of a subfamily of heterodimeric receptor tyrosine kinases (RTKs) and is the receptor for hepatocyte growth factor (HGF). Binding of HGF to its receptor c-Met, initiates a wide range of cellular signalling, including those involved in proliferation, motility, migration and invasion. Importantly, dysregulated HGF/c-Met signalling is a driving factor for numerous malignancies and promotes tumour growth, invasion, dissemination and/or angiogenesis. Dysregulated HGF/c-Met signalling has also been associated with poor clinical outcomes and resistance acquisition to some approved targeted therapies. Thus, c-Met kinase has emerged as a promising target for cancer drug development. Different therapeutic approaches targeting the HGF/c-Met signalling pathway are under development for targeted cancer therapy, among which small molecule inhibitors of c-Met kinase constitute the largest effort within the pharmaceutical industry. The review is an effort to summarize recent advancements in medicinal chemistry development of small molecule c-Met kinase inhibitors as potential anti-cancer agents which would certainly help future researchers to bring further developments in the discovery of small molecule c-Met kinase inhibitors. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Myricetin: A Dietary Molecule with Diverse Biological Activities

Directory of Open Access Journals (Sweden)

Deepak Kumar Semwal

2016-02-01

Full Text Available Myricetin is a common plant-derived flavonoid and is well recognised for its nutraceuticals value. It is one of the key ingredients of various foods and beverages. The compound exhibits a wide range of activities that include strong anti-oxidant, anticancer, antidiabetic and anti-inflammatory activities. It displays several activities that are related to the central nervous system and numerous studies have suggested that the compound may be beneficial to protect against diseases such as Parkinson’s and Alzheimer’s. The use of myricetin as a preserving agent to extend the shelf life of foods containing oils and fats is attributed to the compound’s ability to protect lipids against oxidation. A detailed search of existing literature revealed that there is currently no comprehensive review available on this important molecule. Hence, the present work includes the history, synthesis, pharmaceutical applications and toxicity studies of myricetin. This report also highlights structure-activity relationships and mechanisms of action for various biological activities.

Path-integral approach to resonant electron-molecule scattering

International Nuclear Information System (INIS)

Winterstetter, M.; Domcke, W.

1993-01-01

A path-integral formulation of resonant electron-molecule scattering is developed within the framework of the projection-operator formalism of scattering theory. The formation and decay of resonances is treated in real time as a quantum-mechanical electronic-tunneling process, modified by the coupling of the electronic motion with the nuclear degrees of freedom. It is shown that the electronic continuum can be summed over in the path-integral formulation, resulting formally in the path integral for an effective two-state system with coupling to vibrations. The harmonic-oscillator approximation is adopted for the vibrational motion in the present work. Approximation methods are introduced which render the numerical evaluation of the sum over paths feasible for up to ∼10 3 elementary time slices. The theory is numerically realized for simple but nontrivial models representing the 2 Π g d-wave shape resonance in e - +N 2 collisions and the 2 Σ u + p-wave shape resonance in e - +H 2 collisions, respectively. The accuracy of the path-integral results is assessed by comparison with exact numerical reference data for these models. The essential virtue of the path-integral approach is the fact that the computational effort scales at most linearly with the number of vibrational degrees of freedom. The path-integral method is thus well suited to treat electron collisions with polyatomic molecules and molecular aggregates

Extensive theoretical study on the excited states of the PCl+ molecule including spin-orbit coupling

Science.gov (United States)

Zhang, Xiaomei; Zhai, Hongsheng; Liu, Siyuan; Liu, Yufang

2017-07-01

The entire 23 Λ-S states of the PCl+ molecule have been studied by using the high-level relativistic MRCI+Q method with full-electron aug-cc-pCVQZ-DK basis set. The potential energy curves(PECs) and wavefunctions of the states have been calculated. From the PECs, the spectroscopic constants of the bound states are also determined, and the good agreements could be found with the experiments. The high density region of states exhibits many PECs' crossings, which lead to complicated interaction of the states. Here, the interactions arising from the dipolar interaction and spin-orbit coupling (SOC) effect have been discussed in detail. Under the influence of the SOC effect, the A2Π state is perturbed by the 14Σ- state. Considering the SOC effect, total 45 Ω states are generated from the original 23 Λ-S states. The transition properties are also predicted, including the transition dipole moments, Franck-Condon factors, and radiative lifetimes. The lifetimes of the transitions A2Π1/2-X2Π1/2 and A2Π3/2-X2Π3/2 are determined to be 478.9 ns and 487.0 ns(v'=0), respectively.

Single molecules and nanotechnology

CERN Document Server

Vogel, Horst

2007-01-01

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.

Multi-Excitonic Quantum Dot Molecules

Science.gov (United States)

Scheibner, M.; Stinaff, E. A.; Doty, M. F.; Ware, M. E.; Bracker, A. S.; Gammon, D.; Ponomarev, I. V.; Reinecke, T. L.; Korenev, V. L.

2006-03-01

With the ability to create coupled pairs of quantum dots, the next step towards the realization of semiconductor based quantum information processing devices can be taken. However, so far little knowledge has been gained on these artificial molecules. Our photoluminescence experiments on single InAs/GaAs quantum dot molecules provide the systematics of coupled quantum dots by delineating the spectroscopic features of several key charge configurations in such quantum systems, including X, X^+,X^2+, XX, XX^+ (with X being the neutral exciton). We extract general rules which determine the formation of molecular states of coupled quantum dots. These include the fact that quantum dot molecules provide the possibility to realize various spin configurations and to switch the electron hole exchange interaction on and off by shifting charges inside the molecule. This knowledge will be valuable in developing implementations for quantum information processing.

Collision of hydrogen molecules interacting with two grapheme sheets

Directory of Open Access Journals (Sweden)

Malivuk-Gak Dragana

2017-01-01

Full Text Available It have been performed the computational experiments with two hydrogen molecules and two graphene sheets. Hydrogen - hydrogen and hydrogen - carbon interactions are described by Lennard - Jones potential. Equations of motion of the wave packet centre are solved numerically. The initial molecule velocity was determined by temperature and collisions occur in central point between two sheets. The molecules after collision stay near or get far away of graphene sheets. Then one can find what temperatures, graphene sheet sizes and their distances are favourable for hydrogen storage. It is found that quantum corrections of the molecule classical trajectories are not significant here. Those investigations of possibility of hydrogen storage by physisorption are of interest for improvement of the fuel cell systems. The main disadvantages of computational experiments are: (1 it cannot compute with very large number of C atoms, (2 it is assumed that carbon atoms are placed always in their equilibrium positions and (3 the changes of wave packet width are not considered.

Hierarchical virtual screening approaches in small molecule drug discovery.

Science.gov (United States)

Kumar, Ashutosh; Zhang, Kam Y J

2015-01-01

Virtual screening has played a significant role in the discovery of small molecule inhibitors of therapeutic targets in last two decades. Various ligand and structure-based virtual screening approaches are employed to identify small molecule ligands for proteins of interest. These approaches are often combined in either hierarchical or parallel manner to take advantage of the strength and avoid the limitations associated with individual methods. Hierarchical combination of ligand and structure-based virtual screening approaches has received noteworthy success in numerous drug discovery campaigns. In hierarchical virtual screening, several filters using ligand and structure-based approaches are sequentially applied to reduce a large screening library to a number small enough for experimental testing. In this review, we focus on different hierarchical virtual screening strategies and their application in the discovery of small molecule modulators of important drug targets. Several virtual screening studies are discussed to demonstrate the successful application of hierarchical virtual screening in small molecule drug discovery. Copyright © 2014 Elsevier Inc. All rights reserved.

Single Molecule Electronics and Devices

Science.gov (United States)

Tsutsui, Makusu; Taniguchi, Masateru

2012-01-01

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. PMID:22969345

Quantum Tunneling of Magnetization in Trigonal Single-Molecule Magnets

Science.gov (United States)

Liu, Junjie; Del Barco, Enrique; Hill, Stephen

2012-02-01

We perform a numerical analysis of the quantum tunneling of magnetization (QTM) that occurs in a spin S = 6 single-molecule magnet (SMM) with idealized C3 symmetry. The deconstructive points in the QTM are located by following the Berry-phase interference (BPI) oscillations. We find that the O4^3 (=12[Sz,S+^3 +S-^3 ]) operator unfreezes odd-k QTM resonances and generates three-fold patterns of BPI minima in all resonances, including k = 0! This behavior cannot be reproduced with operators that possess even rotational symmetry about the quantization axis. We find also that the k = 0 BPI minima shift away from zero longitudinal field. The wider implications of these results will be discussed in terms of the QTM behavior observed in other SMMs.

Positron creation in superheavy quasi-molecules

International Nuclear Information System (INIS)

Mueller, B.

1976-01-01

The review of positron creation in superheavy quasi-molecules includes spontaneous positron emission from superheavy atoms, supercritical quasi-molecules, background effects, and some implications of the new ground state. 66 references

Single-Molecule Electronics: Chemical and Analytical Perspectives.

Science.gov (United States)

Nichols, Richard J; Higgins, Simon J

2015-01-01

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.

Kohn-Sham potentials for fullerenes and spherical molecules

International Nuclear Information System (INIS)

Pavlyukh, Y.; Berakdar, J.

2010-01-01

We present a procedure for the construction of accurate Kohn-Sham potentials of quasispherical molecules starting from the first-principles valence densities. The method is demonstrated for the case of icosahedral C 20 2+ and C 60 molecules. Provided the density is N representable the Hohenberg-Kohn theorem guarantees the uniqueness of the obtained potentials. The potential is iteratively built following the suggestion of R. van Leeuwen and E. J. Baerends [Phys. Rev. A 49, 2421 (1994)]. The high symmetry of the molecules allows a parametrization of the angular dependence of the densities and the potentials using a small number of symmetry-adapted spherical harmonics. The radial behavior of these quantities is represented on a grid and the density is reconstructed from the approximate potential by numerically solving the coupled-channel Kohn-Sham equations. Subsequently, the potential is updated and the procedure is continued until convergence is achieved.

Interaction of spin and vibrations in transport through single-molecule magnets.

Science.gov (United States)

May, Falk; Wegewijs, Maarten R; Hofstetter, Walter

2011-01-01

We study electron transport through a single-molecule magnet (SMM) and the interplay of its anisotropic spin with quantized vibrational distortions of the molecule. Based on numerical renormalization group calculations we show that, despite the longitudinal anisotropy barrier and small transverse anisotropy, vibrational fluctuations can induce quantum spin-tunneling (QST) and a QST-Kondo effect. The interplay of spin scattering, QST and molecular vibrations can strongly enhance the Kondo effect and induce an anomalous magnetic field dependence of vibrational Kondo side-bands.

Double ionization of molecule H2 in intense ultrashort laser fields

International Nuclear Information System (INIS)

Le, Thu-Thuy; Nguyen, Ngoc-Ty

2015-01-01

By solving numerically the time-dependent Schrödinger equation (TDSE), we have calculated the double ionization probability when a vibrating hydrogen molecule interacts with intense ultrashort laser pulses. The results show that in the case of vibrating nuclei the double ionization probability is higher than that of the fixed nuclei. Additionally, the double ionization probability is larger if the molecule is vibrating in a higher level. This is due to the decreasing of ionization potential when the inter-nuclei separation increases. (paper)

Isotope separation using vibrationally excited molecules

International Nuclear Information System (INIS)

Woodroffe, J.A.; Keck, J.C.

1979-01-01

Vibrational excitation of molecules having components of a selected isotope type is used to produce a conversion from vibrational to translational excitation of the molecules by collision with the molecules of a heavy carrier gas. The resulting difference in translaton between the molecules of the selected isotope type and all other molecules of the same compound permits their separate collection. When applied to uranium enrichment, a subsonic cryogenic flow of molecules of uranium hexafluoride in combination with an argon carrier gas is directed through a cooled chamber that is illuminated by laser radiaton tuned to vibrationally excite the uranium hexafluoride molecules of a specific uranium isotope. The excited molecules collide with carrier gas molecules, causing a conversion of the excitation energy into a translation of the excited molecule, which results in a higher thermal energy or diffusivity than that of the other uranium hexafluoride molecules. The flowing molecules including the excited molecules directly enter a set of cryogenically cooled channels. The higher thermal velocity of the excited molecules increases the probability of their striking a collector surface. The molecules which strike this surface immediately condense. After a predetermined thickness of molecules is collected on the surface, the flow of uranium hexafluoride is interrupted and the chamber heated to the point of vaporization of the collected hexafluoride, permitting its removal. (LL)

Separation of large DNA molecules by applying pulsed electric field to size exclusion chromatography-based microchip

Science.gov (United States)

Azuma, Naoki; Itoh, Shintaro; Fukuzawa, Kenji; Zhang, Hedong

2018-02-01

Through electrophoresis driven by a pulsed electric field, we succeeded in separating large DNA molecules with an electrophoretic microchip based on size exclusion chromatography (SEC), which was proposed in our previous study. The conditions of the pulsed electric field required to achieve the separation were determined by numerical analyses using our originally proposed separation model. From the numerical results, we succeeded in separating large DNA molecules (λ DNA and T4 DNA) within 1600 s, which was approximately half of that achieved under a direct electric field in our previous study. Our SEC-based electrophoresis microchip will be one of the effective tools to meet the growing demand of faster and more convenient separation of large DNA molecules, especially in the field of epidemiological research of infectious diseases.

Theoretical femtosecond physics atoms and molecules in strong laser fields

CERN Document Server

Grossmann, Frank

2013-01-01

Theoretical investigations of atoms and molecules interacting with pulsed or continuous wave lasers up to atomic field strengths on the order of 10^16 W/cm² are leading to an understanding of many challenging experimental discoveries. This book deals with the basics of femtosecond physics and goes up to the latest applications of new phenomena. The book presents an introduction to laser physics with mode-locking and pulsed laser operation. The solution of the time-dependent Schrödinger equation is discussed both analytically and numerically. The basis for the non-perturbative treatment of laser-matter interaction in the book is the numerical solution of the time-dependent Schrödinger equation. The light field is treated classically, and different possible gauges are discussed. Physical phenonema, ranging from Rabi-oscillations in two-level systems to the ionization of atoms, the generation of high harmonics, the ionization and dissociation of molecules as well as the control of chemical reactions are pre...

Molecule Matters van der Waals Molecules

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 12. Molecule Matters van der Waals Molecules - Noble Gas Clusters are London Molecules! E Arunan. Feature Article Volume 14 Issue 12 December 2009 pp 1210-1222 ...

Strain-induced formation of fourfold symmetric SiGe quantum dot molecules.

Science.gov (United States)

Zinovyev, V A; Dvurechenskii, A V; Kuchinskaya, P A; Armbrister, V A

2013-12-27

The strain field distribution at the surface of a multilayer structure with disklike SiGe nanomounds formed by heteroepitaxy is exploited to arrange the symmetric quantum dot molecules typically consisting of four elongated quantum dots ordered along the [010] and [100] directions. The morphological transition from fourfold quantum dot molecules to continuous fortresslike quantum rings with an increasing amount of deposited Ge is revealed. We examine key mechanisms underlying the formation of lateral quantum dot molecules by using scanning tunneling microscopy and numerical calculations of the strain energy distribution on the top of disklike SiGe nanomounds. Experimental data are well described by a simple thermodynamic model based on the accurate evaluation of the strain dependent part of the surface chemical potential. The spatial arrangement of quantum dots inside molecules is attributed to the effect of elastic property anisotropy.

Dynamical spin accumulation in large-spin magnetic molecules

Science.gov (United States)

Płomińska, Anna; Weymann, Ireneusz; Misiorny, Maciej

2018-01-01

The frequency-dependent transport through a nanodevice containing a large-spin magnetic molecule is studied theoretically in the Kondo regime. Specifically, the effect of magnetic anisotropy on dynamical spin accumulation is of primary interest. Such accumulation arises due to finite components of frequency-dependent conductance that are off diagonal in spin. Here, employing the Kubo formalism and the numerical renormalization group method, we demonstrate that the dynamical transport properties strongly depend on the relative orientation of spin moments in electrodes of the device, as well as on intrinsic parameters of the molecule. In particular, the effect of dynamical spin accumulation is found to be greatly affected by the type of magnetic anisotropy exhibited by the molecule, and it develops for frequencies corresponding to the Kondo temperature. For the parallel magnetic configuration of the device, the presence of dynamical spin accumulation is conditioned by the interplay of ferromagnetic-lead-induced exchange field and the Kondo correlations.

Interaction of spin and vibrations in transport through single-molecule magnets

Directory of Open Access Journals (Sweden)

Falk May

2011-10-01

Full Text Available We study electron transport through a single-molecule magnet (SMM and the interplay of its anisotropic spin with quantized vibrational distortions of the molecule. Based on numerical renormalization group calculations we show that, despite the longitudinal anisotropy barrier and small transverse anisotropy, vibrational fluctuations can induce quantum spin-tunneling (QST and a QST-Kondo effect. The interplay of spin scattering, QST and molecular vibrations can strongly enhance the Kondo effect and induce an anomalous magnetic field dependence of vibrational Kondo side-bands.

Environmental effects on molecules immersed in liquids

International Nuclear Information System (INIS)

Sese, L.M.

1990-01-01

A methodology to study environmental effects is thoroughly discussed. It combines molecular quantum mechanics and classical statistical mechanics of molecular fluids. Pair distribution functions collecting statistical information appear quite naturally in the quantum equations describing a single molecule. As well as allowing the computation of any individual molecular property in a liquid phase, this approach satisfies a number of theoretical requirements (dependence on density and temperature, validity in the thermodynamic limit). In a sense, it can be regarded as a useful alternative to the well-known Monte Carlo averaging processes for calculating molecular properties. Numerical applications studying liquid carbon disulphide and liquid carbon tetrachloride at several state points are given. Results cover typical RHF information (CNDO/2) on molecules, and show the sensitivity of the presented methodology to structural changes in liquids. (orig.)

Spectroscopic and electric properties of the LiCs molecule: a coupled cluster study including higher excitations

Science.gov (United States)

Sørensen, L. K.; Fleig, T.; Olsen, J.

2009-08-01

Aimed at obtaining complete and highly accurate potential energy surfaces for molecules containing heavy elements, we present a new general-order coupled cluster method which can be applied in the framework of the spin-free Dirac formalism. As an initial application we present a systematic study of electron correlation and relativistic effects on the spectroscopic and electric properties of the LiCs molecule in its electronic ground state. In particular, we closely investigate the importance of excitations higher than coupled cluster doubles, spin-free and spin-dependent relativistic effects and the correlation of outer-core electrons on the equilibrium bond length, the harmonic vibrational frequency, the dissociation energy, the dipole moment and the static electric dipole polarizability. We demonstrate that our new implementation allows for highly accurate calculations not only in the bonding region but also along the complete potential curve. The quality of our results is demonstrated by a vibrational analysis where an almost complete set of vibrational levels has been calculated accurately.

Spectroscopic and electric properties of the LiCs molecule: a coupled cluster study including higher excitations

International Nuclear Information System (INIS)

Soerensen, L K; Fleig, T; Olsen, J

2009-01-01

Aimed at obtaining complete and highly accurate potential energy surfaces for molecules containing heavy elements, we present a new general-order coupled cluster method which can be applied in the framework of the spin-free Dirac formalism. As an initial application we present a systematic study of electron correlation and relativistic effects on the spectroscopic and electric properties of the LiCs molecule in its electronic ground state. In particular, we closely investigate the importance of excitations higher than coupled cluster doubles, spin-free and spin-dependent relativistic effects and the correlation of outer-core electrons on the equilibrium bond length, the harmonic vibrational frequency, the dissociation energy, the dipole moment and the static electric dipole polarizability. We demonstrate that our new implementation allows for highly accurate calculations not only in the bonding region but also along the complete potential curve. The quality of our results is demonstrated by a vibrational analysis where an almost complete set of vibrational levels has been calculated accurately.

Improved alternating gradient transport and focusing of neutral molecules

International Nuclear Information System (INIS)

Kalnins, Juris; Lambertson, Glen; Gould, Harvey

2001-01-01

Polar molecules, in strong-field seeking states, can be transported and focused by an alternating sequence of electric field gradients that focus in one transverse direction while defocusing in the other. We show by calculation and numerical simulation, how one may greatly improve the alternating gradient transport and focusing of molecules. We use a new optimized multipole lens design, a FODO lattice beam transport line, and lenses to match the beam transport line to the beam source and the final focus. We derive analytic expressions for the potentials, fields, and gradients that may be used to design these lenses. We describe a simple lens optimization procedure and derive the equations of motion for tracking molecules through a beam transport line. As an example, we model a straight beamline that transports a 560 m/s jet-source beam of methyl fluoride molecules 15 m from its source and focuses it to 2 mm diameter. We calculate the beam transport line acceptance and transmission, for a beam with velocity spread, and estimate the transmitted intensity for specified source conditions. Possible applications are discussed

Memory effects in single-molecule spectroscopy

International Nuclear Information System (INIS)

Schmitt, Daniel T.; Schulz, Michael; Reineker, Peter

2007-01-01

From the time series of LH2 optical single-molecule fluorescence excitation spectra of Rhodospirillum molischianum the memory function of the Mori-Zwanzig equation for the optical intensity is derived numerically. We show that the time dependence of the excited states is determined by at least three different non-Markovian stochastic processes with decay constants for the Mori-Zwanzig kernel on the order of 1-5min -1 . We suggest that this decay stems from the conformational motion of the protein scaffold of LH2

Molecule Matters van der Waals Molecules

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Molecule Matters van der Waals Molecules - Rg•••HF Complexes are Debye Molecules! E Arunan. Feature Article Volume 15 Issue 7 July 2010 pp 667-674. Fulltext. Click here to view fulltext PDF. Permanent link:

Numerical analysis

CERN Document Server

Scott, L Ridgway

2011-01-01

Computational science is fundamentally changing how technological questions are addressed. The design of aircraft, automobiles, and even racing sailboats is now done by computational simulation. The mathematical foundation of this new approach is numerical analysis, which studies algorithms for computing expressions defined with real numbers. Emphasizing the theory behind the computation, this book provides a rigorous and self-contained introduction to numerical analysis and presents the advanced mathematics that underpin industrial software, including complete details that are missing from most textbooks. Using an inquiry-based learning approach, Numerical Analysis is written in a narrative style, provides historical background, and includes many of the proofs and technical details in exercises. Students will be able to go beyond an elementary understanding of numerical simulation and develop deep insights into the foundations of the subject. They will no longer have to accept the mathematical gaps that ex...

Expansion Hamiltonian model for a diatomic molecule adsorbed on a surface: Vibrational states of the CO/Cu(100) system including surface vibrations

Energy Technology Data Exchange (ETDEWEB)

Meng, Qingyong, E-mail: mengqingyong@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, 116023 Dalian (China); Meyer, Hans-Dieter, E-mail: hans-dieter.meyer@pci.uni-heidelberg.de [Theoretische Chemie, Physikalisch-Chemisches Institut, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany)

2015-10-28

Molecular-surface studies are often done by assuming a corrugated, static (i.e., rigid) surface. To be able to investigate the effects that vibrations of surface atoms may have on spectra and cross sections, an expansion Hamiltonian model is proposed on the basis of the recently reported [R. Marquardt et al., J. Chem. Phys. 132, 074108 (2010)] SAP potential energy surface (PES), which was built for the CO/Cu(100) system with a rigid surface. In contrast to other molecule-surface coupling models, such as the modified surface oscillator model, the coupling between the adsorbed molecule and the surface atoms is already included in the present expansion SAP-PES model, in which a Taylor expansion around the equilibrium positions of the surface atoms is performed. To test the quality of the Taylor expansion, a direct model, that is avoiding the expansion, is also studied. The latter, however, requests that there is only one movable surface atom included. On the basis of the present expansion and direct models, the effects of a moving top copper atom (the one to which CO is bound) on the energy levels of a bound CO/Cu(100) system are studied. For this purpose, the multiconfiguration time-dependent Hartree calculations are carried out to obtain the vibrational fundamentals and overtones of the CO/Cu(100) system including a movable top copper atom. In order to interpret the results, a simple model consisting of two coupled harmonic oscillators is introduced. From these calculations, the vibrational levels of the CO/Cu(100) system as function of the frequency of the top copper atom are discussed.

Torsion-inversion tunneling patterns in the CH-stretch vibrationally excited states of the G12 family of molecules including methylamine.

Science.gov (United States)

Dawadi, Mahesh B; Bhatta, Ram S; Perry, David S

2013-12-19

Two torsion-inversion tunneling models (models I and II) are reported for the CH-stretch vibrationally excited states in the G12 family of molecules. The torsion and inversion tunneling parameters, h(2v) and h(3v), respectively, are combined with low-order coupling terms involving the CH-stretch vibrations. Model I is a group theoretical treatment starting from the symmetric rotor methyl CH-stretch vibrations; model II is an internal coordinate model including the local-local CH-stretch coupling. Each model yields predicted torsion-inversion tunneling patterns of the four symmetry species, A, B, E1, and E2, in the CH-stretch excited states. Although the predicted tunneling patterns for the symmetric CH-stretch excited state are the same as for the ground state, inverted tunneling patterns are predicted for the asymmetric CH-stretches. The qualitative tunneling patterns predicted are independent of the model type and of the particular coupling terms considered. In model I, the magnitudes of the tunneling splittings in the two asymmetric CH-stretch excited states are equal to half of that in the ground state, but in model II, they differ when the tunneling rate is fast. The model predictions are compared across the series of molecules methanol, methylamine, 2-methylmalonaldehyde, and 5-methyltropolone and to the available experimental data.

Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy

Science.gov (United States)

Minh, David D. L.; Adib, Artur B.

2008-05-01

An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy—valid for biasing potentials of arbitrary stiffness—are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.

Sequential nonadiabatic excitation of large molecules and ions driven by strong laser fields

International Nuclear Information System (INIS)

Markevitch, Alexei N.; Levis, Robert J.; Romanov, Dmitri A.; Smith, Stanley M.; Schlegel, H. Bernhard; Ivanov, Misha Yu.

2004-01-01

Electronic processes leading to dissociative ionization of polyatomic molecules in strong laser fields are investigated experimentally, theoretically, and numerically. Using time-of-flight ion mass spectroscopy, we study the dependence of fragmentation on laser intensity for a series of related molecules and report regular trends in this dependence on the size, symmetry, and electronic structure of a molecule. Based on these data, we develop a model of dissociative ionization of polyatomic molecules in intense laser fields. The model is built on three elements: (i) nonadiabatic population transfer from the ground electronic state to the excited-state manifold via a doorway (charge-transfer) transition; (ii) exponential enhancement of this transition by collective dynamic polarization of all electrons, and (iii) sequential energy deposition in both neutral molecules and resulting molecular ions. The sequential nonadiabatic excitation is accelerated by a counterintuitive increase of a large molecule's polarizability following its ionization. The generic theory of sequential nonadiabatic excitation forms a basis for quantitative description of various nonlinear processes in polyatomic molecules and ions in strong laser fields

Calculation of Ground State Rotational Populations for Kinetic Gas Homonuclear Diatomic Molecules including Electron-Impact Excitation and Wall Collisions

International Nuclear Information System (INIS)

Farley, David R.

2010-01-01

A model has been developed to calculate the ground-state rotational populations of homonuclear diatomic molecules in kinetic gases, including the effects of electron-impact excitation, wall collisions, and gas feed rate. The equations are exact within the accuracy of the cross sections used and of the assumed equilibrating effect of wall collisions. It is found that the inflow of feed gas and equilibrating wall collisions can significantly affect the rotational distribution in competition with non-equilibrating electron-impact effects. The resulting steady-state rotational distributions are generally Boltzmann for N (ge) 3, with a rotational temperature between the wall and feed gas temperatures. The N = 0,1,2 rotational level populations depend sensitively on the relative rates of electron-impact excitation versus wall collision and gas feed rates.

Quantum Monte-Carlo programming for atoms, molecules, clusters, and solids

International Nuclear Information System (INIS)

Schattke, Wolfgang; Diez Muino, Ricardo

2013-01-01

This is a book that initiates the reader into the basic concepts and practical applications of Quantum Monte Carlo. Because of the simplicity of its theoretical concept, the authors focus on the variational Quantum Monte Carlo scheme. The reader is enabled to proceed from simple examples as the hydrogen atom to advanced ones as the Lithium solid. In between, several intermediate steps are introduced, including the Hydrogen molecule (2 electrons), the Lithium atom (3 electrons) and expanding to an arbitrary number of electrons to finally treat the three-dimensional periodic array of Lithium atoms in a crystal. The book is unique, because it provides both theory and numerical programs. It pedagogically explains how to transfer into computational tools what is usually described in a theoretical textbook. It also includes the detailed physical understanding of methodology that cannot be found in a code manual. The combination of both aspects allows the reader to assimilate the fundamentals of Quantum Monte Carlo not only by reading but also by practice.

Controlling translational motion of neutral molecules in inhomogeneous electric fields

International Nuclear Information System (INIS)

Yamakita, Yoshihiro

2006-01-01

Hydrogen molecules are excited to Rydberg states with n=16, 17 in the presence of inhomogeneous field of an electric dipole by a vacuum ultraviolet-ultraviolet double resonance scheme. The large dipole moment produced in Stark eigenstates leads to strong forces on the molecules in the inhomogeneous electric field. Deflection and deceleration are demonstrated for a pulsed supersonic beam containing the H 2 molecules in the n=16, 17, N + =2, M J =0 Rydberg states. The Rydberg states are found to survive for over 100 μs after the dipole field is switched off. The Rydberg states have a special stability with respect to decay by predissociation. Complete deceleration to the zero mean velocity is numerically demonstrated for H 2 molecules in the higher linear low-field-seeking n=16, M J =0 Rydberg states by using a symplectic integrator of the fourth order. The calculations show that the initial velocity of 900 ms -1 with translational temperature 1 K is decelerated to 0 ms -1 with 13 mK. (author)

Magnetic field modification of ultracold molecule-molecule collisions

International Nuclear Information System (INIS)

Tscherbul, T V; Suleimanov, Yu V; Aquilanti, V; Krems, R V

2009-01-01

We present an accurate quantum mechanical study of molecule-molecule collisions in the presence of a magnetic field. The work focuses on the analysis of elastic scattering and spin relaxation in collisions of O 2 ( 3 Σ g - ) molecules at cold (∼0.1 K) and ultracold (∼10 -6 K) temperatures. Our calculations show that magnetic spin relaxation in molecule-molecule collisions is extremely efficient except at magnetic fields below 1 mT. The rate constant for spin relaxation at T=0.1 K and a magnetic field of 0.1 T is found to be as large as 6.1x10 -11 cm -3 s -1 . The magnetic field dependence of elastic and inelastic scattering cross sections at ultracold temperatures is dominated by a manifold of Feshbach resonances with the density of ∼100 resonances per Tesla for collisions of molecules in the absolute ground state. This suggests that the scattering length of ultracold molecules in the absolute ground state can be effectively tuned in a very wide range of magnetic fields. Our calculations demonstrate that the number and properties of the magnetic Feshbach resonances are dramatically different for molecules in the absolute ground and excited spin states. The density of Feshbach resonances for molecule-molecule scattering in the low-field-seeking Zeeman state is reduced by a factor of 10.

How to Measure Load-Dependent Kinetics of Individual Motor Molecules Without a Force-Clamp

DEFF Research Database (Denmark)

Sung, Jongmin; Mortensen, Kim; Spudich, James A.

Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using a new method, Harmonic Force...... and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human beta-cardiac myosin molecules interacting with an actin filament...... at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load. This points to Kramer's Brownian diffusion model of chemical reactions as explanation why muscle contracts with a velocity inversely proportional to external load....

Some considerations of ''cold fusion'' including the calculation of fusion rates in molecules of hydrogen isotopes

International Nuclear Information System (INIS)

Cowley, S.C.; Kulsrud, R.M.

1989-11-01

We calculate the fusion reaction rates in molecules of hydrogen isotopes. The rates are calculated analytically (for the first time) as an asymptotic expansion in the ratio of the electron mass to the reduced mass of the nucleii. The fusion rates of the P-D, D-D, and D-T reactions are given for a variable electron mass by a simple analytic formula. However, we do not know any mechanism by which a sufficiently localized electron in solid can have an 'effective mass' large enough to explain the result of Fleischman and Pons (FP). This calculation indicates that P-D rates should exceed D-D rates for D-D fusion rates less than approximately 10 -23 per molecule per second. The D-D fusion rate is enhanced by a factor of 10 5 at 10,000 degree K if the excited vibrational states are populated with a Boltzmann distribution and the rotational excitations suppressed. The suggestion that experimental results could be explained by bombardment of cold deuterons by kilovolt deuterons is shown to be an unlikely from an energetic point of view. 12 refs., 3 figs., 1 tab

Polarization properties of below-threshold harmonics from aligned molecules H2+ in linearly polarized laser fields.

Science.gov (United States)

Dong, Fulong; Tian, Yiqun; Yu, Shujuan; Wang, Shang; Yang, Shiping; Chen, Yanjun

2015-07-13

We investigate the polarization properties of below-threshold harmonics from aligned molecules in linearly polarized laser fields numerically and analytically. We focus on lower-order harmonics (LOHs). Our simulations show that the ellipticity of below-threshold LOHs depends strongly on the orientation angle and differs significantly for different harmonic orders. Our analysis reveals that this LOH ellipticity is closely associated with resonance effects and the axis symmetry of the molecule. These results shed light on the complex generation mechanism of below-threshold harmonics from aligned molecules.

Transition probabilities and dissociation energies of MnH and MnD molecules

International Nuclear Information System (INIS)

Nagarajan, K.; Rajamanickam, N.

1997-01-01

The Frank-Condon factors (vibrational transition probabilities) and r-centroids have been evaluated by the more reliable numerical integration procedure for the bands of A-X system of MnH and MnD molecules, using a suitable potential. By fitting the Hulburt- Hirschfelder function to the experimental potential curve using correlation coefficient, the dissociation energy for the electronic ground states of MnH and MnD molecules, respectively have been estimated as D 0 0 =251±5 KJ.mol -1 and D 0 0 =312±6 KJ.mol -1 . (authors)

Double photoionisation spectra of molecules

CERN Document Server

Eland, John

2017-01-01

This book contains spectra of the doubly charged positive ions (dications) of some 75 molecules, including the major constituents of terrestrial and planetary atmospheres and prototypes of major chemical groups. It is intended to be a new resource for research in all areas of molecular spectroscopy involving high energy environments, both terrestrial and extra-terrestrial. All the spectra have been produced by photoionisation using laboratory lamps or synchrotron radiation and have been measured using the magnetic bottle time-of-flight technique by coincidence detection of correlated electron pairs. Full references to published work on the same species are given, though for several molecules these are the first published spectra. Double ionisation energies are listed and discussed in relation to the molecular electronic structure of the molecules. A full introduction to the field of molecular double ionisation is included and the mechanisms by which double photoionisation can occur are examined in detail. A p...

DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences.

Science.gov (United States)

Kunig, Verena; Potowski, Marco; Gohla, Anne; Brunschweiger, Andreas

2018-06-27

DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.

Laboratory Studies of Stabilities of Heterocyclic Aromatic Molecules: Suggested Gas Phase Ion-Molecule Routes to Production in Interstellar Gas Clouds

Science.gov (United States)

Adams, Nigel G.; Fondren, L. Dalila; McLain, Jason L.; Jackson, Doug M.

2006-01-01

Several ring compounds have been detected in interstellar gas clouds, ISC, including the aromatic, benzene. Polycyclic aromatic hydrocarbons, PAHs, have been implicated as carriers of diffuse interstellar bands (DIBs) and unidentified infrared (UIR) bands. Heterocyclic aromatic rings of intermediate size containing nitrogen, possibly PreLife molecules, were included in early searches but were not detected and a recent search for Pyrimidine was unsuccessful. Our laboratory investigations of routes to such molecules could establish their existence in ISC and suggest conditions under which their concentrations would be maximized thus aiding the searches. The stability of such ring compounds (C5H5N, C4H4N2, C5H11N and C4H8O2) has been tested in the laboratory using charge transfer excitation in ion-molecule reactions. The fragmentation paths, including production of C4H4(+), C3H3N(+) and HCN, suggest reverse routes to the parent molecules, which are presently under laboratory investigation as production sources.

Precision analysis for standard deviation measurements of immobile single fluorescent molecule images.

Science.gov (United States)

DeSantis, Michael C; DeCenzo, Shawn H; Li, Je-Luen; Wang, Y M

2010-03-29

Standard deviation measurements of intensity profiles of stationary single fluorescent molecules are useful for studying axial localization, molecular orientation, and a fluorescence imaging system's spatial resolution. Here we report on the analysis of the precision of standard deviation measurements of intensity profiles of single fluorescent molecules imaged using an EMCCD camera.We have developed an analytical expression for the standard deviation measurement error of a single image which is a function of the total number of detected photons, the background photon noise, and the camera pixel size. The theoretical results agree well with the experimental, simulation, and numerical integration results. Using this expression, we show that single-molecule standard deviation measurements offer nanometer precision for a large range of experimental parameters.

Single molecule transcription profiling with AFM

International Nuclear Information System (INIS)

Reed, Jason; Mishra, Bud; Pittenger, Bede; Magonov, Sergei; Troke, Joshua; Teitell, Michael A; Gimzewski, James K

2007-01-01

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

Detecting high-density ultracold molecules using atom–molecule collision

International Nuclear Information System (INIS)

Chen, Jun-Ren; Kao, Cheng-Yang; Chen, Hung-Bin; Liu, Yi-Wei

2013-01-01

Utilizing single-photon photoassociation, we have achieved ultracold rubidium molecules with a high number density that provides a new efficient approach toward molecular quantum degeneracy. A new detection mechanism for ultracold molecules utilizing inelastic atom–molecule collision is demonstrated. The resonant coupling effect on the formation of the X 1 Σ + g ground state 85 Rb 2 allows for a sufficient number of more deeply bound ultracold molecules, which induced an additional trap loss and heating of the co-existing atoms owing to the inelastic atom–molecule collision. Therefore, after the photoassociation process, the ultracold molecules can be investigated using the absorption image of the ultracold rubidium atoms mixed with the molecules in a crossed optical dipole trap. The existence of the ultracold molecules was then verified, and the amount of accumulated molecules was measured. This method detects the final produced ultracold molecules, and hence is distinct from the conventional trap loss experiment, which is used to study the association resonance. It is composed of measurements of the time evolution of an atomic cloud and a decay model, by which the number density of the ultracold 85 Rb 2 molecules in the optical trap was estimated to be >5.2 × 10 11 cm −3 . (paper)

Biofuels: from microbes to molecules

National Research Council Canada - National Science Library

Lu, Xuefeng

2014-01-01

.... The production of different biofuel molecules including hydrogen, methane, ethanol, butanol, higher chain alcohols, isoprenoids and fatty acid derivatives, from genetically engineered microbes...

Bibliography of electron and photon cross sections with atoms and molecules published in the 20th century. Argon

Energy Technology Data Exchange (ETDEWEB)

Hayashi, Makoto [Gaseous Electronics Institute, Nagoya, Aichi (Japan)

2003-01-01

A bibliography of original and review reports of experiments or theories of electron and photon cross sections and also electron swarm data are presented for atomic or molecular species with specified targets. These works covered 17 atoms and 51 molecules. The present bibliography is only for argon (Ar). About 1,960 papers were compiled. A comprehensive author index is included. The bibliography covers the period 1921 through 2000 for Ar. Finally, author's recommended Ar electron collision cross section set is given in numerical tables. (author)

Bibliography of electron and photon cross sections with atoms and molecules published in the 20th century. Argon

International Nuclear Information System (INIS)

Hayashi, Makoto

2003-01-01

A bibliography of original and review reports of experiments or theories of electron and photon cross sections and also electron swarm data are presented for atomic or molecular species with specified targets. These works covered 17 atoms and 51 molecules. The present bibliography is only for argon (Ar). About 1,960 papers were compiled. A comprehensive author index is included. The bibliography covers the period 1921 through 2000 for Ar. Finally, author's recommended Ar electron collision cross section set is given in numerical tables. (author)

Functionalization of Probe Tips and Supports for Single-Molecule Recognition Force Microscopy

Science.gov (United States)

Ebner, Andreas; Wildling, Linda; Zhu, Rong; Rankl, Christian; Haselgrübler, Thomas; Hinterdorfer, Peter; Gruber, Hermann J.

The measuring tip of a force microscope can be converted into a monomolecular sensor if one or few "ligand" molecules are attached to the apex of the tip while maintaining ligand function. Functionalized tips are used to study fine details of receptor-ligand interaction by force spectroscopy or to map cognate "receptor" molecules on the sample surface. The receptor (or target) molecules can be present on the surface of a biological specimen; alternatively, soluble target molecules must be immobilized on ultraflat supports. This review describes the methods of tip functionalization, as well as target molecule immobilization. Silicon nitride tips, silicon chips, and mica have usually been functionalized in three steps: (1) aminofunctionalization, (2) crosslinker attachment, and (3) ligand/receptor coupling, whereby numerous crosslinkers are available to couple widely different ligand molecules. Gold-covered tips and/or supports have usually been coated with a self-assembled monolayer, on top of which the ligand/receptor molecule has been coupled either directly or via a crosslinker molecule. Apart from these general strategies, many simplified methods have been used for tip and/or support functionalization, even single-step methods such as adsorption or chemisorption being very efficient under suitable circumstances. All methods are described with the same explicitness and critical parameters are discussed. In conclusion, this review should help to find suitable methods for specific problems of tip and support functionalization.

Low-energy positron interactions with atoms and molecules

International Nuclear Information System (INIS)

Surko, C M; Gribakin, G F; Buckman, S J

2005-01-01

This paper is a review of low-energy positron interactions with atoms and molecules. Processes of interest include elastic scattering, electronic and vibrational excitation, ionization, positronium formation and annihilation. An overview is presented of the currently available theoretical and experimental techniques to study these phenomena, including the use of trap-based positron beam sources to study collision processes with improved energy resolution. State-resolved measurements of electronic and vibrational excitation cross sections and measurement of annihilation rates in atoms and molecules as a function of incident positron energy are discussed. Where data are available, comparisons are made with analogous electron scattering cross sections. Resonance phenomena, common in electron scattering, appear to be less common in positron scattering. Possible exceptions include the sharp onsets of positron-impact electronic and vibrational excitation of selected molecules. Recent energy-resolved studies of positron annihilation in hydrocarbons containing more than a few carbon atoms provide direct evidence that vibrational Feshbach resonances underpin the anomalously large annihilation rates observed for many polyatomic species. We discuss open questions regarding this process in larger molecules, as well as positron annihilation in smaller molecules where the theoretical picture is less clear. (topical review)

Elliptically polarized high-order harmonics from aligned molecules within the strong-field approximation

DEFF Research Database (Denmark)

Etches, Adam; Madsen, Christian Bruun; Madsen, Lars Bojer

A correction term is introduced in the stationary-point analysis on high-order harmonic generation (HHG) from aligned molecules. Arising from a multi-centre expansion of the electron wave function, this term brings our numerical calculations of the Lewenstein model into qualitative agreement...

Newly detected molecules in dense interstellar clouds

Science.gov (United States)

Irvine, William M.; Avery, L. W.; Friberg, P.; Matthews, H. E.; Ziurys, L. M.

Several new interstellar molecules have been identified including C2S, C3S, C5H, C6H and (probably) HC2CHO in the cold, dark cloud TMC-1; and the discovery of the first interstellar phosphorus-containing molecule, PN, in the Orion "plateau" source. Further results include the observations of 13C3H2 and C3HD, and the first detection of HCOOH (formic acid) in a cold cloud.

Small molecule antagonists of integrin receptors.

Science.gov (United States)

Perdih, A; Dolenc, M Sollner

2010-01-01

The complex and widespread family of integrin receptors is involved in numerous physiological processes, such as tissue remodeling, angiogenesis, development of the immune response and homeostasis. In addition, their key role has been elucidated in important pathological disorders such as cancer, cardiovascular diseases, osteoporosis, autoimmune and inflammatory diseases and in the pathogenesis of infectious diseases, making them highly important targets for modern drug design campaigns. In this review we seek to present a concise overview of the small molecule antagonists of this diverse and highly complex receptor family. Integrin antagonists are classified according to the targeted integrin receptor and are discussed in four sections. First we present the fibrinogen alpha(IIb)beta3 and the vitronectin alpha (V)beta(3) receptor antagonists. The remaining selective integrin antagonists are examined in the third section. The final section is dedicated to molecules with dual or multiple integrin activity. In addition, the use of antibodies and peptidomimetic approaches to modulate the integrin receptors are discussed, as well providing the reader with an overall appreciation of the field.

Observing electron localization in a dissociating H2+ molecule in real time.

Science.gov (United States)

Xu, H; Li, Zhichao; He, Feng; Wang, X; Atia-Tul-Noor, A; Kielpinski, D; Sang, R T; Litvinyuk, I V

2017-06-16

Dissociation of diatomic molecules with odd number of electrons always causes the unpaired electron to localize on one of the two resulting atomic fragments. In the simplest diatomic molecule H 2 + dissociation yields a hydrogen atom and a proton with the sole electron ending up on one of the two nuclei. That is equivalent to breaking of a chemical bond-the most fundamental chemical process. Here we observe such electron localization in real time by performing a pump-probe experiment. We demonstrate that in H 2 + electron localization is complete in just 15 fs when the molecule's internuclear distance reaches 8 atomic units. The measurement is supported by a theoretical simulation based on numerical solution of the time-dependent Schrödinger equation. This observation advances our understanding of detailed dynamics of molecular dissociation.

Nano-manipulation of single DNA molecules

International Nuclear Information System (INIS)

Hu Jun; Shanghai Jiaotong Univ., Shanghai; Lv Junhong; Wang Guohua; Wang Ying; Li Minqian; Zhang Yi; Li Bin; Li Haikuo; An Hongjie

2004-01-01

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 10 nm 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. (authors)

Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS).

Science.gov (United States)

Braun, Joerg E; Serebrov, Victor

2017-01-01

Recent development of single-molecule techniques to study pre-mRNA splicing has provided insights into the dynamic nature of the spliceosome. Colocalization single-molecule spectroscopy (CoSMoS) allows following spliceosome assembly in real time at single-molecule resolution in the full complexity of cellular extracts. A detailed protocol of CoSMoS has been published previously (Anderson and Hoskins, Methods Mol Biol 1126:217-241, 2014). Here, we provide an update on the technical advances since the first CoSMoS studies including slide surface treatment, data processing, and representation. We describe various labeling strategies to generate RNA reporters with multiple dyes (or other moieties) at specific locations.

Growing interstellar molecules with ion-molecule reactions

International Nuclear Information System (INIS)

Bohme, D.K.

1989-01-01

Laboratory measurements of gas-phase ion-molecule reactions continue to provide important insights into the chemistry of molecular growth in interstellar environments. It is also true that the measurements are becoming more demanding as larger molecules capture our interest. While some of these measurements are motivated by current developments in chemical models of interstellar environments or by new molecular observations by astronomers, others explore novel chemistry which can lead to predictions of new interstellar molecules. Here the author views the results of some recent measurements, taken in the Ion Chemistry Laboratory at York University with the SIFT technique, which address some of the current needs of modellers and observers and which also provide some new fundamental insight into molecular growth, particularly when it occurs in the presence of large molecules such as PAH molecules which are now thought to have a major influence on the chemistry of interstellar environments in which they are present

Effects of Electric Field on the Valence-Bond Property of an Electron in a Quantum-Dot Molecule

Institute of Scientific and Technical Information of China (English)

王立民; 罗莹; 马本堃

2002-01-01

The electronic structure of the quantum-dot molecules in an electric field is investigated by the finite element method with the effective mass approximation. The numerical calculation results show that the valence bond of the quantum-dot molecule alternates between covalent bonds and ionic bonds as the electric field increases. The valence-bond property can be reflected by the oscillator strength of the intraband transition. The bound state with the highest energy level in the quantum-dot molecule gradually changes into a quasibound state when the electric field increases.

Pump-probe study of the formation of rubidium molecules by ultrafast photoassociation of ultracold atoms

Science.gov (United States)

McCabe, David J.; England, Duncan G.; Martay, Hugo E. L.; Friedman, Melissa E.; Petrovic, Jovana; Dimova, Emiliya; Chatel, Béatrice; Walmsley, Ian A.

2009-09-01

An experimental pump-probe study of the photoassociative creation of translationally ultracold rubidium molecules is presented together with numerical simulations of the process. The formation of loosely bound excited-state dimers is observed as a first step toward a fully coherent pump-dump approach to the stabilization of Rb2 into its lowest ground vibrational states. The population that contributes to the pump-probe process is characterized and found to be distinct from a background population of preassociated molecules.

Tuning the hybridization bandgap by meta-molecules with in-unit interaction

Energy Technology Data Exchange (ETDEWEB)

Chen, Yongqiang; Li, Yunhui, E-mail: liyunhui@tongji.edu.cn; Wu, Qian; Jiang, Haitao; Zhang, Yewen; Chen, Hong [Key Laboratory of Advanced Micro-Structured Materials, Ministry of Education, School of Physics Science and Engineering, Tongji University, Shanghai 200092 (China)

2015-09-07

In this paper, we demonstrate that the hybridization bandgap (HBG) can be tuned conveniently by deep subwavelength meta-molecules with in-unit interaction. Spontaneous-emission-cancellation-like (SEC-like) effect is realized in a meta-molecule by introducing the destructive interference of two detuned meta-atoms. The meta-atoms consisting of subwavelength zero-index-metamaterial-based resonators are side-coupled to a microstrip. Compared to conventional HBG configurations, the presence of in-unit interaction between meta-atoms provides more flexibility in tuning the bandgap properties, keeping the device volume almost unchanged. Both numerical simulations and microwave experiments confirm that the width, depth, and spectrum shape of HBG can be tuned by simply introducing SEC-like interaction into the meta-molecule. Due to these features, our design may be promising to be applied in microwave or optics communications systems with strict limitation of device volume and flexible bandgap properties.

Dynamics of hadronic molecule in one-boson exchange approach and possible heavy flavor molecules

International Nuclear Information System (INIS)

Ding Guijun; Liu Jiafeng; Yan Mulin

2009-01-01

We extend the one pion exchange model at quark level to include the short distance contributions coming from η, σ, ρ and ω exchange. This formalism is applied to discuss the possible molecular states of DD*/DD*, BB*/BB*, DD*, BB*, the pseudoscalar-vector systems with C=B=1 and C=-B=1 respectively. The ''δ function'' term contribution and the S-D mixing effects have been taken into account. We find the conclusions reached after including the heavier mesons exchange are qualitatively the same as those in the one pion exchange model. The previous suggestion that 1 ++ BB*/BB* molecule should exist, is confirmed in the one-boson exchange model, whereas DD* bound state should not exist. The DD*/DD* system can accommodate a 1 ++ molecule close to the threshold, the mixing between the molecule and the conventional charmonium has to be considered to identify this state with X(3872). For the BB* system, the pseudoscalar-vector systems with C=B=1 and C=-B=1, near threshold molecular states may exist. These bound states should be rather narrow, isospin is violated and the I=0 component is dominant. Experimental search channels for these states are suggested.

Quasiparticle Approach to Molecules Interacting with Quantum Solvents.

Science.gov (United States)

Lemeshko, Mikhail

2017-03-03

Understanding the behavior of molecules interacting with superfluid helium represents a formidable challenge and, in general, requires approaches relying on large-scale numerical simulations. Here, we demonstrate that experimental data collected over the last 20 years provide evidence that molecules immersed in superfluid helium form recently predicted angulon quasiparticles [Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001]. Most important, casting the many-body problem in terms of angulons amounts to a drastic simplification and yields effective molecular moments of inertia as straightforward analytic solutions of a simple microscopic Hamiltonian. The outcome of the angulon theory is in good agreement with experiment for a broad range of molecular impurities, from heavy to medium-mass to light species. These results pave the way to understanding molecular rotation in liquid and crystalline phases in terms of the angulon quasiparticle.

Slowing techniques for loading a magneto-optical trap of CaF molecules

Science.gov (United States)

Truppe, Stefan; Fitch, Noah; Williams, Hannah; Hambach, Moritz; Sauer, Ben; Hinds, Ed; Tarbutt, Mike

2016-05-01

Ultracold molecules in a magneto-optical trap (MOT) are useful for testing fundamental physics and studying strongly-interacting quantum systems. With experiments starting with a relatively fast (50-200 m/s) buffer-gas beam, a primary concern is decelerating molecules to below the MOT capture velocity, typically 10 m/s. Direct laser cooling, where the molecules are slowed via momentum transfer from a chirped counter-propagating narrowband laser, is a natural choice. However, chirping the cooling and repump lasers requires precise control of multiple laser frequencies simultaneously. Another approach, called ``white-light slowing'' uses a broadband laser such that all fast molecules in the beam are decelerated. By addressing numerous velocities no chirping is needed. Unfortunately, both techniques have significant losses as molecules are transversely heated during the optical cycling. Ideally, the slowing method would provide simultaneous deceleration and transverse guiding. A newly developed technique, called Zeeman-Sisyphus deceleration, is potentially capable of both. Using permanent magnets and optical pumping, the number of scattered photons is reduced, lessening transverse heating and relaxing the repump requirements. Here we compare all three options for CaF.

Small molecule annotation for the Protein Data Bank.

Science.gov (United States)

Sen, Sanchayita; Young, Jasmine; Berrisford, John M; Chen, Minyu; Conroy, Matthew J; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A

2014-01-01

The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors. © The Author(s) 2014. Published by Oxford University Press.

Dynamic Control of Synaptic Adhesion and Organizing Molecules in Synaptic Plasticity

Energy Technology Data Exchange (ETDEWEB)

Rudenko, Gabby (Texas-MED)

2017-01-01

Synapses play a critical role in establishing and maintaining neural circuits, permitting targeted information transfer throughout the brain. A large portfolio of synaptic adhesion/organizing molecules (SAMs) exists in the mammalian brain involved in synapse development and maintenance. SAMs bind protein partners, formingtrans-complexes spanning the synaptic cleft orcis-complexes attached to the same synaptic membrane. SAMs play key roles in cell adhesion and in organizing protein interaction networks; they can also provide mechanisms of recognition, generate scaffolds onto which partners can dock, and likely take part in signaling processes as well. SAMs are regulated through a portfolio of different mechanisms that affect their protein levels, precise localization, stability, and the availability of their partners at synapses. Interaction of SAMs with their partners can further be strengthened or weakened through alternative splicing, competing protein partners, ectodomain shedding, or astrocytically secreted factors. Given that numerous SAMs appear altered by synaptic activity, in vivo, these molecules may be used to dynamically scale up or scale down synaptic communication. Many SAMs, including neurexins, neuroligins, cadherins, and contactins, are now implicated in neuropsychiatric and neurodevelopmental diseases, such as autism spectrum disorder, schizophrenia, and bipolar disorder and studying their molecular mechanisms holds promise for developing novel therapeutics.

Machine learning-based screening of complex molecules for polymer solar cells

Science.gov (United States)

Jørgensen, Peter Bjørn; Mesta, Murat; Shil, Suranjan; García Lastra, Juan Maria; Jacobsen, Karsten Wedel; Thygesen, Kristian Sommer; Schmidt, Mikkel N.

2018-06-01

Polymer solar cells admit numerous potential advantages including low energy payback time and scalable high-speed manufacturing, but the power conversion efficiency is currently lower than for their inorganic counterparts. In a Phenyl-C_61-Butyric-Acid-Methyl-Ester (PCBM)-based blended polymer solar cell, the optical gap of the polymer and the energetic alignment of the lowest unoccupied molecular orbital (LUMO) of the polymer and the PCBM are crucial for the device efficiency. Searching for new and better materials for polymer solar cells is a computationally costly affair using density functional theory (DFT) calculations. In this work, we propose a screening procedure using a simple string representation for a promising class of donor-acceptor polymers in conjunction with a grammar variational autoencoder. The model is trained on a dataset of 3989 monomers obtained from DFT calculations and is able to predict LUMO and the lowest optical transition energy for unseen molecules with mean absolute errors of 43 and 74 meV, respectively, without knowledge of the atomic positions. We demonstrate the merit of the model for generating new molecules with the desired LUMO and optical gap energies which increases the chance of finding suitable polymers by more than a factor of five in comparison to the randomised search used in gathering the training set.

Augmented-plane-wave calculations on small molecules

International Nuclear Information System (INIS)

Serena, P.A.; Baratoff, A.; Soler, J.M.

1993-01-01

We have performed ab initio calculations on a wide range of small molecules, demonstrating the accuracy and flexibility of an alternative method for calculating the electronic structure of molecules, solids, and surfaces. It is based on the local-density approximation (LDA) for exchange and correlation and the nonlinear augmented-plane-wave method. Very accurate atomic forces are obtained directly. This allows for implementation of Car-Parrinello-like techniques to determine simultaneously the self-consistent electron wave functions and the equilibrium atomic positions within an iterative scheme. We find excellent agreement with the best existing LDA-based calculations and remarkable agreement with experiment for the equilibrium geometries, vibrational frequencies, and dipole moments of a wide variety of molecules, including strongly bound homopolar and polar molecules, hydrogen-bound and electron-deficient molecules, and weakly bound alkali and noble-metal dimers, although binding energies are overestimated

Chip-based microtrap arrays for cold polar molecules

Science.gov (United States)

Hou, Shunyong; Wei, Bin; Deng, Lianzhong; Yin, Jianping

2017-12-01

Compared to the atomic chip, which has been a powerful platform to perform an astonishing range of applications from rapid Bose-Einstein condensate (BEC) production to the atomic clock, the molecular chip is only in its infant stages. Recently a one-dimensional electric lattice was demonstrated to trap polar molecules on a chip. This excellent work opens up the way to building a molecular chip laboratory. Here we propose a two-dimensional (2D) electric lattice on a chip with concise and robust structure, which is formed by arrays of squared gold wires. Arrays of microtraps that originate in the microsize electrodes offer a steep gradient and thus allow for confining both light and heavy polar molecules. Theoretical analysis and numerical calculations are performed using two types of sample molecules, N D3 and SrF, to justify the possibility of our proposal. The height of the minima of the potential wells is about 10 μm above the surface of the chip and can be easily adjusted in a wide range by changing the voltages applied on the electrodes. These microtraps offer intriguing perspectives for investigating cold molecules in periodic potentials, such as quantum computing science, low-dimensional physics, and some other possible applications amenable to magnetic or optical lattice. The 2D adjustable electric lattice is expected to act as a building block for a future gas-phase molecular chip laboratory.

Physics of Complex Polymeric Molecules

Science.gov (United States)

Kelly, Joshua Walter

The statistical physics of complex polymers with branches and circuits is the topic of this dissertation. An important motivation are large, single-stranded (ss) RNA molecules. Such molecules form complex ``secondary" and ``tertiary" structures that can be represented as branched polymers with circuits. Such structures are in part directly determined by the nucleotide sequence and in part subject to thermal fluctuations. The polymer physics literature on molecules in this class has mostly focused on randomly branched polymers without circuits while there has been minimal research on polymers with specific structures and on polymers that contain circuits. The dissertation is composed of three parts: Part I studies branched polymers with thermally fluctuating structure confined to a potential well as a simple model for the encapsidation of viral RNA. Excluded volume interactions were ignored. In Part II, I apply Flory theory to the study of the encapsidation of viral ss RNA molecules with specific branched structures, but without circuits, in the presence of excluded volume interaction. In Part III, I expand on Part II and consider complex polymers with specific structure including both branching and circuits. I introduce a method based on the mathematics of Laplacian matrices that allows me to calculate density profiles for such molecules, which was not possible within Flory theory.

Numerical calculation of the cross section by the solution of the wave equation

International Nuclear Information System (INIS)

Drewko, J.

1982-01-01

A numerical method of solving of the wave equation is described for chosen vibrational eigenfunctions. A prepared program calculates the total cross sections for the resonant vibrational excitation for diatomic molecules on the basis of introduced molecular data. (author)

Diabatic potential-optimized discrete variable representation: application to photodissociation process of the CO molecule

International Nuclear Information System (INIS)

Bitencourt, Ana Carla P; Prudente, Frederico V; Vianna, Jose David M

2007-01-01

We propose a new numerically optimized discrete variable representation using eigenstates of diabatic Hamiltonians. This procedure provides an efficient method to solve non-adiabatic coupling problems since the generated basis sets take into account information on the diabatic potentials. The method is applied to the B 1 Σ + - D' 1 Σ + Rydberg-valence predissociation interaction in the CO molecule. Here we give an account of the discrete variable representation and present the procedure for the calculation of its optimized version, which we apply to obtain the total photodissociation cross sections of the CO molecule

Investigating single molecule adhesion by atomic force spectroscopy.

Science.gov (United States)

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

2015-02-27

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.

Numerical analysis of ion wind flow using space charge for optimal design

Science.gov (United States)

Ko, Han Seo; Shin, Dong Ho; Baek, Soo Hong

2014-11-01

Ion wind flow has been widly studied for its advantages of a micro fluidic device. However, it is very difficult to predict the performance of the ion wind flow for various conditions because of its complicated electrohydrodynamic phenomena. Thus, a reliable numerical modeling is required to design an otimal ion wind generator and calculate velocity of the ion wind for the proper performance. In this study, the numerical modeling of the ion wind has been modified and newly defined to calculate the veloctiy of the ion wind flow by combining three basic models such as electrostatics, electrodynamics and fluid dynamics. The model has included presence of initial space charges to calculate transfer energy between space charges and air gas molecules using a developed space charge correlation. The simulation has been performed for a geometry of a pin to parallel plate electrode. Finally, the results of the simulation have been compared with the experimental data for the ion wind velocity to confirm the accuracy of the modified numerical modeling and to obtain the optimal design of the ion wind generator. This work was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Korean government (MEST) (No. 2013R1A2A2A01068653).

Post-transcriptional bursting in genes regulated by small RNA molecules

Science.gov (United States)

Rodrigo, Guillermo

2018-03-01

Gene expression programs in living cells are highly dynamic due to spatiotemporal molecular signaling and inherent biochemical stochasticity. Here we study a mechanism based on molecule-to-molecule variability at the RNA level for the generation of bursts of protein production, which can lead to heterogeneity in a cell population. We develop a mathematical framework to show numerically and analytically that genes regulated post transcriptionally by small RNA molecules can exhibit such bursts due to different states of translation activity (on or off), mostly revealed in a regime of few molecules. We exploit this framework to compare transcriptional and post-transcriptional bursting and also to illustrate how to tune the resulting protein distribution with additional post-transcriptional regulations. Moreover, because RNA-RNA interactions are predictable with an energy model, we define the kinetic constants of on-off switching as functions of the two characteristic free-energy differences of the system, activation and formation, with a nonequilibrium scheme. Overall, post-transcriptional bursting represents a distinctive principle linking gene regulation to gene expression noise, which highlights the importance of the RNA layer beyond the simple information transfer paradigm and significantly contributes to the understanding of the intracellular processes from a first-principles perspective.

Photoionization of water molecules by high energy photons

Directory of Open Access Journals (Sweden)

Lara Martini

2017-07-01

Full Text Available We theoretically study the photoionization of water molecules by high energy photon impact. We develop a model in which the final state wavefunction is given by a Coulomb continuum wavefunction with effective charges and the water molecule bound states are represented using the Moccia's monocentric wavefunctions. We obtain analytical expressions for the transition matrix element that enable the computation of cross sections by numerical quadratures. We compare our predictions for photon energies between 20 and 300 eV with more elaborated theoretical results and experiments. We obtain a very good agreement with experiments, in particular, at enough high energies where there is a lack of elaborated results due to their high computational cost. Received: 15 March 2017, Accepted: 25 June 2017; Edited by: S. Kais; DOI: http://dx.doi.org/10.4279/PIP.090006 Cite as: L Martini, D I R Boll, O A Fojón, Papers in Physics 9, 090006 (2017

Symmetries and rotational line intensities in diatomic molecules

International Nuclear Information System (INIS)

Veseth, L.

1986-02-01

The general theory of angular momenta and the full rotation group is used to reconsider the theory of the intensity factors of rotational lines in the spectra of diatomic molecules (Hoenl-London factors). It is shown that the use of the rotational symmetry (rotation matrices) leads to compact derivations of the symmetry properties of the molecular wave functions, as well as the matrix elements of the transitions operator. The present work is restricted to spin-allowed electric dipole transitions, and the general sum rule characteristic of this type of transitions is rederived by use of the general angular momentum theory. A main purpose of the present work has been to provide a unified theoretical basis for exact numerical computations of Hoenl-London factors for all types of spin-allowed electric dipole transitions in diatomic molecules. The computed Hoenl-London factors are then in the next step intended to be the basis for construction of synthetic molecular band spectra, with particular applications to upper atmosperic emissions (aurora)

Spectroscopy and Chemistry of Cold Molecules

Science.gov (United States)

Momose, Takamasa

2012-06-01

Molecules at low temperatures are expected to behave quite differently from those at high temperatures because pronounced quantum effects emerge from thermal averages. Even at 10 K, a significant enhancement of reaction cross section is expected due to tunneling and resonance effects. Chemistry at this temperature is very important in order to understand chemical reactions in interstellar molecular clouds. At temperatures lower than 1 K, collisions and intermolecular interactions become qualitatively different from those at high temperatures because of the large thermal de Broglie wavelength of molecules. Collisions at these temperatures must be treated as the interference of molecular matter waves, but not as hard sphere collisions. A Bose-Einstein condensate is a significant state of matter as a result of coherent matter wave interaction. Especially, dense para-H_2 molecules are predicted to become a condensate even around 1 K. A convenient method to investigate molecules around 1 K is to dope molecules in cold matrices. Among various matrices, quantum hosts such as solid para-H_2 and superfluid He nano-droplets have been proven to be an excellent host for high-resolution spectroscopy. Rovibrational motion of molecules in these quantum hosts is well quantized on account of the weak interactions and the softness of quantum environment. The linewidths of infrared spectra of molecules in the quantum hosts are extremely narrow compared with those in other matrices. The sharp linewidths allow us to resolve fine spectral structures originated in subtle interactions between guest and host molecules. In this talk, I will describe how the splitting and lineshape of high-resolution spectra of molecules in quantum hosts give us new information on the static and dynamical interactions of molecules in quantum medium. The topics include dynamical response of superfluid environment upon rotational excitation, and possible superfluid phase of para-H_2 clusters. I will also

2D Numerical Modelling of the Resin Injection Pultrusion Process Including Experimental Resin Kinetics and Temperature Validation

DEFF Research Database (Denmark)

Rasmussen, Filip Salling; Sonne, Mads Rostgaard; Larsen, Martin

In the present study, a two-dimensional (2D) transient Eulerian thermo-chemical analysis of a carbon fibre epoxy thermosetting Resin Injection Pultrusion (RIP) process is carried out. The numerical model is implemented using the well known unconditionally stable Alternating Direction Implicit (ADI......) scheme. The total heat of reaction and the cure kinetics of the epoxy thermosetting are determined using Differential Scanning Calorimetry (DSC). A very good agreement is observed between the fitted cure kinetic model and the experimental measurements. The numerical steady state temperature predictions...

Diatomic molecule vibrational potentials: Accuracy of representations

International Nuclear Information System (INIS)

Engelke, R.

1978-01-01

A method is presented for increasing the radius of convergence of certain representations of diatomic molecule vibrational potentials. The method relies on using knowledge of the analytic structure of such potentials to the maximum when attempting to approximate them. The known singular point (due to the centrifugal and/or Coulomb potentials) at zero internuclear separation should be included in its exact form in an approximate representation. The efficacy of this idea is tested [using Peek's ''exact'' numerical Born-Oppenheimer potential for the (1ssigma/sub g/) 2 Σ + /sub g/ state of H + 2 as a test problem] when the representational form is the series of (1) Dunham, (2) Simons, Parr, and Finlan, (3) Thakkar, and (4) Ogilvie-Tipping, and also (5) when the form is a [2, 2] or a [3, 3] Pade approximant. Significant improvements in accuracy are obtained in some of these cases, particularly on the inner wall of the potential. A comparison of the effectiveness of the five methods is made both with and without the origin behavior being included exactly. This is useful in itself as no comprehensive accuracy comparison of the standard representations seems to have appeared in the literature. The Ogilvie-Tipping series, corrected at the origin for singular behavior, is the best representation presently available for states analogous to the (1ssigma/sub g/) 2 Σ + /sub g/ state of H + 2

Ion-molecule reactions: their role in radiation chemistry

International Nuclear Information System (INIS)

Lias, S.G.; Ausloos, P.

1975-01-01

A comprehensive review of ion--molecule reactions is presented, including information from mass spectrometric, organic chemistry, and NMR studies, from theoretical calculations, and from gas and liquid phase radiation chemistry. Special emphasis is placed on interpreting the role of ion--molecule reactions in systems under high energy irradiation. The discussion is presented under the following chapter headings: ion--molecule reactions and their role in radiation chemistry; unimolecular processes: the nature and structure of ionic intermediates in radiolysis; ion lifetimes and the fate of unreactive ions; kinetics and mechanisms of ion--molecule reactions; proton transfer reactions; negative atom and two-atom transfer reactions; condensation reactions; and, association or clustering reactions

Peptide binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes, and include HLA-B27-like alleles

OpenAIRE

Mothé, Bianca R.; Southwood, Scott; Sidney, John; English, A. Michelle; Wriston, Amanda; Hoof, Ilka; Shabanowitz, Jeffrey; Hunt, Donald F.; Sette, Alessandro

2013-01-01

Chinese rhesus macaques are of particular interest in SIV/HIV research as these animals have prolonged kinetics of disease progression to AIDS, compared to their Indian counterparts, suggesting that they may be a better model for HIV. Nevertheless, the specific mechanism(s) accounting for these kinetics remains unclear. The study of Major Histocompatibility Complex (MHC) molecules, including their MHC:peptide binding motifs, provides valuable information for measuring cellular immune response...

Organic molecules with abnormal geometric parameters

International Nuclear Information System (INIS)

Komarov, Igor V

2001-01-01

Organic molecules, the structural parameters of which (carbon-carbon bond lengths, bond and torsion angles) differ appreciably from the typical most frequently encountered values, are discussed. Using many examples of 'record-breaking' molecules, the limits of structural distortions in carbon compounds and their unusual chemical properties are demonstrated. Particular attention is devoted to strained compounds not yet synthesised whose properties have been predicted using quantum-chemical calculations. Factors that ensure the stability of such compounds are outlined. The bibliography includes 358 references.

Theoretical and numerical investigations of TAP experiments. New approaches for variable pressure conditions

Energy Technology Data Exchange (ETDEWEB)

Senechal, U.; Breitkopf, C. [Technische Univ. Dresden (Germany). Inst. fuer Energietechnik

2011-07-01

Temporal analysis of products (TAP) is a valuable tool for characterization of porous catalytic structures. Established TAP-modeling requires a spatially constant diffusion coefficient and neglect convective flows, which is only valid in Knudsen diffusion regime. Therefore in experiments, the number of molecules per pulse must be chosen accordingly. New approaches for variable process conditions are highly required. Thus, a new theoretical model is developed for estimating the number of molecules per pulse to meet these requirements under any conditions and at any time. The void volume is calculated as the biggest sphere fitting between three pellets. The total number of pulsed molecules is assumed to fill the first void volume at the inlet immediately. Molecule numbers from these calculations can be understood as maximum possible molecules at any time in the reactor to be in Knudsen diffusion regime, i.e., above the Knudsen number of 2. Moreover, a new methodology for generating a full three-dimensional geometrical representation of beds is presented and used for numerical simulations to investigate spatial effects. Based on a freely available open-source game physics engine library (BULLET), beds of arbitrary-sized pellets can be generated and transformed to CFD-usable geometry. In CFD-software (ANSYS CFX registered) a transient diffusive transport equation with time-dependent inlet boundary conditions is solved. Three different pellet diameters were investigated with 1e18 molecules per pulse, which is higher than the limit from the theoretical calculation. Spatial and temporal distributions of transported species show regions inside the reactor, where non-Knudsen conditions exist. From this results, the distance from inlet can be calculated where the theoretical pressure limit (Knudsen number equals 2) is obtained, i.e., from this point to the end of the reactor Knudsen regime can be assumed. Due to linear dependency of pressure and concentration (assuming ideal

Including screening in van der Waals corrected density functional theory calculations: The case of atoms and small molecules physisorbed on graphene

Energy Technology Data Exchange (ETDEWEB)

Silvestrelli, Pier Luigi; Ambrosetti, Alberto [Dipartimento di Fisica e Astronomia, Università di Padova, via Marzolo 8, I–35131 Padova, Italy and DEMOCRITOS National Simulation Center of the Italian Istituto Officina dei Materiali (IOM) of the Italian National Research Council (CNR), Trieste (Italy)

2014-03-28

The Density Functional Theory (DFT)/van der Waals-Quantum Harmonic Oscillator-Wannier function (vdW-QHO-WF) method, recently developed to include the vdW interactions in approximated DFT by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique, is applied to the cases of atoms and small molecules (X=Ar, CO, H{sub 2}, H{sub 2}O) weakly interacting with benzene and with the ideal planar graphene surface. Comparison is also presented with the results obtained by other DFT vdW-corrected schemes, including PBE+D, vdW-DF, vdW-DF2, rVV10, and by the simpler Local Density Approximation (LDA) and semilocal generalized gradient approximation approaches. While for the X-benzene systems all the considered vdW-corrected schemes perform reasonably well, it turns out that an accurate description of the X-graphene interaction requires a proper treatment of many-body contributions and of short-range screening effects, as demonstrated by adopting an improved version of the DFT/vdW-QHO-WF method. We also comment on the widespread attitude of relying on LDA to get a rough description of weakly interacting systems.

Characterization of Interstellar Organic Molecules

International Nuclear Information System (INIS)

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

2008-01-01

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.

Supersonic molecular beam electric resonance spectroscopy and van der Waals molecules

International Nuclear Information System (INIS)

Luftman, H.S.

1982-09-01

A supersonic molecular beam electric resonance (MBER) spectrometer was built to study the radiofrequency spectra of weakly bound gas phase van der Waals molecules. The instrument and its operating characteristics are described in detail. Sample mass spectra of Ar-ClF gas mixtures are also presented as an illustration of the synthesis of van der Waals molecules. The Stark focusing process for linear polar molecules is discussed and computer-simulated using both second order perturbation and variational methods. Experimental refocusing spectra of OCS and ClF are studied and compared with these trajectory calculations. Though quantitative fitting is poor, there are strong qualitative indicators that the central part of a supersonic beam consists of molecules with a significantly greater population in the lowest energy rotational states than generally assumed. Flop in as opposed to flop out resonance signals for OCS are also numerically predicted and observed. The theoretical properties of the MBER spectrum for linear molecules are elaborated upon with special emphasis on line shape considerations. MBER spectra of OCS and ClF under a variety of conditions are presented and discussed in context to these predictions. There is some uncertainty expressed both in our own modeling and in the manner complex MBER spectra have been analyzed in the past. Finally, an electrostatic potential model is used to quantitatively describe the class of van der Waals molecules Ar-MX, where MX is an alkali halide. Energetics and equilibrium geometries are calculated. The validity of using an electrostatic model to predict van der Waals bond properties is critically discussed

Fixman compensating potential for general branched molecules

Energy Technology Data Exchange (ETDEWEB)

Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [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: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States)

2013-12-28

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.

Reduced order dynamic model for polysaccharides molecule attached to an atomic force microscope

International Nuclear Information System (INIS)

Tang Deman; Li Aiqin; Attar, Peter; Dowell, Earl H.

2004-01-01

A dynamic analysis and numerical simulation has been conducted of a polysaccharides molecular structure (a ten (10) single-α-D-glucose molecule chain) connected to a moving atomic force microscope (AFM). Sinusoidal base excitation of the AFM cantilevered beam is considered. First a linearized perturbation model is constructed for the complex polysaccharides molecular structure. Then reduced order (dynamic) models based upon a proper orthogonal decomposition (POD) technique are constructed using global modes for both the linearized perturbation model and for the full nonlinear model. The agreement between the original and reduced order models (ROM/POD) is very good even when only a few global modes are included in the ROM for either the linear case or for the nonlinear case. The computational advantage of the reduced order model is clear from the results presented

Radiation- and phonon-bottleneck--induced tunneling in the Fe8 single-molecule magnet

Science.gov (United States)

Bal, M.; Friedman, Jonathan R.; Chen, W.; Tuominen, M. T.; Beedle, C. C.; Rumberger, E. M.; Hendrickson, D. N.

2008-04-01

We measure magnetization changes in a single crystal of the single-molecule magnet Fe8 when exposed to intense, short (spin dynamics, allowing observation of thermally assisted resonant tunneling between spin states at the 100 ns time scale. Detailed numerical simulations quantitatively reproduce the data and yield a spin-phonon relaxation time T1~40 ns.

Multiphoton processes in isolated atoms and molecules

International Nuclear Information System (INIS)

Sudbo, A.S.

1979-11-01

The theory of coherent excitation of a multilevel quantum mechanical system is developed. Damping of the system is taken into account by the use of a density matrix formalism. General properties of the wave function and/or the density matrix are discussed. The physical implications for the behavior of the system are described, together with possible applications of the formalism, including the infrared multiphoton excitation of molecules, and optical pumping in alkali atoms. Experimental results are presented on the infrared multiphoton dissociation of molecules, followed by a discussion of the general features of this process. The experimental results were obtained using a crossed laser and molecular beam method, and the emphasis is on determining the properties of the dissociating molecule and the dissociation products. The dissociation process is shown to be described very well by the standard statistical theory (RRKM theory) of unimolecular reactions, a brief presentation of which is also included

Thermal ion-molecule reactions in oxygen-containing molecules

International Nuclear Information System (INIS)

Kumakura, Minoru

1981-02-01

The energetics of ions and the thermal ion-molecule reactions in oxygen-containing molecules have been studied with a modified time-of-flight mass spectrometer. It was found that the translational energy of ion can be easily obtained from analysis of the decay curve using the time-of-flight mass spectrometer. The condensation-elimination reactions proceeded via cross- and homo-elimination mechanism in which the nature of intermediate-complex could be correlated with the nature of reactant ion. It was elucidated that behavior of poly-atomic oxygen-containing ions on the condensation-elimination reactions is considerably influenced by their oxonium ion structures having functional groups. In addition, the rate constants of the condensation-elimination reactions have affected with the energy state of reactant ion and the dipole moment and/or the polarizability of neutral molecule. It was clarified that the rate constants of the ion-molecule clustering reactions in poly-atomic oxygen-containing molecules such as cyclic ether of six member rings are very large and the cluster ions are stable owing to the large number of vibrational degree of freedom in the cluster ions. (author)

Detection of kinetic change points in piece-wise linear single molecule motion

Science.gov (United States)

Hill, Flynn R.; van Oijen, Antoine M.; Duderstadt, Karl E.

2018-03-01

Single-molecule approaches present a powerful way to obtain detailed kinetic information at the molecular level. However, the identification of small rate changes is often hindered by the considerable noise present in such single-molecule kinetic data. We present a general method to detect such kinetic change points in trajectories of motion of processive single molecules having Gaussian noise, with a minimum number of parameters and without the need of an assumed kinetic model beyond piece-wise linearity of motion. Kinetic change points are detected using a likelihood ratio test in which the probability of no change is compared to the probability of a change occurring, given the experimental noise. A predetermined confidence interval minimizes the occurrence of false detections. Applying the method recursively to all sub-regions of a single molecule trajectory ensures that all kinetic change points are located. The algorithm presented allows rigorous and quantitative determination of kinetic change points in noisy single molecule observations without the need for filtering or binning, which reduce temporal resolution and obscure dynamics. The statistical framework for the approach and implementation details are discussed. The detection power of the algorithm is assessed using simulations with both single kinetic changes and multiple kinetic changes that typically arise in observations of single-molecule DNA-replication reactions. Implementations of the algorithm are provided in ImageJ plugin format written in Java and in the Julia language for numeric computing, with accompanying Jupyter Notebooks to allow reproduction of the analysis presented here.

Vibronic interactions proceeding from combined analytical and numerical considerations: Covalent functionalization of graphene by benzene, distortions, electronic transitions

Energy Technology Data Exchange (ETDEWEB)

Krasnenko, V.; Boltrushko, V.; Hizhnyakov, V. [Institute of Physics, University of Tartu, W. Ostwaldi Str 1, 50411 Tartu (Estonia)

2016-04-07

Chemically bound states of benzene molecules with graphene are studied both analytically and numerically. The states are formed by switching off intrabonds of π-electrons in C{sub 6} rings to interbonds. A number of different undistorted and distorted structures are established both with aligned and with transversal mutual orientation of benzene and graphene. The vibronic interactions causing distortions of bound states are found, by using a combination of analytical and numerical considerations. This allows one to determine all electronic transitions of π-electrons without explicit numerical calculations of excited states, to find the conical intersections of potentials, and to show that the mechanism of distortions is the pseudo-Jahn-Teller effect. It is found that the aligned distorted benzene molecule placed between two graphene sheets makes a chemical bond with both of them, which may be used for fastening of graphene sheets together.

Bibliography of electron and photon cross sections with atoms and molecules published in the 20th century. Halogen molecules

International Nuclear Information System (INIS)

Hayashi, Makoto

2003-12-01

A bibliographies of original and review reports of experiments or theories of electron and photon cross sections and also electron swarm data are presented for atomic or molecular species with specified targets. These works covered 17 atoms and 51 molecules. The present bibliography is only for halogen molecules (F 2 , Cl 2 , Br 2 , I 2 ). About 190(F 2 ), 360(Cl 2 ), 140(Br 2 ) and 240(I 2 ) papers were compiled respectively. A comprehensive author indexes for each molecule are included. The bibliography covers the period 1901 through 2000 for F 2 -I 2 . Finally, author's comments for F 2 -I 2 electron collision cross sections are given. (author)

Analytic expression for any pure rotational transition (ΔJ≥1) for a diatomic molecule

International Nuclear Information System (INIS)

Korek, M.; Hamdoun, B.; Fakhreddine, K.

1999-01-01

Full text.The problem of the pure rotational transitions vJ↔vJ' for any spectra |J-J'|≥1 for a diatomic molecule is considered. It is proved that, the wave functions ΨvJ and ΨvJ' are expanded in terms of the running number m=[J'(J'+1)-J(J+1)]/2 as ΨvJ=Σπ n m n (n=0) and ΨvJ'=Σπ n (-m) n (n=0) where π n are expressed in terms of the pure vibrational wave function φ 0 and its rotational corrections φ n (defined in the conventional perturbation theory). By using this m-representation of the wave functions the pure rotational matrix elements of the considered transitions are given by M vJ vJ' = =Σμ 2n m 2n (n=0) where μ 2n are simple combinations of simple integrals of the form i |γ|φ n >. This formulation is valid for any potential (either numerical or analytical), any vibrational level v and any operator γ. The numerical application to the Dunham potential of the molecule H 2 in the Raman transitions and to the Huffaker potential of the molecule CO in the infrared transitions shows the validity and the high accuracy of the present formulation

Numerical calculation of electromagnetic properties including chirality parameters for uniaxial bianisotropic media

International Nuclear Information System (INIS)

Amirkhizi, Alireza V; Nemat-Nasser, Sia

2008-01-01

Through the use of conductive straight wires or coils the electromagnetic properties of a composite material can be modified. The asymmetric geometry of the coils creates an overall chiral response. The polarization vectors rotate as an electromagnetic wave travels through such a medium. To calculate the chirality of a medium prior to its manufacturing, we developed a method to extract all four electromagnetic material parameter tensors for a general uniaxial bianisotropic composite based on the numerical simulation of the electromagnetic fields. Our method uses appropriate line and surface field averages in a single unit cell of the periodic structure of the composite material. These overall field quantities have physical meaning only when the microscopic variation of the electromagnetic fields in the scale of the unit cell is not important, that is when the wavelength of interest is significantly larger than the maximum linear dimension of the unit cell. The overall constitutive relations of the periodic structure can then be obtained from the relations among the average quantities

Bibliography of electron and photon cross sections with atoms and molecules published in the 20th century. Hydrogen halide molecules

International Nuclear Information System (INIS)

Hayashi, Makoto

2004-03-01

Bibliographies of original and review reports of experiments or theories of electron and photon cross sections and also electron swarm data are presented for atomic or molecular species with specified targets. These works covered 17 atoms and 51 molecules. The present bibliography is only for hydrogen halide molecules (HF, HCL, HBr, HI). About 330 (HF), 420 (HCl) 220 (HBr) and 150 (HI) papers were compiled respectively. Comprehensive author indexes for each molecule are included. The bibliography covers the period 1903 through 2000 for HF-HI. Finally, author's comments for HBr electron collision cross sections are given. (author)

Toward Generalization of Iterative Small Molecule Synthesis.

Science.gov (United States)

Lehmann, Jonathan W; Blair, Daniel J; Burke, Martin D

2018-02-01

Small molecules have extensive untapped potential to benefit society, but access to this potential is too often restricted by limitations inherent to the customized approach currently used to synthesize this class of chemical matter. In contrast, the "building block approach", i.e., generalized iterative assembly of interchangeable parts, has now proven to be a highly efficient and flexible way to construct things ranging all the way from skyscrapers to macromolecules to artificial intelligence algorithms. The structural redundancy found in many small molecules suggests that they possess a similar capacity for generalized building block-based construction. It is also encouraging that many customized iterative synthesis methods have been developed that improve access to specific classes of small molecules. There has also been substantial recent progress toward the iterative assembly of many different types of small molecules, including complex natural products, pharmaceuticals, biological probes, and materials, using common building blocks and coupling chemistry. Collectively, these advances suggest that a generalized building block approach for small molecule synthesis may be within reach.

Toward Generalization of Iterative Small Molecule Synthesis

Science.gov (United States)

Lehmann, Jonathan W.; Blair, Daniel J.; Burke, Martin D.

2018-01-01

Small molecules have extensive untapped potential to benefit society, but access to this potential is too often restricted by limitations inherent to the customized approach currently used to synthesize this class of chemical matter. In contrast, the “building block approach”, i.e., generalized iterative assembly of interchangeable parts, has now proven to be a highly efficient and flexible way to construct things ranging all the way from skyscrapers to macromolecules to artificial intelligence algorithms. The structural redundancy found in many small molecules suggests that they possess a similar capacity for generalized building block-based construction. It is also encouraging that many customized iterative synthesis methods have been developed that improve access to specific classes of small molecules. There has also been substantial recent progress toward the iterative assembly of many different types of small molecules, including complex natural products, pharmaceuticals, biological probes, and materials, using common building blocks and coupling chemistry. Collectively, these advances suggest that a generalized building block approach for small molecule synthesis may be within reach. PMID:29696152

Mapping the Small Molecule Interactome by Mass Spectrometry.

Science.gov (United States)

Flaxman, Hope A; Woo, Christina M

2018-01-16

Mapping small molecule interactions throughout the proteome provides the critical structural basis for functional analysis of their impact on biochemistry. However, translation of mass spectrometry-based proteomics methods to directly profile the interaction between a small molecule and the whole proteome is challenging because of the substoichiometric nature of many interactions, the diversity of covalent and noncovalent interactions involved, and the subsequent computational complexity associated with their spectral assignment. Recent advances in chemical proteomics have begun fill this gap to provide a structural basis for the breadth of small molecule-protein interactions in the whole proteome. Innovations enabling direct characterization of the small molecule interactome include faster, more sensitive instrumentation coupled to chemical conjugation, enrichment, and labeling methods that facilitate detection and assignment. These methods have started to measure molecular interaction hotspots due to inherent differences in local amino acid reactivity and binding affinity throughout the proteome. Measurement of the small molecule interactome is producing structural insights and methods for probing and engineering protein biochemistry. Direct structural characterization of the small molecule interactome is a rapidly emerging area pushing new frontiers in biochemistry at the interface of small molecules and the proteome.

Electron-excited molecule interactions

International Nuclear Information System (INIS)

Christophorou, L.G.; Tennessee Univ., Knoxville, TN

1991-01-01

In this paper the limited but significant knowledge to date on electron scattering from vibrationally/rotationally excited molecules and electron scattering from and electron impact ionization of electronically excited molecules is briefly summarized and discussed. The profound effects of the internal energy content of a molecule on its electron attachment properties are highlighted focusing in particular on electron attachment to vibrationally/rotationally and to electronically excited molecules. The limited knowledge to date on electron-excited molecule interactions clearly shows that the cross sections for certain electron-molecule collision processes can be very different from those involving ground state molecules. For example, optically enhanced electron attachment studies have shown that electron attachment to electronically excited molecules can occur with cross sections 10 6 to 10 7 times larger compared to ground state molecules. The study of electron-excited molecule interactions offers many experimental and theoretical challenges and opportunities and is both of fundamental and technological significance. 54 refs., 15 figs

Magnetic quantum tunneling: insights from simple molecule-based magnets.

Science.gov (United States)

Hill, Stephen; Datta, Saiti; Liu, Junjie; Inglis, Ross; Milios, Constantinos J; Feng, Patrick L; Henderson, John J; del Barco, Enrique; Brechin, Euan K; Hendrickson, David N

2010-05-28

This perspectives article takes a broad view of the current understanding of magnetic bistability and magnetic quantum tunneling in single-molecule magnets (SMMs), focusing on three families of relatively simple, low-nuclearity transition metal clusters: spin S = 4 Ni(II)(4), Mn(III)(3) (S = 2 and 6) and Mn(III)(6) (S = 4 and 12). The Mn(III) complexes are related by the fact that they contain triangular Mn(III)(3) units in which the exchange may be switched from antiferromagnetic to ferromagnetic without significantly altering the coordination around the Mn(III) centers, thereby leaving the single-ion physics more-or-less unaltered. This allows for a detailed and systematic study of the way in which the individual-ion anisotropies project onto the molecular spin ground state in otherwise identical low- and high-spin molecules, thus providing unique insights into the key factors that control the quantum dynamics of SMMs, namely: (i) the height of the kinetic barrier to magnetization relaxation; and (ii) the transverse interactions that cause tunneling through this barrier. Numerical calculations are supported by an unprecedented experimental data set (17 different compounds), including very detailed spectroscopic information obtained from high-frequency electron paramagnetic resonance and low-temperature hysteresis measurements. Comparisons are made between the giant spin and multi-spin phenomenologies. The giant spin approach assumes the ground state spin, S, to be exact, enabling implementation of simple anisotropy projection techniques. This methodology provides a basic understanding of the concept of anisotropy dilution whereby the cluster anisotropy decreases as the total spin increases, resulting in a barrier that depends weakly on S. This partly explains why the record barrier for a SMM (86 K for Mn(6)) has barely increased in the 15 years since the first studies of Mn(12)-acetate, and why the tiny Mn(3) molecule can have a barrier approaching 60% of this

Quantum Phases of Atom-Molecule Mixtures of Fermionic Atoms

Science.gov (United States)

Lopez, Nicolas; Tsai, Shan-Wen

2009-11-01

Cold atom experiments have observed atom-molecule mixtures by tuning the interactions between particles.footnotetextM.L. Olsen, J. D. Perreault, T. D. Cumby, and D. S. Jin, Phys. Rev. A 80, 030701(R) (2009) We study many particle interactions by examaning a simple model that describes the destruction of fermionic atom pairs to form single bosonic molecules and vice versa. A set of functional Renomalization Group equationsfootnotetextR. Shankar, Rev. Mod. Phys., Vol 66 No. 1, January 1994^,footnotetextS.W. Tsai, A.H. Castro Neto, R. Shankar, D.K. Campbell, Phys. Rev. B 72, 054531 (2005) describing these processes are set up and solved numerically. The Self Energy of the fermions are attained as a function of frequency and we search for frequency dependent instabilities that could denote a transition from a disordered liquid to a BCS phase. (Financial support from NSF DMR-084781 and UC-Lab Fees Research Program.)

Computer systems for annotation of single molecule fragments

Science.gov (United States)

Schwartz, David Charles; Severin, Jessica

2016-07-19

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.

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

Science.gov (United States)

2011-01-01

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution. PMID:21338175

Single Molecule Nanoelectrochemistry in Electrical Junctions.

Science.gov (United States)

Nichols, Richard J; Higgins, Simon J

2016-11-15

It is now possible to reliably measure single molecule conductance in a wide variety of environments including organic liquids, ultrahigh vacuum, water, ionic liquids, and electrolytes. The most commonly used methods deploy scanning probe microscopes, mechanically formed break junctions, or lithographically formed nanogap contacts. Molecules are generally captured between a pair of facing electrodes, and the junction current response is measured as a function of bias voltage. Gating electrodes can also be added so that the electrostatic potential at the molecular bridge can be independently controlled by this third noncontacting electrode. This can also be achieved in an electrolytic environment using a four-electrode bipotentiostatic configuration, which allows independent electrode potential control of the two contacting electrodes. This is commonly realized using an electrochemical STM and enables single molecule electrical characterization as a function of electrode potential and redox state of the molecular bridge. This has emerged as a powerful tool in modern interfacial electrochemistry and nanoelectrochemistry for studying charge transport across single molecules as a function of electrode potential and the electrolytic environments. Such measurements are possible in electrolytes ranging from aqueous buffers to nonaqueous ionic liquids. In this Account, we illustrate a number of examples of single molecule electrical measurements under electrode potential control use a scanning tunneling microscope (STM) and demonstrate how these can help in the understanding of charge transport in single molecule junctions. Examples showing charge transport following phase coherent tunneling to incoherent charge hopping across redox active molecular bridges are shown. In the case of bipyridinium (or viologen) molecular wires, it is shown how electrochemical reduction leads to an increase of the single molecule conductance, which is controlled by the liquid electrochemical

JSME: a free molecule editor in JavaScript.

Science.gov (United States)

Bienfait, Bruno; Ertl, Peter

2013-01-01

A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript. The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/

Strategies For Immobilization Of Bioactive Organic Molecules On Titanium Implant Surfaces – A Review

Directory of Open Access Journals (Sweden)

Panayotov Ivan V.

2015-03-01

Full Text Available Numerous approaches have been used to improve the tissue-implant interface of titanium (Ti and titanium alloy (Ti6Al4V. They all aim at increasing cell migration and attachment to the metal, preventing unspecific protein adsorption and improving post-implantation healing process. Promising methods for titanium and titanium alloy surface modification are based on the immobilization of biologically active organic molecules. New and interesting biochemical approaches to such surface modification include layer-by-layer deposition of polyelectrolyte films, phage display-selected surface binding peptides and self-assembled DNA monolayer systems. The present review summarizes the scientific information about these methods, which are at in vitro or in vivo development stages, and hopes to promote their future application in dental implantology and in oral and maxillofacial surgery.

Methods to enable the design of bioactive small molecules targeting RNA.

Science.gov (United States)

Disney, Matthew D; Yildirim, Ilyas; Childs-Disney, Jessica L

2014-02-21

RNA is an immensely important target for small molecule therapeutics or chemical probes of function. However, methods that identify, annotate, and optimize RNA-small molecule interactions that could enable the design of compounds that modulate RNA function are in their infancies. This review describes recent approaches that have been developed to understand and optimize RNA motif-small molecule interactions, including structure-activity relationships through sequencing (StARTS), quantitative structure-activity relationships (QSAR), chemical similarity searching, structure-based design and docking, and molecular dynamics (MD) simulations. Case studies described include the design of small molecules targeting RNA expansions, the bacterial A-site, viral RNAs, and telomerase RNA. These approaches can be combined to afford a synergistic method to exploit the myriad of RNA targets in the transcriptome.

Ultra-cold molecule production

International Nuclear Information System (INIS)

Ramirez-Serrano, Jamie; Chandler, David W.; Strecker, Kevin; Rahn, Larry A.

2005-01-01

The production of Ultra-cold molecules is a goal of many laboratories through out the world. Here we are pursuing a unique technique that utilizes the kinematics of atomic and molecular collisions to achieve the goal of producing substantial numbers of sub Kelvin molecules confined in a trap. Here a trap is defined as an apparatus that spatially localizes, in a known location in the laboratory, a sample of molecules whose temperature is below one degree absolute Kelvin. Further, the storage time for the molecules must be sufficient to measure and possibly further cool the molecules. We utilize a technique unique to Sandia to form cold molecules from near mass degenerate collisions between atoms and molecules. This report describes the progress we have made using this novel technique and the further progress towards trapping molecules we have cooled

Molecules in stars

International Nuclear Information System (INIS)

Tsuji, T.

1986-01-01

Recently, research related to molecules in stars has rapidly expanded because of progress in related fields. For this reason, it is almost impossible to cover all the topics related to molecules in stars. Thus, here the authors focus their attention on molecules in the atmospheres of cool stars and do not cover in any detail topics related to circumstellar molecules originating from expanding envelopes located far from the stellar surface. However, the authors do discuss molecules in quasi-static circumstellar envelopes (a recently discovered new component of circumstellar envelopes) located near the stellar surface, since molecular lines originating from such envelopes show little velocity shift relative to photospheric lines, and hence they directly affect the interpretation and analysis of stellar spectra

Semi-empirical γ-ray peak efficiency determination including self-absorption correction based on numerical integration

International Nuclear Information System (INIS)

Noguchi, M.; Takeda, K.; Higuchi, H.

1981-01-01

A method of γ-ray efficiency determination for extended (plane or bulk) samples based on numerical integration of point source efficiency is studied. The proposed method is widely applicable to samples of various shapes and materials. The geometrical factor in the peak efficiency can easily be corrected for by simply changing the integration region, and γ-ray self-absorption is also corrected by the absorption coefficients for the sample matrix. (author)

Molecule Matters

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 4. Molecule Matters – van der Waals Molecules - History and Some Perspectives on Intermolecular Forces. E Arunan. Feature Article Volume 14 Issue 4 April 2009 pp 346-356 ...

Strategies for Discovery of Small Molecule Radiation Protectors and Radiation Mitigators

Directory of Open Access Journals (Sweden)

Joel S Greenberger

2012-01-01

Full Text Available Mitochondrial targeted radiation damage protectors (delivered prior to irradiation and mitigators (delivered after irradiation, but before the appearance of symptoms associated with radiation syndrome have been a recent focus in drug discovery for 1 normal tissue radiation protection during fractionated radiotherapy, and 2 radiation terrorism counter measures. Several categories of such molecules have been discovered: nitroxide-linked hybrid molecules, including GS-nitroxide, GS-nitric oxide synthase inhibitors, p53/mdm2/mdm4 inhibitors, and pharmaceutical agents including inhibitors of the phosphoinositide-3-kinase pathway and the anti-seizure medicine, carbamazepine. Evaluation of potential new irradiation dose modifying molecules to protect normal tissue includes: clonagenic radiation survival curves; assays for apoptosis and DNA repair, and irradiation-induced depletion of antioxidant stores. Studies of organ specific radioprotection and in total body irradiation-induced hematopoietic syndrome in the mouse model for protection/mitigation facilitate rational means by which to move candidate small molecule drugs along the drug discovery pipeline into clinical development.

Strategies for Discovery of Small Molecule Radiation Protectors and Radiation Mitigators

Energy Technology Data Exchange (ETDEWEB)

Greenberger, Joel S.; Clump, David [Radiation Oncology Department, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States); Kagan, Valerian [Environmental and Occupational Health Department, University of Pittsburgh, Pittsburgh, PA (United States); Bayir, Hülya [Critical Care Medicine Department, University of Pittsburgh Medical Center, Pittsburgh, PA (United States); Lazo, John S. [Pharmacology Department, University of Virginia, Charlottesville, VA (United States); Wipf, Peter [Department of Chemistry, Accelerated Chemical Discovery Center, University of Pittsburgh, Pittsburgh, PA (United States); Li, Song; Gao, Xiang [Pharmaceutical Science Department, University of Pittsburgh, Pittsburgh, PA (United States); Epperly, Michael W., E-mail: greenbergerjs@upmc.edu [Radiation Oncology Department, University of Pittsburgh Cancer Institute, Pittsburgh, PA (United States)

2012-01-13

Mitochondrial targeted radiation damage protectors (delivered prior to irradiation) and mitigators (delivered after irradiation, but before the appearance of symptoms associated with radiation syndrome) have been a recent focus in drug discovery for (1) normal tissue radiation protection during fractionated radiotherapy, and (2) radiation terrorism counter measures. Several categories of such molecules have been discovered: nitroxide-linked hybrid molecules, including GS-nitroxide, GS-nitric oxide synthase inhibitors, p53/mdm2/mdm4 inhibitors, and pharmaceutical agents including inhibitors of the phosphoinositide-3-kinase pathway and the anti-seizure medicine, carbamazepine. Evaluation of potential new radiation dose modifying molecules to protect normal tissue includes: clonogenic radiation survival curves, assays for apoptosis and DNA repair, and irradiation-induced depletion of antioxidant stores. Studies of organ specific radioprotection and in total body irradiation-induced hematopoietic syndrome in the mouse model for protection/mitigation facilitate rational means by which to move candidate small molecule drugs along the drug discovery pipeline into clinical development.

Charge transport in polyguanine-polycytosine DNA molecules

International Nuclear Information System (INIS)

Wei, J H; Chan, K S

2007-01-01

A double chain tight-binding model is proposed to interpret the experimental I-V curves for polyguanine-polycytosine DNA molecules reported in Porath et al (2000 Nature 493 635). The proposed model includes the salient features of existing transport models of DNA molecules. The proposed double chain model fits excellently with the experimental I-V curves and provides a theoretical interpretation of features found in the I-V curves, which so far do not have a satisfactory explanation. Steps in the I-V curves are explained as the result of transmission gaps caused by hybridization with reservoirs and inter-chain coupling. Variations in I-V curves are due to the variation of inter-chain and intra-chain hopping parameters caused by structural changes in the DNA molecules

Fluorescent Biosensors Based on Single-Molecule Counting.

Science.gov (United States)

Ma, Fei; Li, Ying; Tang, Bo; Zhang, Chun-Yang

2016-09-20

fluorescence signals by specific in vitro/in vivo fluorescent labeling, and consequently, the fluorescent molecules indicate the presence of target molecules. The resultant fluorescence signals may be simply counted by either microfluidic device-integrated confocal microscopy or total internal reflection fluorescence-based single-molecule imaging. We have developed a series of single-molecule counting-based biosensors which can be classified as separation-free and separation-assisted assays. As a proof-of-concept, we demonstrate the applications of single-molecule counting-based biosensors for sensitive detection of various target biomolecules such as DNAs, miRNAs, proteins, enzymes, and intact cells, which may function as the disease-related biomarkers. Moreover, we give a summary of future directions to expand the usability of single-molecule counting-based biosensors including (1) the development of more user-friendly and automated instruments, (2) the discovery of new fluorescent labels and labeling strategies, and (3) the introduction of new concepts for the design of novel biosensors. Due to their high sensitivity, good selectivity, rapidity, and simplicity, we believe that the single-molecule counting-based fluorescent biosensors will indubitably find wide applications in biological research, clinical diagnostics, and drug discovery.

Formation of Ultracold Molecules

Energy Technology Data Exchange (ETDEWEB)

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

2016-01-28

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.

Introduction to precise numerical methods

CERN Document Server

Aberth, Oliver

2007-01-01

Precise numerical analysis may be defined as the study of computer methods for solving mathematical problems either exactly or to prescribed accuracy. This book explains how precise numerical analysis is constructed. The book also provides exercises which illustrate points from the text and references for the methods presented. All disc-based content for this title is now available on the Web. · Clearer, simpler descriptions and explanations ofthe various numerical methods· Two new types of numerical problems; accurately solving partial differential equations with the included software and computing line integrals in the complex plane.

Molecules for Fluorescence Detection of Specific Chemicals

Science.gov (United States)

Fedor, Steve

2008-01-01

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

Dynamic evolution of temporal dissipative-soliton molecules in large normal path-averaged dispersion fiber lasers

International Nuclear Information System (INIS)

Liu Xueming

2010-01-01

The robust dissipative soliton molecules (DSM's) exhibiting as the quasirectangular spectral profile are investigated numerically and observed experimentally in mode-locked fiber lasers with the large normal path-averaged dispersion and the large net cavity dispersion. These DSM's have an independently evolving phase with a pulse duration T 0 of about 20 ps and a peak-to-peak separation of about 8T 0 . Under laboratory conditions, the proposed laser delivers vibrating DSM's with an oscillating amplitude of less than a percent of peak separation. Numerical simulations show that DSM's are characterized by a spectral modulation pattern with about a 3-dB modulation depth measured as an averaged value. The experimental observations are in excellent agreement with the numerical predictions.

A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile

Directory of Open Access Journals (Sweden)

Rajani Thanissery

2018-06-01

Full Text Available Antibiotics are considered to be the first line of treatment for mild to moderately severe Clostridium difficile infection (CDI in humans. However, antibiotics are also risk factors for CDI as they decrease colonization resistance against C. difficile by altering the gut microbiota and metabolome. Finding compounds that selectively inhibit different stages of the C. difficile life cycle, while sparing the indigenous gut microbiota is important for the development of alternatives to standard antibiotic treatment. 2-aminoimidazole (2-AI molecules are known to disrupt bacterial protection mechanisms in antibiotic resistant bacteria such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus, but are yet to be evaluated against C. difficile. A comprehensive small molecule-screening pipeline was developed to investigate how novel small molecules affect different stages of the C. difficile life cycle (growth, toxin, and sporulation in vitro, and a library of commensal bacteria that are associated with colonization resistance against C. difficile. The initial screening tested the efficacy of eleven 2-AI molecules (compound 1 through 11 against C. difficile R20291 compared to a vancomycin (2 μg/ml control. Molecules were selected for their ability to inhibit C. difficile growth, toxin activity, and sporulation. Further testing included growth inhibition of other C. difficile strains (CD196, M68, CF5, 630, BI9, M120 belonging to distinct PCR ribotypes, and a commensal panel (Bacteroides fragilis, B. thetaiotaomicron, C. scindens, C. hylemonae, Lactobacillus acidophilus, L. gasseri, Escherichia coli, B. longum subsp. infantis. Three molecules compound 1 and 2, and 3 were microbicidal, whereas compounds 4, 7, 9, and 11 inhibited toxin activity without affecting the growth of C. difficile strains and the commensal microbiota. The antimicrobial and anti-toxin effects of 2-AI molecules need to be further characterized for mode of

Electron Scattering From Atoms, Molecules, Nuclei, and Bulk Matter

CERN Document Server

Whelan, Colm T

2005-01-01

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.

Collisions of low-energy antiprotons and protons with atoms and molecules

International Nuclear Information System (INIS)

Luehr, Armin

2010-01-01

Antiproton (anti p) collisions have evolved to a powerful tool for the testing of dynamic electron correlations in atoms and molecules. While advances in the understanding of anti p collisions with the simplest one- and two-electron atoms, H and He, have been achieved experiment and theory did not agree for low-energy anti p+He collisions ( 2 despite its fundamental role in representing the simplest two-electron molecule. The obtained results may be useful for the anti p experiments at CERN (e.g., antihydrogen production) and in particular for the facility design of low-energy anti p storage rings (e.g., at FLAIR) where a precise knowledge of the anti p interaction with the dominant residual-gas molecule H 2 is needed. In this work a nonperturbative, time-dependent numerical approach is developed which describes ionization and excitation of atoms or molecules by either anti p or p impact based on the impact-parameter method. A spectral close-coupling method is employed for solving the time-dependent Schroedinger equation in which the scattering wave function is expanded in (effective) one- or two-electron eigenstates of the target. This includes for the first time a full two-electron, two-center description of the H 2 molecule in anti p collisions. The radial part of the one-electron eigenstates is expanded in B splines while the two-electron basis is obtained with a configurationinteraction approach. Calculations are performed for anti p collisions with H, H 2 + , and H 2 as well as with He and alkali-metal atoms Li, Na, K, and Rb. Additionally, data are obtained for p collisions with H 2 , Li, Na, and K. The developed method is tested and validated by detailed comparison of the present findings for p impacts and for anti p+He collisions with literature data. On the other hand, total and differential cross sections for ionization and excitation of the targets by anti p impact complement the sparse literature data of this kind. Results gained from different targets

X-ray characterization of solid small molecule organic materials

Science.gov (United States)

Billinge, Simon; Shankland, Kenneth; Shankland, Norman; Florence, Alastair

2014-06-10

The present invention provides, inter alia, methods of characterizing a small molecule organic material, e.g., a drug or a drug product. This method includes subjecting the solid small molecule organic material to x-ray total scattering analysis at a short wavelength, collecting data generated thereby, and mathematically transforming the data to provide a refined set of data.

A fluorogenic probe for SNAP-tagged plasma membrane proteins based on the solvatochromic molecule Nile Red.

Science.gov (United States)

Prifti, Efthymia; Reymond, Luc; Umebayashi, Miwa; Hovius, Ruud; Riezman, Howard; Johnsson, Kai

2014-03-21

A fluorogenic probe for plasma membrane proteins based on the dye Nile Red and SNAP-tag is introduced. It takes advantage of Nile Red, a solvatochromic molecule highly fluorescent in an apolar environment, such as cellular membranes, but almost dark in a polar aqueous environment. The probe possesses a tuned affinity for membranes allowing its Nile Red moiety to insert into the lipid bilayer of the plasma membrane, becoming fluorescent, only after its conjugation to a SNAP-tagged plasma membrane protein. The fluorogenic character of the probe was demonstrated for different SNAP-tag fusion proteins, including the human insulin receptor. This work introduces a new approach for generating a powerful turn-on probe for "no-wash" labeling of plasma membrane proteins with numerous applications in bioimaging.

Proteinaceous molecules mediating Bifidobacterium-host interactions

Directory of Open Access Journals (Sweden)

Lorena Ruiz

2016-08-01

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.

Exotic helium molecules; Molecules exotiques d'helium

Energy Technology Data Exchange (ETDEWEB)

Portier, M

2007-12-15

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)

Advances and challenges in electron-molecule scattering physics-A Report of the 14th International Symposium on Electron-Molecule Collisions and Swarms

Energy Technology Data Exchange (ETDEWEB)

Khakoo, M A [Department of Physics, California State University, Fullerton, CA 92831 (United States); Lima, M A P [Departamento de Eletronica Quantica, Instituto de Fisica ' Gleb Wataghin' -UNICAMP, Caixa Postal 6165, 13083-970 Campinas (Brazil); Tennyson, J [Department of Physics and Astronomy, University College, Gower Street, London WC1E 6BT (United Kingdom)

2006-07-15

A report is presented of the 13th International Symposium on Electron-Molecule Collisions Physics (Instituto de Fisica, Unicamp, Campinas, Brazil, 27-30 July 2005). This workshop covered low-energy electron interactions with atoms, molecules and condensed matter systems. Several important aspects of this symposium were to bring together theory and experimental advances in this field for gaseous targets as well as showcasing the increasing diversity of electron-molecule collision applications in condensed matter and biological applications. A summary session was held wherein were discussed aspects of the future of the field, including the development of new theoretical and experimental capabilities.

Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis.

Science.gov (United States)

Cao, Chan; Long, Yi-Tao

2018-02-20

Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis

Investigation on Single-Molecule Junctions Based on Current–Voltage Characteristics

Directory of Open Access Journals (Sweden)

Yuji Isshiki

2018-02-01

Full Text Available The relationship between the current through an electronic device and the voltage across its terminals is a current–voltage characteristic (I–V that determine basic device performance. Currently, I–V measurement on a single-molecule scale can be performed using break junction technique, where a single molecule junction can be prepared by trapping a single molecule into a nanogap between metal electrodes. The single-molecule I–Vs provide not only the device performance, but also reflect information on energy dispersion of the electronic state and the electron-molecular vibration coupling in the junction. This mini review focuses on recent representative studies on I–Vs of the single molecule junctions that cover investigation on the single-molecule diode property, the molecular vibration, and the electronic structure as a form of transmission probability, and electronic density of states, including the spin state of the single-molecule junctions. In addition, thermoelectronic measurements based on I–Vs and identification of the charged carriers (i.e., electrons or holes are presented. The analysis in the single-molecule I–Vs provides fundamental and essential information for a better understanding of the single-molecule science, and puts the single molecule junction to more practical use in molecular devices.

Discrete unified gas kinetic scheme for all Knudsen number flows. III. Binary gas mixtures of Maxwell molecules

Science.gov (United States)

Zhang, Yue; Zhu, Lianhua; Wang, Ruijie; Guo, Zhaoli

2018-05-01

Recently a discrete unified gas kinetic scheme (DUGKS) in a finite-volume formulation based on the Boltzmann model equation has been developed for gas flows in all flow regimes. The original DUGKS is designed for flows of single-species gases. In this work, we extend the DUGKS to flows of binary gas mixtures of Maxwell molecules based on the Andries-Aoki-Perthame kinetic model [P. Andries et al., J. Stat. Phys. 106, 993 (2002), 10.1023/A:1014033703134. A particular feature of the method is that the flux at each cell interface is evaluated based on the characteristic solution of the kinetic equation itself; thus the numerical dissipation is low in comparison with that using direct reconstruction. Furthermore, the implicit treatment of the collision term enables the time step to be free from the restriction of the relaxation time. Unlike the DUGKS for single-species flows, a nonlinear system must be solved to determine the interaction parameters appearing in the equilibrium distribution function, which can be obtained analytically for Maxwell molecules. Several tests are performed to validate the scheme, including the shock structure problem under different Mach numbers and molar concentrations, the channel flow driven by a small gradient of pressure, temperature, or concentration, the plane Couette flow, and the shear driven cavity flow under different mass ratios and molar concentrations. The results are compared with those from other reliable numerical methods. The results show that the proposed scheme is an effective and reliable method for binary gas mixtures in all flow regimes.

The status of molecules

International Nuclear Information System (INIS)

Barnes, T.; Oak Ridge National Lab., TN; Tennessee Univ., Knoxville, TN

1994-06-01

This report summarizes the experimental and theoretical status of hadronic molecules, which are weakly-bound states of two or more hadrons. We begin with a brief history of the subject and discuss a few good candidates, and then abstract some signatures for molecules which may be of interest in the classification of possible molecule states. Next we argue that a more general understanding of 2 → 2 hadron-hadron scattering amplitudes will be crucial for molecule searches, and discuss some of our recent work in this area. We conclude with a discussion of a few more recent molecule candidates (notably the f o (1710)) which are not well established as molecules but satisfy some of the expected signatures. (Author)

A novel method of including Landau level mixing in numerical studies of the quantum Hall effect

International Nuclear Information System (INIS)

Wooten, Rachel; Quinn, John; Macek, Joseph

2013-01-01

Landau level mixing should influence the quantum Hall effect for all except the strongest applied magnetic fields. We propose a simple method for examining the effects of Landau level mixing by incorporating multiple Landau levels into the Haldane pseudopotentials through exact numerical diagonalization. Some of the resulting pseudopotentials for the lowest and first excited Landau levels will be presented

Strategy to discover diverse optimal molecules in the small molecule universe.

Science.gov (United States)

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

2015-03-23

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.

Bibliography of electron and photon cross sections with atoms and molecules published in the 20th century. Nitrogen molecule

International Nuclear Information System (INIS)

Hayashi, Makoto

2003-06-01

A bibliography of original and review reports of experiments or theories of electron and photon cross sections and also electron swarm data are presented for atomic or molecular species with specified targets. These works covered 17 atoms and 51 molecules. The present bibliography is only for nitrogen molecule (N 2 ). About 2240 papers were compiled. A comprehensive author index is include. The bibliography covers the period 1906 through 2000 for N 2 . Finally, author's comments for N 2 electron collision cross section are given. (author)

Numerical problems in physics

CERN Document Server

Singh, Devraj

2015-01-01

Numerical Problems in Physics, Volume 1 is intended to serve the need of the students pursuing graduate and post graduate courses in universities with Physics and Materials Science as subject including those appearing in engineering, medical, and civil services entrance examinations. KEY FEATURES: * 29 chapters on Optics, Wave & Oscillations, Electromagnetic Field Theory, Solid State Physics & Modern Physics * 540 solved numerical problems of various universities and ompetitive examinations * 523 multiple choice questions for quick and clear understanding of subject matter * 567 unsolved numerical problems for grasping concepts of the various topic in Physics * 49 Figures for understanding problems and concept

Toxicology of organic-inorganic hybrid molecules: bio-organometallics and its toxicology.

Science.gov (United States)

Fujie, Tomoya; Hara, Takato; Kaji, Toshiyuki

2016-01-01

Bio-organometallics is a research strategy of biology that uses organic-inorganic hybrid molecules. The molecules are expected to exhibit useful bioactivities based on the unique structure formed by interaction between the organic structure and intramolecular metal(s). However, studies on both biology and toxicology of organic-inorganic hybrid molecules have been incompletely performed. There can be two types of toxicological studies of bio-organometallics; one is evaluation of organic-inorganic hybrid molecules and the other is analysis of biological systems from the viewpoint of toxicology using organic-inorganic hybrid molecules. Our recent studies indicate that cytotoxicity of hybrid molecules containing a metal that is nontoxic in inorganic forms can be more toxic than that of hybrid molecules containing a metal that is toxic in inorganic forms when the structure of the ligand is the same. Additionally, it was revealed that organic-inorganic hybrid molecules are useful for analysis of biological systems important for understanding the toxicity of chemical compounds including heavy metals.

Numerical calculations in quantum field theories

International Nuclear Information System (INIS)

Rebbi, C.

1984-01-01

Four lecture notes are included: (1) motivation for numerical calculations in Quantum Field Theory; (2) numerical simulation methods; (3) Monte Carlo studies of Quantum Chromo Dynamics; and (4) systems with fermions. 23 references

Light incoupling in small molecule organic solar cells

Energy Technology Data Exchange (ETDEWEB)

Allinger, Nikola; Meiss, Jan; Riede, Moritz; Leo, Karl [Institut fuer Angewandte Photophysik, Technische Universitaet Dresden, 01069 Dresden (Germany); Gnehr, Wolf-Michael [Heliatek GmbH, Liebigstrasse 26, 01187 Dresden (Germany)

2008-07-01

Light incoupling is an essential topic for optimization of organic solar cells. In our group, we examine light incoupling of different kinds of transparent contacting materials as well as external dielectric coatings, using optical simulation of thin film systems and experimental methods. Thin films of small molecules are prepared by thermal evaporation in a multi-chamber UHV system. Complex refraction indices of various materials are calculated from reflection and transmission measurements of monolayers. For modelling of optical properties of thin film systems, we developed a numerical simulation program based on the transfer matrix method. The cell structures investigated consist of nanolayers of small molecules, using ZnPc/C60 as an acceptor-donor heterojunction. As contact materials, we compare the expensive standard material indium tin oxide (ITO) with more cost-efficient alternatives like thin Ag layers or spin-coated layers of the polymer PEDOT:PSS, and discuss the resulting cell properties. Additional dielectric layers of varying materials, like tris(8-hydroxy-quinolinate)-aluminum (Alq3) or N,N'-tetrakis(4-methoxyphenyl)-benzidine (MeO-TPD), are deposited on top of the stack and their influence on cell efficiencies is investigated.

Cell Adhesion Molecules of the Immunoglobulin Superfamily in the Nervous System

DEFF Research Database (Denmark)

Walmod, Peter Schledermann; Pedersen, Martin Volmer; Berezin, Vladimir

2007-01-01

Cell adhesion molecules (CAMs) are proteins mediating cell-cell or cell-extracellular matrix (ECM) interactions. CAMs are traditionally divided into four groups, the cadherins, the selectins, the integrins and CAMs belonging to the immunoglobulin superfamily (IgSF). The present chapter describes...... CAMs belonging to IgSF, that exclusively or in part, are expressed in the nervous system. The chapter includes descriptions of myelin protein zero (P0), integrin-associated protein (CD47), neuroplastin, activated leukocyte-cell adhesion molecule (ALCAM), melanoma cell adhesion molecule (MCAM......), myelinassociated glycoprotein (MAG), the neural cell adhesion molecules 1 and 2 (NCAM, NCAM2), Down Syndrome cell adhesion molecule (DSCAM) and Down Syndrome cell adhesion molecule-like-1 (DSCAML1), sidekick 1 and 2 (SDK1, SDK2), signal-regulatory proteins (SIRPs), nectins, nectin-like proteins (necls...

The formation of carbon chain molecules in IRC + 10216

International Nuclear Information System (INIS)

Howe, D.A.; Millar, T.J.

1990-01-01

This paper considers the formation of carbon-chain molecules, including C 2n H, C n S, HC 2n+1 N (n = 1-3) and SiC n (n = 1-4), in the outflowing envelope of the late-type carbon star IRC + 10216. The results suggest that the organo-sulphur species C 2 S and C 3 S can be formed in ion-molecule reactions involving acetylene ions and parent CS and SiS molecules. In addition to ion-molecule processes, neutral-neutral reactions can play a significant role in the formation of hydrocarbons and cyanopolyynes with up to six heavy atoms and in the formation of SiC 4 , and suggest that SiC 3 might be observable. However, the short time-scales available in the outflow are such that the observed abundances of the cyanopolyynes larger than HC 5 N cannot be reproduced using the parent molecules and abundances adopted here. (author)

Bibliography of electron and photon cross sections with atoms and molecules published in the 20th century. Hydrogen molecules

International Nuclear Information System (INIS)

Hayashi, Makoto

2004-02-01

Bibliographies of original and review reports of experiments or theories of electron and photon cross sections and also electron swarm data are presented for atomic or molecular species with specified targets. These works covered 17 atoms and 51 molecules. The present bibliography is only for hydrogen molecules (H 2 , HD, HT, D 2 , DT, T 2 ). About 2200 papers were compiled. A comprehensive author index is included. The bibliography covers the period 1901 through 2000 for H 2 . Finally, author's comments for H 2 electron collision cross sections are given. (author)

Separation and Characterization of DNA Molecules and Intermolecular Interactions in Pressure-Driven Micro Flow

Science.gov (United States)

Friedrich, Sarah; Wang, Tza-Huei

Pressure-driven flow in micron-sized diameter capillaries can be used to separate DNA molecules by size in a technique called Free Solution Hydrodynamic Separation. By coupling this technique with Cylindrical Illumination Confocal Spectroscopy, we have developed a highly sensitive and quantitative platform capable of separating DNA molecules by length over a large dynamic range (25 bp to 48 kbp) in a single run using only picoliters or femtograms of a DNA sample. The optical detection volume completely spans the capillary cross section, enabling highly efficient single molecule detection for enhanced sensitivity and quantification accuracy via single molecule counting. Because each DNA molecule generates its own fluorescent burst, these burst profiles can be further analyzed to individually characterize each DNA molecule's shape as it passes through the detection region. We exploit these burst profiles to visualize fluctuations in conformation under shear flow in microcapillaries, and utilizing combined mobility shift analysis, explore the complex relationship between molecular properties including length and conformation, hydrodynamic mobility, solution conditions including ion species and concentrations, and separation conditions including flow rate and capillary diameter.

Molecule scattering from insulator and metal surfaces

International Nuclear Information System (INIS)

Moroz, Iryna; Ambaye, Hailemariam; Manson, J R

2004-01-01

Calculations are carried out and compared with data for the scattering of CH 4 molecules from a LiF(001) surface and for O 2 scattering from Al(111). The theory is a mixed classical-quantum formalism that includes energy and momentum transfers between the surface and projectile for translational and rotational motions as well as internal mode excitation of the projectile molecule. The translational and rotational degrees of freedom couple most strongly to multiphonon excitations of the surface and are treated with classical dynamics. Internal vibrational excitations of the molecules are treated with a semiclassical formalism with extension to arbitrary numbers of modes and arbitrary quantum numbers. Calculations show good agreement for the dependence on incident translational energy, incident beam angle and surface temperature when compared with data for energy-resolved intensity spectra and angular distributions

Analytic vibrational matrix elements for diatomic molecules

International Nuclear Information System (INIS)

Bouanich, J.P.; Ogilvie, J.F.; Tipping, R.H.

1986-01-01

The vibrational matrix elements and expectation values for a diatomic molecule, including the rotational dependence, are calculated for powers of the reduced displacement in terms of the parameters of the Dunham potential-energy function. (orig.)

Dynamics of Activated Molecules

Energy Technology Data Exchange (ETDEWEB)

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

2016-11-16

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.

Radiational and energetic characteristics of diatomic molecules (data base)

International Nuclear Information System (INIS)

Kuznetsova, L.A.; Pazyuk, E.A.; Stolyarov, A.V.

1993-01-01

Data base on radiational and energetic characteristics of diatomic molecules was created. The base consists of two parts: reference system and recommended data system. The reference system contains the information about studies of radiational and energetic parameters of more than 1500 electronic states and 1700 electron transfers for ∼ 350 diatomic molecules and their ions. The base bibliography includes ∼ 3000 publications. 11 refs., 1 figs

Cell Adhesion Molecules and Ubiquitination—Functions and Significance

Science.gov (United States)

Homrich, Mirka; Gotthard, Ingo; Wobst, Hilke; Diestel, Simone

2015-01-01

Cell adhesion molecules of the immunoglobulin (Ig) superfamily represent the biggest group of cell adhesion molecules. They have been analyzed since approximately 40 years ago and most of them have been shown to play a role in tumor progression and in the nervous system. All members of the Ig superfamily are intensively posttranslationally modified. However, many aspects of their cellular functions are not yet known. Since a few years ago it is known that some of the Ig superfamily members are modified by ubiquitin. Ubiquitination has classically been described as a proteasomal degradation signal but during the last years it became obvious that it can regulate many other processes including internalization of cell surface molecules and lysosomal sorting. The purpose of this review is to summarize the current knowledge about the ubiquitination of cell adhesion molecules of the Ig superfamily and to discuss its potential physiological roles in tumorigenesis and in the nervous system. PMID:26703751

Lanczos-driven coupled-cluster damped linear response theory for molecules in polarizable environments

DEFF Research Database (Denmark)

List, Nanna Holmgaard; Coriani, Sonia; Kongsted, Jacob

2014-01-01

are specifically motivated by a twofold aim: (i) computation of core excitations in realistic surroundings and (ii) examination of the effect of the differential response of the environment upon excitation solely related to the CC multipliers (herein denoted the J matrix) in computations of excitation energies......We present an extension of a previously reported implementation of a Lanczos-driven coupled-cluster (CC) damped linear response approach to molecules in condensed phases, where the effects of a surrounding environment are incorporated by means of the polarizable embedding formalism. We...... and transition moments of polarizable-embedded molecules. Numerical calculations demonstrate that the differential polarization of the environment due to the first-order CC multipliers provides only minor contributions to the solvatochromic shift for all transitions considered. We thus complement previous works...

Mathematical modeling and numerical study of a spray in a rarefied gas. Application to the simulation of dust particle transport in ITER in case of vacuum loss accident

International Nuclear Information System (INIS)

Charles, F.

2009-11-01

The thesis deals with kinetic models describing a rarefied spray. These models rely on coupling two Partial Differential Equations which describe the spatio-temporal evolution of the distribution of molecules and dust particles. The model presented in the first part is described by two Boltzmann-type equations where collisions between molecules and particles are modeled by two collision operators. We suggest two models of this collision operators. In the first one, collisions between dust particles and molecules are supposed to be elastic. In the second one, we assume those collisions are inelastic and given by a diffuse reflexion mechanism on the surface of dust specks. This leads to establish non classical collision operators. We prove that in the case of elastic collisions, the spatially homogeneous system has weak solutions which preserve mass and energy, and which satisfy an entropy inequality. We then describe the numerical simulation of the inelastic model, which is based on a Direct Simulation Method. This brings to light that the numerical simulation of the system becomes too expensive because the typical size of a dust particle is too large. We therefore introduce in the second part of this work a model constituted of a coupling (by a drag force term) between a Boltzmann equation and a Vlasov equation. To this end, we perform a scaling of the Boltzmann/Boltzmann system and an asymptotic expansion of one of the dimensionless collision operators with respect to the ratio of mass between a molecule of gas and a particle. A rigorous proof of the passage to the limit is given in the spatially homogeneous setting, for the elastic model of collision operators. It includes a new variant of Povzner's inequality in which the vanishing mass ratio is taken into account. Moreover, we numerically compare the Boltzmann/Boltzmann and Vlasov/Boltzmann systems with the inelastic collision operators. The simulation of the Vlasov equation is performed with a Particle

Hyperfine structure of 2Σ molecules containing alkaline-earth-metal atoms

Science.gov (United States)

Aldegunde, Jesus; Hutson, Jeremy M.

2018-04-01

Ultracold molecules with both electron spin and an electric dipole moment offer new possibilities in quantum science. We use density-functional theory to calculate hyperfine coupling constants for a selection of molecules important in this area, including RbSr, LiYb, RbYb, CaF, and SrF. We find substantial hyperfine coupling constants for the fermionic isotopes of the alkaline-earth-metal and Yb atoms. We discuss the hyperfine level patterns and Zeeman splittings expected for these molecules. The results will be important both to experiments aimed at forming ultracold open-shell molecules and to their applications.

Numerical methods in software and analysis

CERN Document Server

Rice, John R

1992-01-01

Numerical Methods, Software, and Analysis, Second Edition introduces science and engineering students to the methods, tools, and ideas of numerical computation. Introductory courses in numerical methods face a fundamental problem-there is too little time to learn too much. This text solves that problem by using high-quality mathematical software. In fact, the objective of the text is to present scientific problem solving using standard mathematical software. This book discusses numerous programs and software packages focusing on the IMSL library (including the PROTRAN system) and ACM Algorithm

Electron-molecule collisions

International Nuclear Information System (INIS)

Shimamura, I.; Takayanagi, K.

1984-01-01

The study of collision processes plays an important research role in modern physics. Many significant discoveries have been made by means of collision experiments. Based on theoretical, experimental, and computational studies, this volume presents an overview detailing the basic processes of electron-molecule collisions. The editors have collected papers-written by a group of international experts-that consider a diverse range of phenomena occurring in electronmolecule collisions. The volume discusses first the basic formulation for scattering problems and then gives an outline of the physics of electron-molecule collisions. The main topics covered are rotational transitions, vibrational transitions, dissociation of molecules in slow collisions, the electron-molecule collision as a spectroscopic tool for studying molecular electronic structures, and experimental and computational techniques for determining the cross sections. These well-referenced chapters are self-contained and can be read independently or consecutively. Authoritative and up-to-date, Electron-Molecule Collisions is a useful addition to the libraries of students and researchers in the fields of atomic, molecular, and chemical physics, and physical chemistry

Semiclassical theory of resonance inelastic electron-molecule collisions

International Nuclear Information System (INIS)

Kazanskij, A.K.

1986-01-01

Semiclassical approach to the theory of resonance electron-molecule collisions, unlocal with respect to interatomic distance was developed. Two problems were considered: modified adiabatic approach for sigle-pole approximation of R-matrix and Fano-Feshbach-Bardsley theory. It is shown that these problems are similar in semiclassical approximation. A simple equation system with coefficients expressed in quadratures was obtained. It enables to determine amplitudes of all processes (including dissociation adhesion, association ejection, free-free and free-bound transitions) in energetic representation with respect to nucleus vibrations in molecule with allowance for both descrete and continuous spectra of nucleus motion in molecule. Quantitative investigation of the system results to the notion of dynamic energy curve of intermediate state, generalizing the motion of such curve in boomerang theory

Electronic and magnetic properties of Mn{sub 12} single-molecule magnets on the Au(111) surface

Energy Technology Data Exchange (ETDEWEB)

Voss, Soenke; Burgert, Michael; Fonin, Mikhail; Groth, Ulrich; Ruediger, Ulrich [Universitaet Konstanz (Germany); Michaelis, Christian; Brihuega, Ivan; Kern, Klaus [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany); Dedkov, Yury S. [Institut fuer Festkoerperphysik, Technische Universitaet Dresden (Germany)

2008-07-01

The paramount interest in single-molecule magnets (SMMs) like Mn{sub 12}-acetate and its derivatives was inspired by numerous experimental and theoretical insights indicating the feasibility of addressing quantum effects of magnetism on a molecular scale. Due to its relatively high blocking temperature ({proportional_to}3 K) combined with the ability to identify well-defined spin states, Mn{sub 12} still remains the most favoured SMM possibly allowing the detection of magnetic fingerprints in transport properties of a single molecule. In this work, the electronic properties of Mn{sub 12} molecules chemically grafted on Au(111) surfaces have been studied by means of low temperature as well as room temperature scanning tunneling microscopy and spectroscopy (STS), X-ray absorption spectroscopy and photoelectron spectroscopy. The results revealed signatures from most probably intact Mn{sub 12} molecules while STS measurements in magnetic fields indicate the possibility to identify magnetic fingerprints in scanning tunneling spectra. The results will be discussed with respect to previous attempts to perform transport measurements on Mn{sub 12} SMMs.

Exotic helium molecules; Molecules exotiques d'helium

Energy Technology Data Exchange (ETDEWEB)

Portier, M

2007-12-15

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)

Extracellular Molecules Involved in Cancer Cell Invasion

International Nuclear Information System (INIS)

Stivarou, Theodora; Patsavoudi, Evangelia

2015-01-01

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

Role of chrysin on expression of insulin signaling molecules

Directory of Open Access Journals (Sweden)

Kottireddy Satyanarayana

2015-01-01

Full Text Available Background: Currently available drugs are unsuccessful for the treatment of tye-2 diabetes due to their adverseside-effects. Hence, a search for novel drugs, especially ofplant origin, continues. Chrysin (5,7-dihydroxyflavone is a flavonoid, natural component of traditional medicinal herbs, present in honey, propolis and many plant extracts that hasbeen used in traditional medicine around the world to treat numerous ailments. Objective: The present study was aimed to identify the protective role of chrysin on the expression of insulin-signaling molecules in the skeletal muscle of high fat and sucrose-induced type-2 diabetic adult male rats. Materials and Methods: The oral effective dose of chrysin (100 mg/kg body weight was given once a day until the end of the study (30 days post-induction of diabetes to high fat diet-induced diabetic rats.At the end of the experimental period, fasting blood glucose, oral glucose tolerance, serum lipid profile, lipid peroxidation (LPO and free radical generation, as well as the levels of insulin signaling molecules and tissue glycogen in the gastrocnemius muscle were assessed. Results: Diabetic rats showed impaired glucose tolerance and impairment in insulin signaling molecules (IR, IRS-1, p-IRS-1Tyr 632 , p- Akt Thr308 , glucose transporter subtype 4 [GLUT4] proteins and glycogen concentration. Serum insulin, lipid profile, LPO and free radical generation were found to be increased in diabetic control rats.The treatment with chrysin normalized the altered levels of blood glucose, serum insulin, lipid profile, LPO and insulin signaling molecules as well as GLUT4 proteins. Conclusion: Our present findings indicate that chrysin improves glycemic control through activation of insulin signal transduction in the gastrocnemius muscle of high fat and sucrose-induced type-2 diabetic male rats.

Resonances in electron-molecule scattering and photoionization

International Nuclear Information System (INIS)

Schneider, B.I.; Collins, L.A.

1984-05-01

The development of reliable theoretical models for calculating the decay of quasi-stationary states of molecular systems has become an important endeavor for theoretical chemists. The understanding and analysis of a wide variety of physical and chemical phenomena depend on a knowledge of the behavior of these states in both collisional and photoionization problems. In this article we describe the theory and calculation of these cross sections using our Linear Algebraic/Optical Potential method. The theory makes optimal use of the numerical methods developed to solve large sets of coupled integral equations and the bound state techniques used by quantum chemists. Calculations are presented for a representative class of diatomic and triatomic molecules at varying levels of sophistication and for collisional and photoionization cross sections. 48 references, 11 figures

Elastic scattering of low energy electrons by hydrogen molecule

International Nuclear Information System (INIS)

Freitas, L.C.G.; Mu-Tao, L.; Botelho, L.F.

1987-01-01

The coherent version of the Renormalized Multiple-Centre Potential Model (RMPM) has been extended to treat the elastic scattering of low energy electrons by H2 molecule. The intramolecular Multiple Scattering (MS) effect has also been included. The comparison against the experimental data shows that the inclusion of the MS improves significantly with experiment. The extension of the present method to study electron-polyatomic molecule interaction is also discussed. (author) [pt

Electronic Transport in Single-Stranded DNA Molecule Related to Huntington's Disease

Science.gov (United States)

Sarmento, R. G.; Silva, R. N. O.; Madeira, M. P.; Frazão, N. F.; Sousa, J. O.; Macedo-Filho, A.

2018-04-01

We report a numerical analysis of the electronic transport in single chain DNA molecule consisting of 182 nucleotides. The DNA chains studied were extracted from a segment of the human chromosome 4p16.3, which were modified by expansion of CAG (cytosine-adenine-guanine) triplet repeats to mimics Huntington's disease. The mutated DNA chains were connected between two platinum electrodes to analyze the relationship between charge propagation in the molecule and Huntington's disease. The computations were performed within a tight-binding model, together with a transfer matrix technique, to investigate the current-voltage (I-V) of 23 types of DNA sequence and compare them with the distributions of the related CAG repeat numbers with the disease. All DNA sequences studied have a characteristic behavior of a semiconductor. In addition, the results showed a direct correlation between the current-voltage curves and the distributions of the CAG repeat numbers, suggesting possible applications in the development of DNA-based biosensors for molecular diagnostics.

Multiphoton dissociation of polyatomic molecules

International Nuclear Information System (INIS)

Schulz, P.A.

1979-10-01

The dynamics of infrared multiphoton excitation and dissociation of SF 6 was investigated under collision free conditions by a crossed laser-molecular beam method. In order to understand the excitation mechanism and to elucidate the requirements of laser intensity and energy fluence, a series of experiments were carried out to measure the dissociation yield dependences on energy fluence, vibrational temperature of SF 6 , the pulse duration of the CO 2 laser and the frequency in both one and two laser experiments. Translational energy distributions of the SF 5 dissociation product measured by time of flight and angular distributions and the dissociation lifetime of excited SF 6 as inferred from the observation of secondary dissociation of SF 5 into SF 4 and F during the laser pulse suggest that the dynamics of dissociation of excited molecules is dominated by complete energy randomization and rapid intramolecular energy transfer on a nanosecond timescale, and can be adequately described by RRKM theory. An improved phenomenological model including the initial intensity dependent excitation, a rate equation describing the absorption and stimulated emission of single photons, and the unimolecular dissociation of excited molecules is constructed based on available experimental results. The model shows that the energy fluence of the laser determines the excitation of molecules in the quasi-continuum and the excess energy with which molecules dissociate after the laser pulse. The role played by the laser intensity in multiphoton dissociation is more significant than just that of overcoming the intensity dependent absorption in the lowest levels. 63 references

Coupling single-molecule magnets to quantum circuits

International Nuclear Information System (INIS)

Jenkins, Mark; Martínez-Pérez, María José; Zueco, David; Luis, Fernando; Hümmer, Thomas; García-Ripoll, Juanjo

2013-01-01

In this work we study theoretically the coupling of single-molecule magnets (SMMs) to a variety of quantum circuits, including microwave resonators with and without constrictions and flux qubits. The main result of this study is that it is possible to achieve strong and ultrastrong coupling regimes between SMM crystals and the superconducting circuit, with strong hints that such a coupling could also be reached for individual molecules close to constrictions. Building on the resulting coupling strengths and the typical coherence times of these molecules (∼ μs), we conclude that SMMs can be used for coherent storage and manipulation of quantum information, either in the context of quantum computing or in quantum simulations. Throughout the work we also discuss in detail the family of molecules that are most suitable for such operations, based not only on the coupling strength, but also on the typical energy gaps and the simplicity with which they can be tuned and oriented. Finally, we also discuss practical advantages of SMMs, such as the possibility to fabricate the SMMs ensembles on the chip through the deposition of small droplets. (paper)

Charge transport properties of a twisted DNA molecule: A renormalization approach

Energy Technology Data Exchange (ETDEWEB)

Almeida, M.L. de; Ourique, G.S.; Fulco, U.L. [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN (Brazil); Albuquerque, E.L., E-mail: eudenilson@gmail.com [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN (Brazil); Moura, F.A.B.F. de; Lyra, M.L. [Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió-AL (Brazil)

2016-10-20

In this work we study the charge transport properties of a nanodevice consisting of a finite segment of the DNA molecule sandwiched between two metallic electrodes. Our model takes into account a nearest-neighbor tight-binding Hamiltonian considering the nucleobases twist motion, whose solutions make use of a two-steps renormalization process to simplify the algebra, which can be otherwise quite involved. The resulting variations of the charge transport efficiency are analyzed by numerically computing the main features of the electron transmittance spectra as well as their I × V characteristic curves.

Observation and control of coherent torsional dynamics in a quinquethiophene molecule.

Science.gov (United States)

Cirmi, Giovanni; Brida, Daniele; Gambetta, Alessio; Piacenza, Manuel; Della Sala, Fabio; Favaretto, Laura; Cerullo, Giulio; Lanzani, Guglielmo

2010-07-28

By applying femtosecond pump-probe spectroscopy to a substituted quinquethiophene molecule in solution, we observe in the time domain the coherent torsional dynamics that drives planarization of the excited state. Our interpretation is based on numerical modeling of the ground and excited state potential energy surfaces and simulation of wavepacket dynamics, which reveals two symmetric excited state deactivation pathways per oscillation period. We use the acquired knowledge on torsional dynamics to coherently control the excited state population with a pump-dump scheme, exploiting the non-stationary Franck-Condon overlap between ground and excited states.

Molecules in strong laser fields. In depth study of H2 molecule

International Nuclear Information System (INIS)

Awasthi, Manohar

2009-01-01

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 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 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 2 molecule. By selecting a very small value of the internuclear distance close to zero for the H 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 above

Metal-Controlled Magnetoresistance at Room Temperature in Single-Molecule Devices.

Science.gov (United States)

Aragonès, Albert C; Aravena, Daniel; Valverde-Muñoz, Francisco J; Real, José Antonio; Sanz, Fausto; Díez-Pérez, Ismael; Ruiz, Eliseo

2017-04-26

The appropriate choice of the transition metal complex and metal surface electronic structure opens the possibility to control the spin of the charge carriers through the resulting hybrid molecule/metal spinterface in a single-molecule electrical contact at room temperature. The single-molecule conductance of a Au/molecule/Ni junction can be switched by flipping the magnetization direction of the ferromagnetic electrode. The requirements of the molecule include not just the presence of unpaired electrons: the electronic configuration of the metal center has to provide occupied or empty orbitals that strongly interact with the junction metal electrodes and that are close in energy to their Fermi levels for one of the electronic spins only. The key ingredient for the metal surface is to provide an efficient spin texture induced by the spin-orbit coupling in the topological surface states that results in an efficient spin-dependent interaction with the orbitals of the molecule. The strong magnetoresistance effect found in this kind of single-molecule wire opens a new approach for the design of room-temperature nanoscale devices based on spin-polarized currents controlled at molecular level.

Collisions of low-energy antiprotons and protons with atoms and molecules

Energy Technology Data Exchange (ETDEWEB)

Luehr, Armin

2010-02-18

Antiproton (anti p) collisions have evolved to a powerful tool for the testing of dynamic electron correlations in atoms and molecules. While advances in the understanding of anti p collisions with the simplest one- and two-electron atoms, H and He, have been achieved experiment and theory did not agree for low-energy anti p+He collisions (<40 keV), stimulating a vivid theoretical activity. On the other hand, only very few theoretical anti p studies can be found considering molecular as well as other atomic targets, in contrast to proton (p) collisions. This is in particular true for anti p impacts on H{sub 2} despite its fundamental role in representing the simplest two-electron molecule. The obtained results may be useful for the anti p experiments at CERN (e.g., antihydrogen production) and in particular for the facility design of low-energy anti p storage rings (e.g., at FLAIR) where a precise knowledge of the anti p interaction with the dominant residual-gas molecule H{sub 2} is needed. In this work a nonperturbative, time-dependent numerical approach is developed which describes ionization and excitation of atoms or molecules by either anti p or p impact based on the impact-parameter method. A spectral close-coupling method is employed for solving the time-dependent Schroedinger equation in which the scattering wave function is expanded in (effective) one- or two-electron eigenstates of the target. This includes for the first time a full two-electron, two-center description of the H{sub 2} molecule in anti p collisions. The radial part of the one-electron eigenstates is expanded in B splines while the two-electron basis is obtained with a configurationinteraction approach. Calculations are performed for anti p collisions with H, H{sub 2}{sup +}, and H{sub 2} as well as with He and alkali-metal atoms Li, Na, K, and Rb. Additionally, data are obtained for p collisions with H{sub 2}, Li, Na, and K. The developed method is tested and validated by detailed

Calculation of probabilities of rotational transitions of two-atom molecules in the collision with heavy particles

International Nuclear Information System (INIS)

Vargin, A.N.; Ganina, N.A.; Konyukhov, V.K.; Selyakov, V.I.

1975-01-01

The problem of calculation of collisional probabilities of rotational transitions (CPRT) in molecule-molecule and molecule-atom interactions in a three-dimensional space has been solved in this paper. A quasiclassical approach was used. The calculation of collisional probabilities of rotational transitions trajectory was carried out in the following way. The particle motion trajectory was calculated by a classical method and the time dependence of the perturbation operator was obtained, its averaging over wave functions of initial and finite states produced CPRT. The classical calculation of the molecule motion trajectory was justified by triviality of the de Broglie wavelength, compared with characteristic atomic distances, and by triviality of a transfered rotational quantum compared with the energy of translational motion of particles. The results of calculation depend on the chosen interaction potential of collisional particles. It follows from the Messy criterion that the region of nonadiabaticity of interaction may be compared with internuclear distances of a molecule. Therefore, for the description of the interaction a short-range potential is required. Analytical expressions were obtained appropriate for practical calculations for one- and two-quantum rotational transitions of diatomic molecules. The CPRT was averaged over the Maxwell distribution over velocities and analytical dependences on a gas temperature were obtained. The results of the numerical calculation of probabilities for the HCl-HCl, HCl-He, CO-CO interactions are presented to illustrate the method

Handbook of Single-Molecule Biophysics

CERN Document Server

Hinterdorfer, Peter

2009-01-01

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...

Theoretical femtosecond physics atoms and molecules in strong laser fields

CERN Document Server

Grossmann, Frank

2018-01-01

This textbook extends from the basics of femtosecond physics all the way to some of the latest developments in the field. In this updated edition, the chapter on laser-driven atoms is augmented by the discussion of two-electron atoms interacting with strong and short laser pulses, as well as by a review of ATI rings and low energy structures in photo-electron spectra. In the chapter on laser-driven molecules a discussion of 2D infrared spectroscopy is incorporated. Theoretical investigations of atoms and molecules interacting with pulsed lasers up to atomic field strengths on the order of 10^16 W/cm² are leading to an understanding of many challenging experimental discoveries. The presentation starts with a brief introduction to pulsed laser physics. The basis for the non-perturbative treatment of laser-matter interaction in the book is the time-dependent Schrödinger equation. Its analytical as well as numerical solution are laid out in some detail. The light field is treated classically and different possi...

Single-Molecule Spectroscopy

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! Kankan Bhattacharyya. General Article Volume 20 Issue 2 February 2015 pp 151-164. Fulltext. Click here to view fulltext PDF. Permanent link:

Microfluidic devices and methods including porous polymer monoliths

Science.gov (United States)

Hatch, Anson V; Sommer, Gregory J; Singh, Anup K; Wang, Ying-Chih; Abhyankar, Vinay V

2014-04-22

Microfluidic devices and methods including porous polymer monoliths are described. Polymerization techniques may be used to generate porous polymer monoliths having pores defined by a liquid component of a fluid mixture. The fluid mixture may contain iniferters and the resulting porous polymer monolith may include surfaces terminated with iniferter species. Capture molecules may then be grafted to the monolith pores.

Novel roles for immune molecules in neural development: Implications for neurodevelopmental disoders

Directory of Open Access Journals (Sweden)

Paula A Garay

2010-09-01

Full Text Available Although the brain has classically been considered "immune-privileged," current research suggests extensive communication between the nervous and the immune systems in both health and disease. Recent studies demonstrate that immune molecules are present at the right place and time to modulate the development and function of the healthy and diseased CNS. Indeed, immune molecules play integral roles in the CNS throughout neural development, including affecting neurogenesis, neuronal migration, axon guidance, synapse formation, activity-dependent refinement of circuits, and synaptic plasticity. Moreover, the roles of individual immune molecules in the nervous system may change over development. This review focuses on the effects of immune molecules on neuronal connections in the mammalian central nervous system—specifically the roles for MHCI and its receptors, complement, and cytokines on the function, refinement, and plasticity of cortical and hippocampal synapses and their relationship to neurodevelopmental disorders. These functions for immune molecules during neural development suggest that they could also mediate pathological responses to chronic elevations of cytokines in neurodevelopmental disorders, including autism spectrum disorders (ASD and schizophrenia.

The synthesis of complex molecules in interstellar clouds

Science.gov (United States)

Huntress, W. T., Jr.; Mitchell, G. F.

1979-01-01

The abundances of polyatomic molecules that may be formed by CH3(+) radiative association reactions in dense interstellar molecular clouds are reevaluated. The formation of a number of complex interstellar molecules via radiative association reactions involving ionic precursors other than CH3(+) is also investigated; these additional precursors include CH3O(+), CH3CO(+), CH5(+), HCO(+), NO(+), H2CN(+), C2H2(+), and NH3(+). The results indicate that the postulated gas-phase ion-molecule radiative association reactions could potentially explain the synthesis of most of the more complex species observed in dense molecular clouds such as Sgr B2. It is concluded, however, that in order to be conclusive, laboratory data are needed to show whether or not these reactions proceed at the required rates at low temperatures.

Development of orthogonal 2-dimensional numerical code TFC2D for fluid flow with various turbulence models and numerical schemes

Energy Technology Data Exchange (ETDEWEB)

Park, Ju Yeop; In, Wang Kee; Chun, Tae Hyun; Oh, Dong Seok [Korea Atomic Energy Research Institute, Taejeon (Korea)

2000-02-01

The development of orthogonal 2-dimensional numerical code is made. The present code contains 9 kinds of turbulence models that are widely used. They include a standard k-{epsilon} model and 8 kinds of low Reynolds number ones. They also include 6 kinds of numerical schemes including 5 kinds of low order schemes and 1 kind of high order scheme such as QUICK. To verify the present numerical code, pipe flow, channel flow and expansion pipe flow are solved by this code with various options of turbulence models and numerical schemes and the calculated outputs are compared to experimental data. Furthermore, the discretization error that originates from the use of standard k-{epsilon} turbulence model with wall function is much more diminished by introducing a new grid system than a conventional one in the present code. 23 refs., 58 figs., 6 tabs. (Author)

Ion-Molecule Reaction Dynamics.

Science.gov (United States)

Meyer, Jennifer; Wester, Roland

2017-05-05

We review the recent advances in the investigation of the dynamics of ion-molecule reactions. During the past decade, the combination of single-collision experiments in crossed ion and neutral beams with the velocity map ion imaging detection technique has enabled a wealth of studies on ion-molecule reactions. These methods, in combination with chemical dynamics simulations, have uncovered new and unexpected reaction mechanisms, such as the roundabout mechanism and the subtle influence of the leaving group in anion-molecule nucleophilic substitution reactions. For this important class of reactions, as well as for many fundamental cation-molecule reactions, the information obtained with crossed-beam imaging is discussed. The first steps toward understanding micro-solvation of ion-molecule reaction dynamics are presented. We conclude with the presentation of several interesting directions for future research.

Angle-resolved effective potentials for disk-shaped molecules

Energy Technology Data Exchange (ETDEWEB)

Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de [Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin (Germany); Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de; Dzubiella, Joachim, E-mail: joachim.dzubiella@helmholtz-berlin.de [Institut für Physik, Humboldt Universität zu Berlin, Newtonstraße 15, 12489 Berlin (Germany); Helmholtz Zentrum Berlin (HZB), Institute of Soft Matter and Functional Materials, Hahn-Meitner Platz 1, 14109 Berlin (Germany)

2014-12-07

We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in more efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations.

Nonadiabatic dynamics of electron injection into organic molecules

International Nuclear Information System (INIS)

Zhu Li-Ping; Qiu Yu; Tong Guo-Ping

2012-01-01

We numerically investigate the injection process of electrons from metal electrodes to one-dimensional organic molecules by combining the extended Su—Schrieffer—Heeger (SSH) model with a nonadiabatic dynamics method. It is found that a match between the Fermi level of electrodes and the highest occupied molecular orbital (HOMO) or the lowest unoccupied molecular orbital (LUMO) of organic molecules can be greatly affected by the length of the organic chains, which has a great impact on electron injection. The correlation between oligomers and electrodes is found to open more efficient channels for electron injection as compared with that in polymer/electrode structures. For oligomer/electrode structures, we show that the Schottky barrier essentially does not affect the electron injection as the electrode work function is smaller than a critical value. This means that the Schottky barrier is pinned for a small work-function electrode. For polymer/electrode structures, we find that it is possible for the Fermi level of electrodes to be pinned to the polaronic level. The condition under which the Fermi level of electrodes exceeds the polaronic level of polymers is shown to not always lead to spontaneous electron transfer from electrodes to polymers. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

Electron Accumulative Molecules.

Science.gov (United States)

Buades, Ana B; Sanchez Arderiu, Víctor; Olid-Britos, David; Viñas, Clara; Sillanpää, Reijo; Haukka, Matti; Fontrodona, Xavier; Paradinas, Markos; Ocal, Carmen; Teixidor, Francesc

2018-02-28

With the goal to produce molecules with high electron accepting capacity and low reorganization energy upon gaining one or more electrons, a synthesis procedure leading to the formation of a B-N(aromatic) bond in a cluster has been developed. The research was focused on the development of a molecular structure able to accept and release a specific number of electrons without decomposing or change in its structural arrangement. The synthetic procedure consists of a parallel decomposition reaction to generate a reactive electrophile and a synthesis reaction to generate the B-N(aromatic) bond. This procedure has paved the way to produce the metallacarboranylviologen [M(C 2 B 9 H 11 )(C 2 B 9 H 10 )-NC 5 H 4 -C 5 H 4 N-M'(C 2 B 9 H 11 )(C 2 B 9 H 10 )] (M = M' = Co, Fe and M = Co and M' = Fe) and semi(metallacarboranyl)viologen [3,3'-M(8-(NC 5 H 4 -C 5 H 4 N-1,2-C 2 B 9 H 10 )(1',2'-C 2 B 9 H 11 )] (M = Co, Fe) electron cumulative molecules. These molecules are able to accept up to five electrons and to donate one in single electron steps at accessible potentials and in a reversible way. By targeted synthesis and corresponding electrochemical tests each electron transfer (ET) step has been assigned to specific fragments of the molecules. The molecules have been carefully characterized, and the electronic communication between both metal centers (when this situation applies) has been definitely observed through the coplanarity of both pyridine fragments. The structural characteristics of these molecules imply a low reorganization energy that is a necessary requirement for low energy ET processes. This makes them electronically comparable to fullerenes, but on their side, they have a wide range of possible solvents. The ET from one molecule to another has been clearly demonstrated as well as their self-organizing capacity. We consider that these molecules, thanks to their easy synthesis, ET, self-organizing capacity, wide range of solubility, and easy processability, can

Single molecule conductance

NARCIS (Netherlands)

Willems, R.

2008-01-01

This thesis represents an excursion into the world of molecular electronics, i.e. the field of research trying to use individual (organic) molecules as electronic components; in this work various experimental methods have been explored to connect individual molecules to metallic contacts and

Investigation of polyelectrolyte desorption by single molecule force spectroscopy

International Nuclear Information System (INIS)

Friedsam, C; Seitz, M; Gaub, H E

2004-01-01

Single molecule force spectroscopy has evolved into a powerful method for the investigation of intra- and intermolecular interactions at the level of individual molecules. Many examples, including the investigation of the dynamic properties of complex biological systems as well as the properties of covalent bonds or intermolecular transitions within individual polymers, are reported in the literature. The technique has recently been extended to the systematic investigation of desorption processes of individual polyelectrolyte molecules adsorbed on generic surfaces. The stable covalent attachment of polyelectrolyte molecules to the AFM-tip provides the possibility of performing long-term measurements with the same set of molecules and therefore allows the in situ observation of the impact of environmental changes on the adsorption behaviour of individual molecules. Different types of interactions, e.g. electrostatic or hydrophobic interactions, that determine the adsorption process could be identified and characterized. The experiments provided valuable details that help to understand the nature and the properties of non-covalent interactions, which is helpful with regard to biological systems as well as for technical applications. Apart from this, desorption experiments can be utilized to characterize the properties of surfaces or polymer coatings. Therefore they represent a versatile tool that can be further developed in terms of various aspects

Effect of dipole polarizability on positron binding by strongly polar molecules

International Nuclear Information System (INIS)

Gribakin, G F; Swann, A R

2015-01-01

A model for positron binding to polar molecules is considered by combining the dipole potential outside the molecule with a strongly repulsive core of a given radius. Using existing experimental data on binding energies leads to unphysically small core radii for all of the molecules studied. This suggests that electron–positron correlations neglected in the simple model play a large role in determining the binding energy. We account for these by including the polarization potential via perturbation theory and non-perturbatively. The perturbative model makes reliable predictions of binding energies for a range of polar organic molecules and hydrogen cyanide. The model also agrees with the linear dependence of the binding energies on the polarizability inferred from the experimental data (Danielson et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 235203). The effective core radii, however, remain unphysically small for most molecules. Treating molecular polarization non-perturbatively leads to physically meaningful core radii for all of the molecules studied and enables even more accurate predictions of binding energies to be made for nearly all of the molecules considered. (paper)

Deep superconducting magnetic traps for neutral atoms and molecules

International Nuclear Information System (INIS)

Harris, J.G.E.; Michniak, R.A.; Nguyen, S.V.; Campbell, W.C.; Egorov, D.; Maxwell, S.E.; Buuren, L.D. van; Doyle, J.M.

2004-01-01

We describe the design, construction and performance of three realizations of a high-field superconducting magnetic trap for neutral atoms and molecules. Each of these traps utilizes a pair of coaxial coils in the anti-Helmholtz geometry and achieves depths greater than 4 T, allowing it to capture magnetic atoms and molecules cooled in a cryogenic buffer gas. Achieving this depth requires that the repulsive force between the coils (which can exceed 30 metric tons) be contained. We also describe additional features of the traps, including the elimination of trapped fluxes from the coils and the integration of the coils into a cryogenic vacuum environment suitable for producing cold atoms and molecules

The semiclassical approximation in the local theory of resonance inelastic interaction of slow electrons with molecules

International Nuclear Information System (INIS)

Kazansky, A.K.

1984-01-01

The semiclassical approach is developed to calculate the cross sections of vibrational excitation and dissociative attachment for diatomic molecules within the framework of the 'boomerang model'. The formulae obtained reveal the energy dependence of the cross sections on the parameters of the system. Numerical calculations for N 2 , CO, H 2 , HD and D 2 confirm the high accuracy of the method. (author)

The formation and interactions of cold and ultracold molecules: new challenges for interdisciplinary physics

Energy Technology Data Exchange (ETDEWEB)

Dulieu, O [Laboratoire Aime Cotton, CNRS, Bat. 505, Univ Paris-Sud 11, F-91405 Orsay Cedex (France); Gabbanini, C [Istituto per i processi chimico-fisici del C.N.R., Via Moruzzi 1, 56124 Pisa (Italy)], E-mail: olivier.dulieu@lac.u-psud.fr, E-mail: carlo@ipcf.cnr.it

2009-08-15

Progress on research in the field of molecules at cold and ultracold temperatures is reported in this review. It covers extensively the experimental methods to produce, detect and characterize cold and ultracold molecules including association of ultracold atoms, deceleration by external fields and kinematic cooling. Confinement of molecules in different kinds of traps is also discussed. The basic theoretical issues related to the knowledge of the molecular structure, the atom-molecule and molecule-molecule mutual interactions, and to their possible manipulation and control with external fields, are reviewed. A short discussion on the broad area of applications completes the review.

Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions.

Science.gov (United States)

Li, Xiaohui; Hu, Duan; Tan, Zhibing; Bai, Jie; Xiao, Zongyuan; Yang, Yang; Shi, Jia; Hong, Wenjing

2017-04-01

The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.

Numerical computations with GPUs

CERN Document Server

Kindratenko, Volodymyr

2014-01-01

This book brings together research on numerical methods adapted for Graphics Processing Units (GPUs). It explains recent efforts to adapt classic numerical methods, including solution of linear equations and FFT, for massively parallel GPU architectures. This volume consolidates recent research and adaptations, covering widely used methods that are at the core of many scientific and engineering computations. Each chapter is written by authors working on a specific group of methods; these leading experts provide mathematical background, parallel algorithms and implementation details leading to

Numerical investigation of a double-junction a:SiGe thin-film solar cell including the multi-trench region

International Nuclear Information System (INIS)

Kacha, K.; Djeffal, F.; Ferhati, H.; Arar, D.; Meguellati, M.

2015-01-01

We present a new approach based on the multi-trench technique to improve the electrical performances, which are the fill factor and the electrical efficiency. The key idea behind this approach is to introduce a new multi-trench region in the intrinsic layer, in order to modulate the total resistance of the solar cell. Based on 2-D numerical investigation and optimization of amorphous SiGe double-junction (a-Si:H/a-SiGe:H) thin film solar cells, in the present paper numerical models of electrical and optical parameters are developed to explain the impact of the multi-trench technique on the improvement of the double-junction solar cell electrical behavior for high performance photovoltaic applications. In this context, electrical characteristics of the proposed design are analyzed and compared with conventional amorphous silicon double-junction thin-film solar cells. (paper)

Spin-Spin Cross Relaxation in Single-Molecule Magnets

Science.gov (United States)

Wernsdorfer, W.; Bhaduri, S.; Tiron, R.; Hendrickson, D. N.; Christou, G.

2002-10-01

The one-body tunnel picture of single-molecule magnets (SMMs) is not always sufficient to explain the measured tunnel transitions. An improvement to the picture is proposed by including also two-body tunnel transitions such as spin-spin cross relaxation (SSCR) which are mediated by dipolar and weak superexchange interactions between molecules. A Mn4 SMM is used as a model system. At certain external fields, SSCRs lead to additional quantum resonances which show up in hysteresis loop measurements as well-defined steps. A simple model is used to explain quantitatively all observed transitions.

Extracellular Molecules Involved in Cancer Cell Invasion

Directory of Open Access Journals (Sweden)

Theodora Stivarou

2015-01-01

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.

Numerical Hydrodynamics in General Relativity

Directory of Open Access Journals (Sweden)

Font José A.

2003-01-01

Full Text Available The current status of numerical solutions for the equations of ideal general relativistic hydrodynamics is reviewed. With respect to an earlier version of the article, the present update provides additional information on numerical schemes, and extends the discussion of astrophysical simulations in general relativistic hydrodynamics. Different formulations of the equations are presented, with special mention of conservative and hyperbolic formulations well-adapted to advanced numerical methods. A large sample of available numerical schemes is discussed, paying particular attention to solution procedures based on schemes exploiting the characteristic structure of the equations through linearized Riemann solvers. A comprehensive summary of astrophysical simulations in strong gravitational fields is presented. These include gravitational collapse, accretion onto black holes, and hydrodynamical evolutions of neutron stars. The material contained in these sections highlights the numerical challenges of various representative simulations. It also follows, to some extent, the chronological development of the field, concerning advances on the formulation of the gravitational field and hydrodynamic equations and the numerical methodology designed to solve them.

Simulation of diffusion time of small molecules in protein crystals.

Science.gov (United States)

Geremia, Silvano; Campagnolo, Mara; Demitri, Nicola; Johnson, Louise N

2006-03-01

A simple model for evaluation of diffusion times of small molecule into protein crystals has been developed, which takes into account the physical and chemical properties both of protein crystal and the diffusing molecules. The model also includes consideration of binding and the binding affinity of a ligand to the protein. The model has been validated by simulation of experimental set-ups of several examples found in the literature. These experiments cover a wide range of situations: from small to relatively large diffusing molecules, crystals having low, medium, or high protein density, and different size. The reproduced experiments include ligand exchange in protein crystals by soaking techniques. Despite the simplifying assumptions of the model, theoretical and experimental data are in agreement with available data, with experimental diffusion times ranging from a few seconds to several hours. The method has been used successfully for planning intermediate cryotrapping experiments in maltodextrin phosphorylase crystals.

Numerical simulation of sand jet in water

Energy Technology Data Exchange (ETDEWEB)

Azimi, A.H.; Zhu, D.; Rajaratnam, N. [Alberta Univ., Edmonton, AB (Canada). Dept. of Civil and Environmental Engineering

2008-07-01

A numerical simulation of sand jet in water was presented. The study involved a two-phase flow using two-phase turbulent jets. A literature review was also presented, including an experiment on particle laden air jet using laser doppler velocimetry (LDV); experiments on the effect of particle size and concentration on solid-gas jets; an experimental study of solid-liquid jets using particle image velocimetry (PIV) technique where mean velocity and fluctuations were measured; and an experimental study on solid-liquid jets using the laser doppler anemometry (LDA) technique measuring both water axial and radial velocities. Other literature review results included a photographic study of sand jets in water; a comparison of many two-phase turbulent flow; and direct numerical simulation and large-eddy simulation to study the effect of particle in gas jet flow. The mathematical model and experimental setup were also included in the presentation along with simulation results for sand jets, concentration, and kinetic energy. The presentation concluded with some proposed future studies including numerical simulation of slurry jets in water and numerical simulation of slurry jets in MFT. tabs., figs.

Challenges for single molecule electronic devices with nanographene and organic molecules. Do single molecules offer potential as elements of electronic devices in the next generation?

Science.gov (United States)

Enoki, Toshiaki; Kiguchi, Manabu

2018-03-01

Interest in utilizing organic molecules to fabricate electronic materials has existed ever since organic (molecular) semiconductors were first discovered in the 1950s. Since then, scientists have devoted serious effort to the creation of various molecule-based electronic systems, such as molecular metals and molecular superconductors. Single-molecule electronics and the associated basic science have emerged over the past two decades and provided hope for the development of highly integrated molecule-based electronic devices in the future (after the Si-based technology era has ended). Here, nanographenes (nano-sized graphene) with atomically precise structures are among the most promising molecules that can be utilized for electronic/spintronic devices. To manipulate single small molecules for an electronic device, a single molecular junction has been developed. It is a powerful tool that allows even small molecules to be utilized. External electric, magnetic, chemical, and mechanical perturbations can change the physical and chemical properties of molecules in a way that is different from bulk materials. Therefore, the various functionalities of molecules, along with changes induced by external perturbations, allows us to create electronic devices that we cannot create using current top-down Si-based technology. Future challenges that involve the incorporation of condensed matter physics, quantum chemistry calculations, organic synthetic chemistry, and electronic device engineering are expected to open a new era in single-molecule device electronic technology.

Electron-molecule collisions

CERN Document Server

Takayanagi, Kazuo

1984-01-01

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...

Complex organic molecules toward low-mass and high-mass star forming regions

Science.gov (United States)

Favre, C.; Ceccarelli, C.; Lefloch, B.; Bergin, E.; Carvajal, M.; Brouillet, N.; Despois, D.; Jørgensen, J.; Kleiner, I.

2016-12-01

One of the most important questions in molecular astrophysics is how, when, and where complex organic molecules, COMs (≥ 6 atoms) are formed. In the Interstellar-Earth connection context, could this have a bearing on the origin of life on Earth? Formation mechanisms of COMs, which include potentially prebiotic molecules, are still debated and may include grain-mantle and/or gas-phase chemistry. Understanding the mechanisms that lead to the interstellar molecular complexification, along with the involved physicochemical processes, is mandatory to answer the above questions. In that context, active researches are ongoing in theory, laboratory experiment, chemical modeling and observations. Thanks to recent progress in radioastronomy instrumentation for both single-dish and millimeter array (e.g. Herschel, NOEMA, ALMA), new results have been obtained. I will review some notable results on the detection of COMs, including prebiotic molecules, towards star forming regions.

Preparation of translationally cold neutral molecules.

Science.gov (United States)

Di Domenicantonio, Giulia; Bertsche, Benjamin; Osterwalder, Andreas

2011-01-01

Efforts at EPFL to obtain translationally cold neutral molecules are described. Active deceleration of polar molecules is performed by confining the molecules in moving three-dimensional electrostatic traps, and by appropriately choosing the velocity of those traps. Alternatively, cold molecules can be obtained by velocity filtering. Here, the velocity of the molecules is not changed, but instead the cold molecules are extracted from a thermal sample by using the competition between the electrostatic force and the centrifugal force inside a bent electrostatic guide for polar molecules.

Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications.

Science.gov (United States)

Gilson, Michael K; Irikura, Karl K

2010-12-16

The use of molecular simulations and ab initio calculations to predict thermodynamic properties of molecules has become routine. Such methods rely upon an accurate representation of the molecular partition function or configurational integral, which in turn often includes a rotational symmetry number. However, the reason for including the symmetry number is unclear to many practitioners, and there is also a need for a general prescription for evaluating the symmetry numbers of flexible molecules, i.e., for molecules with thermally active internal degrees of freedom, such as internal rotors. Surprisingly, we have been unable to find any complete and convincing explanations of these important issues in textbooks or the journal literature. The present paper aims to explain why symmetry numbers are needed and how their values should be determined. Both classical and quantum approaches are provided.

Optical Spectroscopy Of Charged Quantum Dot Molecules

Science.gov (United States)

Scheibner, M.; Bracker, A. S.; Stinaff, E. A.; Doty, M. F.; Gammon, D.; Ponomarev, I. V.; Reinecke, T. L.; Korenev, V. L.

2007-04-01

Coupling between two closely spaced quantum dots is observed by means of photoluminescence spectroscopy. Hole coupling is realized by rational crystal growth and heterostructure design. We identify molecular resonances of different excitonic charge states, including the important case of a doubly charged quantum dot molecule.

Electronic structure of molecules using relativistic effective core potentials

International Nuclear Information System (INIS)

Hay, P.J.

1981-01-01

Starting with one-component Cowan-Griffin relativistic Hartree-Fock orbitals, which successfully incorporate the mass-velocity and Darwin terms present in more complicated wavefunctions such as Dirac-Hartree-Fock, one can derive relativistic effective core potentials (RECP's) to carry out molecular calculations. These potentials implicitly include the dominant relativistic terms for molecules while allowing one to use the traditional quantum chemical techniques for studying the electronic structure of molecules. The effects of spin-orbit coupling can then be included using orbitals from such calculations using an effective 1-electron, 1-center spin-orbit operator. Applications to molecular systems involving heavy atoms, show good agreement with available spectroscopic data on molecular geometries and excitation energies

Intercellular communication in Helicobacter pylori: luxS is essential for the production of an extracellular signaling molecule.

Science.gov (United States)

Forsyth, M H; Cover, T L

2000-06-01

Individual bacteria of numerous species can communicate and coordinate their actions via the production, release, and detection of extracellular signaling molecules. In this study, we used the Vibrio harveyi luminescence bioassay to determine whether Helicobacter pylori produces such a factor. Cell-free conditioned media from H. pylori strains 60190 and 26695 each induced >100-fold-greater luminescence in V. harveyi than did sterile culture medium. The H. pylori signaling molecule had a molecular mass of 100-fold-greater luminescence in the V. harveyi bioassay than did conditioned medium from either mutant strain. Production of the signaling molecule was restored in an H. pylori luxS null mutant strain by complementation with a single intact copy of luxS placed in a heterologous site on the chromosome. In addition, Escherichia coli DH5alpha produced autoinducer activity following the introduction of an intact copy of luxS from H. pylori. Production of the signaling molecule by H. pylori was growth phase dependent, with maximal production occurring in the mid-exponential phase of growth. Transcription of H. pylori vacA also was growth phase dependent, but this phenomenon was not dependent on luxS activity. These data indicate that H. pylori produces an extracellular signaling molecule related to AI-2 from V. harveyi. We speculate that this signaling molecule may play a role in regulating H. pylori gene expression.

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

DEFF Research Database (Denmark)

Jørgensen, Jacob Lykkebo

Abstract The idea of using single-molecules as components in electronic devices is fas- cinating. For this idea to come into fruition, a number of technical and theo- retical challenges must be overcome. In this PhD thesis, the electron-phonon interaction is studied for a special class of molecules......, 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......-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...

Block copolymer templated self-assembly of disk-shaped molecules

Science.gov (United States)

Aragones, J. L.; Alexander-Katz, A.

2017-08-01

Stacking of disk-shaped organic molecules is a promising strategy to develop electronic and photovoltaic devices. Here, we investigate the capability of a soft block copolymer matrix that microphase separates into a cylindrical phase to direct the self-assembly of disk-shaped molecules by means of molecular simulations. We show that two disk molecules confined in the cylinder domain experience a depletion force, induced by the polymer chains, which results in the formation of stacks of disks. This entropic interaction and the soft confinement provided by the matrix are both responsible for the structures that can be self-assembled, which include slanted or columnar stacks. In addition, we evidence the transmission of stresses between the different minority domains of the microphase, which results in the establishment of a long-ranged interaction between disk molecules embedded in different domains; this interaction is of the order of the microphase periodicity and may be exploited to direct assembly of disks at larger scales.

Reactive oxygen species, essential molecules, during plant-pathogen interactions.

Science.gov (United States)

Camejo, Daymi; Guzmán-Cedeño, Ángel; Moreno, Alexander

2016-06-01

Reactive oxygen species (ROS) are continually generated as a consequence of the normal metabolism in aerobic organisms. Accumulation and release of ROS into cell take place in response to a wide variety of adverse environmental conditions including salt, temperature, cold stresses and pathogen attack, among others. In plants, peroxidases class III, NADPH oxidase (NOX) locates in cell wall and plasma membrane, respectively, may be mainly enzymatic systems involving ROS generation. It is well documented that ROS play a dual role into cells, acting as important signal transduction molecules and as toxic molecules with strong oxidant power, however some aspects related to its function during plant-pathogen interactions remain unclear. This review focuses on the principal enzymatic systems involving ROS generation addressing the role of ROS as signal molecules during plant-pathogen interactions. We described how the chloroplasts, mitochondria and peroxisomes perceive the external stimuli as pathogen invasion, and trigger resistance response using ROS as signal molecule. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

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

Energy Technology Data Exchange (ETDEWEB)

Awasthi, Manohar

2009-10-29

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

Electronic structure of the Fe2 molecule in the local-spin-density approximation

International Nuclear Information System (INIS)

Dhar, S.; Kestner, N.R.

1988-01-01

Ab initio self-consistent all-electron spin-polarized calculations have been performed for the ground-state properties of the Fe 2 molecule using the local-spin-density approximation. A Gaussian orbital basis is employed and all the two-electron integrals are evaluated analytically. The matrix elements of the exchange-correlation potential are computed numerically. The total energy, the binding energy, the equilibrium distance, vibrational frequency, and the ground-state configurations are reported and compared with other calculations and experimental results

Multi-wavelength search for complex molecules in Titan's Atmosphere

Science.gov (United States)

Nixon, C. A.; Cordiner, M. A.; Greathouse, T. K.; Richter, M.; Kisiel, Z.; Irwin, P. G.; Teanby, N. A.; Kuan, Y. J.; Charnley, S. B.

2017-12-01

Titan's atmosphere is one of the most complex astrochemical environments known: the photochemistry of methane and nitrogen, induced by solar UV and Saturn magnetospheric electron impacts, creates a bonanza of organic molecules like no other place in the solar system. Cassini has unveiled the first glimpses of Titan's chemical wonderland, but many gaps remain. In particular, interpreting the mass spectra of Titan's upper atmosphere requires external knowledge, to disentangle the signature of molecules from their identical-mass brethren. Cassini infrared spectroscopy with CIRS has helped to some extent, but is also limited by low spectral resolution. Potentially to the rescue, comes high-resolution spectroscopy from the Earth at infrared and sub-millimeter wavelengths, where molecules exhibit vibrational and rotational transitions respectively. In this presentation, we describe the quest to make new, unique identifications of large molecules in Titan's atmosphere, focusing specifically on cyclic molecules including N-heterocycles. This molecular family is of high astrobiological significance, forming the basic ring structure for DNA nucleobases. We present the latest spectroscopic observations of Titan from ALMA and NASA's IRTF telescope, discussing present findings and directions for future work.

Molecules and Models The molecular structures of main group element compounds

CERN Document Server

Haaland, Arne

2008-01-01

This book provides a systematic description of the molecular structures and bonding in simple compounds of the main group elements with particular emphasis on bond distances, bond energies and coordination geometries. The description includes the structures of hydrogen, halogen and methyl derivatives of the elements in each group, some of these molecules are ionic, some polar covalent. The survey of molecules whose structures conform to well-established trends is followed byrepresentative examples of molecules that do not conform. We also describe electron donor-acceptor and hydrogen bonded co

Numerically and experimentally analysis of creep

International Nuclear Information System (INIS)

Fontanive, J.A.

1982-11-01

The problems of creep in concrete are analyzed experimentally and numerically, comparing with classical methods and suggesting a numerical procedure for the solution of these problems. Firstly, fundamentals of viscoelasticity and its application to concrete behaviour representation are presented. Then the theories of Dischinger and Arutyunyan are studied, and a computing numerical solutions are compared in several examples. Finally, experiences on creep and relaxation are described, and its result are analyzed. Some coments on possible future developments are included. (Author) [pt

Theory and applications of numerical analysis

CERN Document Server

Phillips, G M

1996-01-01

This text is a self-contained Second Edition, providing an introductory account of the main topics in numerical analysis. The book emphasizes both the theorems which show the underlying rigorous mathematics andthe algorithms which define precisely how to program the numerical methods. Both theoretical and practical examples are included.* a unique blend of theory and applications* two brand new chapters on eigenvalues and splines* inclusion of formal algorithms* numerous fully worked examples* a large number of problems, many with solutions

Studies of interstellar vibrationally-excited molecules

International Nuclear Information System (INIS)

Ziurys, L.M.; Snell, R.L.; Erickson, N.R.

1986-01-01

Several molecules thus far have been detected in the ISM in vibrationally-excited states, including H 2 , SiO, HC 3 N, and CH 3 CN. In order for vibrational-excitation to occur, these species must be present in unusually hot and dense gas and/or where strong infrared radiation is present. In order to do a more thorough investigation of vibrational excitation in the interstellar medium (ISM), studies were done of several mm-wave transitions originating in excited vibrational modes of HCN, an abundant interstellar molecule. Vibrationally-excited HCN was recently detected toward Orion-KL and IRC+10216, using a 12 meter antenna. The J=3-2 rotational transitions were detected in the molecule's lowest vibrational state, the bending mode, which is split into two separate levels, due to l-type doubling. This bending mode lies 1025K above ground state, with an Einstein A coefficient of 3.6/s. The J=3-2 line mode of HCN, which lies 2050K above ground state, was also observed toward IRC+10216, and subsequently in Orion-KL. Further measurements of vibrationally-excited HCN were done using a 14 meter telescope, which include the observations of the (0,1,0) and (0,2,0) modes towards Orion-KL, via their J=3-2 transitions at 265-267 GHz. The spectrum of the J=3-2 line in Orion taken with the 14 meter telescope, is shown, along with a map, which indicates that emission from vibrationally-excited HCN arises from a region probably smaller than the 14 meter telescope's 20 arcsec beam

Curvature contributions to the static electrical properties of push-pull molecules

International Nuclear Information System (INIS)

Squitieri, Emilio

2005-01-01

Calculations of the curvature contribution to the diagonals components of the static dipole moment (μ), polarizability (α), first (β) and second (γ) hyperpolarizability of push-pull molecules are presented. This contribution was obtained from the analytical evaluation of electrical properties method using the harmonic zero-point energy. The valence-bond charge-transfer model was employed to obtain the field-dependent force constant and their derivates with respect to electric field. Our results show a relationship between the curvature and electronic contributions. We have also found that the curvature contribution is important in a numerical estimation of β and γ

Dense Molecular Gas Around Protostars and in Galactic Nuclei European Workshop on Astronomical Molecules 2004

CERN Document Server

Baan, W A; Langevelde, H J

2004-01-01

The phenomena observed in young stellar objects (YSO), circumstellar regions and extra-galactic nuclei show some similarity in their morphology, dynamical and physical processes, though they may differ in scale and energy. The European Workshop on Astronomical Molecules 2004 gave astronomers a unique opportunity to discuss the links among the observational results and to generate common interpretations of the phenomena in stars and galaxies, using the available diagnostic tools such as masers and dense molecular gas. Their theoretical understanding involves physics, numerical simulations and chemistry. Including a dozen introductory reviews, topics of papers in this book also cover: maser and dense gas diagnostics and related phenomena, evolution of circumstellar regions around protostars, evolution of circumnuclear regions of active galaxies, diagnostics of the circumnuclear gas in stars and galactic nuclei. This book summarizes our present knowledge in these topics, highlights major problems to be addressed...

Single ovalbumin molecules exploring nucleoplasm and nucleoli of living cell nuclei.

Science.gov (United States)

Speil, Jasmin; Kubitscheck, Ulrich

2010-03-01

The nucleus is the center of direction and coordination of the cell's metabolic and reproductive activities and contains numerous functionally specialized domains. These subnuclear structures are not delimited by membranes like cytoplasmic organelles and their function is only poorly understood. Here, we studied the most prominent nuclear domains, nucleoli and the remaining nucleoplasm. We used fluorescently labeled ovalbumin-ATTO647N, an inert protein, to examine their physical properties. This inert tracer was microinjected into the cytoplasm of HeLa cells, and after diffusion into the nucleus the tracer distribution and mobility in the two nuclear compartments was examined. Like many macromolecular probes ovalbumin was significantly less abundant in nucleoli compared to the nucleoplasm. High-speed fluorescence microscopy allowed visualizing and analyzing single tracer molecule trajectories within nucleoli and nucleoplasm. In accordance with previous studies we found that the viscosity of the nucleus is sevenfold higher than that of aqueous buffer. Notably, nucleoplasm and nucleoli did not significantly differ in viscosity, however, the fraction of slow or trapped molecules was higher in the nucleoplasm than in nucleoli (6% versus 0.2%). Surprisingly, even a completely inert molecule like ovalbumin showed at times short-lived binding events with a decay time of 8 ms in the nucleoplasm and even shorter-6.3 ms-within the nucleoli. Copyright 2009 Elsevier B.V. All rights reserved.

Method for preparation and readout of polyatomic molecules in single quantum states

Science.gov (United States)

Patterson, David

2018-03-01

Polyatomic molecular ions contain many desirable attributes of a useful quantum system, including rich internal degrees of freedom and highly controllable coupling to the environment. To date, the vast majority of state-specific experimental work on molecular ions has concentrated on diatomic species. The ability to prepare and read out polyatomic molecules in single quantum states would enable diverse experimental avenues not available with diatomics, including new applications in precision measurement, sensitive chemical and chiral analysis at the single-molecule level, and precise studies of Hz-level molecular tunneling dynamics. While cooling the motional state of a polyatomic ion via sympathetic cooling with a laser-cooled atomic ion is straightforward, coupling this motional state to the internal state of the molecule has proven challenging. Here we propose a method for readout and projective measurement of the internal state of a trapped polyatomic ion. The method exploits the rich manifold of technically accessible rotational states in the molecule to realize robust state preparation and readout with far less stringent engineering than quantum logic methods recently demonstrated on diatomic molecules. The method can be applied to any reasonably small (≲10 atoms) polyatomic ion with an anisotropic polarizability.

Single-Molecule Photocurrent at a Metal-Molecule-Semiconductor Junction.

Science.gov (United States)

Vezzoli, Andrea; Brooke, Richard J; Higgins, Simon J; Schwarzacher, Walther; Nichols, Richard J

2017-11-08

We demonstrate here a new concept for a metal-molecule-semiconductor nanodevice employing Au and GaAs contacts that acts as a photodiode. Current-voltage traces for such junctions are recorded using a STM, and the "blinking" or "I(t)" method is used to record electrical behavior at the single-molecule level in the dark and under illumination, with both low and highly doped GaAs samples and with two different types of molecular bridge: nonconjugated pentanedithiol and the more conjugated 1,4-phenylene(dimethanethiol). Junctions with highly doped GaAs show poor rectification in the dark and a low photocurrent, while junctions with low doped GaAs show particularly high rectification ratios in the dark (>10 3 for a 1.5 V bias potential) and a high photocurrent in reverse bias. In low doped GaAs, the greater thickness of the depletion layer not only reduces the reverse bias leakage current, but also increases the volume that contributes to the photocurrent, an effect amplified by the point contact geometry of the junction. Furthermore, since photogenerated holes tunnel to the metal electrode assisted by the HOMO of the molecular bridge, the choice of the latter has a strong influence on both the steady state and transient metal-molecule-semiconductor photodiode response. The control of junction current via photogenerated charge carriers adds new functionality to single-molecule nanodevices.

Numerical Feedback Stabilization with Applications to Networks

Directory of Open Access Journals (Sweden)

Simone Göttlich

2017-01-01

Full Text Available The focus is on the numerical consideration of feedback boundary control problems for linear systems of conservation laws including source terms. We explain under which conditions the numerical discretization can be used to design feedback boundary values for network applications such as electric transmission lines or traffic flow systems. Several numerical examples illustrate the properties of the results for different types of networks.

Role of N2 molecules in pulse discharge production of I atoms for a pulsed chemical oxygen-iodine laser

International Nuclear Information System (INIS)

Kochetov, I V; Napartovich, A P; Vagin, N P; Yuryshev, N N

2011-01-01

A pulsed electric discharge is the most effective means to turn chemical oxygen-iodine laser (COIL) operation into the pulse mode by fast production of iodine atoms. Experimental studies and numerical simulations are performed on a pulsed COIL initiated by an electric discharge in a mixture CF 3 I : N 2 : O 2 ( 3 X) : O 2 (a 1 Δ g ) flowing out of a chemical singlet oxygen generator. A transverse pulsed discharge is realized at various iodide pressures. The model comprises a system of kinetic equations for neutral and charged species, the electric circuit equation, the gas thermal balance equation and the photon balance equation. Reaction rate coefficients for processes involving electrons are repeatedly re-calculated by the electron Boltzmann equation solver when the plasma parameters are changed. The processes accounted for in the Boltzmann equation include direct and stepwise excitation and ionization of atoms and molecules, dissociation of molecules, electron attachment processes, electron-ion recombination, electron-electron collisions and second-kind collisions. The last processes are particularly important because of a high singlet oxygen concentration in gas flow from the singlet oxygen chemical generator. A conclusion is drawn about satisfactory agreement between the theory and the experiment.

Adhesion molecules

CERN Document Server

Preedy, Victor R

2016-01-01

This book covers the structure and classification of adhesion molecules in relation to signaling pathways and gene expression. It discusses immunohistochemical localization, neutrophil migration, and junctional, functional, and inflammatory adhesion molecules in pathologies such as leukocyte decompression sickness and ischemia reperfusion injury. Highlighting the medical applications of current research, chapters cover diabetes, obesity, and metabolic syndrome; hypoxia; kidney disease; smoking, atrial fibrillation, and heart disease, the brain and dementia; and tumor proliferation. Finally, it looks at molecular imaging and bioinformatics, high-throughput technologies, and chemotherapy.

Numerical modeling of AA2024-T3 friction stir welding process for residual stress evaluation, including softening effects

DEFF Research Database (Denmark)

Sonne, Mads Rostgaard; Carlone, Pierpaolo; Palazzo, Gaetano S.

2014-01-01

In the present paper, a numerical finite element model of the precipitation hardenable AA2024-T3 aluminum alloy, consisting of a heat transfer analysis based on the Thermal Pseudo Mechanical model for heat generation, and a sequentially coupled quasi-static stress analysis is proposed. Metallurgi...

Prediction of Physicochemical Properties of Organic Molecules Using Semi-Empirical Methods

International Nuclear Information System (INIS)

Kim, Chan Kyung; Kim, Chang Kon; Kim, Miri; Lee, Hai Whang; Cho, Soo Gyeong

2013-01-01

Prediction of physicochemical properties of organic molecules is an important process in chemistry and chemical engineering. The MSEP approach developed in our lab calculates the molecular surface electrostatic potential (ESP) on van der Waals (vdW) surfaces of molecules. This approach includes geometry optimization and frequency calculation using hybrid density functional theory, B3LYP, at the 6-31G(d) basis set to find minima on the potential energy surface, and is known to give satisfactory QSPR results for various properties of organic molecules. However, this MSEP method is not applicable to screen large database because geometry optimization and frequency calculation require considerable computing time. To develop a fast but yet reliable approach, we have re-examined our previous work on organic molecules using two semi-empirical methods, AM1 and PM3. This new approach can be an efficient protocol in designing new molecules with improved properties

On the Mass of Atoms in Molecules: Beyond the Born-Oppenheimer Approximation

Science.gov (United States)

Scherrer, Arne; Agostini, Federica; Sebastiani, Daniel; Gross, E. K. U.; Vuilleumier, Rodolphe

2017-07-01

Describing the dynamics of nuclei in molecules requires a potential energy surface, which is traditionally provided by the Born-Oppenheimer or adiabatic approximation. However, we also need to assign masses to the nuclei. There, the Born-Oppenheimer picture does not account for the inertia of the electrons, and only bare nuclear masses are considered. Nowadays, experimental accuracy challenges the theoretical predictions of rotational and vibrational spectra and requires the participation of electrons in the internal motion of the molecule. More than 80 years after the original work of Born and Oppenheimer, this issue has still not been solved, in general. Here, we present a theoretical and numerical framework to address this problem in a general and rigorous way. Starting from the exact factorization of the electron-nuclear wave function, we include electronic effects beyond the Born-Oppenheimer regime in a perturbative way via position-dependent corrections to the bare nuclear masses. This maintains an adiabaticlike point of view: The nuclear degrees of freedom feel the presence of the electrons via a single potential energy surface, whereas the inertia of electrons is accounted for and the total mass of the system is recovered. This constitutes a general framework for describing the mass acquired by slow degrees of freedom due to the inertia of light, bounded particles; thus, it is applicable not only in electron-nuclear systems but in light-heavy nuclei or ions as well. We illustrate this idea with a model of proton transfer, where the light particle is the proton and the heavy particles are the oxygen atoms to which the proton is bounded. Inclusion of the light-particle inertia allows us to gain orders of magnitude in accuracy. The electron-nuclear perspective is adopted, instead, to calculate position-dependent mass corrections using density functional theory for a few polyatomic molecules at their equilibrium geometry. These data can serve as input for the

On the Mass of Atoms in Molecules: Beyond the Born-Oppenheimer Approximation

Directory of Open Access Journals (Sweden)

Arne Scherrer

2017-08-01

Full Text Available Describing the dynamics of nuclei in molecules requires a potential energy surface, which is traditionally provided by the Born-Oppenheimer or adiabatic approximation. However, we also need to assign masses to the nuclei. There, the Born-Oppenheimer picture does not account for the inertia of the electrons, and only bare nuclear masses are considered. Nowadays, experimental accuracy challenges the theoretical predictions of rotational and vibrational spectra and requires the participation of electrons in the internal motion of the molecule. More than 80 years after the original work of Born and Oppenheimer, this issue has still not been solved, in general. Here, we present a theoretical and numerical framework to address this problem in a general and rigorous way. Starting from the exact factorization of the electron-nuclear wave function, we include electronic effects beyond the Born-Oppenheimer regime in a perturbative way via position-dependent corrections to the bare nuclear masses. This maintains an adiabaticlike point of view: The nuclear degrees of freedom feel the presence of the electrons via a single potential energy surface, whereas the inertia of electrons is accounted for and the total mass of the system is recovered. This constitutes a general framework for describing the mass acquired by slow degrees of freedom due to the inertia of light, bounded particles; thus, it is applicable not only in electron-nuclear systems but in light-heavy nuclei or ions as well. We illustrate this idea with a model of proton transfer, where the light particle is the proton and the heavy particles are the oxygen atoms to which the proton is bounded. Inclusion of the light-particle inertia allows us to gain orders of magnitude in accuracy. The electron-nuclear perspective is adopted, instead, to calculate position-dependent mass corrections using density functional theory for a few polyatomic molecules at their equilibrium geometry. These data can

Physics of atoms and molecules

International Nuclear Information System (INIS)

Bransden, B.H.; Joachain, C.J.

1983-01-01

This book presents a unified account of the physics of atoms and molecules at a level suitable for second- and third-year undergraduate students of physics and physical chemistry. Following a brief historical introduction to the subject the authors outline the ideas and approximation methods of quantum mechanics to be used later in the book. Six chapters look at the structure of atoms and the interactions between atoms and electromagnetic radiation. The authors then move on to describe the structure of molecules and molecular spectra. Three chapters deal with atomic collisions, the scattering of electrons by atoms and the scattering of atoms by atoms. The concluding chapter considers a few of the many important applications of atomic physics within astrophysics, laser technology, and nuclear fusion. Problems are given at the end of each chapter, with hints at the solutions in an appendix. Other appendices include various special topics and derivations together with useful tables of units. (author)

Numerical modeling and experimental validation of the acoustic transmission of aircraft's double-wall structures including sound package

Science.gov (United States)

Rhazi, Dilal

In the field of aeronautics, reducing the harmful effects of acoustics constitutes a major concern at the international level and justifies the call for further research, particularly in Canada where aeronautics is a key economic sector, which operates in a context of global competition. Aircraft sidewall structure is usually of a double wall construction with a curved ribbed metallic skin and a lightweight composite or sandwich trim separated by a cavity filled with a noise control treatment. The latter is of a great importance in the transport industry, and continues to be of interest in many engineering applications. However, the insertion loss noise control treatment depends on the excitation of the supporting structure. In particular, Turbulent Boundary Layer is of interest to several industries. This excitation is difficult to simulate in laboratory conditions, given the prohibiting costs and difficulties associated with wind tunnel and in-flight tests. Numerical simulation is the only practical way to predict the response to such excitations and to analyze effects of design changes to the response to such excitation. Another kinds of excitations encountered in industrial are monopole, rain on the Roof and diffuse acoustic field. Deterministic methods can calculate in each point the spectral response of the system. Most known are numerical methods such as finite elements and boundary elements methods. These methods generally apply to the low frequency where modal behavior of the structure dominates. However, the high limit of calculation in frequency of these methods cannot be defined in a strict way because it is related to the capacity of data processing and to the nature of the studied mechanical system. With these challenges in mind, and with limitations of the main numerical codes on the market, the manufacturers have expressed the need for simple models immediately available as early as the stage of preliminary drafts. This thesis represents an attempt

Stability of matter-antimatter molecules

International Nuclear Information System (INIS)

Wong, Cheuk-Yin; Lee, Teck-Ghee

2011-01-01

Highlights: → We examine stability of matter-antimatter molecules with four constituents. → The binding of matter-antimatter molecules is a common phenomenon. → Molecules have bound states if ratio of constituent masses greater than ∼4. → We evaluate molecular binding energies and annihilation lifetimes. - Abstract: We examine the stability of matter-antimatter molecules by reducing the four-body problem into a simpler two-body problem with residual interactions. We find that matter-antimatter molecules with constituents (m 1 + ,m 2 - ,m-bar 2 + ,m-bar 1 - ) possess bound states if their constituent mass ratio m 1 /m 2 is greater than about 4. This stability condition suggests that the binding of matter-antimatter molecules is a rather common phenomenon. We evaluate the binding energies and eigenstates of matter-antimatter molecules (μ + e - )-(e + μ - ),(π + e - )-(e + π - ),(K + e - )-(e + K - ),(pe - )-(e + p-bar),(pμ - )-(μ + p-bar), and (K + μ - ) - (μ + K - ), which satisfy the stability condition. We estimate the molecular annihilation lifetimes in their s states.

Modelling of energetic molecule-surface interactions

International Nuclear Information System (INIS)

Kerford, M.

2000-09-01

This thesis contains the results of molecular dynamics simulations of molecule-surface interactions, looking particularly at fullerene molecules and carbon surfaces. Energetic impacts of fullerene molecules on graphite create defect craters. The relationship between the parameters of the impacting molecule and the parameters of the crater axe examined and found to be a function of the energy and velocity of the impacting molecule. Less energetic fullerene molecules can be scattered from a graphite surface and the partitioning of energy after a scattering event is investigated. It is found that a large fraction of the kinetic energy retained after impact is translational energy, with a small fraction of rotational energy and a number of vibrational modes. At impact energies where the surface is not broken and at normal incidence, surface waves axe seen to occur. These waves axe used to develop a method of desorbing molecules from a graphite surface without damage to either the surface or the molecules being desorbed. A number of fullerene molecules are investigated and ways to increase the desorption yield are examined. It is found that this is a successful technique for desorbing large numbers of intact molecules from graphite. This technique could be used for desorbing intact molecules into a gas phase for mass spectrometric analysis. (author)

Numerical integration methods and layout improvements in the context of dynamic RNA visualization.

Science.gov (United States)

Shabash, Boris; Wiese, Kay C

2017-05-30

RNA visualization software tools have traditionally presented a static visualization of RNA molecules with limited ability for users to interact with the resulting image once it is complete. Only a few tools allowed for dynamic structures. One such tool is jViz.RNA. Currently, jViz.RNA employs a unique method for the creation of the RNA molecule layout by mapping the RNA nucleotides into vertexes in a graph, which we call the detailed graph, and then utilizes a Newtonian mechanics inspired system of forces to calculate a layout for the RNA molecule. The work presented here focuses on improvements to jViz.RNA that allow the drawing of RNA secondary structures according to common drawing conventions, as well as dramatic run-time performance improvements. This is done first by presenting an alternative method for mapping the RNA molecule into a graph, which we call the compressed graph, and then employing advanced numerical integration methods for the compressed graph representation. Comparing the compressed graph and detailed graph implementations, we find that the compressed graph produces results more consistent with RNA drawing conventions. However, we also find that employing the compressed graph method requires a more sophisticated initial layout to produce visualizations that would require minimal user interference. Comparing the two numerical integration methods demonstrates the higher stability of the Backward Euler method, and its resulting ability to handle much larger time steps, a high priority feature for any software which entails user interaction. The work in this manuscript presents the preferred use of compressed graphs to detailed ones, as well as the advantages of employing the Backward Euler method over the Forward Euler method. These improvements produce more stable as well as visually aesthetic representations of the RNA secondary structures. The results presented demonstrate that both the compressed graph representation, as well as the Backward

Introduction to numerical analysis

CERN Document Server

Hildebrand, F B

1987-01-01

Well-known, respected introduction, updated to integrate concepts and procedures associated with computers. Computation, approximation, interpolation, numerical differentiation and integration, smoothing of data, other topics in lucid presentation. Includes 150 additional problems in this edition. Bibliography.

Manipulating ultracold polar molecules with microwave radiation: The influence of hyperfine structure

International Nuclear Information System (INIS)

Aldegunde, J.; Hutson, Jeremy M.; Ran Hong

2009-01-01

We calculate the microwave spectra of ultracold 40 K 87 Rb alkali-metal dimers, including hyperfine interactions and in the presence of electric and magnetic fields. We show that microwave transitions may be used to transfer molecules between different hyperfine states, but only because of the presence of nuclear quadrupole interactions. Hyperfine splittings may also complicate the use of ultracold molecules for quantum computing. The spectrum of molecules oriented in electric fields may be simplified dramatically by applying a simultaneous magnetic field.

On the Several Molecules and Nanostructures of Water

Directory of Open Access Journals (Sweden)

Cynthia Kolb Whitney

2012-01-01

Full Text Available This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called ‘Algebraic Chemistry’. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are involved in chemical reactions and in changes of physical state. The model is based on consistent patterns seen in empirical data about ionization potentials, together with rational scaling laws that can interpolate and extrapolate for situations where no data are available. The results of the investigation of the water molecule include comments, both positive and negative, about technologies involving heavy water, poly water, Brown’s gas, and cold fusion.

Impact of the putative cancer stem cell markers and growth factor receptor expression on the sensitivity of ovarian cancer cells to treatment with various forms of small molecule tyrosine kinase inhibitors and cytotoxic drugs

OpenAIRE

Puvanenthiran, Soozana; Essapen, Sharadah; Seddon, Alan M.; Modjtahedi, Helmout

2016-01-01

Increased expression and activation of human epidermal growth factor receptor (EGFR) and HER-2 have been reported in numerous cancers. The aim of this study was to determine the sensitivity of a large panel of human ovarian cancer cell lines (OCCLs) to treatment with various forms of small molecule tyrosine kinase inhibitors (TKIs) and cytotoxic drugs. The aim was to see if there was any association between the protein expression of various biomarkers including three putative ovarian cancer s...

Effects of Magnetic Field on the Valence Bond Property of the Double-Quantum-Dot Molecule

Institute of Scientific and Technical Information of China (English)

王立民; 罗莹; 马本堃

2002-01-01

The effects of the magnetic field on the valence bond property of the double-quantum-dot molecule are numerically studied by the finite element method and perturbation approach because of the absence of cylindrical symmetry in the horizontally coupled dots. The calculation results show that the energy value of the ground state changes differently from that of the first excited state with increasing magnetic field strength, and they cross under a certain magnetic field. The increasing magnetic field makes the covalent bond state change into an ionic bond state, which agrees qualitatively with experimental results and makes ionic bond states remain. The oscillator strength of transition between covalent bond states decreases distinctly with the increasing magnetic field strength, when the molecule is irradiated by polarized light. Such a phenomenon is possibly useful for actual applications.

Single-molecule dynamics in nanofabricated traps

Science.gov (United States)

Cohen, Adam

2009-03-01

The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

Numerical calculations near spatial infinity

International Nuclear Information System (INIS)

Zenginoglu, Anil

2007-01-01

After describing in short some problems and methods regarding the smoothness of null infinity for isolated systems, I present numerical calculations in which both spatial and null infinity can be studied. The reduced conformal field equations based on the conformal Gauss gauge allow us in spherical symmetry to calculate numerically the entire Schwarzschild-Kruskal spacetime in a smooth way including spacelike, null and timelike infinity and the domain close to the singularity

Systems including catalysts in porous zeolite materials within a reactor for use in synthesizing hydrocarbons

Science.gov (United States)

Rolllins, Harry W [Idaho Falls, ID; Petkovic, Lucia M [Idaho Falls, ID; Ginosar, Daniel M [Idaho Falls, ID

2012-07-24

Catalytic structures include a catalytic material disposed within a zeolite material. The catalytic material may be capable of catalyzing a formation of methanol from carbon monoxide and/or carbon dioxide, and the zeolite material may be capable of catalyzing a formation of hydrocarbon molecules from methanol. The catalytic material may include copper and zinc oxide. The zeolite material may include a first plurality of pores substantially defined by a crystal structure of the zeolite material and a second plurality of pores dispersed throughout the zeolite material. Systems for synthesizing hydrocarbon molecules also include catalytic structures. Methods for synthesizing hydrocarbon molecules include contacting hydrogen and at least one of carbon monoxide and carbon dioxide with such catalytic structures. Catalytic structures are fabricated by forming a zeolite material at least partially around a template structure, removing the template structure, and introducing a catalytic material into the zeolite material.

Methods of using structures including catalytic materials disposed within porous zeolite materials to synthesize hydrocarbons

Science.gov (United States)

Rollins, Harry W [Idaho Falls, ID; Petkovic, Lucia M [Idaho Falls, ID; Ginosar, Daniel M [Idaho Falls, ID

2011-02-01

Catalytic structures include a catalytic material disposed within a zeolite material. The catalytic material may be capable of catalyzing a formation of methanol from carbon monoxide and/or carbon dioxide, and the zeolite material may be capable of catalyzing a formation of hydrocarbon molecules from methanol. The catalytic material may include copper and zinc oxide. The zeolite material may include a first plurality of pores substantially defined by a crystal structure of the zeolite material and a second plurality of pores dispersed throughout the zeolite material. Systems for synthesizing hydrocarbon molecules also include catalytic structures. Methods for synthesizing hydrocarbon molecules include contacting hydrogen and at least one of carbon monoxide and carbon dioxide with such catalytic structures. Catalytic structures are fabricated by forming a zeolite material at least partially around a template structure, removing the template structure, and introducing a catalytic material into the zeolite material.

Probabilistic numerics and uncertainty in computations.

Science.gov (United States)

Hennig, Philipp; Osborne, Michael A; Girolami, Mark

2015-07-08

We deliver a call to arms for probabilistic numerical methods : algorithms for numerical tasks, including linear algebra, integration, optimization and solving differential equations, that return uncertainties in their calculations. Such uncertainties, arising from the loss of precision induced by numerical calculation with limited time or hardware, are important for much contemporary science and industry. Within applications such as climate science and astrophysics, the need to make decisions on the basis of computations with large and complex data have led to a renewed focus on the management of numerical uncertainty. We describe how several seminal classic numerical methods can be interpreted naturally as probabilistic inference. We then show that the probabilistic view suggests new algorithms that can flexibly be adapted to suit application specifics, while delivering improved empirical performance. We provide concrete illustrations of the benefits of probabilistic numeric algorithms on real scientific problems from astrometry and astronomical imaging, while highlighting open problems with these new algorithms. Finally, we describe how probabilistic numerical methods provide a coherent framework for identifying the uncertainty in calculations performed with a combination of numerical algorithms (e.g. both numerical optimizers and differential equation solvers), potentially allowing the diagnosis (and control) of error sources in computations.

A study on interaction of DNA molecules and carbon nanotubes for an effective ejection of the molecules

International Nuclear Information System (INIS)

Wu, N.; Wang, Q.

2012-01-01

The ejection of DNA molecules from carbon nanotubes is reported from interaction energy perspectives by molecular dynamics simulations. The critical ejection energy, which is to be applied to a DNA molecule for a successful ejection from a carbon nanotube, is investigated based on a study on the friction and binding energy between the DNA molecule and the tube. An effective ejection is realized by subjecting a kinetic energy on the DNA molecule that is larger than the solved critical ejection energy. In addition, the relationship between ejection energies and sizes of DNA molecules and carbon nanotubes is investigated. -- Highlights: ► Report the ejection of DNA molecules from CNTs from interaction energy perspectives. ► Develop a methodology for the critical energy of an effective ejection of a DNA molecule from a CNT. ► Present the relationship between critical ejection energies and sizes of DNA molecules and CNTs. ► Provide a general guidance on the ejection of encapsulated molecules from CNTs.

Numerical simulations of single and double ionization of H2 in short intense laser pulses

International Nuclear Information System (INIS)

Baier, Silvio

2008-01-01

Rescattering is the dominant process leading to double ionization in atoms and molecules interacting with linearly polarized laser pulses with wavelengths around 800 nm and in an intensity regime of 10 14 to 10 15 W/cm 2 . Using numerical integrations of the two-electron Schroedinger equation of the Hydrogen molecule in appropriate reduced dimensions two mechanisms, namely correlated emission of the electrons and excitation followed by field ionization after rescattering, could be identified and characterized. With the help of a planar model in reduced dimensions these mechanisms were quantitatively compared by their dependence on the molecular alignment with respect to the polarization axis. Two additional mechanisms, which are also related to rescattering, could be identified as well. (orig.)

Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface.

Science.gov (United States)

Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

2015-07-07

The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

A systematic investigation of differential effects of cell culture substrates on the extent of artifacts in single-molecule tracking.

Directory of Open Access Journals (Sweden)

Laura C Zanetti-Domingues

Full Text Available Single-molecule techniques are being increasingly applied to biomedical investigation, notwithstanding the numerous challenges they pose in terms of signal-to-noise ratio issues. Non-specific binding of probes to glass substrates, in particular, can produce experimental artifacts due to spurious molecules on glass, which can be particularly deleterious in live-cell tracking experiments. In order to resolve the issue of non-specific probe binding to substrates, we performed systematic testing of a range of available surface coatings, using three different proteins, and then extended our assessment to the ability of these coatings to foster cell growth and retain non-adhesive properties. Linear PEG, a passivating agent commonly used both in immobilized-molecule single-molecule techniques and in tissue engineering, is able to both successfully repel non-specific adhesion of fluorescent probes and to foster cell growth when functionalized with appropriate adhesive peptides. Linear PEG treatment results in a significant reduction of tracking artifacts in EGFR tracking with Affibody ligands on a cell line expressing EGFR-eGFP. The findings reported herein could be beneficial to a large number of experimental situations where single-molecule or single-particle precision is required.

Organizing and addressing magnetic molecules.

Science.gov (United States)

Gatteschi, Dante; Cornia, Andrea; Mannini, Matteo; Sessoli, Roberta

2009-04-20

Magnetic molecules ranging from simple organic radicals to single-molecule magnets (SMMs) are intensively investigated for their potential applications in molecule-based information storage and processing. The goal of this Article is to review recent achievements in the organization of magnetic molecules on surfaces and in their individual probing and manipulation. We stress that the inherent fragility and redox sensitivity of most SMM complexes, combined with the noninnocent role played by the substrate, ask for a careful evaluation of the structural and electronic properties of deposited molecules going beyond routine methods for surface analysis. Detailed magnetic information can be directly obtained using X-ray magnetic circular dichroism or newly emerging scanning probe techniques with magnetic detection capabilities.

Methods for the selective detection of alkyne-presenting molecules and related compositions and systems

Science.gov (United States)

Valdez, Carlos A.; Vu, Alexander K.

2017-10-17

Provided herein are methods for selectively detecting an alkyne-presenting molecule in a sample and related detection reagents, compositions, methods and systems. The methods include contacting a detection reagent with the sample for a time and under a condition to allow binding of the detection reagent to the one or more alkyne-presenting molecules possibly present in the matrix to the detection reagent. The detection reagent includes an organic label moiety presenting an azide group. The binding of the azide group to the alkyne-presenting molecules results in emission of a signal from the organic label moiety.

Molecular beam studies of ion-molecule reactions

International Nuclear Information System (INIS)

Gentry, W.R.

1978-01-01

A review is presented in which an attempt is made to highlight some of the areas in which molecular beam techniques contribute to the understanding of ion--molecule reaction dynamics. Included are reactant kinetic energy range and resolution, internal state selection and analysis, and new chemical systems and phenomena. 35 references

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

KAUST Repository

Serag, Maged F.

2014-10-06

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

KAUST Repository

Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi

2014-01-01

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

Carbon Nanotube Biosensors for Space Molecule Detection and Clinical Molecular Diagnostics

Science.gov (United States)

Han, Jie

2001-01-01

Both space molecule detection and clinical molecule diagnostics need to develop ultra sensitive biosensors for detection of less than attomole molecules such as amino acids for DNA. However all the electrode sensor systems including those fabricated from the existing carbon nanotubes, have a background level of nA (nanoAmp). This has limited DNA or other molecule detection to nA level or molecules whose concentration is, much higher than attomole level. A program has been created by NASA and NCI (National Cancer Institute) to exploit the possibility of carbon nanotube based biosensors to solve this problem for both's interest. In this talk, I will present our effort on the evaluation and novel design of carbon nanotubes as electrode biosensors with strategies to minimize background currents while maximizing signal intensity.The fabrication of nanotube electrode arrays, immobilization of molecular probes on nanotube electrodes and in vitro biosensor testing will also be discussed.

Numerical simulation of mechatronic sensors and actuators

CERN Document Server

Kaltenbacher, Manfred

2007-01-01

Focuses on the physical modeling of mechatronic sensors and actuators and their precise numerical simulation using the Finite Element Method (FEM). This book discusses the physical modeling as well as numerical computation. It also gives a comprehensive introduction to finite elements, including their computer implementation.

Molecule-by-Molecule Writing Using a Focused Electron Beam

DEFF Research Database (Denmark)

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

2012-01-01

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...... 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...

Fano effect in the transport of an artificial molecule

Science.gov (United States)

Norimoto, Shota; Nakamura, Shuji; Okazaki, Yuma; Arakawa, Tomonori; Asano, Kenichi; Onomitsu, Koji; Kobayashi, Kensuke; Kaneko, Nobu-hisa

2018-05-01

The Fano effect is a ubiquitous phenomenon arising from interference between a discrete energy state and an energy continuum. We explore this effect in an artificial molecule, namely, two lateral quantum dots (QDs) fabricated from a two-dimensional electron gas system and coupled in series. When the coupling between the leads and QDs is small, the charge stability diagram of the system shows a honeycomb lattice structure that is characteristic of a double QD system. As the coupling increases, a honeycomb structure consisting of the Fano resonances emerges. A numerical simulation based on the T-matrix method can satisfactorily reproduce our experimental observation. This report constitutes a clear example of the ubiquitous nature of the Fano effect in mesoscopic transport.

Observation of pendular butterfly Rydberg molecules

Science.gov (United States)

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

2016-01-01

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. PMID:27703143

Passing Current through Touching Molecules

DEFF Research Database (Denmark)

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

2009-01-01

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...

Characterizing cavities in model inclusion molecules: a comparative study.

Science.gov (United States)

Torrens, F; Sánchez-Marín, J; Nebot-Gil, I

1998-04-01

We have selected fullerene-60 and -70 cavities as model systems in order to test several methods for characterizing inclusion molecules. The methods are based on different technical foundations such as a square and triangular tessellation of the molecule taken as a unitary sphere, spherical tessellation of the molecular surface, numerical integration of the atomic volumes and surfaces, triangular tessellation of the molecular surface, and a cubic lattice approach to a molecular space. Accurate measures of the molecular volume and surface area have been performed with the pseudo-random Monte Carlo (MCVS) and uniform Monte Carlo (UMCVS) methods. These calculations serve as a reference for the rest of the methods. The SURMO2 and MS methods have not recognized the cavities and may not be convenient for intercalation compounds. The programs that have detected the cavities never exceed 5% deviation relative to the reference values for molecular volume and surface area. The GEPOL algorithm, alone or combined with TOPO, shows results in good agreement with those of the UMCVS reference. The uniform random number generator provides the fastest convergence for UMCVS and a correct estimate of the standard deviations. The effect of the internal cavity on the accessible surfaces has been calculated.

Use of pseudopotentials in atom-atom (or molecule) collisions

International Nuclear Information System (INIS)

Pascale, J.

1985-09-01

Knowledge of interactions between ions, atoms or molecules is fundamental for interpretating or predicting collisional processes which may occur under various circumstances. The aim of this paper is to demonstrate the usefulness of using semiempirical effective interactions (more particularly, emphasis will be put on the pseudopotential approach) in the study of atom-atom (or molecule) collisions. We would like to show that if the semiempirical effective interactions are carefully defined, their use in molecular-structure calculations and in collision problems can give quite accurate results. We will limit our examples to one-electron systems. We consider the M-atom-He systems as a first example. For these systems, recent molecular-structure calculations have been carried out using an 1-dependent semiempirical pseudopotential approach and they have been tested against numerous experimental data in extensive calculations of cross sections for intra-and-inter-doublet transitions in the M-atom in collisions with He. Our second example will concern the M-H 2 systems, for which semiempirical pseudopotential molecular-structure calculations have been performed very recently using an one-electron two-center model. The results of these calculations are quite encouraging and we foresee the use of the pseudopotential approach in future studies of some reactive scattering processes

Cellular Adhesion and Adhesion Molecules

OpenAIRE

SELLER, Zerrin

2014-01-01

In recent years, cell adhesion and cell adhesion molecules have been shown to be important for many normal biological processes, including embryonic cell migration, immune system functions and wound healing. It has also been shown that they contribute to the pathogenesis of a large number of common human disorders, such as rheumatoid arthritis and tumor cell metastasis in cancer. In this review, the basic mechanisms of cellular adhesion and the structural and functional features of adhes...

On the trends of Fukui potential and hardness potential derivatives in isolated atoms vs. atoms in molecules.

Science.gov (United States)

Bhattacharjee, Rituparna; Roy, Ram Kinkar

2014-10-28

In the present study, trends of electronic contribution to molecular electrostatic potential [Vel(r¯)(r=0)], Fukui potential [v(+)f|(r=0) and v(-)f|(r=0)] and hardness potential derivatives [Δ(+)h(k) and Δ(-)h(k)] for isolated atoms as well as atoms in molecules are investigated. The generated numerical values of these three reactivity descriptors in these two electronically different situations are critically analyzed through the relevant formalism. Values of Vel(r¯) (when r → 0, i.e., on the nucleus) are higher for atoms in molecules than that of isolated atoms. In contrast, higher values of v(+)|(r=0) and v(-)|(r=0) are observed for isolated atoms compared to the values for atoms in a molecule. However, no such regular trend is observed for the Δ(+)h(k) and Δ(-)h(k) values, which is attributed to the uncertainty in the Fukui function values of atoms in molecules. The sum of Fukui potential and the sum of hardness potential derivatives in molecules are also critically analyzed, which shows the efficacy of orbital relaxation effects in quantifying the values of these parameters. The chemical consequence of the observed trends of these descriptors in interpreting electron delocalization, electronic relaxation and non-negativity of atomic Fukui function indices is also touched upon. Several commonly used molecules containing carbon as well as heteroatoms are chosen to make the investigation more insightful.

Enzyme Molecules in Solitary Confinement

Directory of Open Access Journals (Sweden)

Raphaela B. Liebherr

2014-09-01

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.

Ion and electron swarm studies of relevance to plasma processing: positive ion-molecule and electron-molecule studies of SF6 and derivatives

International Nuclear Information System (INIS)

Atterbury, C.; Kennedy, R.A.; Critchley, A.D.J.; Mayhew, C.A.

2002-01-01

Many sequential and parallel chemical reactions involving charged species occur in a plasma. Data needed to model plasma's chemical and physical environment includes cross-section, rate coefficients, and product ion distribution of electron-molecule and ion-molecule processes. Such reactions are studied by our group away from the complexity of the plasma environment, with experimental techniques that allow us to concentrate on a single process, where usually only one or two species are involved. A molecule commonly used in plasma etching applications is SF 6 1,2 . We have performed a series of positive ion-molecule and electron attachment studies on SF 6 and related molecules, including SeF 6 , TeF 6 (i.e. XF 6 molecules), SF 5 CF 3 and SF 5 Cl (i.e. SF 5 X molecules) 3- (. The studies of ion reactions with and electron attachment to SF 6 and physically similar molecules are of value when seeking to understand the ion and electron chemistry occurring in SF 6 containing plasma. The result of these studies are presented in this poster. Ion-molecule reactions. Rate coefficients and ion product branching ratios have been determined with the Selected Ion Flow Tube (SIFT) at room temperature (300 K) for reactions of SF 5 X with the following twenty-two cations; Ne + , F + , Ar + , N 2 + , N + , CO + , CO 2 + , O + , N 2 O + , O 2 + , SF 4 + , CF 2 + , SF + , SF 2 + , NO 2 + , SF 5 + , NO + , CF + , CF 3 + , SF 3 + , and H 3 O + (listed in order of decreasing recombination energy). SF 2 + , NO 2 + , NO + , SF 3 + , and H 3 O + are found to be unreacted with both SF 5 CF 3 and SF 5 Cl. The majority of the other reactions proceed with rate coefficients that are close to the capture value. Those found to occur at rates significantly less than the capture mechanism value re the reactions of O 2 + , SF + , SF 5 + , and CF 3 + with SF 5 CF 3 , and SF 4 + and SF 5 + with SF 5 Cl. Several distinction processes are observed among the large number of reactions studied, including

A Mott-like State of Molecules

International Nuclear Information System (INIS)

Duerr, S.; Volz, T.; Syassen, N.; Bauer, D. M.; Hansis, E.; Rempe, G.

2006-01-01

We prepare a quantum state where each site of an optical lattice is occupied by exactly one molecule. This is the same quantum state as in a Mott insulator of molecules in the limit of negligible tunneling. Unlike previous Mott insulators, our system consists of molecules which can collide inelastically. In the absence of the optical lattice these collisions would lead to fast loss of the molecules from the sample. To prepare the state, we start from a Mott insulator of atomic 87Rb with a central region, where each lattice site is occupied by exactly two atoms. We then associate molecules using a Feshbach resonance. Remaining atoms can be removed using blast light. Our method does not rely on the molecule-molecule interaction properties and is therefore applicable to many systems

Dissociation in small molecules

International Nuclear Information System (INIS)

Dehmer, P.M.

1982-01-01

The study of molecular dissociation processes is one of the most interesting areas of modern spectroscopy owing to the challenges presented bt even the simplest of diatomic molecules. This paper reviews the commonly used descriptions of molecular dissociation processes for diatomic molecules, the selection rules for predissociation, and a few of the principles to be remembered when one is forced to speculate about dissociation mechanisms in a new molecule. Some of these points will be illustrated by the example of dissociative ionization in O 2

Heme as a danger molecule in pathogen recognition.

Science.gov (United States)

Wegiel, Barbara; Hauser, Carl J; Otterbein, Leo E

2015-12-01

Appropriate control of redox mechanisms are critical for and effective innate immune response, which employs multiple cell types, receptors and molecules that recognize danger signals when they reach the host. Recognition of pathogen-associated pattern molecules (PAMPs) is a fundamental host survival mechanism for efficient elimination of invading pathogens and resolution of the infection and inflammation. In addition to PAMPs, eukaryotic cells contain a plethora of intracellular molecules that are normally secured within the confines of the plasma membrane, but if liberated and encountered in the extracellular milieu can provoke rapid cell activation. These are known as Alarmins or Danger-Associated Molecular Patterns (DAMPs) and can be released actively by cells or passively as a result of sterile cellular injury after trauma, ischemia, or toxin-induced cell rupture. Both PAMPs and DAMPs are recognized by a series of cognate receptors that increase the generation of free radicals and activate specific signaling pathways that result in regulation of a variety of stress response, redox sensitive genes. Multiple mediators released, as cells die include, but are not limited to ATP, hydrogen peroxide, heme, formyl peptides, DNA or mitochondria provide the second signal to amplify immune responses. In this review, we will focus on how sterile and infective stimuli activate the stress response gene heme oxygenase-1 (Hmox1, HO-1), a master gene critical to an appropriate host response that is now recognized as one with enormous therapeutic potential. HO-1 gene expression is regulated in large part by redox-sensitive proteins including but not limited to nrf2. Both PAMPs and DAMPs increase the activation of nrf2 and HO-1. Heme is a powerful pro-oxidant and as such should be qualified as a DAMP. With its degradation by HO-1a molecule of carbon monoxide (CO) is generated that in turn serves as a bioactive signaling molecule. PAMPs such as bacterial endotoxin activate HO-1

Susy theories and QCD: numerical approaches

International Nuclear Information System (INIS)

Ita, Harald

2011-01-01

We review on-shell and unitarity methods and discuss their application to precision predictions for Large Hadron Collider (LHC) physics. Being universal and numerically robust, these methods are straightforward to automate for next-to-leading-order computations within standard model and beyond. Several state-of-the-art results including studies of (W/Z+3)-jet and (W+4)-jet production have explicitly demonstrated the effectiveness of the unitarity method for describing multi-parton scattering. Here we review central ideas needed to obtain efficient numerical implementations. This includes on-shell loop-level recursions, the unitarity method, color management and further refined tricks. (review)

Multi-hump potentials for efficient wave absorption in the numerical solution of the time-dependent Schrödinger equation

Science.gov (United States)

Silaev, A. A.; Romanov, A. A.; Vvedenskii, N. V.

2018-03-01

In the numerical solution of the time-dependent Schrödinger equation by grid methods, an important problem is the reflection and wrap-around of the wave packets at the grid boundaries. Non-optimal absorption of the wave function leads to possible large artifacts in the results of numerical simulations. We propose a new method for the construction of the complex absorbing potentials for wave suppression at the grid boundaries. The method is based on the use of the multi-hump imaginary potential which contains a sequence of smooth and symmetric humps whose widths and amplitudes are optimized for wave absorption in different spectral intervals. We show that this can ensure a high efficiency of absorption in a wide range of de Broglie wavelengths, which includes wavelengths comparable to the width of the absorbing layer. Therefore, this method can be used for high-precision simulations of various phenomena where strong spreading of the wave function takes place, including the phenomena accompanying the interaction of strong fields with atoms and molecules. The efficiency of the proposed method is demonstrated in the calculation of the spectrum of high-order harmonics generated during the interaction of hydrogen atoms with an intense infrared laser pulse.

Site-Selection in Single-Molecule Junction for Highly Reproducible Molecular Electronics.

Science.gov (United States)

Kaneko, Satoshi; Murai, Daigo; Marqués-González, Santiago; Nakamura, Hisao; Komoto, Yuki; Fujii, Shintaro; Nishino, Tomoaki; Ikeda, Katsuyoshi; Tsukagoshi, Kazuhito; Kiguchi, Manabu

2016-02-03

Adsorption sites of molecules critically determine the electric/photonic properties and the stability of heterogeneous molecule-metal interfaces. Then, selectivity of adsorption site is essential for development of the fields including organic electronics, catalysis, and biology. However, due to current technical limitations, site-selectivity, i.e., precise determination of the molecular adsorption site, remains a major challenge because of difficulty in precise selection of meaningful one among the sites. We have succeeded the single site-selection at a single-molecule junction by performing newly developed hybrid technique: simultaneous characterization of surface enhanced Raman scattering (SERS) and current-voltage (I-V) measurements. The I-V response of 1,4-benzenedithiol junctions reveals the existence of three metastable states arising from different adsorption sites. Notably, correlated SERS measurements show selectivity toward one of the adsorption sites: "bridge sites". This site-selectivity represents an essential step toward the reliable integration of individual molecules on metallic surfaces. Furthermore, the hybrid spectro-electric technique reveals the dependence of the SERS intensity on the strength of the molecule-metal interaction, showing the interdependence between the optical and electronic properties in single-molecule junctions.

Single-Molecule Chemistry with Surface- and Tip-Enhanced Raman Spectroscopy.

Science.gov (United States)

Zrimsek, Alyssa B; Chiang, Naihao; Mattei, Michael; Zaleski, Stephanie; McAnally, Michael O; Chapman, Craig T; Henry, Anne-Isabelle; Schatz, George C; Van Duyne, Richard P

2017-06-14

Single-molecule (SM) surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) have emerged as analytical techniques for characterizing molecular systems in nanoscale environments. SERS and TERS use plasmonically enhanced Raman scattering to characterize the chemical information on single molecules. Additionally, TERS can image single molecules with subnanometer spatial resolution. In this review, we cover the development and history of SERS and TERS, including the concept of SERS hot spots and the plasmonic nanostructures necessary for SM detection, the past and current methodologies for verifying SMSERS, and investigations into understanding the signal heterogeneities observed with SMSERS. Moving on to TERS, we cover tip fabrication and the physical origins of the subnanometer spatial resolution. Then, we highlight recent advances of SMSERS and TERS in fields such as electrochemistry, catalysis, and SM electronics, which all benefit from the vibrational characterization of single molecules. SMSERS and TERS provide new insights on molecular behavior that would otherwise be obscured in an ensemble-averaged measurement.

Phase properties of elastic waves in systems constituted of adsorbed diatomic molecules on the (001) surface of a simple cubic crystal

Science.gov (United States)

Deymier, P. A.; Runge, K.

2018-03-01

A Green's function-based numerical method is developed to calculate the phase of scattered elastic waves in a harmonic model of diatomic molecules adsorbed on the (001) surface of a simple cubic crystal. The phase properties of scattered waves depend on the configuration of the molecules. The configurations of adsorbed molecules on the crystal surface such as parallel chain-like arrays coupled via kinks are used to demonstrate not only linear but also non-linear dependency of the phase on the number of kinks along the chains. Non-linear behavior arises for scattered waves with frequencies in the vicinity of a diatomic molecule resonance. In the non-linear regime, the variation in phase with the number of kinks is formulated mathematically as unitary matrix operations leading to an analogy between phase-based elastic unitary operations and quantum gates. The advantage of elastic based unitary operations is that they are easily realizable physically and measurable.

Average-case analysis of numerical problems

CERN Document Server

2000-01-01

The average-case analysis of numerical problems is the counterpart of the more traditional worst-case approach. The analysis of average error and cost leads to new insight on numerical problems as well as to new algorithms. The book provides a survey of results that were mainly obtained during the last 10 years and also contains new results. The problems under consideration include approximation/optimal recovery and numerical integration of univariate and multivariate functions as well as zero-finding and global optimization. Background material, e.g. on reproducing kernel Hilbert spaces and random fields, is provided.

Numerical modelling of mine workings.

CSIR Research Space (South Africa)

Lightfoot, N

1999-03-01

Full Text Available to cover most of what is required for a practising rock mechanics engineer to be able to use any of these five programs to solve practical mining problems. The chapters on specific programs discuss their individual strengths and weaknesses and highlight... and applications of numerical modelling in the context of the South African gold and platinum mining industries. This includes an example that utilises a number of different numerical 3 modelling programs to solve a single problem. This particular example...

Neutral molecules in tokamak edge plasma - role of vibrationally excited hydrogen molecules

International Nuclear Information System (INIS)

Cadez, I.; Cercek, M.; Pelicon, P.; Razpet, A.

2003-01-01

The role of neutral molecules in edge plasma is discussed with special emphasis on the vibrationally excited hydrogen. Neutral molecules are formed mostly by surface processes on the walls and then released to the edge plasma where they take part in volumetric reactions with other particles. Typically these molecules are formed in excited states and data are needed for their reactions on the wall and in the volume. Processes in edge plasma determine particle and energy flux what is especially critical issue in tokamak divertor region. Various cross sections and reaction rates are needed for modelling edge plasma and its interaction with walls. (author)

Grand Canonical adaptive resolution simulation for molecules with electrons: A theoretical framework based on physical consistency

Science.gov (United States)

Delle Site, Luigi

2018-01-01

A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic properties of the quantum region are calculated at constant electronic chemical potential equal to that of the corresponding (large) bulk system treated at full quantum level. Instead, the exchange of molecules between the quantum region and the classical environment occurs at the chemical potential of the macroscopic thermodynamic conditions. The Grand Canonical Adaptive Resolution Scheme is proposed for the treatment of the classical environment; such an approach can treat the exchange of molecules according to first principles of statistical mechanics and thermodynamic. The overall scheme is build on the basis of physical consistency, with the corresponding definition of numerical criteria of control of the approximations implied by the coupling. Given the wide range of expertise required, this work has the intention of providing guiding principles for the construction of a well founded computational protocol for actual multiscale simulations from the electronic to the mesoscopic scale.

Single Molecule Analysis Research Tool (SMART: an integrated approach for analyzing single molecule data.

Directory of Open Access Journals (Sweden)

Max Greenfeld

Full Text Available Single molecule studies have expanded rapidly over the past decade and have the ability to provide an unprecedented level of understanding of biological systems. A common challenge upon introduction of novel, data-rich approaches is the management, processing, and analysis of the complex data sets that are generated. We provide a standardized approach for analyzing these data in the freely available software package SMART: Single Molecule Analysis Research Tool. SMART provides a format for organizing and easily accessing single molecule data, a general hidden Markov modeling algorithm for fitting an array of possible models specified by the user, a standardized data structure and graphical user interfaces to streamline the analysis and visualization of data. This approach guides experimental design, facilitating acquisition of the maximal information from single molecule experiments. SMART also provides a standardized format to allow dissemination of single molecule data and transparency in the analysis of reported data.

A novel class of small molecule inhibitors of HDAC6.

Science.gov (United States)

Inks, Elizabeth S; Josey, Benjamin J; Jesinkey, Sean R; Chou, C James

2012-02-17

Histone deacetylases (HDACs) are a family of enzymes that play significant roles in numerous biological processes and diseases. HDACs are best known for their repressive influence on gene transcription through histone deacetylation. Mapping of nonhistone acetylated proteins and acetylation-modifying enzymes involved in various cellular pathways has shown protein acetylation/deacetylation also plays key roles in a variety of cellular processes including RNA splicing, nuclear transport, and cytoskeletal remodeling. Studies of HDACs have accelerated due to the availability of small molecule HDAC inhibitors, most of which contain a canonical hydroxamic acid or benzamide that chelates the metal catalytic site. To increase the pool of unique and novel HDAC inhibitor pharmacophores, a pharmacological active compound screen was performed. Several unique HDAC inhibitor pharmacophores were identified in vitro. One class of novel HDAC inhibitors, with a central naphthoquinone structure, displayed a selective inhibition profile against HDAC6. Here we present the results of a unique class of HDAC6 inhibitors identified using this compound library screen. In addition, we demonstrated that treatment of human acute myeloid leukemia cell line MV4-11 with the selective HDAC6 inhibitors decreases levels of mutant FLT-3 and constitutively active STAT5 and attenuates Erk phosphorylation, all of which are associated with the inhibitor's selective toxicity against leukemia.

High-resolution internal state control of ultracold 23Na87Rb molecules

Science.gov (United States)

Guo, Mingyang; Ye, Xin; He, Junyu; Quéméner, Goulven; Wang, Dajun

2018-02-01

We report the full internal state control of ultracold 23Na87Rb molecules, including vibrational, rotational, and hyperfine degrees of freedom. Starting from a sample of weakly bound Feshbach molecules, we realize the creation of molecules in single hyperfine levels of both the rovibrational ground and excited states with a high-efficiency and high-resolution stimulated Raman adiabatic passage. This capability brings broad possibilities for investigating ultracold polar molecules with different chemical reactivities and interactions with a single molecular species. Moreover, starting from the rovibrational and hyperfine ground state, we achieve rotational and hyperfine control with one- and two-photon microwave spectroscopy to reach levels not accessible by the stimulated Raman transfer. The combination of these two techniques results in complete control over the internal state of ultracold polar molecules, which paves the way to study state-dependent molecular collisions and state-controlled chemical reactions.

Modulation of intermolecular interactions in single-molecule magnets

Science.gov (United States)

Heroux, Katie Jeanne

Polynuclear manganese clusters exhibiting interesting magnetic and quantum properties have been an area of intense research since the discovery of the first single-molecule magnet (SMM) in 1993. These molecules, below their blocking temperature, function as single-domain magnetic particles which exhibit classical macroscale magnetic properties as well as quantum mechanical phenomena such as quantum tunnelling of magnetization (QTM) and quantum phase interference. The union of classical and quantum behavior in these nanomaterials makes SMMs ideal candidates for high-density information storage and quantum computing. However, environmental coupling factors (nuclear spins, phonons, neighboring molecules) must be minimized if such applications are ever to be fully realized. The focus of this work is making small structural changes in well-known manganese SMMs in order to drastically enhance the overall magnetic and quantum properties of the system. Well-isolated molecules of high crystalline quality should lead to well-defined energetic and spectral properties as well. An advantage of SMMs over bulk magnetic materials is that they can be chemically altered from a "bottom-up" approach providing a synthetic tool for tuning magnetic properties. This systematic approach is utilized in the work presented herein by incorporating bulky ligands and/or counterions to "isolate" the magnetic core of [Mn4] dicubane SMMs. Reducing intermolecular interactions in the crystal lattice (neighboring molecules, solvate molecules, dipolar interactions) is an important step toward developing viable quantum computing devices. Detailed bulk magnetic studies as well as single crystal magnetization hysteresis and high-frequency EPR studies on these sterically-isolated complexes show enhanced, and sometimes even unexpected, quantum dynamics. The importance of intra- and intermolecular interactions remains a common theme throughout this work, extending to other SMMs of various topology including

Surface Passivation for Single-molecule Protein Studies

Science.gov (United States)

Chandradoss, Stanley D.; Haagsma, Anna C.; Lee, Young Kwang; Hwang, Jae-Ho; Nam, Jwa-Min; Joo, Chirlmin

2014-01-01

Single-molecule fluorescence spectroscopy has proven to be instrumental in understanding a wide range of biological phenomena at the nanoscale. Important examples of what this technique can yield to biological sciences are the mechanistic insights on protein-protein and protein-nucleic acid interactions. When interactions of proteins are probed at the single-molecule level, the proteins or their substrates are often immobilized on a glass surface, which allows for a long-term observation. This immobilization scheme may introduce unwanted surface artifacts. Therefore, it is essential to passivate the glass surface to make it inert. Surface coating using polyethylene glycol (PEG) stands out for its high performance in preventing proteins from non-specifically interacting with a glass surface. However, the polymer coating procedure is difficult, due to the complication arising from a series of surface treatments and the stringent requirement that a surface needs to be free of any fluorescent molecules at the end of the procedure. Here, we provide a robust protocol with step-by-step instructions. It covers surface cleaning including piranha etching, surface functionalization with amine groups, and finally PEG coating. To obtain a high density of a PEG layer, we introduce a new strategy of treating the surface with PEG molecules over two rounds, which remarkably improves the quality of passivation. We provide representative results as well as practical advice for each critical step so that anyone can achieve the high quality surface passivation. PMID:24797261

Exotic helium molecules

International Nuclear Information System (INIS)

Portier, M.

2007-12-01

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 4 He 2 (2 3 S 1 -2 3 P 0 ) molecule, or a 4 He 2 (2 3 S 1 -2 3 S 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 4 He 2 (2 3 S 1 -2 3 S 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 τ = (1.4 ± 0.3) μs 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)

Targeting of ECM molecules and their metabolizing enzymes and receptors for the treatment of CNS diseases

DEFF Research Database (Denmark)

Berezin, Vladimir; Walmod, Peter Schledermann; Filippov, Mikhail

2014-01-01

Extracellular matrix (ECM) molecules, their receptors at the cell surface, and cell adhesion molecules (CAMs) involved in cell-cell or cell-ECM interactions are implicated in processes related to major diseases of the central nervous system including Alzheimer's disease (AD), epilepsy......, schizophrenia, addiction, multiple sclerosis, Parkinson's disease, and cancer. There are multiple strategies for targeting the ECM molecules and their metabolizing enzymes and receptors with antibodies, peptides, glycosaminoglycans, and other natural and synthetic compounds. ECM-targeting treatments include...... chondroitinase ABC, heparin/heparan sulfate-mimicking oligosaccharides, ECM cross-linking antibodies, and drugs stimulating expression of ECM molecules. The amount or activity of ECM-degrading enzymes like matrix metalloproteinases can be modulated indirectly via the regulation of endogenous inhibitors like...

Cold guided beams of polar molecules

International Nuclear Information System (INIS)

Motsch, Michael

2010-01-01

This thesis reports on experiments characterizing cold guided beams of polar molecules which are produced by electrostatic velocity filtering. This filtering method exploits the interaction between the polar molecules and the electric field provided by an electrostatic quadrupole guide to extract efficiently the slow molecules from a thermal reservoir. For molecules with large and linear Stark shifts such as deuterated ammonia (ND 3 ) or formaldehyde (H 2 CO), fluxes of guided molecules of 10 10 -10 11 molecules/s are produced. The velocities of the molecules in these beams are in the range of 10-200 m/s and correspond to typical translational temperatures of a few Kelvin. The maximum velocity of the guided molecules depends on the Stark shift, the molecular mass, the geometry of the guide, and the applied electrode voltage. Although the source is operated in the near-effusive regime, the number density of the slowest molecules is sensitive to collisions. A theoretical model, taking into account this velocity-dependent collisional loss of molecules in the vicinity of the nozzle, reproduces the density of the guided molecules over a wide pressure range. A careful adjustment of pressure allows an increase in the total number of molecules, whilst yet minimizing losses due to collisions of the sought-for slow molecules. This is an important issue for future applications. Electrostatic velocity filtering is suited for different molecular species. This is demonstrated by producing cold guided beams of the water isotopologs H 2 O, D 2 O, and HDO. Although these are chemically similar, they show linear and quadratic Stark shifts, respectively, when exposed to external electric fields. As a result, the flux of HDO is larger by one order of magnitude, and the flux of the individual isotopologs shows a characteristic dependence on the guiding electric field. The internal-state distribution of guided molecules is studied with a newly developed diagnostic method: depletion

Electron Correlations and Two-Photon States in Polycyclic Aromatic Hydrocarbon Molecules: A Peculiar Role of Geometry

OpenAIRE

Aryanpour, K.; Shukla, A.; Mazumdar, S.

2013-01-01

We present numerical studies of one- and two-photon excited states ordering in a number of polycyclic aromatic hydrocarbon molecules: coronene, hexa-peri-hexabenzocoronene and circumcoronene, all possessing $D_{6h}$ point group symmetry versus ovalene with $D_{2h}$ symmetry, within the Pariser-Parr-Pople model of interacting $\\pi$-electrons. The calculated energies of the two-photon states as well as their relative two-photon absorption cross-sections within the interacting model are qualitat...

Numerical relativity

International Nuclear Information System (INIS)

Piran, T.

1982-01-01

There are many recent developments in numerical relativity, but there remain important unsolved theoretical and practical problems. The author reviews existing numerical approaches to solution of the exact Einstein equations. A framework for classification and comparison of different numerical schemes is presented. Recent numerical codes are compared using this framework. The discussion focuses on new developments and on currently open questions, excluding a review of numerical techniques. (Auth.)

Molecule of the Month

Indian Academy of Sciences (India)

Atoms in a molecule generally prefer, particularly among the neighbouring ones, certain optimmn geometrical relationships. These are manifested in specific ranges of bond lengths, bond angles, torsion angles etc. As it always happens, chemists are interested in making molecules where these 'standard relationships' are ...

Dissociation and decay of ultracold sodium molecules

International Nuclear Information System (INIS)

Mukaiyama, T.; Abo-Shaeer, J.R.; Xu, K.; Chin, J.K.; Ketterle, W.

2004-01-01

The dissociation of ultracold molecules was studied by ramping an external magnetic field through a Feshbach resonance. The observed dissociation energies directly yielded the strength of the atom-molecule coupling. They showed nonlinear dependence on the ramp speed. This was explained by a Wigner threshold law which predicts that the decay rate of the molecules above threshold increases with the density of states. In addition, inelastic molecule-molecule and molecule-atom collisions were characterized

Current and potential uses of bioactive molecules from marine processing waste.

Science.gov (United States)

Suleria, Hafiz Ansar Rasul; Masci, Paul; Gobe, Glenda; Osborne, Simone

2016-03-15

Food industries produce huge amounts of processing waste that are often disposed of incurring expenses and impacting upon the environment. For these and other reasons, food processing waste streams, in particular marine processing waste streams, are gaining popularity amongst pharmaceutical, cosmetic and nutraceutical industries as sources of bioactive molecules. In the last 30 years, there has been a gradual increase in processed marine products with a concomitant increase in waste streams that include viscera, heads, skins, fins, bones, trimmings and shellfish waste. In 2010, these waste streams equated to approximately 24 million tonnes of mostly unused resources. Marine processing waste streams not only represent an abundant resource, they are also enriched with structurally diverse molecules that possess a broad panel of bioactivities including anti-oxidant, anti-coagulant, anti-thrombotic, anti-cancer and immune-stimulatory activities. Retrieval and characterisation of bioactive molecules from marine processing waste also contributes valuable information to the vast field of marine natural product discovery. This review summarises the current use of bioactive molecules from marine processing waste in different products and industries. Moreover, this review summarises new research into processing waste streams and the potential for adoption by industries in the creation of new products containing marine processing waste bioactives. © 2015 Society of Chemical Industry.

Beneficial effects of bacteria-plant communication based on quorum sensing molecules of the N-acyl homoserine lactone group.

Science.gov (United States)

Schikora, Adam; Schenk, Sebastian T; Hartmann, Anton

2016-04-01

Bacterial quorum sensing (QS) mechanisms play a crucial role in the proper performance and ecological fitness of bacterial populations. Many key physiological processes are regulated in a QS-dependent manner by auto-inducers, like the N-acyl homoserine lactones (AHLs) in numerous Gram-negative bacteria. In addition, also the interaction between bacteria and eukaryotic hosts can be regulated by AHLs. Those mechanisms gained much attention, because of the positive effects of different AHL molecules on plants. This positive impact ranges from growth promotion to induced resistance and is quite contrasting to the rather negative effects observed in the interactions between bacterial AHL molecules and animals. Only very recently, we began to understand the molecular mechanisms underpinning plant responses to AHL molecules. In this review, we gathered the latest information in this research field. The first part gives an overview of the bacterial aspects of quorum sensing. Later we focus on the impact of AHLs on plant growth and AHL-priming, as one of the most understood phenomena in respect to the inter-kingdom interactions based on AHL-quorum sensing molecules. Finally, we discuss the potential benefits of the understanding of bacteria-plant interaction for the future agricultural applications.

Electron attachment to the SF{sub 6} molecule

Energy Technology Data Exchange (ETDEWEB)

Smirnov, B. M., E-mail: bmsmirnov@gmail.com; Kosarim, A. V. [Russian Academy of Sciences, Joint Institute for High Temperatures (Russian Federation)

2015-09-15

Various models for transition between electron and nuclear subsystems are compared in the case of electron attachment to the SF{sub 6} molecule. Experimental data, including the cross section of electron attachment to this molecule as a function of the electron energy and vibrational temperature, the rate constants of this process in swarm experiments, and the rates of the chemionization process involving Rydberg atoms and the SF{sub 6} molecule, are collected and treated. Based on the data and on the resonant character of electron capture into an autodetachment ion state in accordance with the Breit–Wigner formula, we find that intersection of the molecule and negative ion electron terms proceeds above the potential well bottom of the molecule with the barrier height 0.05–0.1 eV, and the transition between these electron terms has both the tunnel and abovebarrier character. The limit of small electron energies e for the electron attachment cross section at room vibrational temperature takes place at ε ≪ 2 meV, while in the range 2 meV ≪ ε ≪ 80 meV, the cross section is inversely proportional to ε. In considering the attachment process as a result of the interaction between the electron and vibrational degrees of freedom, we find the coupling factor f between them to be f = aT at low vibrational temperatures T with a ≈ 3 × 10{sup −4} K{sup −1}. The coupling factor is independent of the temperature at T > 400 K.

Single-Molecule Interfacial Electron Transfer

Energy Technology Data Exchange (ETDEWEB)

Lu, H. Peter [Bowling Green State Univ., Bowling Green, OH (United States). Dept. of Chemistry and Center for Photochemical Sciences

2017-11-28

This project is focused on the use of single-molecule high spatial and temporal resolved techniques to study molecular dynamics in condensed phase and at interfaces, especially, the complex reaction dynamics associated with electron and energy transfer rate processes. The complexity and inhomogeneity of the interfacial ET dynamics often present a major challenge for a molecular level comprehension of the intrinsically complex systems, which calls for both higher spatial and temporal resolutions at ultimate single-molecule and single-particle sensitivities. Combined single-molecule spectroscopy and electrochemical atomic force microscopy approaches are unique for heterogeneous and complex interfacial electron transfer systems because the static and dynamic inhomogeneities can be identified and characterized by studying one molecule at a specific nanoscale surface site at a time. The goal of our project is to integrate and apply these spectroscopic imaging and topographic scanning techniques to measure the energy flow and electron flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure. We have been primarily focusing on studying interfacial electron transfer under ambient condition and electrolyte solution involving both single crystal and colloidal TiO₂ and related substrates. The resulting molecular level understanding of the fundamental interfacial electron transfer processes will be important for developing efficient light harvesting systems and broadly applicable to problems in fundamental chemistry and physics. We have made significant advancement on deciphering the underlying mechanism of the complex and inhomogeneous interfacial electron transfer dynamics in dyesensitized TiO₂ nanoparticle systems that strongly involves with and regulated by molecule-surface interactions. We have studied interfacial electron transfer on TiO₂ nanoparticle surfaces by using ultrafast single-molecule

Extraction of gravitational waves in numerical relativity.

Science.gov (United States)

Bishop, Nigel T; Rezzolla, Luciano

2016-01-01

A numerical-relativity calculation yields in general a solution of the Einstein equations including also a radiative part, which is in practice computed in a region of finite extent. Since gravitational radiation is properly defined only at null infinity and in an appropriate coordinate system, the accurate estimation of the emitted gravitational waves represents an old and non-trivial problem in numerical relativity. A number of methods have been developed over the years to "extract" the radiative part of the solution from a numerical simulation and these include: quadrupole formulas, gauge-invariant metric perturbations, Weyl scalars, and characteristic extraction. We review and discuss each method, in terms of both its theoretical background as well as its implementation. Finally, we provide a brief comparison of the various methods in terms of their inherent advantages and disadvantages.

Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing

DEFF Research Database (Denmark)

Łopacińska-Jørgensen, Joanna M; Pedersen, Jonas Nyvold; Bak, Mads

2017-01-01

Next-generation sequencing (NGS) has caused a revolution, yet left a gap: long-range genetic information from native, non-amplified DNA fragments is unavailable. It might be obtained by optical mapping of megabase-sized DNA molecules. Frequently only a specific genomic region is of interest, so......-megabase- to megabase-sized DNA molecules were recovered from the gel and analysed by denaturation-renaturation optical mapping. Size-selected molecules from the same gel were sequenced by NGS. The optically mapped molecules and the NGS reads showed enrichment from regions defined by NotI restriction sites. We...... demonstrate that the unannotated genome can be characterized in a locus-specific manner via molecules partially overlapping with the annotated genome. The method is a promising tool for investigation of structural variants in enriched human genomic regions for both research and diagnostic purposes. Our...

Preface: Special Topic on Single-Molecule Biophysics.

Science.gov (United States)

Makarov, Dmitrii E; Schuler, Benjamin

2018-03-28

Single-molecule measurements are now almost routinely used to study biological systems and processes. The scope of this special topic emphasizes the physics side of single-molecule observations, with the goal of highlighting new developments in physical techniques as well as conceptual insights that single-molecule measurements bring to biophysics. This issue also comprises recent advances in theoretical physical models of single-molecule phenomena, interpretation of single-molecule signals, and fundamental areas of statistical mechanics that are related to single-molecule observations. A particular goal is to illustrate the increasing synergy between theory, simulation, and experiment in single-molecule biophysics.

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

2002-01-01

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

Diatomic-molecule vibrational potentials. II. New representationsa)

International Nuclear Information System (INIS)

Engelke, R.

1979-01-01

Two new representations of diatomic-molecule vibrational potentials are presented. One of these includes most of the previously employed series approximations as special cases. The new representations are tested against older ones by using Peek's ''exact'' numerical Born--Oppenheimer potentials for the 1ssigma/sub g/, 2pπ/sub u/, and 3dsigma/sub g/ states of H 2 + as test problems. Accuracy comparisons are made with Dunham, Thakkar, Ogilvie--Tipping, Coulomb-subtracted Ogilvie--Tipping, and Pade representations. A central idea of the new treatment is that it is not necessary to use a global representation of the potential over the region 0 or =1 and then match them smoothly to each other and to the Dunham expansion at R/R/sub e/=1. Attention is focused on finding improved approximations for R/R/sub e/>1, since this region exerts strong control on the vibrational eigenvalue spectrum and it is here, perhaps, where the older techniques are at their weakest. Known properties of the exact potential such as the R→infinity behavior and the dissociation energy can be built into the new forms a priori. If the dissociation energy is not known, the new methods allow it to be estimated with better accuracy then could be done previously. If one knows only Dunham coefficients, the Coulomb-subtracted Ogilvie--Tipping series is the superior representation. If one knows, in addition, the dissociation energy, the new representations are superior and give more accurate results on the interval R/R/sub e/> or =1

Labelled molecules, modern research implements

International Nuclear Information System (INIS)

Pichat, L.; Langourieux, Y.

1974-01-01

Details of the synthesis of carbon 14- and tritium-labelled molecules are examined. Although the methods used are those of classical organic chemistry the preparation of carbon 14-labelled molecules differs in some respects, most noticeably in the use of 14 CO 2 which requires very special handling techniques. For the tritium labelling of organic molecules the methods are somewhat different, very often involving exchange reactions. The following are described in turn: the so-called Wilzbach exchange method; exchange by catalysis in solution; catalytic hydrogenation with tritium; reductions with borotritides. Some applications of labelled molecules in organic chemistry, biochemistry and pharmacology are listed [fr

Abundant expression of guidance and synaptogenic molecules in the injured spinal cord.

Directory of Open Access Journals (Sweden)

Anne Jacobi

Full Text Available BACKGROUND: Spinal interneurons have emerged as crucial targets of supraspinal input during post-injury axonal remodelling. For example, lesioned corticospinal projections use propriospinal neurons as relay stations to form intraspinal detour circuits that circumvent the lesion site and contribute to functional recovery. While a number of the molecules that determine the formation of neuronal circuits in the developing nervous system have been identified, it is much less understood which of these cues are also expressed in the injured spinal cord and can thus guide growing collaterals and initiate synaptogenesis during circuit remodelling. METHODOLOGY/PRINCIPAL FINDINGS: To address this question we characterized the expression profile of a number of guidance and synaptogenic molecules in the cervical spinal cord of healthy and spinal cord-injured mice by in situ hybridization. To assign the expression of these molecules to distinct populations of interneurons we labeled short and long propriospinal neurons by retrograde tracing and glycinergic neurons using a transgenically expressed fluorescent protein. Interestingly, we found that most of the molecules studied including members of slit-, semaphorin-, synCAM-, neuroligin- and ephrin- families as well as their receptors are also present in the adult CNS. While many of these molecules were abundantly expressed in all interneurons examined, some molecules including slits, semaphorin 7a, synCAM4 and neuroligin 1 showed preferential expression in propriospinal interneurons. Overall the expression pattern of guidance and synaptogenic molecules in the cervical spinal cord appeared to be stable over time and was not substantially altered following a midthoracic spinal cord injury. CONCLUSIONS: Taken together, our study indicates that many of the guidance and synaptogenic cues that regulate neuronal circuit formation in development are also present in the adult CNS and therefore likely contribute to the

Molecular eigenstate spectroscopy: Application to the intramolecular dynamics of some polyatomic molecules in the 3000 to 7000 cm-1 region

International Nuclear Information System (INIS)

Perry, D.S.

1991-05-01

This project uses high resolution infrared spectroscopy to probe the mechanism of intramolecular vibrational redistribution (IVR) in isolated polyatomic molecules. We have found only vibrationally anharmonic coupling in the C-H stretch region of 1-butyne but rotationally mediated coupling is evident in similar spectra of ethanol. The ''keyhole'' model of IVR was developed to account for the similarities and differences between these molecules. The concepts of the model are being implemented numerically in random matrix calculations. A second F-center laser has been purchased and is now being set up to develop an infrared double resonance technique which can be applied to this problem. 4 refs., 5 figs

Hybrid molecule/superconductor assemblies

International Nuclear Information System (INIS)

McDevitt, J.T.; Haupt, S.G.; Riley, D.R.; Zhao, J.; Zhou, J.P., Jones, C.

1993-01-01

The fabrication of electronic devices from molecular materials has attracted much attention recently. Schottky diodes, molecular transistors, metal-insulator-semiconductor diodes, MIS field effect transistors and light emitting diodes have all been prepared utilizing such substances. The active elements in these devices have been constructed by depositing the molecular phase onto the surface of a metal, semiconductor or insulating substrate. With the recent discovery of high temperature superconductivity, new opportunities now exist for the study of molecule/superconductor interactions as well as for the construction of novel hybrid molecule/superconductor devices. In this paper, methods for preparing the initial two composite molecule/semiconductor devices will be reported. Consequently, light sensors based on dye-coated superconductor junctions as well as molecular switches fashioned from conductive polymer coated superconductor junctions as well as molecular switches fashioned from conductive polymer coated superconductor microbridges will be discussed. Moreover, molecule/superconductor energy and electron transfer phenomena will be illustrated also for the first time

Single-molecule conductivity of non-redox and redox molecules at pure and gold-mined Au(111)-electrode surfaces

DEFF Research Database (Denmark)

Zhang, Jingdong; Chi, Qijin; Ulstrup, Jens

The structure, two-dimensional organization, and function of molecules immobilized on solid surfaces can be addressed in a degree of detail that has reached the level of the single-molecule. In this context redox molecules are “smart” molecules adding sophisticated electronic function. Redox meta...

MHC-like molecules in some nonmammalian vertebrates can be detected by some cross-reactive xenoantisera

DEFF Research Database (Denmark)

Kaufman, J; Skjoedt, K; Salomonsen, J

1990-01-01

in the contact regions between the chains. These latter antibodies recognized biosynthetic intermediates and also a variety of unusual cell surface MHC-like molecules present in reptile and amphibian, but absent in the mammal and chicken cells tested. These included E homodimers whose relationship to chicken B......-G molecules is unknown. 5) MHC-like molecules were identified in a bird, three reptiles, and two amphibians, but no molecules with the expected properties were found with these reagents in any of the fish tested. Udgivelsesdato: 1990-Mar-15...

Neoclassical transport including collisional nonlinearity.

Science.gov (United States)

Candy, J; Belli, E A

2011-06-10

In the standard δf theory of neoclassical transport, the zeroth-order (Maxwellian) solution is obtained analytically via the solution of a nonlinear equation. The first-order correction δf is subsequently computed as the solution of a linear, inhomogeneous equation that includes the linearized Fokker-Planck collision operator. This equation admits analytic solutions only in extreme asymptotic limits (banana, plateau, Pfirsch-Schlüter), and so must be solved numerically for realistic plasma parameters. Recently, numerical codes have appeared which attempt to compute the total distribution f more accurately than in the standard ordering by retaining some nonlinear terms related to finite-orbit width, while simultaneously reusing some form of the linearized collision operator. In this work we show that higher-order corrections to the distribution function may be unphysical if collisional nonlinearities are ignored.

Small molecule-guided thermoresponsive supramolecular assemblies

KAUST Repository

Rancatore, Benjamin J.

2012-10-23

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.

Small molecule-guided thermoresponsive supramolecular assemblies

KAUST Repository

Rancatore, Benjamin J.; Mauldin, Clayton E.; Frechet, Jean; Xu, Ting

2012-01-01

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.

A literature survey on numerical heat transfer

Science.gov (United States)

Shih, T. M.

1982-12-01

Technical papers in the area of numerical heat transfer published from 1977 through 1981 are reviewed. The journals surveyed include: (1) ASME Journal of Heat Transfer, (2) International Journal of Heat and Mass Transfer, (3) AIAA Journal, (4) Numerical Heat Transfer, (5) Computers and Fluids, (6) International Journal for Numerical Methods in Engineering, (7) SIAM Journal of Numerical Analysis, and (8) Journal of Computational Physics. This survey excludes experimental work in heat transfer and numerical schemes that are not applied to equations governing heat transfer phenomena. The research work is categorized into the following areas: (A) conduction, (B) boundary-layer flows, (C) momentum and heat transfer in cavities, (D) turbulent flows, (E) convection around cylinders and spheres or within annuli, (F) numerical convective instability, (G) radiation, (H) combustion, (I) plumes, jets, and wakes, (J) heat transfer in porous media, (K) boiling, condensation, and two-phase flows, (L) developing and fully developed channel flows, (M) combined heat and mass transfer, (N) applications, (O) comparison and properties of numerical schemes, and (P) body-fitted coordinates and nonuniform grids.

Spin- and energy-dependent tunneling through a single molecule with intramolecular spatial resolution.

Science.gov (United States)

Brede, Jens; Atodiresei, Nicolae; Kuck, Stefan; Lazić, Predrag; Caciuc, Vasile; Morikawa, Yoshitada; Hoffmann, Germar; Blügel, Stefan; Wiesendanger, Roland

2010-07-23

We investigate the spin- and energy-dependent tunneling through a single organic molecule (CoPc) adsorbed on a ferromagnetic Fe thin film, spatially resolved by low-temperature spin-polarized scanning tunneling microscopy. Interestingly, the metal ion as well as the organic ligand show a significant spin dependence of tunneling current flow. State-of-the-art ab initio calculations including also van der Waals interactions reveal a strong hybridization of molecular orbitals and substrate 3d states. The molecule is anionic due to a transfer of one electron, resulting in a nonmagnetic (S=0) state. Nevertheless, tunneling through the molecule exhibits a pronounced spin dependence due to spin-split molecule-surface hybrid states.

The origin of small and large molecule behavior in the vibrational relaxation of highly excited molecules

International Nuclear Information System (INIS)

Gordon, R.J.

1990-01-01

An explanation is proposed for the qualitatively different types of behavior that have been reported for the vibrational relaxation of highly excited diatomic and polyatomic molecules. It is argued that all of the diatomic molecules that have been studied in bulk relax adiabatically at room temperature. In contrast, large polyatomic molecules have low frequency modes which act at ''doorway'' modes for the rest of the molecules, producing an impulsive relaxation mechanism. The theoretical work of Nesbitt and Hynes showed that impulsive collisions result in an exponential decay of the average vibrational energy of a Morse oscillator, whereas adiabatic collisions produce nonexponential power law behavior. We propose that this result explains a large body of data for the vibrational relaxation of small and large molecules

Protection of a PWR nuclear power stations against corrosion using hydrogen molecules to capture oxygen molecules

International Nuclear Information System (INIS)

Nahili, M.

2004-01-01

A protection method for the primary loops metals of nuclear power plants from corrosion was investigated. Hydrogen molecules were added to the primary circuit to eliminate oxygen molecules produced by radiolysis of coolant at the reactor core. The hydrogen molecules were produced by electrolyses of water and then added when the coolant water was passing through the primary coolant circuit. Thermodynamical process and the protection methods from corrosion were discussed, the discussion emphasized on the removal of oxygen molecules as one of the protection methods, and compared with other methods. The amount of hydrogen molecules needed for complete removal of oxygen was estimated in two cases: in the case without passing the water through the oxygen removal system, and in the case of passing water through the system. A pressurized water reactor VVER was chosen to be investigated in this study. The amount of hydrogen molecules was estimated so as to eliminate completely the oxygen molecules from coolant water. The estimated value was found to be less than the permissible range for coolant water for such type of reactors. A simulation study for interaction mechanism between hydrogen and oxygen molecules as water flowing in a tube similar to that of coolant water was performed with different water flow velocities. The interaction between the molecules of hydrogen and oxygen was described. The gas diffusion at the surface of the tube was found to play a major role in the interaction. A mathematical model was found to give full description of the change of oxygen concentration through the tube, as well as, to calculate the length of the tube where the concentration of oxygen reduced to few order of magnitude. (Author)

Numerical relativity

CERN Document Server

Shibata, Masaru

2016-01-01

This book is composed of two parts: First part describes basics in numerical relativity, that is, the formulations and methods for a solution of Einstein's equation and general relativistic matter field equations. This part will be helpful for beginners of numerical relativity who would like to understand the content of numerical relativity and its background. The second part focuses on the application of numerical relativity. A wide variety of scientific numerical results are introduced focusing in particular on the merger of binary neutron stars and black holes.

Numerical analysis

CERN Document Server

Khabaza, I M

1960-01-01

Numerical Analysis is an elementary introduction to numerical analysis, its applications, limitations, and pitfalls. Methods suitable for digital computers are emphasized, but some desk computations are also described. Topics covered range from the use of digital computers in numerical work to errors in computations using desk machines, finite difference methods, and numerical solution of ordinary differential equations. This book is comprised of eight chapters and begins with an overview of the importance of digital computers in numerical analysis, followed by a discussion on errors in comput

Infrared-x-ray pump-probe spectroscopy of the NO molecule

International Nuclear Information System (INIS)

Guimaraes, F.F.; Felicissimo, V.C.; Kimberg, V.; Gel'mukhanov, F.; Aagren, H.; Cesar, A.

2005-01-01

Two color infrared-x-ray pump-probe spectroscopy of the NO molecule is studied theoretically and numerically in order to obtain a deeper insight of the underlying physics and of the potential of this suggested technology. From the theoretical investigation a number of conclusions could be drawn: It is found that the phase of the infrared field strongly influences the trajectory of the nuclear wave packet, and hence, the x-ray spectrum. The trajectory experiences fast oscillations with the vibrational frequency with a modulation due to the anharmonicity of the potential. The dependences of the x-ray spectra on the delay time, the duration, and the shape of the pulses are studied in detail. It is shown that the x-ray spectrum keep memory about the infrared phase after the pump field left the system. This memory effect is sensitive to the time of switching-off the pump field and the Rabi frequency. The phase effect takes maximum value when the duration of the x-ray pulse is one-fourth of the infrared field period, and can be enhanced by a proper control of the duration and intensity of the pump pulse. The manifestation of the phase is different for oriented and disordered molecules and depends strongly on the intensity of the pump radiation

Infrared x-ray pump-probe spectroscopy of the NO molecule

Science.gov (United States)

Guimarães, F. F.; Kimberg, V.; Felicíssimo, V. C.; Gel'Mukhanov, F.; Cesar, A.; Ågren, H.

2005-07-01

Two color infrared x-ray pump-probe spectroscopy of the NO molecule is studied theoretically and numerically in order to obtain a deeper insight of the underlying physics and of the potential of this suggested technology. From the theoretical investigation a number of conclusions could be drawn: It is found that the phase of the infrared field strongly influences the trajectory of the nuclear wave packet, and hence, the x-ray spectrum. The trajectory experiences fast oscillations with the vibrational frequency with a modulation due to the anharmonicity of the potential. The dependences of the x-ray spectra on the delay time, the duration, and the shape of the pulses are studied in detail. It is shown that the x-ray spectrum keep memory about the infrared phase after the pump field left the system. This memory effect is sensitive to the time of switching-off the pump field and the Rabi frequency. The phase effect takes maximum value when the duration of the x-ray pulse is one-fourth of the infrared field period, and can be enhanced by a proper control of the duration and intensity of the pump pulse. The manifestation of the phase is different for oriented and disordered molecules and depends strongly on the intensity of the pump radiation.

How to assess good candidate molecules for self-activated optical power limiting

Science.gov (United States)

Lundén, Hampus; Glimsdal, Eirik; Lindgren, Mikael; Lopes, Cesar

2018-03-01

Reverse saturable absorbers have shown great potential to attenuate laser radiation. Good candidate molecules and various particles have successfully been incorporated into different glass matrices, enabling the creation of self-activated filters against damaging laser radiation. Although the performance of such filters has been impressive, work is still ongoing to improve the performance in a wider range of wavelengths and pulse widths. The purpose of this tutorial is, from an optical engineering perspective, to give an understanding of the strengths and weaknesses of this class of smart materials, how relevant photophysical parameters are measured and influence system performance and comment on the pitfalls in experimental evaluation of materials. A numerical population model in combination with simple physical formulas is used to demonstrate system behavior from a performance standpoint. Geometrical reasoning shows the advantage of reverse saturable absorption over nonlinear scattering due to a fraction of scattered light being recollected by imaging system optics. The numerical population model illustrates the importance of the optical power limiting performance during the leading edge of a nanosecond pulse, which is most strongly influenced by changes in the two-photon absorption cross section and the triplet linear absorption cross section for a modeled Pt-acetylide. This tutorial not only targets optical engineers evaluating reverse saturable absorbing materials but also aims to assist researchers with a chemistry background working on optical power limiting materials. We also present photophysical data for a series of coumarins that can be useful for the determination of quantum yields and two-photon cross sections and show examples of characterization of molecules with excited triplet states.

Small molecules as therapy for uveitis: a selected perspective of new and developing agents.

Science.gov (United States)

Pleyer, Uwe; Algharably, Engi Abdel-Hady; Feist, Eugen; Kreutz, Reinhold

2017-09-01

Intraocular inflammation (uveitis) remains a significant burden of legal blindness. Because of its immune mediated and chronic recurrent nature, common therapy includes corticosteroids, disease-modifying anti-rheumatic drugs and more recently biologics as immune modulatory agents. The purpose of this article is to identify the role of new treatment approaches focusing on small molecules as therapeutic option in uveitis. Areas covered: A MEDLINE database search was conducted through February 2017 using the terms 'uveitis' and 'small molecule'. To provide ongoing and future perspectives in treatment options, also clinical trials as registered at ClinicalTrials.gov were included. Both, results from experimental as well as clinical research in this field were included. Since this field is rapidly evolving, a selection of promising agents had to be made. Expert opinion: Small molecules may interfere at different steps of the inflammatory cascade and appear as an interesting option in the treatment algorithm of uveitis. Because of their highly targeted molecular effects and their favorable bioavailability with the potential of topical application small molecules hold great promise. Nevertheless, a careful evaluation of these agents has to be made, since current experience is almost exclusively based on experimental uveitis models and few registered trials.

Radiotherapy- and chemotherapy-induced normal tissue damage. The role of cytokines and adhesion molecules

International Nuclear Information System (INIS)

Plevova, P.

2002-01-01

Background. Ionising radiation and cytostatic agents used in cancer therapy exert damaging effects on normal tissues and induce a complex response at the cellular and molecular levels. Cytokines and adhesion molecules are involved in this response. Methods. Published data on the given topic have been reviewed. Results and conclusions. Various cytokines and adhesion molecules, including tumor necrosis factor α, interleukins- 1,-2,-4, and -6, interferon γ, granulocyte macrophage- and macrophage- colony stimulating factors, transforming growth factor β, platelet-derived growth factor, insulin-like growth factor I, fibroblast and epidermal growth factors, platelet-activating factor, intercellular adhesion molecule-1, vascular cell adhesion molecule-1, E- and P-selectins are involved in the response of normal tissues to ionizing radiation- and chemotherapy- induced normal tissues damage and are co-responsible for some side effects of these treatment modalities, including fever, anorexia and fatigue, suppression of hematopoiesis, both acute and late local tissue response. (author)

Molecule condensate production from an atomic Bose-Einstein condensate via Feshbach scattering in an optical lattice: Gap solitons

International Nuclear Information System (INIS)

Tasgal, Richard S.; Menabde, G.; Band, Y. B.

2006-01-01

We propose a scheme for making a Bose-Einstein condensate (BEC) of molecules from a BEC of atoms in a strongly confining two-dimensional optical lattice and a weak one-dimensional optical lattice in the third dimension. The stable solutions obtained for the order parameters take the form of a different type of gap soliton, with both atomic and molecular BECs, and also standard gap solitons with only a molecular BEC. The strongly confining dimensions of the lattice stabilize the BEC against inelastic energy transfer in atom-molecule collisions. The solitons with atoms and molecules may be obtained by starting with an atomic BEC, and gradually tuning the resonance by changing the external magnetic-field strength until the desired atom-molecule soliton is obtained. A gap soliton of a BEC of only molecules may be obtained nonadiabatically by starting from an atom-only gap soliton, far from a Feshbach resonance and adjusting the magnetic field to near Feshbach resonance. After a period of time in which the dimer field grows, change the magnetic field such that the detuning is large and negative and Feshbach effects wash out, turn off the optical lattice in phase with the atomic BEC, and turn on an optical lattice in phase with the molecules. The atoms disperse, leaving a gap soliton composed of a molecular BEC. Regarding instabilities in the dimension of the weak optical lattice, the solitons which are comprised of both atoms and molecules are sometimes stable and sometimes unstable--we present numerically obtained results. Gap solitons comprised of only molecules have the same stability properties as the standard gap solitons: stable from frequencies slightly below the middle of the band gap to the top, and unstable below that point. Instabilities are only weakly affected by the soliton velocities, and all instabilities are oscillatory

Ellipticity of near-threshold harmonics from stretched molecules.

Science.gov (United States)

Li, Weiyan; Dong, Fulong; Yu, Shujuan; Wang, Shang; Yang, Shiping; Chen, Yanjun

2015-11-30

We study the ellipticity of near-threshold harmonics (NTH) from aligned molecules with large internuclear distances numerically and analytically. The calculated harmonic spectra show a broad plateau for NTH which is several orders of magnitude higher than that for high-order harmonics. In particular, the NTH plateau shows high ellipticity at small and intermediate orientation angles. Our analyses reveal that the main contributions to the NTH plateau come from the transition of the electron from continuum states to these two lowest bound states of the system, which are strongly coupled together by the laser field. Besides continuum states, higher excited states also play a role in the NTH plateau, resulting in a large phase difference between parallel and perpendicular harmonics and accordingly high ellipticity of the NTH plateau. The NTH plateau with high intensity and large ellipticity provides a promising manner for generating strong elliptically-polarized extreme-ultraviolet (EUV) pulses.

Molecule of the Month

Indian Academy of Sciences (India)

Cyclo bu tadiene (1) has been one of the most popular molecules for experimentalists and theoreticians. This molecule is unstable as . it is antiaromatic ( 4,n electrons in a cyclic array). Even though some highly substituted cyclobutadienes, for example, compound 2 and the Fe(CO)3 complex of cyclobutadiene (3) are ...

Numerical Analysis Objects

Science.gov (United States)

Henderson, Michael

1997-08-01

The Numerical Analysis Objects project (NAO) is a project in the Mathematics Department of IBM's TJ Watson Research Center. While there are plenty of numerical tools available today, it is not an easy task to combine them into a custom application. NAO is directed at the dual problems of building applications from a set of tools, and creating those tools. There are several "reuse" projects, which focus on the problems of identifying and cataloging tools. NAO is directed at the specific context of scientific computing. Because the type of tools is restricted, problems such as tools with incompatible data structures for input and output, and dissimilar interfaces to tools which solve similar problems can be addressed. The approach we've taken is to define interfaces to those objects used in numerical analysis, such as geometries, functions and operators, and to start collecting (and building) a set of tools which use these interfaces. We have written a class library (a set of abstract classes and implementations) in C++ which demonstrates the approach. Besides the classes, the class library includes "stub" routines which allow the library to be used from C or Fortran, and an interface to a Visual Programming Language. The library has been used to build a simulator for petroleum reservoirs, using a set of tools for discretizing nonlinear differential equations that we have written, and includes "wrapped" versions of packages from the Netlib repository. Documentation can be found on the Web at "http://www.research.ibm.com/nao". I will describe the objects and their interfaces, and give examples ranging from mesh generation to solving differential equations.

High resolution SPM imaging of organic molecules with functionalized tips

Czech Academy of Sciences Publication Activity Database

Jelínek, Pavel

2017-01-01

Roč. 29, č. 34 (2017), 1-18, č. článku 343002. ISSN 0953-8984 R&D Projects: GA MŠk LM2015087; GA MŠk 8E15B010; GA ČR(CZ) GC14-16963J Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : atomic- force microscopy * scanning tunneling microscope * on-surface synthesis * single-molecule * AFM * STM * high resolution * molecules * surfaces Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 2.649, year: 2016

Isotope separation using vibrationally excited molecules

International Nuclear Information System (INIS)

Woodroffe, J.A.; Keck, J.C.

1977-01-01

A system for isotope separation or enrichment wherein molecules of a selected isotope type in a flow of molecules of plural isotope types are vibrationally excited and collided with a background gas to provide enhanced diffusivity for the molecules of the selected isotope type permitting their separate collection. The system typically is for the enrichment of uranium using a uranium hexafluoride gas in combination with a noble gas such as argon. The uranium hexafluoride molecules having a specific isotope of uranium are vibrationally excited by laser radiation. The vibrational energy is converted to a translation energy upon collision with a particle of the background gas and the added translation energy enhances the diffusivity of the selected hexafluoride molecules facilitating its condensation on collection surfaces provided for that purpose. This process is periodically interrupted and the cryogenic flow halted to permit evaporation of the collected molecules to provide a distinct, enriched flow

Strong plasmonic enhancement of single molecule photostability in silver dimer optical antennas

Directory of Open Access Journals (Sweden)

Kaminska Izabela

2018-02-01

Full Text Available Photobleaching is an effect terminating the photon output of fluorophores, limiting the duration of fluorescence-based experiments. Plasmonic nanoparticles (NPs can increase the overall fluorophore photostability through an enhancement of the radiative rate. In this work, we use the DNA origami technique to arrange a single fluorophore in the 12-nm gap of a silver NP dimer and study the number of emitted photons at the single molecule level. Our findings yielded a 30× enhancement in the average number of photons emitted before photobleaching. Numerical simulations are employed to rationalize our results. They reveal the effect of silver oxidation on decreasing the radiative rate enhancement.

Rotational state dependence of ion-polar molecule reactions at very low temperature

International Nuclear Information System (INIS)

Dubernet, M.L.; McCarroll, R.

1989-01-01

The adiabatic rotational state method is used to investigate the rotational state dependence of the rate coefficients for ion-polar molecule reactions in the very low temperature regime characteristic of interstellar molecular clouds. Results obtained for the systems H 3 + +HCl and H 3 + +HCN indicate that all the methods based on the adiabatic separation of the rotational and radial motion of the collision complex - adiabatic capture centrifugal sudden approximation (ACCSA), statistical adiabatic channel model, classical adiabatic invariance method - agree very satisfactorily in the low temperature limit. Discrepancies observed between some of the published data would appear to arise from numerical inaccuracies rather than from any defect of the theory. (orig.)

Trapping molecules in two and three dimensions

International Nuclear Information System (INIS)

Pinkse, PW.H.; Junglen, T.; Rieger, T.; Rangwala, S.A.; Windpassinger, P.; Rempe, G.

2005-01-01

Full text: Cold molecules offer a new testing ground for quantum-physical effects in nature. For example, producing slow beams of large molecules could push experiments studying the boundary between quantum interference and classical particles up towards ever heavier particles. Moreover, cold molecules, in particular YbF, seem an attractive way to narrow down the constraints on the value of the electron dipole moment and finally, quantum information processing using chains of cold polar molecules or vibrational states in molecules have been proposed. All these proposals rely on advanced production and trapping techniques, most of which are still under development. Therefore, novel production and trapping techniques for cold molecules could offer new possibilities not found in previous methods. Electric traps hold promise for deep trap potentials for neutral molecules. Recently we have demonstrated two-dimensional trapping of polar molecules in a four-wire guide using electrostatic and electrodynamic trapping techniques. Filled from a thermal effusive source, such a guide will deliver a beam of slow molecules, which is an ideal source for interferometry experiments with large molecules, for instance. Here we report about the extension of this work to three-dimensional trapping. Polar molecules with a positive Stark shift can be trapped in the minimum of an electrostatic field. We have successfully tested a large volume electrostatic trap for ND3 molecules. A special feature of this trap is that it can be loaded continuously from an electrostatic guide, at a temperature of a few hundred mK. (author)

Numerical MHD study for plasmoid instability in uniform resistivity

Science.gov (United States)

Shimizu, Tohru; Kondoh, Koji; Zenitani, Seiji

2017-11-01

The plasmoid instability (PI) caused in uniform resistivity is numerically studied with a MHD numerical code of HLLD scheme. It is shown that the PI observed in numerical studies may often include numerical (non-physical) tearing instability caused by the numerical dissipations. By increasing the numerical resolutions, the numerical tearing instability gradually disappears and the physical tearing instability remains. Hence, the convergence of the numerical results is observed. Note that the reconnection rate observed in the numerical tearing instability can be higher than that of the physical tearing instability. On the other hand, regardless of the numerical and physical tearing instabilities, the tearing instability can be classified into symmetric and asymmetric tearing instability. The symmetric tearing instability tends to occur when the thinning of current sheet is stopped by the physical or numerical dissipations, often resulting in the drastic changes in plasmoid chain's structure and its activity. In this paper, by eliminating the numerical tearing instability, we could not specify the critical Lundquist number Sc beyond which PI is fully developed. It suggests that Sc does not exist, at least around S = 105.

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...... interfere destructively or constructively. Destructive interference effects in electron transport could potentially improve thermo-electrics, organic logic circuits and energy harvesting. We have investigated destructive interference in off-resonant transport through organic molecules, and have found a set...

Growth and Destruction of PAH Molecules in Reactions with Carbon Atoms

Energy Technology Data Exchange (ETDEWEB)

Krasnokutski, Serge A.; Huisken, Friedrich; Jäger, Cornelia; Henning, Thomas [Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Helmholtzweg 3, D-07743 Jena (Germany)

2017-02-10

A very high abundance of atomic carbon in the interstellar medium (ISM), and the high reactivity of these species toward different hydrocarbon molecules including benzene, raise questions regarding the stability of polycyclic aromatic hydrocarbon (PAH) molecules in space. To test the efficiency of destruction of PAH molecules via reactions with atomic carbon, we performed a set of laboratory and computational studies of the reactions of naphthalene, anthracene, and coronene molecules with carbon atoms in the ground state. The reactions were investigated in liquid helium droplets at T = 0.37 K and by quantum chemical computations. Our studies suggest that all small and all large catacondensed PAHs react barrierlessly with atomic carbon, and therefore should be efficiently destroyed by such reactions in a broad temperature range. At the same time, large compact pericondensed PAHs should be more inert toward such a reaction. In addition, taking into account their higher photostability, much higher abundances of pericondensed PAHs should be expected in various astrophysical environments. The barrierless reactions between carbon atoms and small PAHs also suggest that, in the ISM, these reactions could lead to the bottom-up formation of PAH molecules.

Numerical methods for metamaterial design

CERN Document Server

2013-01-01

This book describes a relatively new approach for the design of electromagnetic metamaterials.  Numerical optimization routines are combined with electromagnetic simulations to tailor the broadband optical properties of a metamaterial to have predetermined responses at predetermined wavelengths. After a review of both the major efforts within the field of metamaterials and the field of mathematical optimization, chapters covering both gradient-based and derivative-free design methods are considered.  Selected topics including surrogate-base optimization, adaptive mesh search, and genetic algorithms are shown to be effective, gradient-free optimization strategies.  Additionally, new techniques for representing dielectric distributions in two dimensions, including level sets, are demonstrated as effective methods for gradient-based optimization.  Each chapter begins with a rigorous review of the optimization strategy used, and is followed by numerous examples that combine the strategy with either electromag...

Numerical integration of asymptotic solutions of ordinary differential equations

Science.gov (United States)

Thurston, Gaylen A.

1989-01-01

Classical asymptotic analysis of ordinary differential equations derives approximate solutions that are numerically stable. However, the analysis also leads to tedious expansions in powers of the relevant parameter for a particular problem. The expansions are replaced with integrals that can be evaluated by numerical integration. The resulting numerical solutions retain the linear independence that is the main advantage of asymptotic solutions. Examples, including the Falkner-Skan equation from laminar boundary layer theory, illustrate the method of asymptotic analysis with numerical integration.

The Neural Cell Adhesion Molecule NCAM2/OCAM/RNCAM, a Close Relative to NCAM

DEFF Research Database (Denmark)

Kulahin, Nikolaj; Walmod, Peter

2008-01-01

molecule (NCAM) is a well characterized, ubiquitously expressed CAM that is highly expressed in the nervous system. In addition to mediating cell adhesion, NCAM participates in a multitude of cellular events, including survival, migration, and differentiation of cells, outgrowth of neurites, and formation......Cell adhesion molecules (CAMs) constitute a large class of plasma membrane-anchored proteins that mediate attachment between neighboring cells and between cells and the surrounding extracellular matrix (ECM). However, CAMs are more than simple mediators of cell adhesion. The neural cell adhesion...... and plasticity of synapses. NCAM shares an overall sequence identity of approximately 44% with the neural cell adhesion molecule 2 (NCAM2), a protein also known as olfactory cell adhesion molecule (OCAM) and Rb-8 neural cell adhesion molecule (RNCAM), and the region-for-region sequence homology between the two...

Manipulation of Origin of Life Molecules: Recognizing Single-Molecule Conformations in β-Carotene and Chlorophyll-a/β-Carotene Clusters

Energy Technology Data Exchange (ETDEWEB)

Ngo, Anh T.; Skeini, Timur [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States; Iancu, Violeta [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States; Redfern, Paul C.; Curtiss, Larry A.; Hla, Saw Wai [Nanoscale; amp, Quantum Phenomena Institute and Physics & amp, Astronomy Department, Ohio University, Athens, Ohio 45701, United States

2018-01-11

Carotenoids and chlorophyll are essential parts of plant leaves and are involved in photosynthesis, a vital biological process responsible for the origin of life on Earth. Here, we investigate how beta-carotene and chlorophyll-a form mixed molecular phases On a Au(111) surface using low-temperature scanning tunneling microscopy and molecular manipulation at the single-molecule level supported by density functional theory calculations. By isolating individual molecules from nanoscale molecular clusters with a scanning tunneling microscope tip, we are able to identify five beta-carotene conformations including a structure exhibiting a three-dimensional conformation. Furthermore, molecular resolution images enable direct visualization of beta-carotene/chlorophyll-a clsuters, with intimate structural details highlighting how they pair: beta-carotene preferentially positions next to chlorophyll-a and induces switching of chlorophyll-a from straight to several bent tail conformations in the molecular clusters.

Process systems engineering studies for catalytic production of bio-based platform molecules from lignocellulosic biomass

International Nuclear Information System (INIS)

Han, Jeehoon

2017-01-01

Highlights: • A process-systems engineering study for production of bio-based platform molecules to is presented. • Experimentally verified catalysis studies for biomass conversion are investigated. • New separations for effective recovery of bio-based platform molecules are developed. • Separations are integrated with catalytic biomass conversions. • Proposed process can compete economically with the current production approaches. - Abstract: This work presents a process-system engineering study of an integrated catalytic conversion strategy to produce bio-based platform molecules (levulinic acid (LA), furfural (FF), and propyl guaiacol (PG)) from hemicellulose (C_5), cellulose (C_6), and lignin fractions of lignocellulosic biomass. A commercial-scale process based on the strategy produces high numerical carbon yields (overall yields: 35.2%; C_6-to-LA: 20.4%, C_5-to-FF: 69.2%, and Lignin-to-PG: 13.3%) from a dilute concentration of solute (1.3–30.0 wt.% solids), but a high recovery of these molecules requires an efficient separation system with low energy requirement. A heat exchanger network significantly reduced the total energy requirements of the process. An economic analysis showed that the minimum selling price of LA as the highest value-added product (42.3 × 10"3 t of LA/y using 700 × 10"3 dry t/y of corn stover) is US$1707/t despite using negative economic parameters, and that this system can be cost-competitive with current production approaches.

Magnitude Knowledge: The Common Core of Numerical Development

Science.gov (United States)

Siegler, Robert S.

2016-01-01

The integrated theory of numerical development posits that a central theme of numerical development from infancy to adulthood is progressive broadening of the types and ranges of numbers whose magnitudes are accurately represented. The process includes four overlapping trends: (1) representing increasingly precisely the magnitudes of non-symbolic…

Electron-molecule interactions and their applications

CERN Document Server

Christophorou, L G

1984-01-01

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

Polyad quantum numbers and multiple resonances in anharmonic vibrational studies of polyatomic molecules.

Science.gov (United States)

Krasnoshchekov, Sergey V; Stepanov, Nikolay F

2013-11-14

In the theory of anharmonic vibrations of a polyatomic molecule, mixing the zero-order vibrational states due to cubic, quartic and higher-order terms in the potential energy expansion leads to the appearance of more-or-less isolated blocks of states (also called polyads), connected through multiple resonances. Such polyads of states can be characterized by a common secondary integer quantum number. This polyad quantum number is defined as a linear combination of the zero-order vibrational quantum numbers, attributed to normal modes, multiplied by non-negative integer polyad coefficients, which are subject to definition for any particular molecule. According to Kellman's method [J. Chem. Phys. 93, 6630 (1990)], the corresponding formalism can be conveniently described using vector algebra. In the present work, a systematic consideration of polyad quantum numbers is given in the framework of the canonical Van Vleck perturbation theory (CVPT) and its numerical-analytic operator implementation for reducing the Hamiltonian to the quasi-diagonal form, earlier developed by the authors. It is shown that CVPT provides a convenient method for the systematic identification of essential resonances and the definition of a polyad quantum number. The method presented is generally suitable for molecules of significant size and complexity, as illustrated by several examples of molecules up to six atoms. The polyad quantum number technique is very useful for assembling comprehensive basis sets for the matrix representation of the Hamiltonian after removal of all non-resonance terms by CVPT. In addition, the classification of anharmonic energy levels according to their polyad quantum numbers provides an additional means for the interpretation of observed vibrational spectra.

Two-body tunnel transitions in a Mn 4 single-molecule magnet

Science.gov (United States)

Wernsdorfer, W.; Bhaduri, S.; Tiron, R.; Hendrickson, D. N.; Christou, G.

2004-05-01

The one-body tunnel picture of single-molecule magnets (SMMs) is not always sufficient to explain the measured tunnel transitions. An improvement to the picture is proposed by including also two-body tunnel transitions such as spin-spin cross-relaxation (SSCR) which are mediated by dipolar and weak superexchange interactions between molecules. A Mn 4 SMM is used as a model system. At certain external fields, SSCRs lead to additional quantum resonances which show up in hysteresis loop measurements as well-defined steps.

Domain-based small molecule binding site annotation

Directory of Open Access Journals (Sweden)

Dumontier Michel

2006-03-01

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 http://smid.blueprint.org. 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

A review of numerical techniques approaching microstructures of crystalline rocks

Science.gov (United States)

Zhang, Yahui; Wong, Louis Ngai Yuen

2018-06-01

The macro-mechanical behavior of crystalline rocks including strength, deformability and failure pattern are dominantly influenced by their grain-scale structures. Numerical technique is commonly used to assist understanding the complicated mechanisms from a microscopic perspective. Each numerical method has its respective strengths and limitations. This review paper elucidates how numerical techniques take geometrical aspects of the grain into consideration. Four categories of numerical methods are examined: particle-based methods, block-based methods, grain-based methods, and node-based methods. Focusing on the grain-scale characters, specific relevant issues including increasing complexity of micro-structure, deformation and breakage of model elements, fracturing and fragmentation process are described in more detail. Therefore, the intrinsic capabilities and limitations of different numerical approaches in terms of accounting for the micro-mechanics of crystalline rocks and their phenomenal mechanical behavior are explicitly presented.

Interstellar Molecules

Science.gov (United States)

Solomon, Philip M.

1973-01-01

Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

Numerical simulation of high Reynolds number bubble motion

Energy Technology Data Exchange (ETDEWEB)

McLaughlin, J.B. [Clarkson Univ., Potsdam, NY (United States)

1995-12-31

This paper presents the results of numerical simulations of bubble motion. All the results are for single bubbles in unbounded fluids. The liquid phase is quiescent except for the motion created by the bubble, which is axisymmetric. The main focus of the paper is on bubbles that are of order 1 mm in diameter in water. Of particular interest is the effect of surfactant molecules on bubble motion. Results for the {open_quotes}insoluble surfactant{close_quotes} model will be presented. These results extend research by other investigators to finite Reynolds numbers. The results indicate that, by assuming complete coverage of the bubble surface, one obtains good agreement with experimental observations of bubble motion in tap water. The effect of surfactant concentration on the separation angle is discussed.

Computer simulation of molecular absorption spectra for asymmetric top molecules

International Nuclear Information System (INIS)

Bende, A.; Tosa, V.; Cosma, V.

2001-01-01

The effective Hamiltonian formalism has been used to develop a model for infrared multiple-photon absorption (IRMPA) process in asymmetric top molecules. Assuming a collisionless regime, the interaction between the molecule and laser field can be described by the time-dependent Schroedinger equation. By using the rotating wave approximation and Laplace transformation, the time-dependent problem reduces to a time-independent eigen problem for an effective Hamiltonian which can be solved only numerically for a real vibrational-rotational structure of polyatomic molecule. The vibrational-rotational structure is assumed to be an anharmonic oscillator coupled to an asymmetric rigid rotor. The main assumptions taken into account for this model are the following: (1) the excitation is coherent, i.e. the collision (if present during the laser pulse) does not influence the excitation; (2) the excitation starts from the ground state and is near resonant to a normal mode, thus, the rotating wave approximation can be applied; (3) after absorbing N photons the vibrational energy of the excited mode leak into a quasicontinuum; (4) the thermal population of the ground state is given by the Maxwell-Boltzmann distribution law. The energy levels of the asymmetric top molecules cannot be represented by an explicit formula analogous to that for the symmetric top, according to quantum mechanics, but we can consider it a deviation from the prolate or oblate case of the symmetric top, and we can find in the same manner the selection rules of the asymmetric case using the selection rules for the symmetric case. The infrared bands of asymmetric top molecules are not resolved, but if the dispersion used is not too small, so that the envelopes of the bands can be distinguished from simple maxima, it is possible to draw conclusions as to the type of the bands. In this case, the simulation of the absorption spectra can give us some important information about the types of these bands. In

Approaches to Validate and Manipulate RNA Targets with Small Molecules in Cells.

Science.gov (United States)

Childs-Disney, Jessica L; Disney, Matthew D

2016-01-01

RNA has become an increasingly important target for therapeutic interventions and for chemical probes that dissect and manipulate its cellular function. Emerging targets include human RNAs that have been shown to directly cause cancer, metabolic disorders, and genetic disease. In this review, we describe various routes to obtain bioactive compounds that target RNA, with a particular emphasis on the development of small molecules. We use these cases to describe approaches that are being developed for target validation, which include target-directed cleavage, classic pull-down experiments, and covalent cross-linking. Thus, tools are available to design small molecules to target RNA and to identify the cellular RNAs that are their targets.

Stochastic numerical methods an introduction for students and scientists

CERN Document Server

Toral, Raul

2014-01-01

Stochastic Numerical Methods introduces at Master level the numerical methods that use probability or stochastic concepts to analyze random processes. The book aims at being rather general and is addressed at students of natural sciences (Physics, Chemistry, Mathematics, Biology, etc.) and Engineering, but also social sciences (Economy, Sociology, etc.) where some of the techniques have been used recently to numerically simulate different agent-based models. Examples included in the book range from phase-transitions and critical phenomena, including details of data analysis (extraction of critical exponents, finite-size effects, etc.), to population dynamics, interfacial growth, chemical reactions, etc. Program listings are integrated in the discussion of numerical algorithms to facilitate their understanding. From the contents: Review of Probability ConceptsMonte Carlo IntegrationGeneration of Uniform and Non-uniformRandom Numbers: Non-correlated ValuesDynamical MethodsApplications to Statistical MechanicsIn...

Electrochemically-gated single-molecule electrical devices

International Nuclear Information System (INIS)

Guo, Shaoyin; Artés, Juan Manuel; Díez-Pérez, Ismael

2013-01-01

In the last decade, single-molecule electrical contacts have emerged as a new experimental platform that allows exploring charge transport phenomena in individual molecular blocks. This novel tool has evolved into an essential element within the Molecular Electronics field to understand charge transport processes in hybrid (bio)molecule/electrode interfaces at the nanoscale, and prospect the implementation of active molecular components into functional nanoscale optoelectronic devices. Within this area, three-terminal single-molecule devices have been sought, provided that they are highly desired to achieve full functionality in logic electronic circuits. Despite the latest experimental developments offer consistent methods to bridge a molecule between two electrodes (source and drain in a transistor notation), placing a third electrode (gate) close to the single-molecule electrical contact is still technically challenging. In this vein, electrochemically-gated single-molecule devices have emerged as an experimentally affordable alternative to overcome these technical limitations. In this review, the operating principle of an electrochemically-gated single-molecule device is presented together with the latest experimental methodologies to built them and characterize their charge transport characteristics. Then, an up-to-date comprehensive overview of the most prominent examples will be given, emphasizing on the relationship between the molecular structure and the final device electrical behaviour

Large quantum systems: a mathematical and numerical perspective

International Nuclear Information System (INIS)

Lewin, M.

2009-06-01

This thesis is devoted to the mathematical study of variational models for large quantum systems. The mathematical methods are that of nonlinear analysis, calculus of variations, partial differential equations, spectral theory, and numerical analysis. The first part contains some results on finite systems. We study several approximations of the N-body Schroedinger equation for electrons in an atom or a molecule, and then the so-called Hartree-Fock- Bogoliubov model for a system of fermions interacting via the gravitational force. In a second part, we propose a new method allowing to prove the existence of the thermodynamic limit of Coulomb quantum systems. Then, we construct two Hartree-Fock-type models for infinite systems. The first is a relativistic theory deduced from Quantum Electrodynamics, allowing to describe the behavior of electrons, coupled to that of Dirac's vacuum which can become polarized. The second model describes a nonrelativistic quantum crystal in the presence of a charged defect. A new numerical method is also proposed. The last part of the thesis is devoted to spectral pollution, a phenomenon which is observed when trying to approximate eigenvalues in a gap of the essential spectrum of a self-adjoint operator, for instance for periodic Schroedinger operators or Dirac operators. (author)

Calculations on isotope separation by laser induced photodissociation of polyatomic molecules. Final report

International Nuclear Information System (INIS)

Lamb, W.E. Jr.

1978-11-01

This report describes research on the theory of isotope separation produced by the illumination of polyatomic molecules by intense infrared laser radiation. Newton's equations of motion were integrated for the atoms of the SF 6 molecule including the laser field interaction. The first year's work has been largely dedicated to obtaining a suitable interatomic potential valid for arbitrary configurations of the seven particles. This potential gives the correct symmetry of the molecule, the equilibrium configuration, the frequencies of the six distinct normal modes of oscillation and the correct (or assumed) value of the total potential energy of the molecule. Other conditions can easily be imposed in order to obtain a more refined potential energy function, for example, by making allowance for anharmonicity data. A suitable expression was also obtained for the interaction energy between a laser field and the polyatomic molecule. The electromagnetic field is treated classically, and it would be easily possible to treat the cases of time dependent pulses, frequency modulation and noise

Atlas cross section for scattering of muonic hydrogen atoms on hydrogen isotope molecules

International Nuclear Information System (INIS)

Adamczak, A.; Faifman, M.P.; Ponomarev, L.I.

1996-01-01

The total cross sections of the elastic, spin-flip, and charge-exchange processes for the scattering of muonic hydrogen isotope atoms (pμ, dμ, tμ) in the ground state on the hydrogen isotope molecules (H 2 , D 2 , T 2 , HD, HT, DT) are calculated. The scattering cross sections of muonic hydrogen isotope atoms on hydrogen isotope nuclei obtained earlier in the multichannel adiabatic approach are used in the calculations. Molecular effects (electron screening, rotational and vibrational excitations of target molecules, etc.) are taken into account. The spin effects of the target molecules and of the incident muonic atoms are included. the cross sections are averaged over the Boltzmann distribution of the molecule rotational states and the Maxwellian distribution of the target molecule kinetic energies for temperatures 30, 100, 300, and 1000 K. The cross sections are given for kinetic energies of the incident muonic atoms ranging from 0.001 to 100 eV in the laboratory frame. 45 refs., 6 tabs

FlavorDB: a database of flavor molecules.

Science.gov (United States)

Garg, Neelansh; Sethupathy, Apuroop; Tuwani, Rudraksh; Nk, Rakhi; Dokania, Shubham; Iyer, Arvind; Gupta, Ayushi; Agrawal, Shubhra; Singh, Navjot; Shukla, Shubham; Kathuria, Kriti; Badhwar, Rahul; Kanji, Rakesh; Jain, Anupam; Kaur, Avneet; Nagpal, Rashmi; Bagler, Ganesh

2018-01-04

Flavor is an expression of olfactory and gustatory sensations experienced through a multitude of chemical processes triggered by molecules. Beyond their key role in defining taste and smell, flavor molecules also regulate metabolic processes with consequences to health. Such molecules present in natural sources have been an integral part of human history with limited success in attempts to create synthetic alternatives. Given their utility in various spheres of life such as food and fragrances, it is valuable to have a repository of flavor molecules, their natural sources, physicochemical properties, and sensory responses. FlavorDB (http://cosylab.iiitd.edu.in/flavordb) comprises of 25,595 flavor molecules representing an array of tastes and odors. Among these 2254 molecules are associated with 936 natural ingredients belonging to 34 categories. The dynamic, user-friendly interface of the resource facilitates exploration of flavor molecules for divergent applications: finding molecules matching a desired flavor or structure; exploring molecules of an ingredient; discovering novel food pairings; finding the molecular essence of food ingredients; associating chemical features with a flavor and more. Data-driven studies based on FlavorDB can pave the way for an improved understanding of flavor mechanisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Engineering and control of cold molecules. Making manipulating and exploiting ultra-cold polar molecules

International Nuclear Information System (INIS)

Bigelow, N.P.; Haimberger, C.; Kleinert, J.; Tscherneck, M.; Holmes, M.E.

2005-01-01

In the last 12 months several groups have demonstrated the use of photo association to create cold heteronuclear (polar) molecules. We report on the formation of translationally cold NaCs molecules starting from a laser-cooled atomic vapor of Na and Cs atoms. Colliding atoms are transferred into bound molecular states in a two-step photoactivated process. We find a translational temperature of T ≅ 260 mK. To increase the density and number of trapped atoms, dark-spot techniques are used on the MOT and a Zeeman slowed sodium beam is used to load the sodium atoms into the trap. Spectroscopy of these molecules is underway using time-of-flight ion detection and trap-loss. Initial REMPI measurements indicate that both singlet and triplet states are being populated by the spontaneous-decay driven process. We measure a rate constant for molecule formation of K NaCs = 7.43 · 10 15 cm 3 s -1 . (author)

Gaseous Electronics Tables, Atoms, and Molecules

CERN Document Server

Raju, Gorur Govinda

2011-01-01

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,

How to measure load-dependent kinetics of individual motor molecules without a force clamp

DEFF Research Database (Denmark)

Sung, J.; Mortensen, Kim; Spudich, J.A.

2017-01-01

Single-molecule force spectroscopy techniques, including optical trapping, magnetic trapping, and atomic force microscopy, have provided unprecedented opportunities to understand biological processes at the smallest biological length scales. For example, they have been used to elucidate the molec......Single-molecule force spectroscopy techniques, including optical trapping, magnetic trapping, and atomic force microscopy, have provided unprecedented opportunities to understand biological processes at the smallest biological length scales. For example, they have been used to elucidate...... functions at the single molecule level, such as conformational changes and force-generation of individual motor proteins or force-dependent kinetics in molecular interactions. Here, we describe a new method, “Harmonic Force Spectroscopy (HFS).” With a conventional dual-beam optical trap and a simple...... concepts, experimental setup, step-by-step experimental protocol, theory, data analysis, and results....

Formation of ultracold NaRb Feshbach molecules

International Nuclear Information System (INIS)

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

2015-01-01

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 (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. (paper)

Quantum transport through organic molecules

International Nuclear Information System (INIS)

Maiti, Santanu K.

2007-01-01

We investigate the electronic transport for the model of benzene-1, 4-dithiolate (BDT) molecule and some other geometric models of benzene molecule attached with two semi-infinite metallic electrodes by the use of Green's function technique. An analytic approach for the electronic transport through the molecular bridges is presented, based on the tight-binding model. Transport of electrons in such molecular bridges is strongly affected by the geometry of the molecules and their coupling strength with the electrodes. Conductance (g) shows resonance peaks associated with the molecular energy eigenstates. In the weak molecule-to-electrodes coupling limit current (I) passing through the molecules shows staircase-like behavior with sharp steps, while, it varies quite continuously in the limit of strong molecular coupling with the applied bias voltage (V). In presence of the transverse magnetic field conductance gives oscillatory behavior with flux φ, threaded by the molecular ring, showing φ 0 ( = ch/e) flux-quantum periodicity. Though conductance changes with the application of transverse magnetic field, but the current-voltage characteristics remain same in presence of this magnetic field for these molecular bridge systems

Single-molecule techniques in biophysics: a review of the progress in methods and applications

Science.gov (United States)

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J. M.; Leake, Mark C.

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in ‘force spectroscopy’ techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including

Nanospectroscopy of thiacyanine dye molecules adsorbed on silver nanoparticle clusters

Science.gov (United States)

Ralević, Uroš; Isić, Goran; Anicijević, Dragana Vasić; Laban, Bojana; Bogdanović, Una; Lazović, Vladimir M.; Vodnik, Vesna; Gajić, Radoš

2018-03-01

The adsorption of thiacyanine dye molecules on citrate-stabilized silver nanoparticle clusters drop-cast onto freshly cleaved mica or highly oriented pyrolytic graphite surfaces is examined using colocalized surface-enhanced Raman spectroscopy and atomic force microscopy. The incidence of dye Raman signatures in photoluminescence hotspots identified around nanoparticle clusters is considered for both citrate- and borate-capped silver nanoparticles and found to be substantially lower in the former case, suggesting that the citrate anions impede the efficient dye adsorption. Rigorous numerical simulations of light scattering on random nanoparticle clusters are used for estimating the electromagnetic enhancement and elucidating the hotspot formation mechanism. The majority of the enhanced Raman signal, estimated to be more than 90%, is found to originate from the nanogaps between adjacent nanoparticles in the cluster, regardless of the cluster size and geometry.

Quenched spin tunneling and diabolical points in magnetic molecules. I. Symmetric configurations

Science.gov (United States)

Garg, Anupam

2001-09-01

The perfect quenching of spin tunneling that has previously been discussed in terms of interfering instantons, and has recently been observed in the magnetic molecule Fe8, is treated using a discrete phase integral (or Wentzel-Kramers-Brillouin) method. The simplest model Hamiltonian for the phenomenon leads to a Schrödinger equation that is a five-term recursion relation. This recursion relation is reflection symmetric when the magnetic field applied to the molecule is along the hard magnetic axis. A completely general Herring formula for the tunnel splittings for all reflection-symmetric five-term recursion relations is obtained. Using connection formulas for a nonclassical turning point that may be described as lying ``under the barrier,'' and which underlies the oscillations in the splitting as a function of magnetic field, this Herring formula is transformed into two other formulas that express the splittings in terms of a small number of action and actionlike integrals. These latter formulas appear to be generally valid, even for problems where the recursion contains more than five terms. The results for the model Hamiltonian are compared with experiment, numerics, previous instanton based approaches, and the limiting case of no magnetic field.

Andreev molecules in semiconductor nanowire double quantum dots.

Science.gov (United States)

Su, Zhaoen; Tacla, Alexandre B; Hocevar, Moïra; Car, Diana; Plissard, Sébastien R; Bakkers, Erik P A M; Daley, Andrew J; Pekker, David; Frolov, Sergey M

2017-09-19

Chains of quantum dots coupled to superconductors are promising for the realization of the Kitaev model of a topological superconductor. While individual superconducting quantum dots have been explored, control of longer chains requires understanding of interdot coupling. Here, double quantum dots are defined by gate voltages in indium antimonide nanowires. High transparency superconducting niobium titanium nitride contacts are made to each of the dots in order to induce superconductivity, as well as probe electron transport. Andreev bound states induced on each of dots hybridize to define Andreev molecular states. The evolution of these states is studied as a function of charge parity on the dots, and in magnetic field. The experiments are found in agreement with a numerical model.Quantum dots in a nanowire are one possible approach to creating a solid-state quantum simulator. Here, the authors demonstrate the coupling of electronic states in a double quantum dot to form Andreev molecule states; a potential building block for longer chains suitable for quantum simulation.

Plasmonics and single-molecule detection in evaporated silver-island films

Energy Technology Data Exchange (ETDEWEB)

Moula, G.; Aroca, R.F. [Materials and Surface Science Group, University of Windsor, Ontario (Canada); Rodriguez-Oliveros, R.; Sanchez-Gil, J.A. [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas, Serrano 121, 28006 Madrid (Spain); Albella, P. [Centro de Fisica de Materiales (CSIC-UPV/EHU) and Donostia International Physics Center (DIPC), 20018 Donostia, San Sebastian (Spain)

2012-11-15

The plasmonic origin of surface-enhanced Raman scattering (SERS) leads to the concept of hotspots and plasmon coupling that can be realized in the interstitial regions, or on specially engineered, silver and gold nanostructures. It is also possible to achieve spatial locations of high local field or hotspots on silver-island films (SIF) allowing single-molecule detection (SMD). When a single monomolecular layer coating the SIFs contains dye molecules dispersed in it, single-molecule impurities, (with an average of one hundred dye molecules in 1 {mu}m{sup 2}, which is the field of view of the micro-Raman system), SMD is observed as a rare statistical event. Here, the SMD results for silver-island films are presented, with the same nominal mass thickness, but differing in the localized surface plasmon resonance that is a function of the temperature of substrate during deposition. A blue-shifted plasmon can be seen as a decrease in plasmon coupling for deposition at higher temperature. A simple two-particle model for localized plasmon resonance coupling calculations, including the shape and substrate effects seems to explain the trend of observations. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Control Strategy for Small Molecule Impurities in Antibody-Drug Conjugates.

Science.gov (United States)

Gong, Hai H; Ihle, Nathan; Jones, Michael T; Kelly, Kathleen; Kott, Laila; Raglione, Thomas; Whitlock, Scott; Zhang, Qunying; Zheng, Jie

2018-04-01

Antibody-drug conjugates (ADCs) are an emerging class of biopharmaceuticals. As such, there are no specific guidelines addressing impurity limits and qualification requirements. The current ICH guidelines on impurities, Q3A (Impurities in New Drug Substances), Q3B (Impurities in New Drug Products), and Q6B (Specifications: Test Procedures and Acceptance Criteria for Biotechnological/Biological Products) do not adequately address how to assess small molecule impurities in ADCs. The International Consortium for Innovation and Quality in Pharmaceutical Development (IQ) formed an impurities working group (IWG) to discuss this issue. This white paper presents a strategy for evaluating the impact of small molecule impurities in ADCs. This strategy suggests a science-based approach that can be applied to the design of control systems for ADC therapeutics. The key principles that form the basis for this strategy include the significant difference in molecular weights between small molecule impurities and the ADC, the conjugation potential of the small molecule impurities, and the typical dosing concentrations and dosing schedule. The result is that exposure to small impurities in ADCs is so low as to often pose little or no significant safety risk.

Electron correlation in molecules and condensed phases

CERN Document Server

March, N H

1996-01-01

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

Energy storage and redistribution in molecules

International Nuclear Information System (INIS)

Hinze, J.

1983-01-01

This book presents information on the following topics: chemistry and spectroscopy of molecules at high levels of excitation; energy and phase randomization in large molecules as probed by laser spectroscopy; intramolecular processes in isolated polyatomic molecules; pulse-probe measurements in low-temperature, low-pressure SF 6 ; the photodissociation dynamics of H 2 S and CF 3 NO; photofragment spectroscopy of the NO 2 dissociation; preparation, laser spectroscopy and predissociation of alkali dimers in supersonic nozzle beams; excited states of small molecules - collisional quenching and photodissociation; quantum-state-resolved scattering of lithium hydride; and molecular negative ions

Numerical Modelling of Flow and Settling in Secondary Settling Tanks

DEFF Research Database (Denmark)

Dahl, Claus Poulsen

This thesis discusses the development of a numerical model for the simulation of secondary settling tanks. In the first part, the status on the development of numerical models for settling tanks and a discussion of the current design practice are presented. A study of the existing numerical models...... and design practice proved a demand for further development to include numerical models in the design of settling tanks, thus improving the future settling tanks....

Molecule-oriented programming in Java

NARCIS (Netherlands)

Bergstra, J.A.

2002-01-01

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

Numerical investigation of high temperature synthesis gas premixed combustion via ANSYS Fluent

Directory of Open Access Journals (Sweden)

Pashchenko Dmitry

2018-01-01

Full Text Available A numerical model of the synthesis gas pre-mixed combustion is developed. The research was carried out via ANSYS Fluent software. Verification of the numerical results was carried out using experimental data. A visual comparison of the flame contours that obtained by the synthesis gas combustion for Re = 600; 800; 1000 was performed. A comparison of the wall temperature of the combustion chamber, obtained with the help of the developed model, with the results of a physical experiment was also presented. For all cases, good convergence of the results is observed. It is established that a change in the temperature of the syngas/air mixture at the inlet to the combustion chamber does not significantly affect the temperature of the combustion products due to the dissipation of the H2O and CO2 molecules. The obtained results are of practical importance for the design of heat engineering plants with thermochemical heat recovery.

Highly sensitivity adhesion molecules detection in hereditary haemochromatosis patients reveals altered expression.

LENUS (Irish Health Repository)

Norris, S

2012-02-01

Several abnormalities in the immune status of patients with hereditary haemochromatosis (HH) have been reported, suggesting an imbalance in their immune function. This may include persistent production of, or exposure to, altered immune signalling contributing to the pathogenesis of this disorder. Adhesion molecules L-, E- and P-Selectin, intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1) are some of the major regulators of the immune processes and altered levels of these proteins have been found in pathological states including cardiovascular diseases, arthritis and liver cancer. The aim of this study was to assess L-, E- and P-Selectin, ICAM-1 and VCAM-1 expression in patients with HH and correlate these results with HFE mutation status and iron indexes. A total of 139 subjects were diagnosed with HH (C282Y homozygotes = 87, C282Y\\/H63D = 26 heterozygotes, H63D homozygotes = 26), 27 healthy control subjects with no HFE mutation (N\\/N), 18 normal subjects heterozygous for the H63D mutation served as age-sex-matched controls. We observed a significant decrease in L-selectin (P = 0.0002) and increased E-selectin and ICAM-1 (P = 0.0006 and P = 0.0059) expression in HH patients compared with healthy controls. This study observes for the first time that an altered adhesion molecules profile occurs in patients with HH that is associated with specific HFE genetic component for iron overload, suggesting that differential expression of adhesion molecules may play a role in the pathogenesis of HH.

MOLECULES IN η CARINAE

International Nuclear Information System (INIS)

Loinard, Laurent; Menten, Karl M.; Güsten, Rolf; Zapata, Luis A.; Rodríguez, Luis F.

2012-01-01

We report the detection toward η Carinae of six new molecules, CO, CN, HCO + , HCN, HNC, and N 2 H + , and of two of their less abundant isotopic counterparts, 13 CO and H 13 CN. The line profiles are moderately broad (∼100 km s –1 ), 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 underabundant in η Carinae. On the other hand, molecules containing nitrogen or the 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 η Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

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

International Nuclear Information System (INIS)

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

2012-01-01

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

Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data.

Science.gov (United States)

Greenfeld, Max; van de Meent, Jan-Willem; Pavlichin, Dmitri S; Mabuchi, Hideo; Wiggins, Chris H; Gonzalez, Ruben L; Herschlag, Daniel

2015-01-16

Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38:30-37, 2013; Nat Rev Genet 14:9-22, 2013; Curr Opin Struct Biol 2014, 28C:112-121; Annu Rev Biophys 43:19-39, 2014]. The analysis and interpretation of raw single-molecule data benefits greatly from the ongoing development of sophisticated statistical analysis tools that enable accurate inference at the low signal-to-noise ratios frequently associated with these measurements. While a number of groups have released analysis toolkits as open source software [J Phys Chem B 114:5386-5403, 2010; Biophys J 79:1915-1927, 2000; Biophys J 91:1941-1951, 2006; Biophys J 79:1928-1944, 2000; Biophys J 86:4015-4029, 2004; Biophys J 97:3196-3205, 2009; PLoS One 7:e30024, 2012; BMC Bioinformatics 288 11(8):S2, 2010; Biophys J 106:1327-1337, 2014; Proc Int Conf Mach Learn 28:361-369, 2013], it remains difficult to compare analysis for experiments performed in different labs due to a lack of standardization. Here we propose a standardized single-molecule dataset (SMD) file format. SMD is designed to accommodate a wide variety of computer programming languages, single-molecule techniques, and analysis strategies. To facilitate adoption of this format we have made two existing data analysis packages that are used for single-molecule analysis compatible with this format. Adoption of a common, standard data file format for sharing raw single-molecule data and analysis outcomes is a critical step for the emerging and powerful single-molecule field, which will benefit both sophisticated users and non-specialists by allowing standardized, transparent, and reproducible analysis practices.

Are Humans too Numerous to Become Extinct?

OpenAIRE

Cairns, John

2009-01-01

Some claim that humans are too numerous to become extinct. However, passenger pigeon, once the most numerous birds on the planet, are now extinct. For years, humankind has been damaging its habitat, discharging toxic chemicals into the environment, and having harmful effects on agricultural productivity due to climate change. Humankind s extinction depends on the continuation of various human activities including economic growth, addiction to fossil fuel, over consumption, overpopulation, oc...

CHIRON: a package for ChPT numerical results at two loops

Energy Technology Data Exchange (ETDEWEB)

Bijnens, Johan [Lund University, Department of Astronomy and Theoretical Physics, Lund (Sweden)

2015-01-01

This document describes the package CHIRON which includes two libraries, chiron itself and jbnumlib.chiron is a set of routines useful for two-loop numerical results in chiral perturbation theory (ChPT). It includes programs for the needed one- and two-loop integrals as well as routines to deal with the ChPT parameters. The present version includes everything needed for the masses, decay constants and quark-antiquark vacuum-expectation-values. An added routine calculates consistent values for the masses and decay constants when the pion and kaon masses are varied. In addition a number of finite volume results are included: one-loop tadpole integrals, two-loop sunset integrals and the results for masses and decay constants. The numerical routine library jbnumlib contains the numerical routines used in chiron. Many are to a large extent simple C++ versions of routines in the CERNLIB numerical library. Notable exceptions are the dilogarithm and the Jacobi theta function implementations. This paper describes what is included in CHIRON v0.50. (orig.)

Conserved water molecules in bacterial serine hydroxymethyltransferases.

Science.gov (United States)

Milano, Teresa; Di Salvo, Martino Luigi; Angelaccio, Sebastiana; Pascarella, Stefano

2015-10-01

Water molecules occurring in the interior of protein structures often are endowed with key structural and functional roles. We report the results of a systematic analysis of conserved water molecules in bacterial serine hydroxymethyltransferases (SHMTs). SHMTs are an important group of pyridoxal-5'-phosphate-dependent enzymes that catalyze the reversible conversion of l-serine and tetrahydropteroylglutamate to glycine and 5,10-methylenetetrahydropteroylglutamate. The approach utilized in this study relies on two programs, ProACT2 and WatCH. The first software is able to categorize water molecules in a protein crystallographic structure as buried, positioned in clefts or at the surface. The other program finds, in a set of superposed homologous proteins, water molecules that occur approximately in equivalent position in each of the considered structures. These groups of molecules are referred to as 'clusters' and represent structurally conserved water molecules. Several conserved clusters of buried or cleft water molecules were found in the set of 11 bacterial SHMTs we took into account for this work. The majority of these clusters were not described previously. Possible structural and functional roles for the conserved water molecules are envisaged. This work provides a map of the conserved water molecules helpful for deciphering SHMT mechanism and for rational design of molecular engineering experiments. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Double-valence-fluctuating molecules and superconductivity

International Nuclear Information System (INIS)

Hirsch, J.E.; Scalapino, D.J.

1985-01-01

We discuss the possibility of ''double-valence-fluctuating'' molecules, having two ground-state configurations differing by two electrons. We propose a possible realization of such a molecule, and experimental ways to look for it. We argue that a weakly coupled array of such molecules should give rise to a strong-coupling Shafroth-Blatt-Butler superconductor, with a high transition temperature

Tunnel ionization of atoms and molecules: How accurate are the weak-field asymptotic formulas?

Science.gov (United States)

Labeye, Marie; Risoud, François; Maquet, Alfred; Caillat, Jérémie; Taïeb, Richard

2018-05-01

Weak-field asymptotic formulas for the tunnel ionization rate of atoms and molecules in strong laser fields are often used for the analysis of strong field recollision experiments. We investigate their accuracy and domain of validity for different model systems by confronting them to exact numerical results, obtained by solving the time dependent Schrödinger equation. We find that corrections that take the dc-Stark shift into account are a simple and efficient way to improve the formula. Furthermore, analyzing the different approximations used, we show that error compensation plays a crucial role in the fair agreement between exact and analytical results.

Study of the electronic properties of organic molecules within a metal-molecule-metal junction

International Nuclear Information System (INIS)

Lambert, Mathieu

2003-01-01

This ph-D thesis is about electronic transport through organic molecules inserted in a metal molecule-metal junction. We describe first a simple process to prepare sub-3 nm gaps by controllable breakage (under an electrical stress) of gold wires lithographed on a SiO 2 Si substrate at low temperature (4.2 K). We show that the involved mechanism is thermally assisted electromigration. We observe that current-voltage (I-V) characteristics of resulting electrodes are stable up to ∼5 V. which gives access to the well-known Fowler-Nordheim regime in the I-V, allowing an accurate characterisation of the gap size. The average gap is found lo be between 1.5 nm in width and 2.5 eV in height. Molecules and nanoparticles have then been inserted in the junction in the case of nanoparticles for example. The resulting IV clearly shows the suppression of electrical current at low bias known as Coulomb blockade. Characteristic of single-electron tunnelling through nanometer-sized structures, finally we fabricated a single-electron tunneling device based on Au nanoparticles connected to the electrodes via terthiophene (T3) molecule. We use the silicon substrate, separated from the planar structure by a silicon oxide of 200 nm, as an electrostatic gate and observed clear current modulation with possible signature of the transport properties of the terthiophene molecules. (author) [fr

Ionization in positron- and positronium- collisions with atoms and molecules

Energy Technology Data Exchange (ETDEWEB)

Laricchia, G; Brawley, S; Cooke, D A; Murtagh, D J; Williams, A I [UCL Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom); Koever, A [permanent address: ATOMKI, Institute for Nuclear Research, Debrecen (Hungary)

2009-11-15

Recent progress in the experimental study of positron- and positronium-induced ionization of atoms and molecules is outlined. Investigations include integral and differential cross-sections, as well as formation of positronium in the first excited state. Future prospects are discussed.

Numerical methods in simulation of resistance welding

DEFF Research Database (Denmark)

Nielsen, Chris Valentin; Martins, Paulo A.F.; Zhang, Wenqi

2015-01-01

Finite element simulation of resistance welding requires coupling betweenmechanical, thermal and electrical models. This paper presents the numerical models and theircouplings that are utilized in the computer program SORPAS. A mechanical model based onthe irreducible flow formulation is utilized...... a resistance welding point of view, the most essential coupling between the above mentioned models is the heat generation by electrical current due to Joule heating. The interaction between multiple objects is anothercritical feature of the numerical simulation of resistance welding because it influences...... thecontact area and the distribution of contact pressure. The numerical simulation of resistancewelding is illustrated by a spot welding example that includes subsequent tensile shear testing...

Numerical studies of the linear theta pinch

International Nuclear Information System (INIS)

Brackbill, J.U.; Menzel, M.T.; Barnes, D.C.

1975-01-01

Aspects of several physical problems associated with linear theta pinches were studied using recently developed numerical methods for the solution of the nonlinear equations for time-dependent magnetohydrodynamic flow in two- and three-dimensions. The problems studied include the propagation of end-loss produced rarefaction waves, the flow produced in a proposed injection experiment geometry, and the linear growth and nonlinear saturation of instabilities in rotating plasmas, all in linear geometries. The studies illustrate how numerical computations aid in flow visualization, and how the small amplitude behavior and nonlinear fate of plasmas in unstable equilibria can be connected through the numerical solution of the dynamical equations. (auth)

Coincidental match of numerical simulation and physics

Science.gov (United States)

Pierre, B.; Gudmundsson, J. S.

2010-08-01

Consequences of rapid pressure transients in pipelines range from increased fatigue to leakages and to complete ruptures of pipeline. Therefore, accurate predictions of rapid pressure transients in pipelines using numerical simulations are critical. State of the art modelling of pressure transient in general, and water hammer in particular include unsteady friction in addition to the steady frictional pressure drop, and numerical simulations rely on the method of characteristics. Comparison of rapid pressure transient calculations by the method of characteristics and a selected high resolution finite volume method highlights issues related to modelling of pressure waves and illustrates that matches between numerical simulations and physics are purely coincidental.

Analysis of experimental positron-molecule binding energies

International Nuclear Information System (INIS)

Danielson, J R; Surko, C M; Young, J A

2010-01-01

Experiments show that positron annihilation on molecules frequently occurs via capture into vibrational Feshbach resonances. In these cases, the downshifts in the annihilation spectra from the vibrational mode spectra provide measures of the positron-molecule binding energies. An analysis of these binding energy data is presented in terms of the molecular dipole polarizability, the permanent dipole moment, and the number of π bonds in aromatic molecules. The results of this analysis are in reasonably good agreement with other information about positron-molecule bound states. Predictions for other targets and promising candidate molecules for further investigation are discussed.

2012 Gordon Research Conference, Single molecule approaches to biology, July 15-20 2012

Energy Technology Data Exchange (ETDEWEB)

Fernandez, Julio M. [Columbia Univ., New York, NY (United States)

2012-04-20

Single molecule techniques are rapidly occupying a central role in biological research at all levels. This transition was made possible by the availability and dissemination of robust techniques that use fluorescence and force probes to track the conformation of molecules one at a time, in vitro as well as in live cells. Single-molecule approaches have changed the way many biological problems are studied. These novel techniques provide previously unobtainable data on fundamental biochemical processes that are essential for all forms of life. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of the molecular systems that underpin the functioning of living cells. Hence, our conference seeks to disseminate the implementation and use of single molecule techniques in the pursuit of new biological knowledge. Topics covered include: Molecular Motors on the Move; Origin And Fate Of Proteins; Physical Principles Of Life; Molecules and Super-resolution Microscopy; Nanoswitches In Action; Active Motion Or Random Diffusion?; Building Blocks Of Living Cells; From Molecular Mechanics To Physiology; Tug-of-war: Force Spectroscopy Of Single Proteins.

Towards standard testbeds for numerical relativity

International Nuclear Information System (INIS)

Alcubierre, Miguel; Allen, Gabrielle; Bona, Carles; Fiske, David; Goodale, Tom; Guzman, F Siddhartha; Hawke, Ian; Hawley, Scott H; Husa, Sascha; Koppitz, Michael; Lechner, Christiane; Pollney, Denis; Rideout, David; Salgado, Marcelo; Schnetter, Erik; Seidel, Edward; Shinkai, Hisa-aki; Shoemaker, Deirdre; Szilagyi, Bela; Takahashi, Ryoji; Winicour, Jeff

2004-01-01

In recent years, many different numerical evolution schemes for Einstein's equations have been proposed to address stability and accuracy problems that have plagued the numerical relativity community for decades. Some of these approaches have been tested on different spacetimes, and conclusions have been drawn based on these tests. However, differences in results originate from many sources, including not only formulations of the equations, but also gauges, boundary conditions, numerical methods and so on. We propose to build up a suite of standardized testbeds for comparing approaches to the numerical evolution of Einstein's equations that are designed to both probe their strengths and weaknesses and to separate out different effects, and their causes, seen in the results. We discuss general design principles of suitable testbeds, and we present an initial round of simple tests with periodic boundary conditions. This is a pivotal first step towards building a suite of testbeds to serve the numerical relativists and researchers from related fields who wish to assess the capabilities of numerical relativity codes. We present some examples of how these tests can be quite effective in revealing various limitations of different approaches, and illustrating their differences. The tests are presently limited to vacuum spacetimes, can be run on modest computational resources and can be used with many different approaches used in the relativity community

Towards standard testbeds for numerical relativity

Energy Technology Data Exchange (ETDEWEB)

Alcubierre, Miguel [Inst. de Ciencias Nucleares, Univ. Nacional Autonoma de Mexico, Apartado Postal 70-543, Mexico Distrito Federal 04510 (Mexico); Allen, Gabrielle; Goodale, Tom; Guzman, F Siddhartha; Hawke, Ian; Husa, Sascha; Koppitz, Michael; Lechner, Christiane; Pollney, Denis; Rideout, David [Max-Planck-Inst. fuer Gravitationsphysik, Albert-Einstein-Institut, 14476 Golm (Germany); Bona, Carles [Departament de Fisica, Universitat de les Illes Balears, Ctra de Valldemossa km 7.5, 07122 Palma de Mallorca (Spain); Fiske, David [Dept. of Physics, Univ. of Maryland, College Park, MD 20742-4111 (United States); Hawley, Scott H [Center for Relativity, Univ. of Texas at Austin, Austin, Texas 78712 (United States); Salgado, Marcelo [Inst. de Ciencias Nucleares, Univ. Nacional Autonoma de Mexico, Apartado Postal 70-543, Mexico Distrito Federal 04510 (Mexico); Schnetter, Erik [Inst. fuer Astronomie und Astrophysik, Universitaet Tuebingen, 72076 Tuebingen (Germany); Seidel, Edward [Max-Planck-Inst. fuer Gravitationsphysik, Albert-Einstein-Inst., 14476 Golm (Germany); Shinkai, Hisa-aki [Computational Science Div., Inst. of Physical and Chemical Research (RIKEN), Hirosawa 2-1, Wako, Saitama 351-0198 (Japan); Shoemaker, Deirdre [Center for Radiophysics and Space Research, Cornell Univ., Ithaca, NY 14853 (United States); Szilagyi, Bela [Dept. of Physics and Astronomy, Univ. of Pittsburgh, Pittsburgh, PA 15260 (United States); Takahashi, Ryoji [Theoretical Astrophysics Center, Juliane Maries Vej 30, 2100 Copenhagen, (Denmark); Winicour, Jeff [Max-Planck-Inst. fuer Gravitationsphysik, Albert-Einstein-Institut, 14476 Golm (Germany)

2004-01-21

In recent years, many different numerical evolution schemes for Einstein's equations have been proposed to address stability and accuracy problems that have plagued the numerical relativity community for decades. Some of these approaches have been tested on different spacetimes, and conclusions have been drawn based on these tests. However, differences in results originate from many sources, including not only formulations of the equations, but also gauges, boundary conditions, numerical methods and so on. We propose to build up a suite of standardized testbeds for comparing approaches to the numerical evolution of Einstein's equations that are designed to both probe their strengths and weaknesses and to separate out different effects, and their causes, seen in the results. We discuss general design principles of suitable testbeds, and we present an initial round of simple tests with periodic boundary conditions. This is a pivotal first step towards building a suite of testbeds to serve the numerical relativists and researchers from related fields who wish to assess the capabilities of numerical relativity codes. We present some examples of how these tests can be quite effective in revealing various limitations of different approaches, and illustrating their differences. The tests are presently limited to vacuum spacetimes, can be run on modest computational resources and can be used with many different approaches used in the relativity community.

Adsorption of CO molecules on doped graphene: A first-principles study

Directory of Open Access Journals (Sweden)

Weidong Wang

2016-02-01

Full Text Available As a typical kinds of toxic gases, CO plays an important role in environmental monitoring, control of chemical processes, space missions, agricultural and medical applications. Graphene is considered a potential candidate of gases sensor, so the adsorption of CO molecules on various graphene, including pristine graphene, Nitrogen-doped graphene (N-doped graphene and Aluminum-doped graphene (Al-doped graphene, are studied by using first-principles calculations. The optimal configurations, adsorption energies, charge transfer, and electronic properties including band structures, density of states and differential charge density are obtained. The adsorption energies of CO molecules on pristine graphene and N-doped graphene are −0.01 eV, and −0.03 eV, respectively. In comparison, the adsorption energy of CO on Al-doped graphene is much larger, −2.69 eV. Our results also show that there occurs a large amount of charge transfer between CO molecules and graphene sheet after the adsorption, which suggests Al-doped graphene is more sensitive to the adsorption of CO than pristine graphene and N-doped graphene. Therefore, the sensitivity of gases on graphene can be drastically improved by introducing the suitable dopants.

Molecules cooled below the Doppler limit

Science.gov (United States)

Truppe, S.; Williams, H. J.; Hambach, M.; Caldwell, L.; Fitch, N. J.; Hinds, E. A.; Sauer, B. E.; Tarbutt, M. R.

2017-12-01

Magneto-optical trapping and sub-Doppler cooling have been essential to most experiments with quantum degenerate gases, optical lattices, atomic fountains and many other applications. A broad set of new applications await ultracold molecules, and the extension of laser cooling to molecules has begun. A magneto-optical trap (MOT) has been demonstrated for a single molecular species, SrF, but the sub-Doppler temperatures required for many applications have not yet been reached. Here we demonstrate a MOT of a second species, CaF, and we show how to cool these molecules to 50 μK, well below the Doppler limit, using a three-dimensional optical molasses. These ultracold molecules could be loaded into optical tweezers to trap arbitrary arrays for quantum simulation, launched into a molecular fountain for testing fundamental physics, and used to study collisions and chemistry between atoms and molecules at ultracold temperatures.

OMG: Open Molecule Generator.

Science.gov (United States)

Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

2012-09-17

Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

OMG: Open Molecule Generator

Directory of Open Access Journals (Sweden)

Peironcely Julio E

2012-09-01

Full Text Available Abstract Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG, which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

Numerical analysis of electromagnetic fields

CERN Document Server

Zhou Pei Bai

1993-01-01

Numerical methods for solving boundary value problems have developed rapidly. Knowledge of these methods is important both for engineers and scientists. There are many books published that deal with various approximate methods such as the finite element method, the boundary element method and so on. However, there is no textbook that includes all of these methods. This book is intended to fill this gap. The book is designed to be suitable for graduate students in engineering science, for senior undergraduate students as well as for scientists and engineers who are interested in electromagnetic fields. Objective Numerical calculation is the combination of mathematical methods and field theory. A great number of mathematical concepts, principles and techniques are discussed and many computational techniques are considered in dealing with practical problems. The purpose of this book is to provide students with a solid background in numerical analysis of the field problems. The book emphasizes the basic theories ...

Numerical Modelling Of Pumpkin Balloon Instability

Science.gov (United States)

Wakefield, D.

Tensys have been involved in the numerical formfinding and load analysis of architectural stressed membrane structures for 15 years. They have recently broadened this range of activities into the `lighter than air' field with significant involvement in aerostat and heavy-lift hybrid airship design. Since early 2004 they have been investigating pumpkin balloon instability on behalf of the NASA ULDB programme. These studies are undertaken using inTENS, an in-house finite element program suite based upon the Dynamic Relaxation solution method and developed especially for the non-linear analysis and patterning of membrane structures. The paper describes the current state of an investigation that started with a numerical simulation of the lobed cylinder problem first studied by Calladine. The influence of material properties and local geometric deformation on stability is demonstrated. A number of models of complete pumpkin balloons have then been established, including a 64-gore balloon with geometry based upon Julian Nott's Endeavour. This latter clefted dramatically upon initial inflation, a phenomenon that has been reproduced in the numerical model. Ongoing investigations include the introduction of membrane contact modelling into inTENS and correlation studies with the series of large-scale ULDB models currently in preparation.

Alkaline pH sensor molecules.

Science.gov (United States)

Murayama, Takashi; Maruyama, Ichiro N

2015-11-01

Animals can survive only within a narrow pH range. This requires continual monitoring of environmental and body-fluid pH. Although a variety of acidic pH sensor molecules have been reported, alkaline pH sensor function is not well understood. This Review describes neuronal alkaline pH sensors, grouped according to whether they monitor extracellular or intracellular alkaline pH. Extracellular sensors include the receptor-type guanylyl cyclase, the insulin receptor-related receptor, ligand-gated Cl- channels, connexin hemichannels, two-pore-domain K+ channels, and transient receptor potential (TRP) channels. Intracellular sensors include TRP channels and gap junction channels. Identification of molecular mechanisms underlying alkaline pH sensing is crucial for understanding how animals respond to environmental alkaline pH and how body-fluid pH is maintained within a narrow range. © 2015 Wiley Periodicals, Inc.

Single Molecule Spectroscopy of Electron Transfer

International Nuclear Information System (INIS)

Holman, Michael; Zang, Ling; Liu, Ruchuan; Adams, David M.

2009-01-01

The objectives of this research are threefold: (1) to develop methods for the study electron transfer processes at the single molecule level, (2) to develop a series of modifiable and structurally well defined molecular and nanoparticle systems suitable for detailed single molecule/particle and bulk spectroscopic investigation, (3) to relate experiment to theory in order to elucidate the dependence of electron transfer processes on molecular and electronic structure, coupling and reorganization energies. We have begun the systematic development of single molecule spectroscopy (SMS) of electron transfer and summaries of recent studies are shown. There is a tremendous need for experiments designed to probe the discrete electronic and molecular dynamic fluctuations of single molecules near electrodes and at nanoparticle surfaces. Single molecule spectroscopy (SMS) has emerged as a powerful method to measure properties of individual molecules which would normally be obscured in ensemble-averaged measurement. Fluctuations in the fluorescence time trajectories contain detailed molecular level statistical and dynamical information of the system. The full distribution of a molecular property is revealed in the stochastic fluctuations, giving information about the range of possible behaviors that lead to the ensemble average. In the case of electron transfer, this level of understanding is particularly important to the field of molecular and nanoscale electronics: from a device-design standpoint, understanding and controlling this picture of the overall range of possible behaviors will likely prove to be as important as designing ia the ideal behavior of any given molecule.

Isatin, a versatile molecule: studies in Brazil

Energy Technology Data Exchange (ETDEWEB)

Silva, Barbara, E-mail: barbara.iq@gmail.com [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil)

2013-05-15

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)

Alternative types of molecule-decorated atomic chains in Au–CO–Au single-molecule junctions

Directory of Open Access Journals (Sweden)

Zoltán Balogh

2015-06-01

Full Text Available We investigate the formation and evolution of Au–CO single-molecule break junctions. The conductance histogram exhibits two distinct molecular configurations, which are further investigated by a combined statistical analysis. According to conditional histogram and correlation analysis these molecular configurations show strong anticorrelations with each other and with pure Au monoatomic junctions and atomic chains. We identify molecular precursor configurations with somewhat higher conductance, which are formed prior to single-molecule junctions. According to detailed length analysis two distinct types of molecule-affected chain-formation processes are observed, and we compare these results to former theoretical calculations considering bridge- and atop-type molecular configurations where the latter has reduced conductance due to destructive Fano interference.

Individual Magnetic Molecules on Ultrathin Insulating Surfaces

Science.gov (United States)

El Hallak, Fadi; Warner, Ben; Hirjibehedin, Cyrus

2012-02-01

Single molecule magnets have attracted ample interest because of their exciting magnetic and quantum properties. Recent studies have demonstrated that some of these molecules can be evaporated on surfaces without losing their magnetic properties [M. Mannini et al., Nature 468, 417, (2010)]. This remarkable progress enhances the chances of real world applications for these molecules. We present STM imaging and spectroscopy data on iron phthalocyanine molecules deposited on Cu(100) and on a Cu2N ultrathin insulating surface. These molecules have been shown to display a large magnetic anisotropy on another thin insulating surface, oxidized Cu(110) [N. Tsukahara et al., Phys. Rev. Lett. 102, 167203 (2009)]. By using a combination of elastic and inelastic electron tunnelling spectroscopy, we investigate the binding of the molecules to the surface and the impact that the surface has on their electronic and magnetic properties.

Experimental decoherence in molecule interferometry

International Nuclear Information System (INIS)

Hackermueller, L.; Hornberger, K.; Stibor, A.; Zeilinger, A.; Arndt, M.; Kiesewetter, G.

2005-01-01

Full text: We present three mechanisms of decoherence that occur quite naturally in matter wave interferometer with large molecules. One way molecules can lose coherence is through collision with background gas particles. We observe a loss of contrast with increasing background pressure for various types of gases. We can understand this phenomenon quantitatively with a new model for collisional decoherence which corrects older models by a factor of 2 π;. The second experiment studies the thermal emission of photons related to the high internal energy of the interfering molecules. When sufficiently many or sufficiently short photons are emitted inside the interferometer, the fringe contrast is lost. We can continuously vary the temperature of the molecules and compare the loss of contrast with a model based on decoherence theory. Again we find good quantitative agreement. A third mechanism that influences our interference pattern is dephasing due to vibrations of the interference gratings. By adding additional vibrations we study this effect in more detail. (author)

Numerical analysis

CERN Document Server

Rao, G Shanker

2006-01-01

About the Book: This book provides an introduction to Numerical Analysis for the students of Mathematics and Engineering. The book is designed in accordance with the common core syllabus of Numerical Analysis of Universities of Andhra Pradesh and also the syllabus prescribed in most of the Indian Universities. Salient features: Approximate and Numerical Solutions of Algebraic and Transcendental Equation Interpolation of Functions Numerical Differentiation and Integration and Numerical Solution of Ordinary Differential Equations The last three chapters deal with Curve Fitting, Eigen Values and Eigen Vectors of a Matrix and Regression Analysis. Each chapter is supplemented with a number of worked-out examples as well as number of problems to be solved by the students. This would help in the better understanding of the subject. Contents: Errors Solution of Algebraic and Transcendental Equations Finite Differences Interpolation with Equal Intervals Interpolation with Unequal Int...

Molecules in the Spotlight

Energy Technology Data Exchange (ETDEWEB)

Cryan, James

2010-01-26

SLAC has just unveiled the world's first X-ray laser, the LCLS. This machine produces pulses of X-rays that are ten billion times brighter than those from conventional sources. One of the goals of this machine is to make movies of chemical reactions, including reactions necessary for life and reactions that might power new energy technologies. This public lecture will show the first results from the LCLS. As a first target, we have chosen nitrogen gas, the main component of the air we breathe. Using the unprecedented power of the LCLS X-rays as a blasting torch, we have created new forms of this molecule and with unique electronic arrangements. Please share with us the first insights from this new technology.

Extracting Models in Single Molecule Experiments

Science.gov (United States)

Presse, Steve

2013-03-01

Single molecule experiments can now monitor the journey of a protein from its assembly near a ribosome to its proteolytic demise. Ideally all single molecule data should be self-explanatory. However data originating from single molecule experiments is particularly challenging to interpret on account of fluctuations and noise at such small scales. Realistically, basic understanding comes from models carefully extracted from the noisy data. Statistical mechanics, and maximum entropy in particular, provide a powerful framework for accomplishing this task in a principled fashion. Here I will discuss our work in extracting conformational memory from single molecule force spectroscopy experiments on large biomolecules. One clear advantage of this method is that we let the data tend towards the correct model, we do not fit the data. I will show that the dynamical model of the single molecule dynamics which emerges from this analysis is often more textured and complex than could otherwise come from fitting the data to a pre-conceived model.

Functional recombinant MHC class II molecules and high-throughput peptide-binding assays

DEFF Research Database (Denmark)

Justesen, Sune; Harndahl, Mikkel; Lamberth, Kasper

2009-01-01

BACKGROUND: Molecules of the class II major histocompability complex (MHC-II) specifically bind and present exogenously derived peptide epitopes to CD4+ T helper cells. The extreme polymorphism of the MHC-II hampers the complete analysis of peptide binding. It is also a significant hurdle......-II molecules and accompanying HTS peptide-binding assay were successfully developed for nine different MHC-II molecules including the DPA1*0103/DPB1*0401 (DP401) and DQA1*0501/DQB1*0201, where both alpha and beta chains are polymorphic, illustrating the advantages of producing the two chains separately....... CONCLUSION: We have successfully developed versatile MHC-II resources, which may assist in the generation of MHC class II -wide reagents, data, and tools....

Comparative Energetics of Carbon Storage Molecules in Green Algae

Energy Technology Data Exchange (ETDEWEB)

Laurens, Lieve M [National Renewable Energy Laboratory (NREL), Golden, CO (United States); McKie-Krisberg, Zaid M. [City University of New York; Huang, Andy [City University of New York; Polle, Jurgen E. W. [City University of New York

2018-02-28

Several members of the green algae possess the ability to produce lipids and/or high value compounds in significant quantities. While for several of these green algal species induction of increased lipid production has been shown, and cultivation of species for high value molecules occurs at production scale, the molecular mechanisms governing over-accumulation of molecules synthesized from isoprenoid precursors, carotenoids, for example, have received far less attention. Here, we present a calculation of the required ATP equivalencies per carbon atom and reducing power equivalencies as NADH/NADPH (NAD(P)H) per carbon atom for the isoprenoid molecules ..beta..-carotene (C40), astaxanthin (C40), and squalene (C30). We compared energetic requirements of carbohydrates, triacylglycerol, and isoprenoid molecules under a gradient of conditions of cellular stress. Our calculations revealed slightly less ATP and NAD(P)H equivalency per carbon atom between triacylglycerol and the three isoprenoid molecules. Based on our results, we propose that the driving force for differences in accumulation patterns of carotenoids vs. triacylglycerols in algal cells under stress is largely dependent on the presence and regulation of bypass mechanisms at metabolic junction bottlenecks, like pyruvate dehydrogenase (PDH), within particular species. We provide a discussion of several molecular mechanisms that may influence carbon partitioning within different groups of green algae, including metabolic inhibition through accumulation of specific substrates related to ATP and reducing equivalent production (NAD(P)H) as well as cellular compartmentalization. This work contributes to the ongoing discussion of cellular homeostatic regulation during stress, as well as the potential mechanisms driving long-term carbon storage as it relates to energy and redox states within the algal cell.

[Progress in sample preparation and analytical methods for trace polar small molecules in complex samples].

Science.gov (United States)

Zhang, Qianchun; Luo, Xialin; Li, Gongke; Xiao, Xiaohua

2015-09-01

Small polar molecules such as nucleosides, amines, amino acids are important analytes in biological, food, environmental, and other fields. It is necessary to develop efficient sample preparation and sensitive analytical methods for rapid analysis of these polar small molecules in complex matrices. Some typical materials in sample preparation, including silica, polymer, carbon, boric acid and so on, are introduced in this paper. Meanwhile, the applications and developments of analytical methods of polar small molecules, such as reversed-phase liquid chromatography, hydrophilic interaction chromatography, etc., are also reviewed.

On Numerical Methods for Including the Effect of Capillary Pressure Forces on Two-phase, Immiscible Flow in a Layered Porous Medium

Energy Technology Data Exchange (ETDEWEB)

Ersland, B.G.

1996-05-01

This mathematical doctoral thesis contains the theory, algorithms and numerical simulations for a heterogeneous oil reservoir. It presents the equations, which apply to immiscible and incompressible two-phase fluid flow in the reservoir, including the effect of capillary pressure forces, and emphasises in particular the interior boundary conditions at the interface between two sediments. Two different approaches are discussed. The first approach is to decompose the computational domain along the interior boundary and iterate between the subdomains until mass balance is achieved. The second approach accounts for the interior boundary conditions in the basis in which the solution is expanded, the basis being discontinuous over the interior boundaries. An overview of the construction of iterative solvers for partial differential equations by means of Schwartz methods is given, and the algorithm for local refinement with Schwartz iterations as iterative solver is described. The theory is then applied to a core plug problem in one and two space dimensions and the results of different methods compared. A general description is given of the computer simulation model, which is implemented in C++. 64 refs., 49 figs., 7 tabs.

Levels Of Serum Intercellular And Vascular Adhesion Molecules In ...

African Journals Online (AJOL)

The study evaluated the possible significant role of soluble intercellular and vascular adhesion molecule-1 (sICAM-1 and sVCAM-1), sE-selectin and interluekin-1β in development nephropathy in patients with insulin dependent diabetes mellitus (IDDM). This study included 60 patients with type 1 diabetes mellitus (IDDM) ...

Nonempirical calculations of the LiBO molecule

International Nuclear Information System (INIS)

Nemukhin, A.V.; Stepanov, N.F.

1987-01-01

Problems of nonempirical calculations of molecule energies, related to the use of limited basis AO set and configurations were considered taking the LiBO molecule as an example. The version of optimizing parameters of basis functions of the base of the concept of ''atoms in molecules'' was suggested. It is shown that correct description of the potential surface of LiBO molecule is impossible without consideration of electron correlation; main contributions to correlation corrections were distinguished