Electrondriven processes in polyatomic molecules
Energy Technology Data Exchange (ETDEWEB)
McKoy, Vincent [California Inst. of Technology (CalTech), Pasadena, CA (United States)
2017-03-20
This project developed and applied scalable computational methods to obtain information about low-energy electron collisions with larger polyatomic molecules. Such collisions are important in modeling radiation damage to living systems, in spark ignition and combustion, and in plasma processing of materials. The focus of the project was to develop efficient methods that could be used to obtain both fundamental scientific insights and data of practical value to applications.
Electron Interactions with Non-Linear Polyatomic Molecules and Their Radicals
1993-12-01
Phys. (NY) 19, 262 (1962). 14. T. Koga and T. Matsuhashi, J. Chem. Phys. 88, 1110 (1988). 15. G. Arfken , Mathematical Methods For Physicists, Third...Luther, and J.0. Wilkes, Applied Numerical Methods , New York, N.Y., Wiley, (1969). 4. M. Abramowitz and I. Stegun, Handbook of Mathematical ...approximation for electron scattering from molecules in the gas phase. In addition, a method for calculating the required cross sections by solving the Schr
Sisyphus Laser Cooling of a Polyatomic Molecule
Kozyryev, Ivan; Matsuda, Kyle; Augenbraun, Benjamin L; Anderegg, Loic; Sedlack, Alexander P; Doyle, John M
2016-01-01
We perform magnetically-assisted Sisyphus laser cooling of the triatomic free radical strontium monohydroxide (SrOH). This is achieved with principal optical cycling in the rotationally closed $P\\left(N"=1\\right)$ branch of either the $\\tilde{X}^{2}\\Sigma^{+}\\left(000\\right)\\leftrightarrow\\tilde{A}^{2}\\Pi_{1/2}\\left(000\\right)$ or the $\\tilde{X}^{2}\\Sigma^{+}\\left(000\\right)\\leftrightarrow\\tilde{B}^{2}\\Sigma^{+}\\left(000\\right)$ vibronic transitions. Molecules lost into the excited vibrational states during the cooling process are repumped back through the $\\tilde{B}\\left(000\\right)$ state for both the $\\left(100\\right)$ level of the Sr-O stretching mode and the $\\left(02^{0}0\\right)$ level of the bending mode. The transverse temperature of a SrOH molecular beam is reduced in one dimension by two orders of magnitude to $\\sim700\\ {\\rm \\mu K}$. This approach opens a path towards creating a variety of ultracold polyatomic molecules, including much larger ones, by means of direct laser cooling.
Sisyphus Laser Cooling of a Polyatomic Molecule.
Kozyryev, Ivan; Baum, Louis; Matsuda, Kyle; Augenbraun, Benjamin L; Anderegg, Loic; Sedlack, Alexander P; Doyle, John M
2017-04-28
We perform magnetically assisted Sisyphus laser cooling of the triatomic free radical strontium monohydroxide (SrOH). This is achieved with principal optical cycling in the rotationally closed P(N^{''}=1) branch of either the X[over ˜]^{2}Σ^{+}(000)↔A[over ˜]^{2}Π_{1/2}(000) or the X[over ˜]^{2}Σ^{+}(000)↔B[over ˜]^{2}Σ^{+}(000) vibronic transitions. Molecules lost into the excited vibrational states during the cooling process are repumped back through the B[over ˜](000) state for both the (100) level of the Sr-O stretching mode and the (02^{0}0) level of the bending mode. The transverse temperature of a SrOH molecular beam is reduced in one dimension by 2 orders of magnitude to ∼750 μK. This approach opens a path towards creating a variety of ultracold polyatomic molecules by means of direct laser cooling.
Laser-coolable polyatomic molecules with heavy nuclei
Isaev, T A; Eliav, E
2016-01-01
Recently a number of diatomic and polyatomics molecules has been identified as a prospective systems for Doppler cooling. Polyatomic molecules with heavy nuclei present great interest for search for new physics outside of Standard Model and a large variety of other applications including cold chemistry, quantum informatics etc. Herein we propose radium monohydroxide molecule (RaOH) which is on the one hand amenable for Doppler cooling and on the other hand has considerable potential for searching for $\\cal P$-odd and $\\cal P,T$-odd effects.
Attosecond-recollision-controlled selective fragmentation of polyatomic molecules.
Xie, Xinhua; Doblhoff-Dier, Katharina; Roither, Stefan; Schöffler, Markus S; Kartashov, Daniil; Xu, Huailiang; Rathje, Tim; Paulus, Gerhard G; Baltuška, Andrius; Gräfe, Stefanie; Kitzler, Markus
2012-12-14
Control over various fragmentation reactions of a series of polyatomic molecules (acetylene, ethylene, 1,3-butadiene) by the optical waveform of intense few-cycle laser pulses is demonstrated experimentally. We show both experimentally and theoretically that the responsible mechanism is inelastic ionization from inner-valence molecular orbitals by recolliding electron wave packets, whose recollision energy in few-cycle ionizing laser pulses strongly depends on the optical waveform. Our work demonstrates an efficient and selective way of predetermining fragmentation and isomerization reactions in polyatomic molecules on subfemtosecond time scales.
Attosecond-recollision-controlled selective fragmentation of polyatomic molecules
Xie, Xinhua; Roither, Stefan; Schöffler, Markus S; Kartashov, Daniil; Xu, Huailiang; Rathje, Tim; Paulus, Gerhard G; Baltuška, Andrius; Gräfe, Stefanie; Kitzler, Markus
2012-01-01
Control over various fragmentation reactions of a series of polyatomic molecules (acetylene, ethylene, 1,3-butadiene) by the optical waveform of intense few-cycle laser pulses is demonstrated experimentally. We show both experimentally and theoretically that the responsible mechanism is inelastic ionization from inner-valence molecular orbitals by recolliding electron wavepackets, whose recollision energy in few-cycle ionizing laser pulses strongly depends on the optical waveform. Our work demonstrates an efficient and selective way of pre-determining fragmentation and isomerization reactions in polyatomic molecules on sub-femtosecond time-scales.
Proposal for Laser Cooling of Complex Polyatomic Molecules.
Kozyryev, Ivan; Baum, Louis; Matsuda, Kyle; Doyle, John M
2016-11-18
An experimentally feasible strategy for direct laser cooling of polyatomic molecules with six or more atoms is presented. Our approach relies on the attachment of a metal atom to a complex molecule, where it acts as an active photon cycling site. We describe a laser cooling scheme for alkaline earth monoalkoxide free radicals taking advantage of the phase space compression of a cryogenic buffer-gas beam. Possible applications are presented including laser cooling of chiral molecules and slowing of molecular beams using coherent photon processes. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Rotational cooling of trapped polyatomic molecules
Glöckner, Rosa; Englert, Barbara G U; Rempe, Gerhard; Zeppenfeld, Martin
2015-01-01
Controlling the internal degrees of freedom is a key challenge for applications of cold and ultracold molecules. Here, we demonstrate rotational-state cooling of trapped methyl fluoride molecules (CH3F) by optically pumping the population of 16 M-sublevels in the rotational states J=3,4,5, and 6 into a single level. By combining rotational-state cooling with motional cooling, we increase the relative number of molecules in the state J=4, K=3, M=4 from a few percent to over 70%, thereby generating a translationally cold (~30mK) and nearly pure state ensemble of about 10^6 molecules. Our scheme is extendable to larger sets of initial states, other final states and a variety of molecule species, thus paving the way for internal-state control of ever larger molecules.
Vacuum ultraviolet photoionization and photodissociation of polyatomic molecules and radicals
Energy Technology Data Exchange (ETDEWEB)
Ng, C.Y. [Iowa State Univ., Ames (United States)
1993-12-01
In the past decade, tremendous progress has been made in understanding the photodissociation (PD) dynamics of triatomic molecules. However, the PD study of radicals, especially polyatomic radicals, has remained essentially an unexplored research area. Detailed state-to-state PD cross sections for radicals in the UV and VUV provide challenges not only for dynamical calculations, but also for ab initio quantum chemical studies. The authors have developed a laser based pump-probe apparatus for the measurement of absolute PD cross sections for CH{sub 3}S and HS is summarized.
Rotational state detection of electrically trapped polyatomic molecules
Glöckner, Rosa; Rempe, Gerhard; Zeppenfeld, Martin
2014-01-01
Detecting the internal state of polar molecules is a substantial challenge when standard techniques such as resonance-enhanced multi photon ionization (REMPI) or laser-induced fluorescense (LIF) do not work. As this is the case for most polyatomic molecule species, we here investigate an alternative based on state selective removal of molecules from an electrically trapped ensemble. Specifically, we deplete molecules by driving rotational and/or vibrational transitions to untrapped states. Fully resolving the rotational state with this method can be a considerable challenge as the frequency differences between various transitions is easily substantially less than the Stark broadening in an electric trap. However, making use of a unique trap design providing homogeneous fields in a large fraction of the trap volume, we successfully discriminate all rotational quantum numbers, including the rotational M-substate.
Dissociative Electron Attachment to Polyatomic Molecules - I : Water
Ram, N Bhargava; Krishnakumar, E
2010-01-01
Using the velocity map imaging technique, we studied and characterized the process of Dissociative Electron Attachment (DEA) in polyatomic molecules like Water, Hydrogen Sulphide, Ammonia, Methane, Formic Acid and Propyl Amine. We present the details of these studies in a series of 5 articles. In the first article here, we discuss the DEA process in gas phase water ($H_{2}O$ and $D_{2}O$) molecules. Electrons of 6.5 eV, 8.5 eV and 12 eV are captured by water molecules in neutral ground state to form $H_{2}O^{-*}$ ($D_{2}O^{-*}$) resonant states which dissociate into an anion fragment and one or more neutrals. Kinetic energy and angular distributions of the fragment anions $H^{-}$($D^{-}$) and $O^{-}$ produced from the three negative ion resonant states in the entire $2\\pi$ scattering range are obtained. Unique angular distribution patterns are observed at the 8.5 eV and 11.8 eV resonances showing dissociation dynamics beyond the axial recoil approximation.
New Ro-Vibrational Kinetic Energy Operators using Polyspherical Coordinates for Polyatomic Molecules
Schwenke, David W.; Kwak, Dochan (Technical Monitor)
2002-01-01
We illustrate how one can easily derive kinetic energy operators for polyatomic molecules using polyspherical coordinates with very general choices for z-axis embeddings arid angles used to specify relative orientations of internal vectors. Computer algebra is not required.
Strong-field-approximation theory of high-order harmonic generation by polyatomic molecules
Odžak, S.; Hasović, E.; Milošević, D. B.
2016-04-01
A theory of high-order harmonic generation by arbitrary polyatomic molecules is introduced. A polyatomic molecule is modeled by an (N +1 ) -particle system, which consists of N heavy atomic (ionic) centers and an electron. After the separation of the center-of-mass coordinate, the dynamics of this system is reduced to the relative electronic and nuclear coordinates. Various versions (with or without the dressing of the initial and/or final molecular state) of the molecular strong-field approximation are introduced. For neutral polyatomic molecules the derived expression for the T -matrix element takes a simple form. The interference minima in the harmonic spectrum are explained as a multiple-slit type of interference. This is illustrated by numerical examples for the ozone (O3) and carbon dioxide (CO2) molecules.
Polyatomic Candidates for Cooling of Molecules with Lasers from Simple Theoretical Concepts.
Isaev, Timur A; Berger, Robert
2016-02-12
A rational approach to identify polyatomic molecules that appear to be promising candidates for direct Doppler cooling with lasers is outlined. First-principles calculations for equilibrium structures and Franck-Condon factors of selected representatives with different point-group symmetries (including the chiral nonsymmetric C1) have been performed and a high potential for laser cooling of these molecules is indicated.
Polyatomic candidates for cooling of molecules with lasers from simple theoretical concepts
Isaev, Timur
2015-01-01
We have outlined a rational approach to identify polyatomic molecules that appear to be promising candidates for direct Doppler cooling with lasers. Explicit numerical calculations for structures and Franck--Condon factors of selected representatives indicates high potential for laser-cooling of such molecules for even opening up the third spatial dimension for ultra-cold molecules generated by direct Doppler cooling with lasers.
Potential energy surfaces and reaction dynamics of polyatomic molecules
Energy Technology Data Exchange (ETDEWEB)
Chang, Yan-Tyng.
1991-11-01
A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.
High-order harmonic generation in polyatomic molecules induced by a bicircular laser field
Odžak, Senad; Milošević, Dejan B
2016-01-01
High-order harmonic generation by a bicircular field, which consists of two coplanar counter-rotating circularly polarized fields of frequency $r\\omega$ and $s\\omega$ ($r$ and $s$ are integers), is investigated for a polyatomic molecule. This field possesses dynamical symmetry, which can be adjusted to the symmetry of the molecular Hamiltonian and used to investigate the molecular symmetry. For polyatomic molecules having the $C_{r+s}$ symmetry only the harmonics $n=q(r+s)\\pm r$, $q=1,2,\\ldots$, are emitted having the ellipticity $\\varepsilon_n=\\pm 1$. We illustrate this using the example of the planar molecules BH$_3$ and BF$_3$, which obey the $C_3$ symmetry. We show that for the BF$_3$ molecule, similarly to atoms with a $p$ ground state, there is a strong asymmetry in the emission of high harmonics with opposite helicities. This asymmetry depends on the molecular orientation.
High-order harmonic generation in polyatomic molecules induced by a bicircular laser field
Odžak, S.; Hasović, E.; Milošević, D. B.
2016-09-01
High-order harmonic generation by a bicircular field, which consists of two coplanar counter-rotating circularly polarized fields of frequency r ω and s ω (r and s are integers), is investigated for a polyatomic molecule. This field possesses dynamical symmetry, which can be adjusted to the symmetry of the molecular Hamiltonian and used to investigate the molecular symmetry. For polyatomic molecules having the Cr +s symmetry, only the harmonics n =q (r +s )±r ,q =1 ,2 ,..., are emitted having the ellipticity ɛn=±1 . We illustrate this using the example of the planar molecules BH3 and BF3, which obey the C3 symmetry. We show that for the BF3 molecule, similarly to atoms with a p ground state, there is a strong asymmetry in the emission of high harmonics with opposite helicities. This asymmetry depends on the molecular orientation.
Imaging an aligned polyatomic molecule with laser-induced electron diffraction
Pullen, Michael; Le, Anh-Thu; Baudisch, Matthias; Hemmer, Michaël; Senftleben, Arne; Schröter, Claus Dieter; Ullrich, Joachim; Moshammer, Robert; Lin, Chii-Dong; Biegert, Jens
2015-01-01
Laser-induced electron diffraction is an evolving tabletop method, which aims to image ultrafast structural changes in gas-phase polyatomic molecules with sub-{\\AA}ngstr\\"om spatial and femtosecond temporal resolution. Here, we provide the general foundation for the retrieval of multiple bond lengths from a polyatomic molecule by simultaneously measuring the C-C and C-H bond lengths in aligned acetylene. Our approach takes the method beyond the hitherto achieved imaging of simple diatomic molecules and is based upon the combination of a 160 kHz mid-IR few-cycle laser source with full three-dimensional electron-ion coincidence detection. Our technique provides an accessible and robust route towards imaging ultrafast processes in complex gas phase molecules with atto- to femto-second temporal resolution.
Energy Technology Data Exchange (ETDEWEB)
Marinkovic, B P, E-mail: bratislav.marinkovic@phy.bg.ac.y [Institute of Physics, Belgrade 11080, Pregrevica 118 (Serbia) and College for Electrical Engineering and Computing, Belgrade 11010, Vojvode Stepe 283 (Serbia)
2009-04-01
Studies of higher excited states of some polyatomic molecules relevant for plasma physics and environment have been presented. Spectra of chlorofluorocarbons are discussed together with their influence on ozone layer depletion and global warming. Tetrahydrofuran molecule was studied by photoabsorption and electron energy loss spectroscopy while the states are assigned following extensive ab initio calculations. Nitrous oxide and hydrogen sulphide spectra are discussed in terms of identifying valence and Rydberg character of excited states.
The UBI QEP treatment of polyatomic molecules without bond-energy partitioning
Shustorovich, Evgeny; Zeigarnik, Andrew V.
2003-03-01
Bond-energy partitioning in polyatomic molecules is a mathematical construct realizing intuitive chemical reasoning but having no physical justification. The bond order conservation-Morse potential method [1,2] and its generalization as the unity bond index-quadratic exponential potential (UBI-QEP) method [3,4] treat polyatomic molecules as quasi-diatomic and often use some bond-energy partitioning, which creates conceptual and numerical uncertainty. We present a new UBI-QEP formalism to calculate binding energies of polyatomic molecules without bond-energy partitioning. We discuss the types of molecules best suited for the new treatment and the nature and values of the relevant parameters. Examples include both symmetric molecules such as ethylene, acetylene and hydrazine and non-symmetric molecules such as nitrous oxide on various metal fcc(1 1 1) surfaces. The calculated binding energies were compared with those obtained by the previous UBI-QEP formulas (using some bond-energy partitioning). The older and new UBI-QEP values typically were found to be close. The scarcity of appropriate experimental data prevents a systematic comparison in order to decide where each approximation can be used most efficiently. One thing is certain, however, that the new UBI-QEP formalism, conceptually superior and quantitatively more reasonable than the older ones, expands opportunities of the practitioners.
Radiation Pressure Force from Optical Cycling on a Polyatomic Molecule SrOH
Kozyryev, Ivan; Baum, Louis; Matsuda, Kyle; Sedlack, Alex; Hemmerling, Boerge; Doyle, John
2016-05-01
Polyatomic molecules hold promise for many applications in physics and chemistry due to their rotational and vibrational degrees of freedom. The starting point for our approach to the production of ultracold strontium monohydroxide (SrOH) is buffer-gas cooling followed by laser manipulation. Linear geometry, diagonal Franck-Condon factors, short radiative lifetimes and unresolved hyperfine splittings make SrOH a particularly attractive candidate for direct laser cooling. We report deflection of the SrOH beam through radiative force from optical cycling on the X~2Σ+ Ã2Π1 / 2 transition. We observe × 12 fluorescence enhancement with closed spin-rotation splitting and demonstrate cycling between different vibrational levels with the Sr O mode repumping laser. Observed deflection and detection signals correspond to the scattering of ~ 100 photons. Additional repumping laser for the bending mode would lead to scattering of ~ 1 , 000 photons allowing for transverse laser cooling of the SrOH beam. We will also describe our experimental efforts towards laser slowing and trapping of SrOH.
Konar, Arkaprabha
The goal of my research is to obtain a better understanding of the various processes that occur during and following laser-matter interactions from both the physical and chemical point of view. In particular I focused my research on understanding two very important aspects of laser-matter interaction; 1) Intense laser-matter interactions for polyatomic molecules in the gas phase in order to determine to what extent processes like excitation, ionization and fragmentation can be controlled by modifying the phase and amplitude of the laser field according to the timescales for electronic, vibrational and rotational energy transfer. 2) Developing pulse shaping based single beam methods aimed at studying solvated molecules in order to elucidate processes like inhomogeneous broadening, solvatochromic shift and to determine the electronic coherence lifetimes of solvated molecules. The effect of the chirped femtosecond pulses on fluorescence and stimulated emission from solvated dye molecules was studied and it was observed that the overall effect depends quadratically on pulse energy, even where excitation probabilities range from 0.02 to 5%, in the so-called "linear excitation regime". The shape of the chirp dependence is found to be independent of the energy of the pulse. It was found that the chirp dependence reveals dynamics related to solvent rearrangement following excitation and also depends on electronic relaxation of the chromophore. Furthermore, the chirped pulses were found to be extremely sensitive to solvent environment and that the complementary phases having the opposite sign provide information about the electronic coherence lifetimes. Similar to chirped pulses, the effects of a phase step on the excitation spectrum and the corresponding changes to the stimulated emission spectrum were also studied and it was found that the coherent feature on the spectrum is sensitive to the dephasing time of the system. Therefore a single phase scanning method can
Williams, J. B.; Trevisan, C. S.; Schöffler, M. S.; Jahnke, T.; Bocharova, I.; Kim, H.; Ulrich, B.; Wallauer, R.; Sturm, F.; Rescigno, T. N.; Belkacem, A.; Dörner, R.; Weber, Th.; McCurdy, C. W.; Landers, A. L.
2012-06-01
We demonstrate a method for determining the full three-dimensional molecular-frame photoelectron angular distribution in polyatomic molecules using methane as a prototype. Simultaneous double Auger decay and subsequent dissociation allow measurement of the initial momentum vectors of the ionic fragments and the photoelectron in coincidence, allowing full orientation by observing a three-ion decay pathway, (H+, H+, CH2+). We find the striking result that at low photoelectron energies the molecule is effectively imaged by the focusing of photoelectrons along bond directions.
Radiation Pressure Force from Optical Cycling on a Polyatomic Molecule
Kozyryev, Ivan; Matsuda, Kyle; Hemmerling, Boerge; Doyle, John M
2016-01-01
We demonstrate multiple photon cycling and radiative force deflection on the triatomic free radical strontium monohydroxide (SrOH). Optical cycling is achieved on SrOH in a cryogenic buffer-gas beam by employing the rotationally closed $P\\left(N''=1\\right)$ branch of the vibronic transition $\\tilde{X}^{2}\\Sigma^{+}\\left(000\\right)\\leftrightarrow\\tilde{A}^{2}\\Pi_{1/2}\\left(000\\right)$. A single repumping laser excites the Sr-O stretching vibrational mode, and photon cycling of the molecule deflects the SrOH beam by an angle of $0.2^{\\circ}$ via scattering of $\\sim100$ photons per molecule. This approach can be used for direct laser cooling of SrOH and more complex, isoelectronic species.
Spectroscopic and dynamical studies of highly energized small polyatomic molecules
Energy Technology Data Exchange (ETDEWEB)
Field, R.W.; Silbey, R.J. [Massachusetts Institute of Technology, Cambridge (United States)
1993-12-01
The authors have initiated a program to perform spectroscopic and dynamic studies of small molecules. Large amplitude motions in excited acetylene were discussed along with plans to record the dispersed fluorescence (DF) and the stimulated emission pumping (SEP) spectra. SEP spectra were reported for the formyl radical. A Fourier transform spectrometer was discussed with respect to its ability to probe the structure of radicals. This instrument is capable of performing studies using various techniques such as magnetic rotation spectroscopy and sub-Doppler sideband-OODR Zeman (SOODRZ) spectroscopy.
Semiempirical models in theory of intensities of rotation—vibration spectra of polyatomic molecules
Berezin, V. I.; El'kin, M. D.
1992-10-01
Two fundamental models in the theory of intensities of rotation—vibration spectra of polyatomic molecules are considered: a valence-optical scheme (Volkenstein—Elyashevitch—Stepanov scheme) and the Mayants—Averbukh method. The mathematics of the tensor analysis are proposed for the reception of the calculated formulae of overtonic spectroscopy in the limit of the debated models. It is shown that the difference in these formulae is conditioned by the form of the system of curvilinear coordinates, which are used to describe the different kinds of molecular motion.
Theorectical Studies of Excitation in Low-Energy Electron-Polyatomic Molecule Collisions
Energy Technology Data Exchange (ETDEWEB)
Rescigno, T N; McCurdy, C W; Isaacs, W A; Orel, A E; Meyer, H D
2001-08-13
This paper focuses on the channeling of energy from electronic to nuclear degrees of freedom in electron-polyatomic molecule collisions. We examine the feasibility of attacking the full scattering problem, both the fixed-nuclei electronic problem and the post-collision nuclear dynamics, entirely from first principles. The electron-CO{sub 2} system is presented as an example. We study resonant vibrational excitation, showing how a6 initio, fixed-nuclei electronic cross sections can provide the necessary input for a multi-dimensional treatment of the nuclear vibrational dynamics.
Sensitivity and resolution in frequency comb spectroscopy of buffer gas cooled polyatomic molecules
Changala, P. Bryan; Spaun, Ben; Patterson, David; Doyle, John M.; Ye, Jun
2016-12-01
We discuss the use of cavity-enhanced direct frequency comb spectroscopy in the mid-infrared region with buffer gas cooling of polyatomic molecules for high-precision rovibrational absorption spectroscopy. A frequency comb coupled to an optical enhancement cavity allows us to collect high-resolution, broad-bandwidth infrared spectra of translationally and rotationally cold (10-20 K) gas-phase molecules with high absorption sensitivity and fast acquisition times. The design and performance of the combined apparatus are discussed in detail. Recorded rovibrational spectra in the CH stretching region of several organic molecules, including vinyl bromide (CH_2CHBr), adamantane (C_{10}H_{16}), and diamantane (C_{14}H_{20}) demonstrate the resolution and sensitivity of this technique, as well as the intrinsic challenges faced in extending the frontier of high-resolution spectroscopy to large complex molecules.
IR multiple-photon excitation of polyatomic molecules: a route towards nanostructures
Energy Technology Data Exchange (ETDEWEB)
Borsella, Elisabetta; Botti, Sabina; Caneve, Luisa; De Dominicis, Luigi; Fantoni, Roberta [ENEA, Applied Physics and New Materials Department, Via E Fermi 45, Frascati 00044 (Italy)], E-mail: fantoni@frascati.enea.it
2008-10-15
The availability of high power IR laser sources in the 1980s paved the way to new attractive experiments for driving chemical reactions, based on the selective excitation of vibrational modes in polyatomic molecules up to and above the dissociation threshold. The process was first studied in the collisionless regime for applications to laser isotope separation and selective chemistry, and later in collision-assisted conditions leading to the synthesis of nanostructures. In particular, the mechanisms of IR laser pyrolysis of SiH{sub 4} and hydrocarbons were investigated in order to control the production of silicon- and carbon-based nanoaggregates. For this purpose, different on-line diagnostics were utilized to monitor the gas-phase reaction intermediates and the process of particle nucleation and growth. The basic principles of the process of multiple-photon excitation of polyatomic molecules and its applications to the synthesis of nanostructures will be reviewed in this paper. Peculiar optical properties of silicon nanoparticles and carbon nanotubes obtained as final products of the developed processes will be described in relation to remarkable applications in several fields.
Yu, Hua-Gen
2016-08-01
We report a new full-dimensional variational algorithm to calculate rovibrational spectra of polyatomic molecules using an exact quantum mechanical Hamiltonian. The rovibrational Hamiltonian of system is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame. It is expressed in an explicitly Hermitian form. The Hamiltonian has a universal formulation regardless of the choice of orthogonal polyspherical coordinates and the number of atoms in molecule, which is suitable for developing a general program to study the spectra of many polyatomic systems. An efficient coupled-state approach is also proposed to solve the eigenvalue problem of the Hamiltonian using a multi-layer Lanczos iterative diagonalization approach via a set of direct product basis set in three coordinate groups: radial coordinates, angular variables, and overall rotational angles. A simple set of symmetric top rotational functions is used for the overall rotation whereas a potential-optimized discrete variable representation method is employed in radial coordinates. A set of contracted vibrationally diabatic basis functions is adopted in internal angular variables. Those diabatic functions are first computed using a neural network iterative diagonalization method based on a reduced-dimension Hamiltonian but only once. The final rovibrational energies are computed using a modified Lanczos method for a given total angular momentum J, which is usually fast. Two numerical applications to CH4 and H2CO are given, together with a comparison with previous results.
Intense 2-cycle laser pulses induce time-dependent bond-hardening in a polyatomic molecule
Dota, K; Tiwari, A K; Dharmadhikari, J A; Dharmadhikari, A K; Mathur, D
2012-01-01
A time-dependent bond-hardening process is discovered in a polyatomic molecule (tetramethyl silane, TMS) using few-cycle pulses of intense 800 nm light. In conventional mass spectrometry, symmetrical molecules like TMS do not exhibit a prominent molecular ion (TMS$^+$) as unimolecular dissociation into [Si(CH$_3$)$_3]^+$ proceeds very fast. Under strong field and few-cycle conditions, this dissociation channel is defeated by time-dependent bond-hardening: a field-induced potential well is created in the TMS$^+$ potential energy curve that effectively traps a wavepacket. The time-dependence of this bond hardening process is verified using longer-duration ($\\geq$ 100 fs) pulses; the relatively "slower" fall-off of optical field in such pulses allows the initially trapped wavepacket to leak out, thereby rendering TMS$^+$ unstable once again. Our results are significant as they demonstrate (i) optical generation of polyatomic ions that are normally inaccessible and (ii) optical control of dynamics in strong field...
Rapid-Adiabatic Control of Ro-Vibrational Populations in Polyatomic Molecules
Zak, Emil J.; Yachmenev, Andrey
2017-06-01
We present a simple method for control of ro-vibrational populations in polyatomic molecules in the presence of inhomogeneous electric fields [1]. Cooling and trapping of heavy polar polyatomic molecules has become one of the frontier goals in high-resolution molecular spectroscopy, especially in the context of parity violation measurement in chiral compounds [2]. A key step toward reaching this goal would be development of a robust and efficient protocol for control of populations of ro-vibrational states in polyatomic, often floppy molecules. Here we demonstrate a modification of the stark-chirped rapid-adiabatic-passage technique (SCRAP) [3], designed for achieving high levels of control of ro-vibrational populations over a selected region in space. The new method employs inhomogeneous electric fields to generate space- and time- controlled Stark-shifts of energy levels in molecules. Adiabatic passage between ro-vibrational states is enabled by the pump pulse, which raises the value of the Rabi frequency. This Stark-chirped population transfer can be used in manipulation of population differences between high-field-seeking and low-field-seeking states of molecules in the Stark decelerator [4]. Appropriate timing of voltages on electric rods located along the decelerator combined with a single pump laser renders our method as potentially more efficient than traditional Stark decelerator techniques. Simulations for NH_3 show significant improvement in effectiveness of cooling, with respect to the standard 'moving-potential' method [5]. At the same time a high phase-space acceptance of the molecular packet is maintained. E. J. Zak, A. Yachmenev (submitted). C. Medcraft, R. Wolf, M. Schnell, Angew. Chem. Int. Ed., 53, 43, 11656-11659 (2014) M. Oberst, H. Munch, T. Halfman, PRL 99, 173001 (2007). K. Wohlfart, F. Grätz, F. Filsinger, H. Haak, G. Meijer, J. Küpper, Phys. Rev. A 77, 031404(R) (2008). H. L. Bethlem, F. M. H. Crompvoets, R. T. Jongma, S. Y. T. van de
Le, Anh-Thu; Lin, Chii-Dong
2016-10-01
Molecular structure determination of chemical reactions or processes has been one of the grand challenges in physics, chemistry, and biology. To image these processes, it typically requires sub-Angstrom spatial and femtosecond temporal resolutions. One of the standard imaging techniques, X-ray diffraction, however, currently suffers from temporal jitters and is available only at large facilities. Furthermore, it also suffers from very low elastic scattering cross sections, which make it difficult to apply to gas phase molecules. Another technique, ultrafast electron diffraction (UED), overcomes this low cross section problem, but the temporal resolution is still limited to hundreds of femtoseconds, mainly due to Coulomb repulsion in electron beam and velocity mismatch between laser-pump pulse and electron probe pulse in a typical pump-probe scheme. The recently proposed laser-induced electron diffraction (LIED) is based on two basic ideas. First, an electron wave packet can be generated from a target itself by an intense laser pulse and driven back within the subsequent half-cycle of the laser to rescatter from the parent ion, thus realizing a self-imaging process. Laser-free elastic differential cross sections (DCS) can then be extracted from high-energy electron spectra, as demonstrated by the Quantitative Rescattering theory (QRS). Second, the target structure information can be retrieved from the DCS. This retrieval is further simplified by using back-scattered electrons with collision energy of about 100 eV, for which the independent-atom model (IAM) can be employed to quite accurately simulate the DCS. Demonstration of ultrafast imaging with the LIED has been reported so far on simple diatomic molecules. Here we discuss recent progress in LIED with polyatomic molecules in two examples. The first one is aligned acetylene (C2H2) and the second one is benzene (C6H6). In both cases, two bond lengths, C-C and C-H have been successfully retrieved. For even more
Intense two-cycle laser pulses induce time-dependent bond hardening in a polyatomic molecule.
Dota, K; Garg, M; Tiwari, A K; Dharmadhikari, J A; Dharmadhikari, A K; Mathur, D
2012-02-17
A time-dependent bond-hardening process is discovered in a polyatomic molecule (tetramethyl silane, TMS) using few-cycle pulses of intense 800 nm light. In conventional mass spectrometry, symmetrical molecules such as TMS do not exhibit a prominent molecular ion (TMS(+)) as unimolecular dissociation into [Si(CH(3))(3)](+) proceeds very fast. Under a strong field and few-cycle conditions, this dissociation channel is defeated by time-dependent bond hardening: a field-induced potential well is created in the TMS(+) potential energy curve that effectively traps a wave packet. The time dependence of this bond-hardening process is verified using longer-duration (≥100 fs) pulses; the relatively slower falloff of optical field in such pulses allows the initially trapped wave packet to leak out, thereby rendering TMS(+) unstable once again.
Energy Technology Data Exchange (ETDEWEB)
Clabo, D.A. Jr.
1987-04-01
Inclusion of the anharmonicity normal mode vibrations (i.e., the third and fourth (and higher) derivatives of a molecular Born-Oppenheimer potential energy surface) is necessary in order to theoretically reproduce experimental fundamental vibrational frequencies of a molecule. Although ab initio determinations of harmonic vibrational frequencies may give errors of only a few percent by the inclusion of electron correlation within a large basis set for small molecules, in general, molecular fundamental vibrational frequencies are more often available from high resolution vibration-rotation spectra. Recently developed analytic third derivatives methods for self-consistent-field (SCF) wavefunctions have made it possible to examine with previously unavailable accuracy and computational efficiency the anharmonic force fields of small molecules.
DEFF Research Database (Denmark)
Madsen, Christian Bruun; Abu-Samha, Mahmoud; Madsen, Lars Bojer
2010-01-01
We present a generic approach for treating the effect of nuclear motion in high-order harmonic generation from polyatomic molecules. Our procedure relies on a separation of nuclear and electron dynamics where we account for the electronic part using the Lewenstein model and nuclear motion enters...... as a nuclear correlation function. We express the nuclear correlation function in terms of Franck-Condon factors, which allows us to decompose nuclear motion into modes and identify the modes that are dominant in the high-order harmonic generation process. We show results for the isotopes CH4 and CD4...... and thereby provide direct theoretical support for a recent experiment [S. Baker et al., Science 312, 424 (2006)] that uses high-order harmonic generation to probe the ultrafast structural nuclear rearrangement of ionized methane....
Indian Academy of Sciences (India)
L R Botha; L E De Clercq; A M Smit; N Botha; E Ronander; H J Strydom
2014-02-01
We simulate adaptive feedback control to coherently shape a femtosecond infrared laser pulse by means of a 4f-spatial light modulator in order to selectively excite the rovibrational modes of a polyatomic molecule. We preferentially populate an arbitrarily chosen upper rovibrational level by only employing these tailored temporally shaped pulses. A second laser would then allow for mode selective chemistry to interact selectively with the excited population. Alternatively the excited molecules enhanced reactivity could be exploited for selective chemistry.
CSIR Research Space (South Africa)
de Clercq, L
2010-09-01
Full Text Available of a Vibrational Level Within the Electronic Ground State of a Polyatomic Molecule with Ultra Short Pulses Ludwig de Clercq1,2, Lourens Botha1,2, Hermann Uys1, Anton Du Plessis1,2, Erich Rohwer2 1CSIR National Laser Centre, PO BOX 395, Pretoria... al lbl d i I e I e dt ? , )? ? ? ? ?=?= ??h (1) where, , .a b a b? ? ?= ? , (2) ?ab gives the elements of the density matrix, ?a the frequencies...
Yu, Chao; Wei, Hui; Wang, Xu; Le, Anh-Thu; Lu, Ruifeng; Lin, C. D.
2015-01-01
Imaging the transient process of molecules has been a basic way to investigate photochemical reactions and dynamics. Based on laser-induced electron diffraction and partial one-dimensional molecular alignment, here we provide two effective methods for reconstructing two-dimensional structure of polyatomic molecules. We demonstrate that electron diffraction images in both scattering angles and broadband energy can be utilized to retrieve complementary structure information, including positions of light atoms. With picometre spatial resolution and the inherent femtosecond temporal resolution of lasers, laser-induced electron diffraction method offers significant opportunities for probing atomic motion in a large molecule in a typical pump-probe measurement. PMID:26503116
Laser induced rovibrational cooling of the linear polyatomic ion C2H2(+).
Deb, Nabanita; Heazlewood, Brianna R; Rennick, Christopher J; Softley, Timothy P
2014-04-28
The laser-induced blackbody-assisted rotational cooling of a linear polyatomic ion, C2H2(+), in its (2)Π ground electronic state in the presence of the blackbody radiation field at 300 K and 77 K is investigated theoretically using a rate-equations model. Although pure rotational transitions are forbidden in this non-polar species, the ν5 cis-bending mode is infrared active and the (1-0) band of this mode strongly overlaps the 300 K blackbody spectrum. Hence the lifetimes of state-selected rotational levels are found to be short compared to the typical timescale of ion trapping experiments. The ν5 (1-0) transition is split by the Renner-Teller coupling of vibrational and electronic angular momentum, and by the spin-orbit coupling, into six principal components and these effects are included in the calculations. In this paper, a rotational-cooling scheme is proposed that involves simultaneous pumping of a set of closely spaced Q-branch transitions on the (2)Δ5/2 - (2)Π3/2 band together with two Q-branch lines in the (2)Σ(+) - (2)Π1/2 band. It is shown that this should lead to >70% of total population in the lowest rotational level at 300 K and over 99% at 77 K. In principle, the multiple Q-branch lines could be pumped with just two broad-band (∼Δν = 0.4-3 cm(-1)) infrared lasers.
Martin, Jan M. L.
The quartic force fields of a number of small polyatomic molecules (specifically, rm H _2O, NH_2, NH_3, CH_4, BH_3, BeH_2, H_2CO, N_2O, CO_2, CS_2, OCS, H_2S, FNO, ClNO, and H_2CS) have been computed ab initio using large basis sets and augmented coupled cluster methods. It has been established throughout that harmonic and fundamental frequencies can consistently be reproduced to within about 10 cm^{ -1} of experimental using spdf basis sets, except in such inherently problematic cases as the umbrella motion in NH_3; such problems are solved by recomputing the harmonic frequencies with an spdf g basis set. Coupled cluster frequencies using small basis sets of spd quality agree surprisingly well with experiment (mean absolute error of 26 cm^ {-1}), but bond distances are generally seriously overestimated. Using spdf basis sets, they are consistently overestimated by 0.002 and 0.006-7 A for single and multiple bonds, respectively; for spdf g basis sets this drops to 0.001 and 0.003-4 A, respectively. Geometries and harmonic frequencies for highly polar fluorine compounds such as HF and FNO are qualitatively wrong unless special anion functions are added to the fluorine basis set. Anharmonicity, rovibrational coupling, and centrifugal distortion constants are consistently predicted well; the anharmonic portions of the computed force fields are probably more reliable than their experimental counterparts in many cases. Remaining errors in the computed geometries and harmonic frequencies are shown to be almost entirely due to a combination of core correlation and residual deficiencies in the electron correlation treatment. A 3-term correction for remaining basis set incompleteness to computed total atomization energies is proposed by the author, and is shown to result in mean absolute errors of as little as 0.5 kcal/mol for spdf g basis sets. Example applications on rm HCO^+, HOC^+, B_2C, BCN, and BNC testify to the predictive power of the methods used in this work.
Ultrafast photochemistry of polyatomic molecules containing labile halogen atoms in solution
Mereshchenko, Andrey S.
Because breaking and making of chemical bonds lies at the heart of chemistry, this thesis focuses on dynamic studies of labile molecules in solutions using ultrafast transient absorption spectroscopy. Specifically, my interest is two-fold: (i) novel reaction intermediates of polyhalogenated carbon, boron and phosphorus compounds; (ii) photophysics and photochemistry of labile copper(II) halide complexes. Excitation of CH2Br2, CHBr3, BBr 3, and PBr3 into n(Br)sigma*(X-Br) states, where X=C, B, or P, leads to direct photoisomerization with formation of isomers having Br-Br bonds as well as rupture of one of X-Br bonds with the formation of a Br atom and a polyatomic radical fragment, which subsequently recombine to form similar isomer products. Nonpolar solvation stabilizes the isomers, consistent with intrinsic reaction coordinate calculations of the isomer ground state potential energy surfaces at the density functional level of theory, and consequently, the involvement of these highly energetic species on chemically-relevant time scales needs to be taken into account. Monochlorocomplexes in methanol solutions promoted to the ligand-to-metal charge transfer (LMCT) excited state predominantly undergo internal conversion via back electron transfer, giving rise to vibrationally hot ground-state parent complexes. Copper-chloride homolitical bond dissociation yielding the solvated copper(I) and Cl- atom/solvent CT complexes constitutes a minor pathway. Insights into ligand substitution mechanisms were acquired by monitoring the recovery of monochloro complexes at the expense of two unexcited dichloro- and unsubstituted forms of Cu(II) complexes also present in the solution. Detailed description of ultrafast excited-state dynamics of CuCl 42- complexes in acetonitrile upon excitation into all possible Ligand Field (LF) excited states and two most intense LMCT transitions is reported. The LF states were found to be nonreactive with lifetimes remarkably longer than those
Klamroth, Tillmann
2006-04-01
We report time-dependent configuration interaction singles calculations for the ultrafast laser driven many-electron dynamics in a polyatomic molecule, N-methyl-6-quinolone. We employ optimal control theory to achieve a nearly state-selective excitation from the S0 to the S1 state, on a time scale of a few (≈6) femtoseconds. The optimal control scheme is shown to correct for effects opposing a state-selective transition, such as multiphoton transitions and other, nonlinear phenomena, which are induced by the ultrashort and intense laser fields. In contrast, simple two-level π pulses are not effective in state-selective excitations when very short pulses are used. Also, the dependence of multiphoton and nonlinear effects on the number of states included in the dynamical simulations is investigated.
Time-resolved photoelectron spectroscopy of non-adiabatic dynamics in polyatomic molecules
Stolow, Albert
2015-01-01
This review article discusses advances in the use of time-resolved photoelectron spectroscopy for the study of non-adiabatic processes in molecules. A theoretical treatment of the experiments is presented together with a number of experimental examples.
High-order harmonic spectroscopy for molecular imaging of polyatomic molecules
Negro, M; Faccialà, D; De Silvestri, S; Vozzi, C; Stagira, S
2014-01-01
High-order harmonic generation is a powerful and sensitive tool for probing atomic and molecular structures, combining in the same measurement an unprecedented attosecond temporal resolution with a high spatial resolution, of the order of the angstrom. Imaging of the outermost molecular orbital by high-order harmonic generation has been limited for a long time to very simple molecules, like nitrogen. Recently we demonstrated a technique that overcame several of the issues that have prevented the extension of molecular orbital tomography to more complex species, showing that molecular imaging can be applied to a triatomic molecule like carbon dioxide. Here we report on the application of such technique to nitrous oxide (N2O) and acetylene (C2H2). This result represents a first step towards the imaging of fragile compounds, a category which includes most of the fundamental biological molecules.
Higher Electric Multipole Moments for Some Polyatomic Molecules from Accurate SCF Calculations
Institute of Scientific and Technical Information of China (English)
Telhat Ozdogan
2002-01-01
Higher electric multipole moments for the ground-state electronic configuration of some polyatomicmolecules, i.e. CH4, NH3, H2O, were calculated from SCF-HFR wavefunctions using Slater-type orbital basis sets.The calculated results for electric multipole moments of these molecules are in good agreement with the theoretical andexperimental ones.
Portnov, Alexander; Epshtein, Michael; Bar, Ilana
2017-06-01
Nonadiabatic processes, dominated by dynamic passage of reactive fluxes through conical intersections (CIs) are considered to be appealing means for manipulating reaction paths. One approach that is considered to be effective in controlling the course of dissociation processes is the selective excitation of vibrational modes containing a considerable component of motion. Here, we have chosen to study the predissociation of the model test molecule, methylamine and its deuterated isotopologues, excited to well-characterized quantum states on the first excited electronic state, S_{1}, by following the N-H(D) bond fission dynamics through sensitive H(D) photofragment probing. The branching ratios between slow and fast H(D) photofragments, the internal energies of their counter radical photofragments and the anisotropy parameters for fast H photofragments, confirm correlated anomalies for predissociation initiated from specific rovibronic states, reflecting the existence of a dynamic resonance in each molecule. This resonance strongly depends on the energy of the initially excited rovibronic states, the evolving vibrational mode on the repulsive S_{1} part during N-H(D) bond elongation, and the manipulated passage through the CI that leads to radicals excited with C-N-H(D) bending and preferential perpendicular bond breaking, relative to the photolyzing laser polarization, in molecules containing the NH_{2} group. The indicated resonance plays an important role in the bifurcation dynamics at the CI and can be foreseen to exist in other photoinitiated processes and to control their outcome.
Shustorovich, Evgeny
1988-10-01
Within the bond-order conservation Morse-potential (BOC-MP) model of chemisorption, the analytic interrelations for diatomic admolecules (at low coverages) are rigorous. Here we extend these interrelations to treat polyatomic adsorbates partitioned into two effective fragments. We discuss a partitioning scheme involving the averaging of chemical structures representing reasonable limits (upper and lower) of two-center bond energies. It is shown that, by using this scheme, one can efficiently determine the preferred coordination modes of polyatomic adsorbates (monoversus dicoordination) and the preferred pathways of complex surface reactions (e.g. hydrogenation of CO and transformations of C 2 hydrocarbons). Relations to other theoretical approaches are briefly discussed.
Fermi Resonances and Vibrational Spectrum of a Polyatomic Molecule XY4: an Algebraic Approach
Institute of Scientific and Technical Information of China (English)
WAN Ming-Fang; CHEN Jing-Hua; HOU Xi-Wen
2005-01-01
A U(2) algebraic model is introduced for the spectrum of a molecule XY4, where the interactions between the stretch and bend modes are described by Td symmetric Fermi resonance terms. The presented algebraic model in a limit corresponds to another model in recent literature. The vibrational spectrum of methane (CH4) measured recently with modern spectroscopy techniques is employed to test those models. The obtained standard deviation between the observed and the calculated vibrational energy levels in the algebraic model is smaller than that in the corresponding model.
Pavlyuchko, A I; Tennyson, Jonathan
2014-01-01
A procedure for calculation of rotation-vibration states of medium sized molecules is presented. It combines the advantages of variational calculations and perturbation theory. The vibrational problem is solved by diagonalizing a Hamiltonian matrix, which is partitioned into two sub-blocks. The first, smaller sub-block includes matrix elements with the largest contribution to the energy levels targeted in the calculations. The second, larger sub-block comprises those basis states which have little effect on these energy levels. Numerical perturbation theory, implemented as a Jacobi rotation, is used to compute the contributions from the matrix elements of the second sub-block. Only the first sub-block needs to be stored in memory and diagonalized. Calculations of the vibrational-rotational energy levels also employ a partitioning of the Hamiltonian matrix into sub-blocks, each of which corresponds either to a single vibrational state or a set of resonating vibrational states, with all associated rotational le...
Universal imaging: Dissociative ionization of polyatomic molecules, chemical dynamics beamline 9.0.2
Energy Technology Data Exchange (ETDEWEB)
Ahmed, M.; Chen, D.; Suits, A.G. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States)
1997-04-01
A third endstation was recently added to the Chemical Dynamics beamline, designed to exploit the high flux broadband undulator light for a range of studies of reactive scattering, photochemistry and photoionization processes using time-of-flight mass spectroscopy coupled with position-sensitive detection. Two molecular beam sources are fixed at right angles, with the undulator light, or laser beams, intersecting the molecular beams at 45{degrees}. To date, beamline experiments have included a study of dissociative photoionization of a variety of molecules including N{sub 2}O and SF{sub 6}. In this mode, a single molecular beam source is used, with the tunable undulator light inducing, in SF{sub 6} for example, the process SF{sub 6} {r_arrow} SF{sub 6}{sup +} + e{sup {minus}} {r_arrow} SF{sub 5}{sup +} + F + e{sup {minus}}. The SF{sub 5}{sup +} ions are accelerated up the flight tube, mass selected and detected as a function of position on a phosphor screen viewed by a CCD camera. The position directly reveals the recoil speed (or translational energy release) and angular distribution for the dissociative ionization process. Furthermore, this measurement is obtained for all recoil speeds and angles simultaneously. Such detailed angular information has not previously been obtained for dissociative ionization processes; typically ion time-of-flight profiles are deconvoluted to yield rough insight into the angular distributions. The recorded image is actually a 2-dimensional projection of the nascent 3-dimensional velocity distribution, but established tomographic techniques enable the authors to reconstruct the 3-D distribution.
Spectra of Linear Polyene Molecule-canthaxanthin
Institute of Scientific and Technical Information of China (English)
OUYANG Shun-li; LI Zuo-wei; CHEN Yuan-zheng; MEN Zhi-wei; WU Nan-nan; SUN Cheng-lin
2011-01-01
Raman spectra and ultraviolet-visible(UV-Vis) absorption spectra of linear polyene molecule-canthaxanthin in n-hexane are measured and analyzed.In addition,the optimized structure of canthaxanthin was calculated via density functional theory(DFT) functional B3LYP.With decreasing the concentration,Raman scattering cross section (RSCS) of fundamental frequency is extremely high,and the UV-Vis absorption bands become narrower.The results of coherent weakly damped electron-Lattice vibration model were analyzed.
Energy Technology Data Exchange (ETDEWEB)
Perry, D.S. [Univ. of Akron, OH (United States)
1993-12-01
Intramolecular vibrational redistribution (IVR) appears to be a universal property of polyatomic molecules in energy regions where the vibrational density of states is greater than about 5 to 30 states per cm{sup {minus}1}. Interest in IVR stems from its central importance to the spectroscopy, photochemistry, and reaction kinetics of these molecules. A bright state, {var_phi}{sub s}, which may be a C-H stretching vibration, carries the oscillator strength from the ground state. This bright state may mix with bath rotational-vibrational levels to form a clump of molecular eigenstates, each of which carries a portion of the oscillator strength from the ground state. In this work the authors explicitly resolve transitions to each of these molecular eigenstates. Detailed information about the nature of IVR is contained in the frequencies and intensities of the observed discrete transitions. The primary goal of this research is to probe the coupling mechanisms by which IVR takes place. The most fundamental distinction to be made is between anharmonic coupling which is independent of molecular rotation and rotationally-mediated coupling. The authors are also interested in the rate at which IVR takes place. Measurements are strictly in the frequency domain but information is obtained about the decay of the zero order state, {var_phi}{sub s}, which could be prepared in a hypothetical experiment as a coherent excitation of the clump of molecular eigenstates. As the coherent superposition dephases, the energy would flow from the initially prepared mode into nearby overtones and combinations of lower frequency vibrational modes. The decay of the initially prepared mode is related to a pure sequence infrared absorption spectrum by a Fourier transform.
CSIR Research Space (South Africa)
De Clercq, L
2010-09-01
Full Text Available molecules for which spectroscopic data for the vibrational modes are available in literature. A density matrix approach was followed. The time evolution of the density matrix is given by the Von Neumann equation [1] , , 1 ( )a l b lN i t i tab lb al... of the individual vibrational levels, and Iab the matrix elements of the interaction Hamiltonian [2] which include the detailed time dependence of the shaped femtosecond pulse. 2. Simulation results A transform limited 150 femtosecond laser pulse with a...
Wehbe, Nimer; Heile, Andreas; Arlinghaus, Heinrich F; Bertrand, Patrick; Delcorte, Arnaud
2008-08-15
A model alkane molecule, triacontane, is used to assess the effects of condensed gold and silver nanoparticles on the molecular ion yields upon atomic (Ga(+) and In(+)) and polyatomic (C60(+) and Bi3(+)) ion bombardment in metal-assisted secondary ion mass spectrometry (MetA-SIMS). Molecular films spin-coated on silicon were metallized using a sputter-coater system, in order to deposit controlled quantities of gold and silver on the surface (from 0 to 15 nm equivalent thickness). The effects of gold and silver islets condensed on triacontane are also compared to the situation of thin triacontane overlayers on metallic substrates (gold and silver). The results focus primarily on the measured yields of quasi-molecular ions, such as (M - H)(+) and (2M - 2H)(+), and metal-cationized molecules, such as (M + Au)(+) and (M + Ag)(+), as a function of the quantity of metal on the surface. They confirm the absence of a simple rule to explain the secondary ion yield improvement in MetA-SIMS. The behavior is strongly dependent on the specific projectile/metal couple used for the experiment. Under atomic bombardment (Ga(+), In(+)), the characteristic ion yields an increase with the gold dose up to approximately 6 nm equivalent thickness. The yield enhancement factor between gold-metallized and pristine samples can be as large as approximately 70 (for (M - H)(+) under Ga(+) bombardment; 10 nm of Au). In contrast, with cluster projectiles such as Bi3(+) and C60(+), the presence of gold and silver leads to a dramatic molecular ion yield decrease. Cluster projectiles prove to be beneficial for triacontane overlayers spin-coated on silicon or metal substrates (Au, Ag) but not in the situation of MetA-SIMS. The fundamental difference of behavior between atomic and cluster primary ions is tentatively explained by arguments involving the different energy deposition mechanisms of these projectiles. Our results also show that Au and Ag nanoparticles do not induce the same behavior in Met
Energy Technology Data Exchange (ETDEWEB)
Pruemper, G. [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980 8577 (Japan)]. E-mail: pruemper@tagen.tohoku.ac.jp; Ueda, K. [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980 8577 (Japan)
2007-05-01
In molecular photofragmentation processes by soft X-rays, a number of ionic fragments can be produced, each having a different abundance and correlation with the kinetic energy of the emitted electron. For investigating these fragmentation processes, electron-ion and electron-ion-ion coincidence experiments, in which the kinetic energy of electrons are analyzed using an electrostatic analyzer while the mass of the ions is analyzed using a pulsed electric field, are very powerful. For such measurements, however, the contribution of random coincidences is substantial and affects the data in a non-trivial way. Simple intuitive subtraction methods cannot be applied. In the present paper, we describe these electron-ion and electron-ion-ion coincidence experiments together with a subtraction method for the contribution from random coincidences. We provide a comprehensive set of equations for the data treatment, including equations for the calculation of error-bars. We demonstrate the method by applying it to the fragmentation of free CF{sub 3}SF{sub 5} molecules.
Conserved linear dynamics of single-molecule Brownian motion
Serag, Maged F.
2017-06-06
Macromolecular diffusion in homogeneous fluid at length scales greater than the size of the molecule is regarded as a random process. The mean-squared displacement (MSD) of molecules in this regime increases linearly with time. Here we show that non-random motion of DNA molecules in this regime that is undetectable by the MSD analysis can be quantified by characterizing the molecular motion relative to a latticed frame of reference. Our lattice occupancy analysis reveals unexpected sub-modes of motion of DNA that deviate from expected random motion in the linear, diffusive regime. We demonstrate that a subtle interplay between these sub-modes causes the overall diffusive motion of DNA to appear to conform to the linear regime. Our results show that apparently random motion of macromolecules could be governed by non-random dynamics that are detectable only by their relative motion. Our analytical approach should advance broad understanding of diffusion processes of fundamental relevance.
Institute of Scientific and Technical Information of China (English)
MENG; Qingtian
2001-01-01
［1］Iachello, F, Levine, R. D., Algebraic approach to molecular rotation-vibration spectra, I. Diatomic molecules, J, Chem.Phys.. 1982, 77: 3046.［2］Iachello. F.. Oss, S., Overtone frequencies and intensities of bent XY2 molecules in the vibron model, J. Mol. Spectrosc.,1990,142: 85.［3］Van Roosmalen, O. S., Iachello, F., Levine, R. D. et al., Algebraic approach to molecular rotation-vibration spectra, II. Triatomic molecules, J. Chem. Phys., 1983, 79: 2515.［4］Iachello, F., Levine, R. D., Algebraic approach to molecular rotation-vibration spectra, Int. J. Quantum Chem., 1983, 23:1679.［5］Cooper, I. L., Levine, R. D., Computed overtone spectra of linear triatomic molecules by dynamical symmetry, J. Mol. Spectrosc., 1991, 148: 391.［6］Iachello. F., Manini. N., Oss, S., Quasi-linear four-atomic molecules in the vibron model, J. Mol. Spectrosc., 1992, 156:190.［7］Wiesenfeld, L.. The vibron model for methane: stretch-bend interactions, J. Mol. Spectrosc., 1997, 184: 277.［8］Zheng, Y.. Ding, S., Vibrational spectra of HCN and OCS from second-order expansion of the U1(4) U2(4) algebra,Phys. Lett. A. 1999. 256: 197.［9］Zheng, Y.. Ding. S., Algebraic method for determining the potential energy surface for nonlinear triatomic molecules, Chem. Phys., 1999, 247: 225.［10］Zheng, Y.. Ding, S.. Algebraic description of stretching and bending vibrational spectra of H2O and H2S, J. Mol. Spectrosc.,2000. 201: 109.［11］Meng. Q., Zheng, Y., Ding, S., Lie algebraic approach to Fermi resonance levels of CS2 and CO2, Int. J. Quantum Chem.,2001, 81: 154.［12］Ding, S., Zheng, Y., Lie algebraic approach to potential energy surface for symmetric triatomic molecules, J. Chem. Phys.,1999. 111: 4466.［13］Zheng. Y., Ding, S., Algebraic approach to the potential energy surface for the electronic ground state of ozone, Chem.Phys.. 2000. 255: 217.［14］Zheng. Y., Ding, S., Theoretical study of nonlinear triatomic molecular potential energy surfaces: Lie
Half-space problem of unsteady evaporation and condensation of polyatomic gas
Inaba, Masashi; Yano, Takeru
2016-11-01
On the basis of polyatomic version of the ellipsoidal-statistical Bhatnager-Gross-Krook (ES-BGK) model, we consider time-periodic gas flows in a semi-infinite expanse of an initially equilibrium polyatomic gas (methanol) bounded by its planar condensed phase. The kinetic boundary condition at the vapor-liquid interface is assumed to be the complete condensation condition with periodically time-varying macroscopic variables (temperature, saturated vapor density and velocity of the interface), and the boundary condition at infinity is the local equilibrium distribution function. The time scale of variation of macroscopic variables is assumed to be much larger than the mean free time of gas molecules, and the variations of those from a reference state are assumed to be sufficiently small. We numerically investigate thus formulated time-dependent half-space problem for the polyatomic version of linearized ES-BGK model equation with the finite difference method for the case of the Strouhal number Sh=0.01 and 0.1. It is shown that the amplitude of the mass flux at the interface is the maximum, and the phase difference in time between the mass flux and v∞ - vℓ (v∞: vapor velocity at infinity, vℓ: velocity of the vapor-liquid interface) is the minimum absolute value, when the phase difference in time between the liquid surface temperature (the saturated vapor density) and the velocity of interface is close to zero.
Translation and integration of numerical atomic orbitals in linear molecules
Energy Technology Data Exchange (ETDEWEB)
Heinäsmäki, Sami, E-mail: sami.heinasmaki@gmail.com [Department of Physics, University of Oulu, FIN-90014, Oulu (Finland)
2014-02-14
We present algorithms for translation and integration of atomic orbitals for LCAO calculations in linear molecules. The method applies to arbitrary radial functions given on a numerical mesh. The algorithms are based on pseudospectral differentiation matrices in two dimensions and the corresponding two-dimensional Gaussian quadratures. As a result, multicenter overlap and Coulomb integrals can be evaluated effectively.
Energy Technology Data Exchange (ETDEWEB)
Cao, Siqin [The HKUST Shenzhen Research Institute, Shenzhen (China); Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Sheong, Fu Kit [Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Huang, Xuhui, E-mail: xuhuihuang@ust.hk [The HKUST Shenzhen Research Institute, Shenzhen (China); Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Division of Biomedical Engineering, Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong)
2015-08-07
Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achieve this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute.
Lamb, W. E. Jr.
1981-12-01
This final report describes research on the theory of isotope separation produced by the illumination of polyatomic molecules by intense infrared laser radiation. This process is investigated by treating the molecule, sulfur hexafluoride, as a system of seven classical particles that obey the Newtonian equations of motion. A minicomputer is used to integrate these differential equations. The particles are acted on by interatomic forces, and by the time-dependent electric field of the laser. We have a very satisfactory expression for the interaction of the laser and the molecule which is compatible with infrared absorption and spectroscopic data. The interatomic potential is capable of improvement, and progress on this problem is still being made. We have made several computer runs of the dynamical behavior of the molecule using a reasonably good model for the interatomic force law. For the laser parameters chosen, we find that typically the molecule passes quickly through the resonance region into the quasi-continuum and even well into the real continuum before dissociation actually occurs. When viewed on a display terminal, the motions are exceedingly complex. As an aid to the visualization of the process, we have made a number of 16 mm movies depicting a three-dimensional representation of the motion of the seven particles. These show even more clearly the enormous complexity of the motions, and make clear the desirability of finding ways of characterizing the motion in simple ways without giving all of the numerical detail. One of the ways to do this is to introduce statistical parameters such as a temperature associated with the distribution of kinetic energies of the single particle. We have made such an analysis of our data runs, and have found favorable indications that such methods will prove useful in keeping track of the dynamical histories.
Detecting chirality in molecules by linearly polarized laser fields
Yachmenev, Andrey
2016-01-01
A new scheme for enantiomer differentiation of chiral molecules using a pair of linearly polarized intense ultrashort laser pulses with skewed mutual polarization is presented. The technique relies on the fact that the off-diagonal anisotropic contributions to the electric polarizability tensor for two enantiomers have different signs. Exploiting this property, we are able to excite a coherent unidirectional rotation of two enantiomers with a {\\pi} phase difference in the molecular electric dipole moment. The approach is robust and suitable for relatively high temperatures of molecular samples, making it applicable for selective chiral analysis of mixtures, and to chiral molecules with low barriers between enantiomers. As an illustration, we present nanosecond laser-driven dynamics of a tetratomic non-rigid chiral molecule with short-lived chirality. The ultrafast time scale of the proposed technique is well suited to study parity violation in molecular systems in short-lived chiral states.
Structural changes of linear DNA molecules induced by cisplatin
Energy Technology Data Exchange (ETDEWEB)
Liu, Zhiguo, E-mail: cn.zguoliu@yahoo.com [State Engineering Laboratory of Bio-Resource Eco-Utilization, Harbin 150040 (China); Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040 (China); Key Laboratory of Forest Plant Ecology of Ministry of Education, Northeast Forestry University, Harbin 150040 (China); Liu, Ruisi; Zhou, Zhen; Zu, Yuangang; Xu, Fengjie [State Engineering Laboratory of Bio-Resource Eco-Utilization, Harbin 150040 (China); Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040 (China); Key Laboratory of Forest Plant Ecology of Ministry of Education, Northeast Forestry University, Harbin 150040 (China)
2015-02-20
Interaction between long DNA molecules and activated cisplatin is believed to be crucial to anticancer activity. However, the exact structural changes of long DNA molecules induced by cisplatin are still not very clear. In this study, structural changes of long linear double-stranded DNA (dsDNA) and short single-stranded DNA (ssDNA) induced by activated cisplatin have been investigated by atomic force microscopy (AFM). The results indicated that long DNA molecules gradually formed network structures, beads-on-string structures and their large aggregates. Electrostatic and coordination interactions were considered as the main driving forces producing these novel structures. An interesting finding in this study is the beads-on-string structures. Moreover, it is worth noting that the beads-on-string structures were linked into the networks, which can be ascribed to the strong DNA–DNA interactions. This study expands our knowledge of the interactions between DNA molecules and cisplatin. - Highlights: • We investigate structural changes of dsDNA and ssDNA induced by cisplatin. • AFM results indicated long dsDNA formed network, beads-on-string and aggregates. • ssDNA can form very similar structures as those of long linear dsDNA. • A possible formation process of theses novel structure is proposed.
Non-linear irreversible thermodynamics of single-molecule experiments
Santamaria-Holek, I; Hidalgo-Soria, M; Perez-Madrid, A
2015-01-01
Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the non-linear case of systems under non-equilibrium external constraints, we are able to calculate the entropy production and the general non-linear kinetic equations for the variables involved. In particular, we analyze the case of RNA stretching protocols obtaining critical oscillations between di?erent con?gurational states when forced by external means to remain in the unstable region of its free-energy landscape, as observed in experiments. We also calculate the entropy produced during these hopping events, and show how resonant phenomena in stretching experiments of single RNA macromolecules may arise. We also calculate the hopping rates using Kramer's approach obtaining a good comparison with experiments.
Institute of Scientific and Technical Information of China (English)
SUN Jin-Feng; XU Bin; LIU Yu-Fang; SHI De-Heng
2005-01-01
A new modified formulation of the Additivity Rule (AR) was proposed to calculate the total electron scattering cross sections for CH4, CO2, NO2, and N2O, considering the overlapping between atoms in molecules and the not fully transparency of the molecules. The present calculation covers the range of impact energy from 10 to 3000 eV. The results are compared with experimental data and other theories where available. The atoms are presented by spherical complex optical potential, which is composed of static, exchange, polarization, and absorption terms.
Linear trinuclear cobalt(II) single molecule magnet.
Zhang, Yuan-Zhu; Brown, Andrew J; Meng, Yin-Shan; Sun, Hao-Ling; Gao, Song
2015-02-14
The introduction of NaBPh(4) into a methanolic solution of CoCl(2)·(6)H(2)O and 2-[(pyridine-2-ylimine)-methyl]phenol (Hpymp) afforded {[Co(II)(3)(pymp)(4)(MeOH)(2)][BPh(4)](2)}·(2)MeOH (1) with a centro-symmetrically linear trinuclear structure. Magnetic analysis of 1 exhibited significant intracluster ferromagnetic exchange (2.4 cm(-1)) and slow relaxation of magnetization in both zero and non-zero static fields below 5 K, giving the first [Co(II)(3)] single molecule magnet with an effective energy barrier of 17.2(3) cm(-1) under a 500 Oe dc field.
Yoo, Hyejin
2012-10-25
Perylenediimide (PDI) molecules are promising building blocks for photophysical studies of electronic interactions within multichromophore arrays. Such PDI arrays are important materials for fabrication of molecular nanodevices such as organic light-emitting diodes, organic semiconductors, and biosensors because of their high photostability, chemical and physical inertness, electron affinity, and high tinctorial strength over the entire visible spectrum. In this work, PDIs have been organized into linear (L3) and trefoil (T3) trimer molecules and investigated by single-molecule fluorescence microscopy to probe the relationship between molecular structures and interchromophoric electronic interactions. We found a broad distribution of coupling strengths in both L3 and T3 and hence strong/weak coupling between PDI units by monitoring spectral peak shifts in single-molecule fluorescence spectra upon sequential photobleaching of each constituent chromophore. In addition, we used a wide-field defocused imaging technique to resolve heterogeneities in molecular structures of L3 and T3 embedded in a PMMA polymer matrix. A systematic comparison between the two sets of experimental results allowed us to infer the correlation between intermolecular interactions and molecular structures. Our results show control of the PDI intermolecular interactions using suitable multichromophoric structures. © 2012 American Chemical Society.
Madzunkov, S. M.; Chutjian, A.; Darrach, M. R.; MacAskill, J. A.; Ehrenfreund, P.; Vidali, G.
2011-05-01
Carbon dioxide (CO2), formaldehyde (H2CO), methanol (CH3OH), ethanol (CH3CH2OH), and formic acid (HCOOH) have been formed in separate measurements involving collisions of superthermal beams of H(2S) atoms and O(3P) atoms with CO and CH4 molecules adsorbed on a gold surface at 4.8K. The collision products are detected using temperature-programmed desorption and mass spectrometry. Identification of the species is made through use of the Metropolis random-walk algorithm as constrained by the fractionation patterns. The relevance of this work to the recent discovery of H2O at the star IRC+10216 by PACS-SPIRE/Herschel will be discussed in terms of the grain-mediated reaction O(3P, 1-5 eV) + H2(grain) → H2O(grain), in which the O(3P) arises from stellar UV photodissociation.
Braunstein, M.; Pack, R. T.
1992-05-01
A simple model for the photodissociation absorption spectra of bent symmetric triatomic molecules to the Wulf-Chappuis band system of ozone (10,000-22,000/cm) is applied to assign the electronic states and the diffuse vibrational bands involved. The conical intersection between the two lowest 1A-double prime states is treated in an approximate way, and the role of the lowest excited triplet states is explored. The results indicate that the Wulf band is probably due to the 3A2 state of ozone which gains intensity through spin-orbit coupling. The 1 1A-double prime (1A2) state gives rise to the featureless red wing of the Chappuis band. Most of the structure in the Chappuis band is reproduced in the model and is due to the 2 1A-double prime (1B1) state as was previously supposed.
The linear and non-linear magnetic response of a tri-uranium single molecule magnet
Shivaram, B. S.; Colineau, E.; Griveau, J.; Kumar, P.; Celli, V.
2017-03-01
We report here low temperature magnetization isotherms for the single molecule magnet, (UO2-L)3. By analyzing the low temperature magnetization in terms of M = χ 1 B + χ 3 B 3 we extract the linear susceptibility χ 1 and the leading order nonlinear susceptibility χ 3. We find that χ 1 exhibits a peak at a temperature of T 1 = 10.4 K with χ 3 also exhibiting a peak but at a reduced temperature T 3 = 5 K. At the lowest temperatures the isotherms exhibit a critical field B c = 11.5 T marked by a clear point of inflection. A minimal Hamiltonian employing S = 1 (pseudo) spins with only a single energy scale (successfully used to model the behavior of bulk f-electron metamagnets) is shown to provide a good description of the observed linear scaling between T 1, T 3 and B c. We further show that a Heisenberg Hamiltonian previously employed by Carretta et al (2013 J. Phys.: Condens. Matter 25 486001) to model this single molecule magnet gives formulas for the angle averaged susceptibilities (in the Ising limit) very similar to those of the minimal model.
Infrared absorption line intensities for U (5) model of linear triatomic molecules
Institute of Scientific and Technical Information of China (English)
于少英
1999-01-01
The symmetry of the rotation-vibration spectra for linear triatomic molecules is described by means of the group U(5). The rotation-vibration levels of linear triatomic molecules HCN and COS are calculated. The infrared absorption line intensities are calculated for the COS molecule. The results are in good agreement with the experimental values.
Linear Ion Trap for the Mars Organic Molecule Analyzer
Brinckerhoff, William; Arevalo, Ricardo; Danell, Ryan; van Amerom, Friso; Pinnick, Veronica; Li, Xiang; Hovmand, Lars; Getty, Stephanie; Mahaffy, Paul; Goesmann, Fred; Steininger, Harald
2014-05-01
The 2018 ExoMars rover mission includes the Mars Organic Molecule Analyzer (MOMA) investigation. MOMA will examine the chemical composition of samples acquired from depths of up to two meters below the martian surface, where organics may be protected from radiative and oxidative degradation. When combined with the complement of instruments in the rover's Pasteur Payload, MOMA has the potential to reveal the presence of a wide range of organics preserved in a variety of mineralogical environments, and to begin to understand the structural character and potential origin of those compounds. MOMA includes a linear, or 2D, ion trap mass spectrometer (ITMS) that is designed to analyze molecular composition of (i) gas evolved from pyrolyzed powder samples and separated on a gas chromatograph and (ii) ions directly desorbed from solid samples at Mars ambient pressure using a pulsed laser and a fast-valve capillary ion inlet system. This "dual source" approach gives MOMA unprecedented breadth of detection over a wide range of molecular weights and volatilities. Analysis of nonvolatile, higher-molecular weight organics such as carboxylic acids and peptides even in the presence of significant perchlorate concentrations is enabled by the extremely short (~1 ns) pulses of the desorption laser. Use of the ion trap's tandem mass spectrometry mode permits selective focus on key species for isolation and controlled fragmentation, providing structural analysis capabilities. The flight-like engineering test unit (ETU) of the ITMS, now under construction, will be used to verify breadboard performance with high fidelity, while simultaneously supporting the development of analytical scripts and spectral libraries using synthetic and natural Mars analog samples guided by current results from MSL. ETU campaign data will strongly advise the specifics of the calibration applied to the MOMA flight model as well as the science operational procedures during the mission.
Quasi-chemical approximation for polyatomic mixtures
Dávila, M V; Matoz-Fernandez, D A; Ramirez-Pastor, A J
2016-01-01
The statistical thermodynamics of binary mixtures of polyatomic species was developed on a generalization in the spirit of the lattice-gas model and the quasi-chemical approximation (QCA). The new theoretical framework is obtained by combining: (i) the exact analytical expression for the partition function of non-interacting mixtures of linear $k$-mers and $l$-mers (species occupying $k$ sites and $l$ sites, respectively) adsorbed in one dimension, and its extension to higher dimensions; and (ii) a generalization of the classical QCA for multicomponent adsorbates and multisite-occupancy adsorption. The process is analyzed through the partial adsorption isotherms corresponding to both species of the mixture. Comparisons with analytical data from Bragg-Williams approximation (BWA) and Monte Carlo simulations are performed in order to test the validity of the theoretical model. Even though a good fitting is obtained from BWA, it is found that QCA provides a more accurate description of the phenomenon of adsorpti...
Investigation of Electron Attachment in Polyatomic Molecules.
1980-05-30
expected from the theory . In the sense of O’Malley’s theory , the slopes D(E) could be called activation energies, in that they are interpreted for a...project and useful discussions. Dr. D. A. Vroom , Dr. S . M. Trujillo, and R. L. Palmer have also contributed through informative discussions, as have Dr...Ref. B2) S log P = 7.766 1499.9 T where P is in torr, and WF6 (b.p. 17.1 0C) is entirely a gas at room temperature. * Thus, it was expected that a
On the symmetrization of rotational spectra for freely rotating linear molecules
Borysow, Aleksandra; Moraldi, Massimo
It is demonstrated that the symmetrization of a quantum mechanical rotational spectrum of freely rotating linear molecules by means of the Egelstaff transformation produces a symmetric spectrum whose first two even moments coincide with the corresponding classical moments.
Studies of a linear single-molecule magnet.
Prescimone, Alessandro; Wolowska, Joanna; Rajaraman, Gopalan; Parsons, Simon; Wernsdorfer, Wolfgang; Murugesu, Murlaee; Christou, George; Piligkos, Stergios; McInnes, Eric J L; Brechin, Euan K
2007-12-07
Reaction of the dinuclear complex [Mn2O2(bpy)4](ClO4)3 with H3cht (cis,cis-l,3,5-cyclohexanetriol) in MeCN produces the complex [Mn3(Hcht)2(bpy)4](ClO4)3.Et2O.2MeCN (1.Et2O.2MeCN). Dc magnetic susceptibility measurements reveal the existence of weak ferromagnetic exchange between the three Mn ions, leading to a spin ground state of S = 7, with D = -0.23 cm(-1). W-Band (94 GHz) EPR measurements on restrained powdered crystalline samples confirm the S = 7 ground state and determine the ground state zero-field splitting (ZFS) parameters of D = -0.14 cm(-1) and B4(0)= +1.5 x 10(-5) cm(-1). The apparent 4th order behaviour is due to a breakdown of the strong exchange limit approximation (J approximately d, the single-ion ZFS). Single crystal dc relaxation decay and hysteresis loop measurements reveal the molecule to have an appreciable energy barrier to magnetization relaxation, displaying low temperature sweep rate and temperature-dependent hysteresis loops. Density functional studies confirm the ferromagnetic exchange coupling between the Mn ions.
Lo, Sui-Sang
The polyatomic gas model equations developed by Hansen and Morse were used in the linearized Wang-Chang and Uhlenbeck equation to study the thermal transpiration and mechanocaloric effects in various geometries with different boundary conditions. The phenomenological coefficients for mass and energy flows at all degrees of rarefaction are reported. It is shown, on a theoretical basis, that the thermal transpiration effect ratio has a strong dependence on f(,tr), the translational Eucken factor, and only a weak dependence on f(,tr), the total Eucken factor. The cross coefficients (,MQ) = (,QM) for all calculations but the energy flux near the wall was found negative for inverse Knudsen numbers greater than 3. Flow of polyatomic gases was studied in a long cylindrical tube with the Maxwell's diffuse scattering boundary conditions. Experimental thermal transpiration effect ratios ((DELTA)p/p(,0))/((DELTA)T/T(,0)) are nearly represented by the Hansen-Morse model for simple gases, argon, air and carbon dioxide. The sulfur dioxide data are not quantitatively given by the theory due to inadequacy of the Hansen-Morse model for strongly polar gases. The work was also extended to a cylindrical annulus where comparisons were made with the Poiseuille flow data for helium, air, hydrogen and carbon dioxide. The cross effects were also studied for arbitrary (alpha), the fraction of molecules that are diffusely reflected from the surface, for a gas confined between parallel plates and in a cylindrical tube. The comparisons of the experimental thermal transpiration data with the theoretical results yielded (alpha) values which lie between 0.8 and 1.0, as expected for the "engineering surfaces.".
NATO Advanced Research Workshop on Dynamics of Polyatomic Van der Waals Complexes
Janda, Kenneth
1991-01-01
This publication is the Proceedings of the NATO Advanced Research Workshop (ARW) on the Dynamics of Polyatomic Van der Waals Molecules held at the Chateau de Bonas, Castera-Verduzan, France, from August 21 through August 26, 1989. Van der Waals complexes provide important model problems for understanding energy transfer and dissipation. These processes can be described in great detail for Van der Waals complexes, and the insight gained from such studies can be applied to more complicated chemical problems that are not amenable to detailed study. The workshop concentrated on the current questions and future prospects for extend ing our highly detailed knowledge of triatomic Van der Waals molecule dynamics to polyatomic molecules and clusters (one molecule surrounded by several, or up to sev eral tens of, atoms). Both experimental and theoretical studies were discussed, with particular emphasis on the dynamical behavior of dissociation as observed in the dis tributions of quantum states of the dissociatio...
Institute of Scientific and Technical Information of China (English)
Chen Jian-Xin; Ma Ri; Ren Hai-Zhen; Li Xia; Wu Cheng-Yin; Yang Hong; Gong Qi-Huang
2004-01-01
@@ The kinetic energy release of fragment ions produced by the interaction of femtosecond laser pulse radiation with diatomic and linear triatomic molecules N2, CO, CO2 and CS2 is investigated. In the case of linear polarization, angles at which the kinetic energy release of ions has the maximum value are different from the alignment of molecules though the kinetic energy release of fragment atomic ions depends on the angle between the laser polarization vector and the detection axis of the time-of-flight.
McGuyer, B H; McDonald, M; Reinaudi, G; Skomorowski, W; Moszynski, R; Zelevinsky, T
2013-01-01
Anomalously large linear and quadratic Zeeman shifts are measured for weakly bound ultracold $^{88}$Sr$_2$ molecules near the intercombination line asymptote. Nonadiabatic Coriolis coupling and the nature of long-range molecular potentials explain how this effect arises and scales roughly cubically with the size of the molecule. The linear shifts yield nonadiabatic mixing angles of the molecular states. The quadratic shifts are sensitive to fourth-order contributions and to nearby opposite $f$-parity states, and provide a stringent test of a state-of-the-art ab initio model.
Institute of Scientific and Technical Information of China (English)
Metin Orbay; Telhat Ozdogan
2003-01-01
In this paper, the symmetry properties of linear combination coefficients for molecular orbitals of diatomicmolecules, using Slater type orbitals, are presented with the help of the symmetry operations in group theory. In order totest the presented symmetry properties, the linear combination coefficients of molecular orbitalsfor the ground electronicstate of pilot molecules F2 and CO are calculated using constructed computer programs for Hartree-Fock-Roothaanequation. It is seen that the obtained computing results satisfy the presented symmetry properties.
Choi, Yongki; Moody, Issa S; Sims, Patrick C; Hunt, Steven R; Corso, Brad L; Seitz, David E; Blaszczak, Larry C; Blaszcazk, Larry C; Collins, Philip G; Weiss, Gregory A
2012-02-01
The dynamic processivity of individual T4 lysozyme molecules was monitored in the presence of either linear or cross-linked peptidoglycan substrates. Single-molecule monitoring was accomplished using a novel electronic technique in which lysozyme molecules were tethered to single-walled carbon nanotube field-effect transistors through pyrene linker molecules. The substrate-driven hinge-bending motions of lysozyme induced dynamic electronic signals in the underlying transistor, allowing long-term monitoring of the same molecule without the limitations of optical quenching or bleaching. For both substrates, lysozyme exhibited processive low turnover rates of 20-50 s(-1) and rapid (200-400 s(-1)) nonproductive motions. The latter nonproductive binding events occupied 43% of the enzyme's time in the presence of the cross-linked peptidoglycan but only 7% with the linear substrate. Furthermore, lysozyme catalyzed the hydrolysis of glycosidic bonds to the end of the linear substrate but appeared to sidestep the peptide cross-links to zigzag through the wild-type substrate.
A Simple Reduction Process for the Normal Vibrational Modes Occurring in Linear Molecules
McInerny, William
2005-01-01
The students in molecular spectroscopy courses are often required to determine the permitted normal vibrations for linear molecules that belong to particular groups. The reducible group representations generated by the use of Cartesian coordinates can be reduced by the use of a simple algebraic process applied to the group representations. The…
Hexapole State-Selection and Beam Focus of Linear Triatomic Molecules
Institute of Scientific and Technical Information of China (English)
LIU Fu-Chun; JIN Ming-Xing; DING Da-Jun
2006-01-01
@@ The state selection and beam focus of linear triatomic molecules (OCS, HCN, CICN, BrCN and ICN) with doubling states in a hexapole electric field have been numerically realized. The method is based on a quantum mechanical treatment of the molecular Stark energy and a classical mechanical treatment for the molecular trajectory in the field. In linear molecules with doubling states, the second-order Stark effect can be neglected and the doubling states have the same value of J and M. The influences of the molecular properties, state energies, and the apparatus parameters such as molecular beam temperature and length of the hexapole, on the role of state selection and focus have been discussed. The method established here can be taken as a guide for hexapole experiment of orientation of polar molecules.
Developing Density of Laser-Cooled Neutral Atoms and Molecules in a Linear Magnetic Trap
Velasquez, Joe, III; Walstrom, Peter; di Rosa, Michael
2013-05-01
In this poster we show that neutral particle injection and accumulation using laser-induced spin flips may be used to form dense ensembles of ultracold magnetic particles, i.e., laser-cooled paramagnetic atoms and molecules. Particles are injected in a field-seeking state, are switched by optical pumping to a field-repelled state, and are stored in the minimum-B trap. The analogous process in high-energy charged-particle accumulator rings is charge-exchange injection using stripper foils. The trap is a linear array of sextupoles capped by solenoids. Particle-tracking calculations and design of our linear accumulator along with related experiments involving 7Li will be presented. We test these concepts first with atoms in preparation for later work with selected molecules. Finally, we present our preliminary results with CaH, our candidate molecule for laser cooling. This project is funded by the LDRD program of Los Alamos National Laboratory.
Reaction dynamics in polyatomic molecular systems
Energy Technology Data Exchange (ETDEWEB)
Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
Energy Technology Data Exchange (ETDEWEB)
Grohmann, Thomas
2012-05-31
In this thesis the wave packet dynamics of nuclear spin isomers of polyatomic molecules after interaction with static and time-dependent magnetic fields and moderate intense nonresonant laser pulses is investigated. In particular, the process of inducing (internal) molecular rotation as well as alignment of molecules by manipulating their rotational or rotational-torsional degrees of freedom is studied. In the first part of the thesis all theoretical concepts for identifying nuclear spin isomers and for describing their quantum dynamics will be discussed. Especially the symmetrization postulate and themolecular symmetry group will be introduced and illustrated for some examples of molecules. These concepts will be extended to the case of identifying nuclear spin isomers in the presence of an external field. In the second part it is shown for nitromethane that magnetic fields are able to induce unidirectional rotations in opposite directions for different nuclear spin isomers of molecules containing methyl groups if the dipolar interaction is included. Additionally, it is demonstrated that different nuclear spin isomers of a chemical compound may show different alignment after the interaction with a moderate intense laser pulse. As shown for the rigid symmetric top propadien and the rigid asymmetric tops ethene and analogues, distinct pairs of nuclear spin isomers show at certain points in time a complementary behavior: while one isomer is showing alignment the partner isomer is showing anti-alignment. Moreover, it is illustrated that not every nuclear spin isomer can be aligned equally efficient. The alignment of non-rigid molecules is considered as well. As an example for a molecule with feasible torsion in the electronic ground state, the alignment of diboron tetrafluoride is investigated. It becomes apparent that not only rotational but also the torsional dynamics of the molecules is nuclear spin selective; different nuclear spin isomers have at distinct points
Energy Technology Data Exchange (ETDEWEB)
Ferguson, Jill Wisnewski [Iowa State Univ., Ames, IA (United States)
2006-01-01
The inductively coupled plasma (ICP) is an atmospheric pressure ionization source. Traditionally, the plasma is sampled via a sampler cone. A supersonic jet develops behind the sampler, and this region is pumped down to a pressure of approximately one Torr. A skimmer cone is located inside this zone of silence to transmit ions into the mass spectrometer. The position of the sampler and skimmer cones relative to the initial radiation and normal analytical zones of the plasma is key to optimizing the useful analytical signal [1]. The ICP both atomizes and ionizes the sample. Polyatomic ions form through ion-molecule interactions either in the ICP or during ion extraction [l]. Common polyatomic ions that inhibit analysis include metal oxides (MO^{+}), adducts with argon, the gas most commonly used to make up the plasma, and hydride species. While high resolution devices can separate many analytes from common interferences, this is done at great cost in ion transmission efficiency--a loss of 99% when using high versus low resolution on the same instrument [2]. Simple quadrupole devices, which make up the bulk of ICP-MS instruments in existence, do not present this option. Therefore, if the source of polyatomic interferences can be determined and then manipulated, this could potentially improve the figures of merit on all ICP-MS devices, not just the high resolution devices often utilized to study polyatomic interferences.
On the state selection of linear triatomic molecules by electrostatic hexapole fields
Tsai, Po-Yu
2016-09-01
Electrostatic hexapole state-selector is a versatile tool in experimental stereodynamics. The requirement of appropriate models to correctly predict the behavior of molecules in the hexapole motivated us to realize a treatment that predicts the Stark effect of linear triatomic molecules with rotational doublet states. Various perturbative approximations are conventionally adopted to obtain analytic Stark energy derivatives of a truncated Hamiltonian matrix, without utilizing numerical diagonalization of the full Hamiltonian matrix. By including both the low and high field effects, which were alternatively ignored in the analytical formulae of such approximate approaches, herein we demonstrate that the performance of hexapole state selector to linear triatomic molecules can be appropriately predicted via Van Vleck transformation. This method can provide analytic Stark energy derivatives that are acceptably in consistent with the ones obtained via numerical diagonalization of the full Hamiltonian matrix. Particularly, this work is suitable for v2 = 1 level of linear triatomic molecules, due to the following reasons: (1) the Stark energy derivative and the molecular orientation as a function of the electric field are expressed in analytical formulae, hence it is suitable for implementation without involving numerical diagonalization of the full Hamiltonian matrix; (2) a better prediction of the focusing curves with respect to conventional analytical treatments is provided, allowing a reliable determination of the selected state compositions and molecular orientation.
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
The Hamiltonian describing rotational spectra of linear triatomic molecules has been derived by using the dynamical Lie algebra of symmetry group U1(4)U,(4). After rovibrational interactions being considered, the eigenvalue expression of the Hamiltonian has the form of term value equation commonly used in spectrum analysis. The molecular rotational constants can be obtained by using the expression and fitting it to the observed lines. As an example, the rotational levels of v2 band for transition (0200-0110) of molecules N2O and HCN have been fitted and the fitting root-mean-square errors (RMS) are 0.00001 and 0.0014 cm-1, respectively.
Institute of Scientific and Technical Information of China (English)
冯东太; 丁世良; 王美山
2003-01-01
The highly excited vibrational states of asymmetric linear tetratomic molecules are studied in the framework of Lie algebra. By using symmetric group U1(4) U2(4) U3(4), we construct the Hamiltonian that includes not only Casimir operators but also Majorana operators M12,M13 and M23, which are useful for getting potential energy surface and force constants in Lie algebra method. By Lie algebra treatment, we obtain the eigenvalues of the Hamiltonian, and make the concrete calculation for molecule C2HF.
Mixed-field orientation of a thermal ensemble of linear polar molecules
Omiste, Juan J
2013-01-01
We present a theoretical study of the impact of an electrostatic field combined with nonresonant linearly polarized laser pulses on the rotational dynamics of a thermal ensemble of linear molecules. We solve the time-dependent Schr\\"odinger equation within the rigid rotor approximation for several rotational states. Using the carbonyl sulfide (OCS) molecule as a prototype, the mixed-field orientation of a thermal sample is analyzed in detail for experimentally accessible static field strengths and laser pulses. We demonstrate that for the characteristic field configuration used in current mixed-field orientation experiments, a significant orientation is obtained for rotational temperatures below 0.7K or using stronger dc fields.
Key components for nano-assembled plasmon-excited single molecule non-linear devices
Kewes, Günter; Mazzamuto, Giacomo; Neitzke, Oliver; Schönfeld, Rolf-Simon; Schell, Andreas W; Probst, Jürgen; Wolters, Janik; Löchel, Bernd; Toninelli, Costanza; Benson, Oliver
2015-01-01
Tremendous enhancement of light-matter interaction in plasmon-excited molecular hybrid devices allows for non-linearities on the level of single emitters and few photons. This promises a plethora of novel applications like single photon transistors. Nevertheless, building the components of such devices is technologically extremely challenging. We tackle this task by lithographically fabricating on-chip plasmonic waveguides, efficiently connected to far-field in- and out-coupling ports via low-loss dielectric waveguides. Furthermore, a nano-assembling technology is developed, enabling the controlled coupling of single organic emitters to the plasmonic waveguides. Dibenzoterrylene fluorescent molecules hosted in anthracene crystals are investigated for this purpose. Here we present all key-components and technologies for a plasmon-excited single molecule non-linear device.
Meng, Qingtian; Guan, Daren; Ding, Shiliang
2001-04-01
An algebraic construction of a Hamiltonian is used to study the rotational spectra of linear triatomic molecules on the basis of the subgroup chain of symmetry U1(4)⊗ U2(4). After considering the rotation-vibration interaction which gives the l splittings, the eigenvalue expression of the Hamiltonian has a form of the term value equation commonly used in the calculation of molecular spectra. The method is applied to calculate the rotational energy levels of vibrational transitions (0 1 10-0 0 00) for C 34S 2, (1 1 13-0 1 10) and (1 0 03-0 0 00) for C 32S 2. The obtained rotational constants can represent the rotational spectra of the three bands with small root-mean-square frequency errors. The results show that the algebraic Hamiltonian can provide an alternative description of rovibrational spectra for linear triatomic molecules.
Crystal chemistry of layered structures formed by linear rigid silyl-capped molecules
Directory of Open Access Journals (Sweden)
Daniel Lumpi
2015-09-01
Full Text Available The crystallization behavior of methylthio- or methylsulfonyl-containing spacer extended Z,Z-bis-ene–yne molecules capped with trimethylsilyl groups obtained by (tandem thiophene ring fragmentation and of two non-spacer extended analogs were investigated. The rigid and linear molecules generally crystallized in layers whereby the flexibility of the layer interfaces formed by the silyl groups leads to a remarkably rich crystal chemistry. The molecules with benzene and thiophene spacers both crystallized with C2/c symmetry and can be considered as merotypes. Increasing the steric bulk of the core by introduction of ethylenedioxythiophene (EDOT gave a structure incommensurately modulated in the [010] direction. Further increase of steric demand in the case of a dimethoxythiophene restored periodicity along [010] but resulted in a doubling of the c vector. Two different polytypes were observed, which feature geometrically different layer interfaces (non-OD, order–disorder, polytypes, one with a high stacking fault probability. Oxidation of the methylthio groups of the benzene-based molecule to methylsulfonyl groups led to three polymorphs (two temperature-dependent, which were analyzed by Hirshfeld surface de/di fingerprint plots. The analogously oxidized EDOT-based molecule crystallized as systematic twins owing to its OD polytypism. Shortening of the backbone by removal of the aryl core resulted in an enantiomorphic structure and a further shortening by removal of a methylthio-ene fragment again in a systematically twinned OD polytype.
On the linear response and scattering of an interacting molecule-metal system
Energy Technology Data Exchange (ETDEWEB)
Masiello, David J.; Schatz, George C.
2010-01-01
A many-body Green’s function approach to the microscopic theory of plasmon-enhanced spectroscopy is presented within the context of localized surface-plasmon resonancespectroscopy and applied to investigate the coupling between quantum-molecular and classical-plasmonic resonances in monolayer-coated silver nanoparticles. Electronic propagators or Green’s functions, accounting for the repeated polarizationinteraction between a single molecule and its image in a nearby nanoscale metal, are explicitly computed and used to construct the linear-response properties of the combined molecule-metal system to an external electromagnetic perturbation. Shifting and finite lifetime of states appear rigorously and automatically within our approach and reveal an intricate coupling between molecule and metal not fully described by previous theories. Self-consistent incorporation of this quantum-molecular response into the continuum-electromagnetic scattering of the molecule-metal target is exploited to compute the localized surface-plasmon resonance wavelength shift with respect to the bare metal from first principles.
Lo, S. S.; Loyalka, S. K.; Storvick, T. S.
1984-09-01
Thermal transpiration and mechanocaloric effect in a long cylindrical tube are studied by use of the Hansen and Morse polyatomic gas model of the linearized Wang-Chang and Uhlenbeck equation and Maxwellian diffuse-specular reflection model for the gas-surface interaction. For all rarefactions, the dimensionless phenomenological coefficients for mass and energy flows due to axial pressure and temperature gradients are calculated as a function of the fraction of incident molecules that are reflected diffusely at the surface. The calculated thermal transpiration effect ratios were compared with the experimental data to obtain α for Xe, Ar, Ne, He, and H2, and CO2 in the transition flow regime, and Kr, Ar, Ne, and He in the near-continuum regime. The values of α were found to lie in the range of 0.8-1.0 and are in general agreement with the reported experimental results.
Pseudo Jahn-Teller versus Renner-Teller effects in the instability of linear molecules
Liu, Yang; Bersuker, Isaac B.; Zou, Wenli; Boggs, James E.
2010-11-01
It is shown that for linear molecules in degenerate states the Renner-Teller effect (RTE) is not the only (and not even the main) source of bending instability; the pseudo Jahn-Teller effect (PJTE) is most important in the bending. Numerical estimates demonstrate that π- σ interactions with a limited number of excited states does not solve the problem. For a Π term with two perturbations a general formula of combined RTE plus PJTE is derived which does not involve excited states explicitly. It shows that the PJTE lowers the curvature of the energy surface in the direction of bending and contributes also to its splitting. By means of ab initio calculations the contributions of the RTE and PJTE to the bending instability are estimated for HBF, HNN, HCO, BH 2, NH 2, and AlH 2 molecules. The PJTE influence is significantly larger than the RTE one. This result may be similarly important for nonlinear systems.
DEFF Research Database (Denmark)
List, Nanna Holmgaard; Coriani, Sonia; Kongsted, Jacob
2014-01-01
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...... 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...
Electron transport through a linear tri-quantum-dot molecule Aharonov-Bohm interference
Bai, Jiyuan; He, Zelong; Li, Li; Ye, Shujiang; Sun, Weimin
2017-09-01
Using the non-equilibrium Keldysh Green's function technique, electron transport properties through a two-terminal linear tri-quantum-dot molecule Aharonov-Bohm (A-B) interference are investigated. The conductance as a function of electron energy is numerically calculated. The influence of magnetic flux and interdot coupling strength on the conductance is researched. Fano resonances emerge in the conductance spectrum, and two bound states in the continuum form simultaneously when the interdot couplings take appropriate values. A conductance dip is observed and evolves into an antiresonance band with increasing magnetic flux. The system can be designed as a quantum switch by adjusting the intramolecular couplings.
Thermal transpiration and mechanocaloric effect. IV. Flow of a polyatomic gas in a cylindrical tube
Loyalka, S. K.; Storvick, T. S.; Lo, S. S.
1982-04-01
The phenomenological coefficients for mass and energy flows due to axial pressure and to temperature gradients on long capillary tubes containing a polyatomic gas at all degrees of rarefaction are reported. The Hansen and Morse polyatomic gas model of the linearized Wang Chang and Uhlenbeck equation was used together with Maxwell's diffuse scattering boundary conditions. The results are consistent with previous results obtained for flow between parallel plates. Experimental isothermal flow data are nearly quantitatively represented by the theory in the transition flow regime (Knudsen number ˜ 1). Experimental thermal transpiration effect ratios (Δp/p0)/(ΔT/T0) are also quantitatively represented for simple gases, argon, air, and carbon dioxide. Thermal transpiration measurements on sulfur dioxide correlate as the other gases but the transpiration effect ratio is not quantitatively given by the theory due to inadequacy of the Hansen-Morse model and the continuum theory for strongly polar gases.
Tellgren, Erik I; Fliegl, Heike
2013-10-28
In the present study a non-perturbative approach to ab initio calculations of molecules in strong, linearly varying, magnetic fields is developed. The use of London atomic orbitals (LAOs) for non-uniform magnetic fields is discussed and the standard rationale of gauge-origin invariance is generalized to invariance under arbitrary constant shifts of the magnetic vector potential. Our approach is applied to study magnetically induced anapole moments (or toroidal moments) and the related anapole susceptibilities for a test set of chiral and nonchiral molecules. For the first time numerical anapole moments are accessible on an ab initio level of theory. Our results show that the use of London atomic orbitals dramatically improves the basis set convergence also for magnetic properties related to non-uniform magnetic fields, at the cost that the Hellmann-Feynman theorem does not apply for a finite LAO basis set. It is shown that the mixed anapole susceptibility can be related to chirality, since its trace vanishes for an achiral molecule.
Gorman, C B; Marder, S R
1993-01-01
A computational method was devised to explore the relationship of charge separation, geometry, molecular dipole moment (mu), polarizability (alpha), and hyperpolariz-abilities (beta, gamma) in conjugated organic molecules. We show that bond-length alternation (the average difference in length between single and double bonds in the molecule) is a key structurally observable parameter that can be correlated with hyperpolarizabilities and is thus relevant to the optimization of molecules and materials. By using this method, the relationship of bond-length alternation, mu, alpha, beta, and gamma for linear conjugated molecules is illustrated, and those molecules with maximized alpha, beta, and gamma are described. PMID:11607441
Gorman, Christopher B.; Marder, Seth R.
1993-12-01
A computational method was devised to explore the relationship of charge separation, geometry, molecular dipole moment (μ), polarizability (α), and hyperpolariz-abilities (β, γ) in conjugated organic molecules. We show that bond-length alternation (the average difference in length between single and double bonds in the molecule) is a key structurally observable parameter that can be correlated with hyperpolarizabilities and is thus relevant to the optimization of molecules and materials. By using this method, the relationship of bond-length alternation, μ, α, β, and γ for linear conjugated molecules is illustrated, and those molecules with maximized α, β, and γ are described.
Interpreting linear support vector machine models with heat map molecule coloring
Directory of Open Access Journals (Sweden)
Rosenbaum Lars
2011-03-01
Full Text Available Abstract Background Model-based virtual screening plays an important role in the early drug discovery stage. The outcomes of high-throughput screenings are a valuable source for machine learning algorithms to infer such models. Besides a strong performance, the interpretability of a machine learning model is a desired property to guide the optimization of a compound in later drug discovery stages. Linear support vector machines showed to have a convincing performance on large-scale data sets. The goal of this study is to present a heat map molecule coloring technique to interpret linear support vector machine models. Based on the weights of a linear model, the visualization approach colors each atom and bond of a compound according to its importance for activity. Results We evaluated our approach on a toxicity data set, a chromosome aberration data set, and the maximum unbiased validation data sets. The experiments show that our method sensibly visualizes structure-property and structure-activity relationships of a linear support vector machine model. The coloring of ligands in the binding pocket of several crystal structures of a maximum unbiased validation data set target indicates that our approach assists to determine the correct ligand orientation in the binding pocket. Additionally, the heat map coloring enables the identification of substructures important for the binding of an inhibitor. Conclusions In combination with heat map coloring, linear support vector machine models can help to guide the modification of a compound in later stages of drug discovery. Particularly substructures identified as important by our method might be a starting point for optimization of a lead compound. The heat map coloring should be considered as complementary to structure based modeling approaches. As such, it helps to get a better understanding of the binding mode of an inhibitor.
DEFF Research Database (Denmark)
Madsen, Lars Bojer; Tolstikhin, Oleg I.; Morishita, Toru
2012-01-01
The recently developed weak-field asymptotic theory [ Phys. Rev. A 84 053423 (2011)] is applied to the analysis of tunneling ionization of a molecular ion (H2+), several homonuclear (H2, N2, O2) and heteronuclear (CO, HF) diatomic molecules, and a linear triatomic molecule (CO2) in a static...
DEFF Research Database (Denmark)
Hansen, Jonas Lerche; Holmegaard, Lotte; Nielsen, Jens Hedegaard
2012-01-01
The yield of strong-field ionization, by a linearly polarized probe pulse, is studied experimentally and theoretically as a function of the relative orientation between the laser field and the molecule. Experimentally, carbonyl sulphide (OCS), benzonitrile and naphthalene molecules are aligned in...
Zolot, Alexander M.
, whereby newly formed molecules leave the surface without equilibrating, and (ii) a partially accommodated fraction that shares vibrational, rotational, and translational energy with the liquid surface before returning to the gas phase. Finally, a velocity map ion imaging apparatus has been implemented to investigate reaction dynamics in crossed molecular beams. Resonantly enhanced multiphoton ionization (REMPI) results in rotational, vibrational, and electronic state selectivity. Velocity map imaging measurements provide differential cross sections and information about the internal energy distribution of the undetected collision partner.
Accurate Structure Parameters for Tunneling Ionization Rates of Gas-Phase Linear Molecules
Zhao, Song-Feng; Li, Jian-Ke; Wang, Guo-Li; Li, Peng-Cheng; Zhou, Xiao-Xin
2017-03-01
In the molecular Ammosov–Delone–Krainov (MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402], the ionization rate depends on the structure parameters of the molecular orbital from which the electron is removed. We determine systematically and tabulate accurate structure parameters of the highest occupied molecular orbital (HOMO) for 123 gas-phase linear molecules by solving time-independent Schrödinger equation with B-spline functions and molecular potentials which are constructed numerically using the modified Leeuwen–Baerends (LBα) model. Supported by National Natural Science Foundation of China under Grant Nos. 11664035, 11674268, 11465016, 11364038, 11364039, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001 and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province
The Time Evolution of the Surface Segregation of Hyperbranched Molecules from a Linear Matrix
Swader, Onome; Dadmun, Mark; Hutchings, Lian; Thompson, Richard
2010-03-01
Modification of a surface by the selective surface segregation of an additive in a mixture is a process with many commercial applications including biocompatibility, wettability, and anti-fouling in coatings. In a blend of branched and linear polymers, there exists an entropic driving force for the selective surface segregation of the branched polymer. Unfortunately, a systematic study of the impact of the branched copolymer structure on the dynamics and thermodynamics of this surface segregation is not currently available. Neutron reflectivity experiments that seek to fill this void have been completed and will be discussed. High molecular weight poly(styrene) (PS) hyperbranched molecules, hypermacs (HM) and dendrimacs (DM), with 10 % HM or DM and 90 % deuterated PS are the model systems studied. Reflectivity profiles for all blends were obtained as a function of annealing time from 30 minutes up to 48 hours.
Thankachan, P. P.; Narasimhan, P. T.
The electric field gradients (EFG) at the D. Li. N and O sites in the linear molecules LID, DF, DCN, DCCD. OCCF, N 2, CO and NCCN have been rigorously evaluated with the inclusion of all integrals using four different semi-empirical SCFMO methods with a view to assess their suitability for EFG calculations. The methods chosen are the CNDO/2 and INDO methods of Pople, a method using explicitly orthogonalised AO's and distinguishing s and p orbitals in the valence shell due to Nanda and Narasimhan (NN-INDO) and a reparametrisation of the same using Clementi-Raimondi exponents. It is found that orbital exponents play a crucial role in semi-empirical EFG calculations. Use of explicitly orthogonalised basis sets as in the NN-INDO schemes is seen to improve the EFG values for the first-row atoms. A few comments are made on population-based methods for EFG calculations.
A nomenclature for Λ-doublet levels in rotating linear molecules
Alexander, M. H.; Andresen, P.; Bacis, R.; Bersohn, R.; Comes, F. J.; Dagdigian, P. J.; Dixon, R. N.; Field, R. W.; Flynn, G. W.; Gericke, K.-H.; Grant, E. R.; Howard, B. J.; Huber, J. R.; King, D. S.; Kinsey, J. L.; Kleinermanns, K.; Kuchitsu, K.; Luntz, A. C.; McCaffery, A. J.; Pouilly, B.; Reisler, H.; Rosenwaks, S.; Rothe, E. W.; Shapiro, M.; Simons, J. P.; Vasudev, R.; Wiesenfeld, J. R.; Wittig, C.; Zare, R. N.
1988-08-01
It is proposed that the two Λ-doublet levels of linear molecules with nonzero electronic orbital angular momentum be labeled Λ(A') and Λ(A`), e.g., Π(A') and Π(A`) for Π states, etc., according to the following prescription: All series of levels in which the electronic wave function at high J is symmetric with reflection of the spatial coordinates of the electrons in the plane of rotation will be designated Λ(A') for all values of J, and all those for which the electronic wave function is antisymmetric with respect to reflection will be denoted Λ(A`). It is emphasized that this notation is meant to supplement, and not replace, the accepted spectroscopic e/f labeling and the parity quantum number. The utility of the Λ(A')/Λ(A`) notation is that it is of most relevance in the mechanistic interpretation of reactive or photodissociative processes involving open-shell molecules.
Influence of a magnetic field on the viscosity of a dilute gas consisting of linear molecules.
Hellmann, Robert; Vesovic, Velisa
2015-12-07
The viscomagnetic effect for two linear molecules, N2 and CO2, has been calculated in the dilute-gas limit directly from the most accurate ab initio intermolecular potential energy surfaces presently available. The calculations were performed by means of the classical trajectory method in the temperature range from 70 K to 3000 K for N2 and 100 K to 2000 K for CO2, and agreement with the available experimental data is exceptionally good. Above room temperature, where no experimental data are available, the calculations provide the first quantitative information on the magnitude and the behavior of the viscomagnetic effect for these gases. In the presence of a magnetic field, the viscosities of nitrogen and carbon dioxide decrease by at most 0.3% and 0.7%, respectively. The results demonstrate that the viscomagnetic effect is dominated by the contribution of the jj¯ polarization at all temperatures, which shows that the alignment of the rotational axes of the molecules in the presence of a magnetic field is primarily responsible for the viscomagnetic effect.
Xiao, Yunlong; Liu, Wenjian
2013-07-21
The relativistic molecular Hamiltonian written in the body-fixed frame of reference is the basis for high-precision calculations of spectroscopic parameters involving nuclear vibrations and/or rotations. Such a Hamiltonian that describes electrons fully relativistically and nuclei quasi-relativistically is just developed for semi-rigid nonlinear molecules [Y. Xiao and W. Liu, J. Chem. Phys. 138, 134104 (2013)]. Yet, the formulation should somewhat be revised for linear molecules thanks to some unusual features arising from the redundancy of the rotation around the molecular axis. Nonetheless, the resulting isomorphic Hamiltonian is rather similar to that for nonlinear molecules. Consequently, the relativistic formulation of nuclear spin-rotation (NSR) tensor for linear molecules is very much the same as that for nonlinear molecules. So is the relativistic mapping between experimental NSR and NMR.
Turning on single-molecule magnet behavior in a linear {Mn3} compound.
Habib, Fatemah; Brunet, Gabriel; Loiseau, Francis; Pathmalingam, Thushan; Burchell, Tara J; Beauchemin, André M; Wernsdorfer, Wolfgang; Clérac, Rodolphe; Murugesu, Muralee
2013-02-04
The synthesis, structure, and magnetic properties are reported for a new manganese compound with a mixed-valent {Mn(3)} core arranged in a linear fashion. The previously reported complex 1, [Mn(IV)(3)(dpo)(6)]·2MeCN, where H(2)dpo is (E)-1-hydroxy-1,1-diphenylpropan-2-one oxime, served as a starting point for the isolation of a {Mn(3)} compound with an analogous core arrangement through the reaction of Mn(OAc)(2)·4H(2)O, H(3)oxol ((E)-2,5-dihydroxy-2,5-dimethylhexan-3-one oxime), and NaOH in MeOH and MeCN. By using these reaction conditions, compound 2, Na[Mn(IV)(2)Mn(III)(Hoxol)(6)](n)·MeOH·H(2)O, was successfully isolated revealing a central Mn(III) ion thereby introducing structural and magnetic anisotropy to the system. The structure of 2 reveals linear trinuclear Mn(IV)-Mn(III)-Mn(IV) units connected through Na(+) ions forming a linear one-dimensional coordination polymer. The Jahn-Teller axes of each trinuclear unit are aligned parallel within the same chain and form a 75° angle between the two symmetry related chains. Magnetic susceptibility measurements of 1 and 2 in the temperature range 1.9-300 K reveal that only the reduced compound, 2, is a single-molecule magnet (SMM) largely due to the anisotropy introduced by the Jahn-Teller distortions on the Mn(III) ions, which effectively induce this magnet behavior. Weak antiferromagnetic interactions along the chains through the Na(+) cations lead to a modulation of the intrinsic properties of the Mn(IV)-Mn(III)-Mn(IV) SMMs.
Do Highly Excited Reactive Polyatomic Molecules Behave Ergodically.
1978-10-01
Chein . Phys., 61, 3114 (1974). 38. 14. 1. Hase, Private coninunication . 39. J. H. Parsons, K. Shobatake, V. 1. Lee and S. A. R ice , J. Chem. Phys...1402, 1416 (1973). - - 80. S. A. Safron, N. D. WeInstein, 0. R. Herschbach and 3. C. Tully, Chein . Phys. Lett., 12, 564 (1972). 81. 1. Donohue, 14. S
Birnbaum, G.; Borysow, A.; Buechele, A.
1993-01-01
The far infrared absorption of a CH4-N2 mixture was measured at 297, 195, and 162 K from 30 to 650/cm. The spectral invariants gamma1 and alpha1, proportional, respectively, to the zeroth and first spectral moments, due to bimolecular collisions between CH4 and N2 were obtained from these data and compared with theoretical values. The theory for collision-induced dipoles between a tetrahedral and a diatomic or symmetrical linear molecule includes contributions not previously considered. Whereas the theoretical values of gamma1 are only somewhat greater than experiment at all temperatures, the theoretical values of alpha1 are significantly lower than the experimental values. From the theoretical spectral moments for the various induced dipole components, the parameters of the BC shape were computed, and theoretical spectra were constructed. Good agreement was obtained at the lower frequencies, but with increasing frequencies the theoretical spectra were increasingly less intense than the experimental spectra. Although the accuracy of the theoretical results may suffer from the lack of a reliable potential function, it does not appear that this high frequency discrepancy can be removed by any conceivable modification in the potential.
Ultracold Molecules: Physics in the Quantum Regime
Energy Technology Data Exchange (ETDEWEB)
Doyle, John [Harvard Univ., Cambridge, MA (United States). Dept. of Physics
2014-11-17
Our research encompasses approaches to the trapping of diatomic molecules at low temperature plus the cooling and detection of polyatomic molecules in the kelvin temperature regime. We have cooled and trapped CaF and/or CaH molecules, loaded directly from a molecular beam. As part of this work, we are continuing to develop an important trapping technique, optical loading from a buffer-gas beam. This method was invented in our lab. We are also studying cold polyatomic molecules and their interactions with cold atoms.
Yumura, Takashi; Yamamoto, Wataru
2017-09-20
We employed density functional theory (DFT) calculations with dispersion corrections to investigate energetically preferred alignments of certain p,p'-dimethylaminonitrostilbene (DANS) molecules inside an armchair (m,m) carbon nanotube (n × DANS@(m,m)), where the number of inner molecules (n) is no greater than 3. Here, three types of alignments of DANS are considered: a linear alignment in a parallel fashion and stacking alignments in parallel and antiparallel fashions. According to DFT calculations, a threshold tube diameter for containing DANS molecules in linear or stacking alignments was found to be approximately 1.0 nm. Nanotubes with diameters smaller than 1.0 nm result in the selective formation of linearly aligned DANS molecules due to strong confinement effects within the nanotubes. By contrast, larger diameter nanotubes allow DANS molecules to align in a stacking and linear fashion. The type of alignment adopted by the DANS molecules inside a nanotube is responsible for their second-order non-linear optical properties represented by their static hyperpolarizability (β0 values). In fact, we computed β0 values of DANS assemblies taken from optimized n × DANS@(m,m) structures, and their values were compared with those of a single DANS molecule. DFT calculations showed that β0 values of DANS molecules depend on their alignment, which decrease in the following order: linear alignment > parallel stacking alignment > antiparallel stacking alignment. In particular, a linear alignment has a β0 value more significant than that of the same number of isolated molecules. Therefore, the linear alignment of DANS molecules, which is only allowed inside smaller diameter nanotubes, can strongly enhance their second-order non-linear optical properties. Since the nanotube confinement determines the alignment of DANS molecules, a restricted nanospace can be utilized to control their second-order non-linear optical properties. These DFT findings can assist in the design
Semiconductor-metal nanoparticle molecules: hybrid excitons and non-linear Fano effect
Zhang, Wei; Govorov, Alexander O.; Bryant, Garnett W.
2006-01-01
Modern nanotechnology opens the possibility of combining nanocrystals of various materials with very different characteristics in one superstructure. The resultant superstructure may provide new physical properties not encountered in homogeneous systems. Here we study theoretically the optical properties of hybrid molecules composed of semiconductor and metal nanoparticles. Excitons and plasmons in such a hybrid molecule become strongly coupled and demonstrate novel properties. At low inciden...
Banik, Subrata; Pal, Sourav; Prasad, M Durga
2008-10-07
Vibrational excited state energies have been calculated using vibrational coupled cluster linear response theory (CCLRT). The method has been implemented on formaldehyde and water molecule. Convergence studies have been shown with varying the cluster operator from S(4) to S(6) as well as the excitation operator from four bosons to six bosons. A good agreement with full configuration interaction results has been observed with S(6) truncation at coupled-cluster method level and six bosonic excitations at CCLRT level.
Hansen, Jonas L; Nielsen, Jens H; Stapelfeldt, Henrik; Dimitrovski, Darko; Madsen, Lars Bojer
2011-01-01
The yield of strong-field ionization, by a linearly polarized probe pulse, is studied experimentally and theoretically, as a function of the relative orientation between the laser field and the molecule. Experimentally, carbonyl sulfide, benzonitrile and naphthalene molecules are aligned in one or three dimensions before being singly ionized by a 30 fs laser pulse centered at 800 nm. Theoretically, we address the behaviour of these three molecules. We consider the degree of alignment and orientation and model the angular dependence of the total ionization yield by molecular tunneling theory accounting for the Stark shift of the energy level of the ionizing orbital. For naphthalene and benzonitrile the orientational dependence of the ionization yield agrees well with the calculated results, in particular the observation that ionization is maximized when the probe laser is polarized along the most polarizable axis. For OCS the observation of maximum ionization yield when the probe is perpendicular to the intern...
DEFF Research Database (Denmark)
Madsen, Lars Bojer; Tolstikhin, Oleg I.; Morishita, Toru
2012-01-01
electric field. The dependence of the ionization rate on the angle between the molecular axis and the field is determined by a structure factor for the highest occupied molecular orbital. This factor is calculated using a virtually exact discrete variable representation wave function for H2+, very accurate...... Hartree-Fock wave functions for the diatomics, and a Hartree-Fock quantum chemistry wave function for CO2. The structure factors are expanded in terms of standard functions and the associated structure coefficients, allowing the determination of the ionization rate for any orientation of the molecule......The recently developed weak-field asymptotic theory [ Phys. Rev. A 84 053423 (2011)] is applied to the analysis of tunneling ionization of a molecular ion (H2+), several homonuclear (H2, N2, O2) and heteronuclear (CO, HF) diatomic molecules, and a linear triatomic molecule (CO2) in a static...
Institute of Scientific and Technical Information of China (English)
LIANG ZHAO-YAN; FANG KUN; XUAN LI; HUANG XI-MIN; DING BAO-QUAN; LU RAN; ZHAO YING-YING
2000-01-01
A new technique to uniformly align liquid crystal molecules is presented.The technique is based on producing an anisotropic surface on the glass substrate coated with photo-polymers by photo-polymerization of linear polarized UVlight.The orientation of liquid crystal molecules is governed by the direction of the polarized vector of UV-light.Using this method,we have studied the photo-polymer PSi-CM aligning LC 6710A molecules.The liquid crystal microscopic texture between crossed polarizers,optical retardation from liquid crystal layers and electro-optical properties of twisted nematic liquid crystal display cell are obtained,which was prepared with one side -photo-alignment and the other siderebbed substrate.
Spectrum Generating Algebra for X$_{3}$ Molecules
Bijker, R; Leviatan, A
1995-01-01
A new spectrum generating algebra for a unified description of rotations and vibrations in polyatomic molecules is introduced. An application to nonlinear X$_3$ molecules shows that this model (i) incorporates exactly the relevant point group, (ii) provides a complete classification of oblate top states, and (iii) treats properly both degenerate and nondegenerate vibrations.
Murina, Ezequiel L.; Fernández-Prini, Roberto; Pastorino, Claudio
2017-08-01
We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface. In bulk water, their conformations up to dodecane are mainly extended. However, larger alkanes like eicosane present a more stable collapsed conformation as they approach bulk water. We have characterized the more probable configurations in all interface and bulk regions. The results obtained are of interest for the study of biomatter processes requiring the transfer of hydrophobic matter, especially chain-like molecules like LCAs, from gas to bulk aqueous systems through the interface.
Modeling Linear Molecules as Carriers of the λ5797 Å and λ6613 Å Diffuse Interstellar Bands
Huang, Jane; Oka, Takeshi
2014-06-01
Electronic transitions of polar linear molecules have been modeled and compared to archival high resolution spectra of the diffuse interstellar bands (DIBs) at 5797 and 6613 Å. These two bands are notable for fine structure that has most commonly been attributed to the rotational structure of electronic transitions of gas-phase molecules. Most strikingly, the 5797 DIB has a sharp, narrow center peak that is characteristic of the Q branch of parallel transitions with non-zero Λ. This work is also motivated by Oka et al.'s analysis of the anomalously extended redward tails seen in certain DIBs toward Herschel 36, which are reminiscent of electronic transitions of polar linear molecules at high radiative temperatures. The determination of rotational distributions, which includes radiative and collisional effects, is based on the model presented in the earlier work. Thus far, the most promising models are a ^2Π ← ^2Π transition for the 5797 DIB and a ^2Δ ← ^2Π transition for the 6613 DIB, with the effects of spin-orbit coupling examined in each case. The degree of consistency of these transitions with respect to the anomalous DIBs toward Herschel 36 is also discussed. Sarre, P. J., Miles, J. R., Kerr, T. H. et al. 1995, MNRAS, 177L 41 Oka, T., Welty, D. E., Johnson, S. et al. 2013, ApJ, 773 42
Renato, Lemus; María del Mar, Estezez-Fregozo
2017-06-01
An approach to connect the su(3) dynamical group- used to describe the bending modes of linear molecules- with configuration space is discussed. The SU(3) group may be seen as a consequence of adding a scalar boson to the SU(2) space of two degenerate harmonic oscillators. The resulting SU(3) group becomes the dynamical group for the bending degrees of freedom of linear molecules, but the connection to configuration space is not obvious. This work aims at providing this connection. Our approach is based on the basis of establishing a mapping between the algebraic and configuration states. An arbitrary operator in configuration space is then expanded in terms of generators of the dynamical algebra. The coefficients are determined through a minimization procedure and given in terms of matrix elements defined in configuration space. As an application we consider the vibrational description of the bending modes of the acetylene molecule, where the force constants are estimated in the framework of the U(3) × U(3) model.
Liu, Kunlong; Barth, Ingo
2016-10-01
We derive the analytical formula of the ratio of the ionization rates of degenerate valence π± orbitals of prealigned linear molecules in strong circularly polarized (CP) laser fields. Interestingly, our theory shows that the ionization ratio for molecular orbitals with opposite azimuthal quantum numbers ±|m | (e.g., π±) is identical to that for atomic orbitals with the same ±|m | (e.g., p±). In general, the electron counter-rotating to the CP laser field tunnels more easily, not only for atoms but also for linear molecules. Our theoretical predictions are then verified by numerically solving the three-dimensional time-dependent Schrödinger equation for the ionization of the prealigned nitric oxide (NO) molecule in strong CP laser fields. Due to the spin-orbital coupling in the electronic ground state of NO and the sensitivity of ionization to the sense of electron rotation, the ionization of NO in CP fields can produce spin-polarized photoelectrons with high controllability of spin polarization up to 100 % .
A Linear Tetranuclear Dysprosium(III) Compound Showing Single-Molecule Magnet Behavior
Energy Technology Data Exchange (ETDEWEB)
Ke, Hongshan; Xu, Gong Feng; Guo, Yun-Nan; Gamez, Patrick; Beavers, Christine M; Teat, Simon J; Tang, Jinkui
2010-04-20
Although magnetic measurements reveal a single-relaxation time for a linear tetranuclear Dy(III) compound, the wide distribution of the relaxation time observed clearly suggests the presence of two slightly different anisotropic centres, therefore opening new avenues for investigating the relaxation dynamics of lanthanide aggregates.
Electrostatic forces and the frequency spectrum of a monolayer solid of linear molecules on graphite
DEFF Research Database (Denmark)
Hansen, Flemming Yssing; Bruch, Ludwig Walter; Roosevelt, S. E.
1992-01-01
Electrostatic energies which arise from aspherical atomic charge distributions in a graphite substrate are included in the modeling of a commensurate molecular monolayer. For the planar (two-in) herringbone lattice of nitrogen on graphite such terms may resolve a discrepancy with experimental data...... for the Brillouin-zone-center frequency gap. The treatment includes consideration of a generalized (two-out) herringbone lattice and of the screening by the graphite of electrostatic fields from the multipole moments of adsorbed molecules. A small adjustment to a previous approximation for the latter process leads...... to stable modeling of the commensurate monolayer solid of carbon monoxide on graphite....
Inversed linear dichroism in F K-edge NEXAFS spectra of fluorinated planar aromatic molecules
DEFF Research Database (Denmark)
de Oteyza, D. G.; Sakko, A.; El-Sayed, A.
2012-01-01
orbitals with significant density of states on the fluorine atoms show different symmetry from those mainly located on C and N atoms. As a result, the angle-dependent linear dichroism in NEXAFS F K-edge spectra is inversed with respect to that in the C and N K-edges. In addition, the significant overlap...... in energy of π* and σ* orbitals throughout the F K-edge spectrum hampers its use for analysis of molecular orientations from angle-dependent NEXAFS measurements....
Ejection of Coulomb Crystals from a Linear Paul Ion Trap for Ion-Molecule Reaction Studies.
Meyer, K A E; Pollum, L L; Petralia, L S; Tauschinsky, A; Rennick, C J; Softley, T P; Heazlewood, B R
2015-12-17
Coulomb crystals are being increasingly employed as a highly localized source of cold ions for the study of ion-molecule chemical reactions. To extend the scope of reactions that can be studied in Coulomb crystals-from simple reactions involving laser-cooled atomic ions, to more complex systems where molecular reactants give rise to multiple product channels-sensitive product detection methodologies are required. The use of a digital ion trap (DIT) and a new damped cosine trap (DCT) are described, which facilitate the ejection of Coulomb-crystallized ions onto an external detector for the recording of time-of-flight (TOF) mass spectra. This enables the examination of reaction dynamics and kinetics between Coulomb-crystallized ions and neutral molecules: ionic products are typically cotrapped, thus ejecting the crystal onto an external detector reveals the masses, identities, and quantities of all ionic species at a selected point in the reaction. Two reaction systems are examined: the reaction of Ca(+) with deuterated isotopologues of water, and the charge exchange between cotrapped Xe(+) with deuterated isotopologues of ammonia. These reactions are examples of two distinct types of experiment, the first involving direct reaction of the laser-cooled ions, and the second involving reaction of sympathetically-cooled heavy ions to form a mixture of light product ions. Extensive simulations are conducted to interpret experimental results and calculate optimal operating parameters, facilitating a comparison between the DIT and DCT approaches. The simulations also demonstrate a correlation between crystal shape and image shape on the detector, suggesting a possible means for determining crystal geometry for nonfluorescing ions.
CALCULATIONS OF ION TRAJECTORIES AT MAGNETOPLASMA SEPARATION AND EXPERIMENTS WITH POLYATOMIC GASES
Directory of Open Access Journals (Sweden)
Vladimir Yuferov
2017-02-01
Full Text Available Calculated trajectories of ions with different masses, indicating the possibility of a mixture separation, are obtained. Comparative experiments for plasma of monatomic and polyatomic gases (Ar, N2, CO2, upon combination of pulsed discharge with a stationary one with incandescent cathode, are carried out. The oscillograms of discharge current and voltage at low emission currents and a constant energy input show that energy is spent on other processes different from ionization. With an increase of emission current, the nonlinear character of the discharge current and voltage, which may be indicative of the role of dissociation and vibrational levels in energy consumption, is observed. In addition, there is connection between the number of atoms in molecule and the values of maximum discharge current and the pressure of injected gas.
Institute of Scientific and Technical Information of China (English)
SAIZ Andrés
2011-01-01
In this study, we found regular behavior, from a statistical point of view, in the intensities of rotational spectra for several organic and inorganic molecules at room temperature. Non-linear molecules, for which a common intensity behavior was derived, were especially interesting. We provided theoretical support for the obtained results based on the Boltzmann distribution. Boltzmann power laws were used to reproduce the statistical behavior of the intensities from the spectra of linear and non-linear molecules. We only used statistical arguments and no specific details of any molecule were used. Therefore, these results are applicable to a large class of atoms and molecules and the model is valid when considering similar conditions to those used in this study.
How linear molecules resist to shear:the origin of nanoscale friction
Institute of Scientific and Technical Information of China (English)
Linmao; QIAN; G.; Luengo; E.; Perez
2004-01-01
Friction force measurements between smooth surfaces across two layers of linear alkanes over five decades of speeds are presented. A maximum friction dissipation is observed at a characteristic speed. The behaviour is described by a new approach: the formation and destruction of molecular bridges between confined alkane layers. The bridges interdigitated between the layers exhibit a thermally activated resistance to shear.An analytical model involving activation barriers accounts for the overall behaviour of the forces over four decades of speed. This first simple semi-quantitative description sheds new light on the subtle mechanisms of friction at the nanoscale level and shows how the molecular length influences the tribological properties of the liquid.
Mineo, Hirobumi; Yamaki, Masahiro; Kim, Gap-Sue; Teranishi, Yoshiaki; Lin, Sheng Hsien; Fujimura, Yuichi
2016-09-29
A new laser-control scenario of unidirectional π-electron rotations in a low-symmetry aromatic ring molecule having no degenerate excited states is proposed. This scenario is based on dynamic Stark shifts of two relevant excited states using two linearly polarized stationary lasers. Each laser is set to selectively interact with one of the two electronic states, the lower and higher excited states are shifted up and down with the same rate, respectively, and the two excited states become degenerate at their midpoint. One of the four control parameters of the two lasers, i.e. two frequencies and two intensities, determines the values of all the other parameters. The direction of π-electron rotations, clockwise or counter-clockwise rotation, depends on the sign of the relative phase of the two lasers at the initial time. An analytical expression for the time-dependent expectation value of the rotational angular momentum operator is derived using the rotating wave approximation (RWA). The control scenario depends on the initial condition of the electronic states. The control scenario with the ground state as the initial condition was applied to toluene molecules. The derived time-dependent angular momentum consists of a train of unidirectional angular momentum pulses. The validity of the RWA was checked by numerically solving the time-dependent Schrödinger equation. The simulation results suggest an experimental realization of the induction of unidirectional π-electron rotations in low-symmetry aromatic ring molecules without using any intricate quantum-optimal control procedure. This may open up an effective generation method of ring currents and current-induced magnetic fields in biomolecules such as amino acids having aromatic ring molecules for searching their interactions.
Liu, Fupin; Wang, Song; Gao, Cong‐Li; Deng, Qingming; Zhu, Xianjun; Kostanyan, Aram; Westerström, Rasmus; Jin, Fei
2017-01-01
Abstract Fused‐pentagons results in an increase of local steric strain according to the isolated pentagon rule (IPR), and for all reported non‐IPR clusterfullerenes multiple (two or three) metals are required to stabilize the strained fused‐pentagons, making it difficult to access the single‐atom properties. Herein, we report the syntheses and isolations of novel non‐IPR mononuclear clusterfullerenes MNC@C76 (M=Tb, Y), in which one pair of strained fused‐pentagon is stabilized by a mononuclear cluster. The molecular structures of MNC@C76 (M=Tb, Y) were determined unambiguously by single‐crystal X‐ray diffraction, featuring a non‐IPR C 2v(19138)‐C76 cage entrapping a nearly linear MNC cluster, which is remarkably different from the triangular MNC cluster within the reported analogous clusterfullerenes based on IPR‐obeying C82 cages. The TbNC@C76 molecule is found to be a field‐induced single‐molecule magnet (SMM). PMID:28079303
Long-range interactions between an atom in its ground S state and an open-shell linear molecule
Skomorowski, Wojciech
2010-01-01
Theory of long-range interactions between an atom in its ground S state and a linear molecule in a degenerate state with a non-zero projection of the electronic orbital angular momentum is presented. It is shown how the long-range coefficients can be related to the first and second-order molecular properties. The expressions for the long-range coefficients are written in terms of all components of the static and dynamic multipole polarizability tensor, including the nonadiagonal terms connecting states with the opposite projection of the electronic orbital angular momentum. It is also shown that for the interactions of molecules in excited states that are connected to the ground state by multipolar transition moments additional terms in the long-range induction energy appear. All these theoretical developments are illustrated with the numerical results for systems of interest for the sympathetic cooling experiments: interactions of the ground state Rb($^2$S) atom with CO($^3\\Pi$), OH($^2\\Pi$), NH($^1\\Delta$),...
Zhang, Shanshan; Niu, Qingfen; Sun, Tao; Li, Yang; Li, Tianduo; Liu, Haixia
2017-08-05
A novel linear A-π-D-π-A-type organic small molecule Ph2(PDPP)2 consisting diketopyrrolopyrrole (DPP) as acceptor unit, biphenylene as donor unit and acetylene unit as π-linkage has been successfully designed and synthesized. Its corresponding thermal, photophysical and electrochemical properties as well as the photoinduced charge-separation process were investigated. Ph2(PDPP)2 exhibits high thermal stability and it can be soluble in common organic solvents such as chloroform and tetrahydrofuran. The photophysical properties show that DPP2Ph2 harvests sunlight over the entire visible spectrum range in the thin-film state (300-800nm). DPP2Ph2 has lower band gaps and appropriate energy levels to satisfy the requirement of solution-processable organic solar cells. The efficient photoinduced charge separation process was clearly observed between DPP2Ph2 with PC61BM and the Ksv value was found to be as high as 2.13×10(4)M(-1). Therefore, these excellent properties demonstrate that the designed A-π-D-π-A-type small molecule Ph2(PDPP)2 is the prospective candidate as donor material for organic photovoltaic material. Copyright © 2017 Elsevier B.V. All rights reserved.
Hölzel, Ralph; Gajovic-Eichelmann, Nenad; Bier, Frank F
2003-05-01
The ability to control molecules at a resolution well below that offered by photolithography has gained much interest recently. DNA is a promising candidate for this task since it offers excellent specificity in base-pairing combined with addressability at the nanometer scale. New applications in biosensing, e.g. interaction analysis at the single molecule level, or nanobiotechnology, e.g. ultradense DNA microarrays, have been devised that rely on stretched DNA bridges. The basic technology required is the ability to deposit spatially defined, stretched DNA-bridges between anchoring structures on surfaces. In this paper we present two techniques for spanning 2 microm long dsDNA bridges between neighboring interdigitated electrodes (IDEs). The extended DNA used was linearized M13 dsDNA (M13mp18 7231 bp, ca. 2.5 microm length), either unmodified, or with chemical modifications at both ends. The first approach is based on the dielectrophoretic (DEP) concentration and alignment of linearized wild-type dsDNA. IDEs with 1.7 microm spacing are driven with an AC voltage around 1 MHz leading to field strengths in the order of 1 MV m(-1). The dsDNA is polarized and linearized by the force field and accumulates in the gap between two neighboring electrodes. This process is reversible and was visualized by fluorescence staining of M13 DNA using PicoGreen, as intercalating dye. The resulting dsDNA bridges and their orientation are discernible under the fluorescence microscope using fluorescent particles of different color. The particles are tagged with sequence specific peptide nucleic acid (PNA) probes that bind to the DNA double strand at specific sites. The second approach is based on asymmetric electrochemical modification of a gold IDE with 2.0 microm spacings followed by spontaneous or stimulated deposition of a chemically modified M13-DNA. One side of the IDE was selectively coated with streptavidin by electropolymerization of a novel hydrophilic conductive polymer in
Krantzman, K D; Delcorte, A; Garrison, B J
2003-01-01
Our previous molecular dynamics simulations on initial test systems have laid the foundation for understanding some of the effects of polyatomic bombardment. In this paper, we describe simulations of the bombardment of a more realistic model system, an overlayer of sec-butyl-terminated polystyrene tetramers on a Ag left brace 1 1 1 right brace substrate. We have used this model system to study the bombardment with Xe and SF sub 5 projectiles at kinetic energies ranging from 0.50 to 5.0 keV. SF sub 5 sputters more molecules than Xe, but a higher percentage of these are damaged rather than ejected intact when the bombarding energy is greater than 0.50 keV. Therefore, at energies comparable to experimental values, the efficiency, measured as the yield-to-damage ratio, is greater with Xe than SF sub 5. Stable and intact molecules are generally produced by upward moving substrate atoms, while fragments are produced by the upward and lateral motion of reflected projectile atoms and fragments from the target molecul...
SPECTRUM-GENERATING ALGEBRA FOR X(3) MOLECULES
DIEPERINK, AEL; LEVIATAN, A
1995-01-01
A spectrum-generating algebra for a unified description of rotations and vibrations in polyatomic molecules is introduced. An application to nonlinear X(3) molecules shows that this model (i) incorporates exactly the relevant point group, (ii) provides a complete classification of oblate top states,
SPECTRUM-GENERATING ALGEBRA FOR X(3) MOLECULES
DIEPERINK, AEL; LEVIATAN, A
1995-01-01
A spectrum-generating algebra for a unified description of rotations and vibrations in polyatomic molecules is introduced. An application to nonlinear X(3) molecules shows that this model (i) incorporates exactly the relevant point group, (ii) provides a complete classification of oblate top states,
Investigations into the origins of polyatomic ions in inductively coupled plasma-mass spectrometry
Energy Technology Data Exchange (ETDEWEB)
McIntyre, Sally M. [Iowa State Univ., Ames, IA (United States)
2010-01-01
An inductively coupled plasma-mass spectrometer (ICP-MS) is an elemental analytical instrument capable of determining nearly all elements in the periodic table at limits of detection in the parts per quadrillion and with a linear analytical range over 8-10 orders of magnitude. Three concentric quartz tubes make up the plasma torch. Argon gas is spiraled through the outer tube and generates the plasma powered by a looped load coil operating at 27.1 or 40.6 MHz. The argon flow of the middle channel is used to keep the plasma above the innermost tube through which solid or aqueous sample is carried in a third argon stream. A sample is progressively desolvated, atomized and ionized. The torch is operated at atmospheric pressure. To reach the reduced pressures of mass spectrometers, ions are extracted through a series of two, approximately one millimeter wide, circular apertures set in water cooled metal cones. The space between the cones is evacuated to approximately one torr. The space behind the second cone is pumped down to, or near to, the pressure needed for the mass spectrometer (MS). The first cone, called the sampler, is placed directly in the plasma plume and its position is adjusted to the point where atomic ions are most abundant. The hot plasma gas expands through the sampler orifice and in this expansion is placed the second cone, called the skimmer. After the skimmer traditional MS designs are employed, i.e. quadrupoles, magnetic sectors, time-of-flight. ICP-MS is the leading trace element analysis technique. One of its weaknesses are polyatomic ions. This dissertation has added to the fundamental understanding of some of these polyatomic ions, their origins and behavior. Although mainly continuing the work of others, certain novel approaches have been introduced here. Chapter 2 includes the first reported efforts to include high temperature corrections to the partition functions of the polyatomic ions in ICP-MS. This and other objections to preceeding
Park, G Barratt
2014-10-07
Franck-Condon vibrational overlap integrals for the Ã Au1-X̃ 1Σg+ transition in acetylene have been calculated in full dimension in the harmonic normal mode basis. The calculation uses the method of generating functions first developed for polyatomic Franck-Condon factors by Sharp and Rosenstock [J. Chem. Phys. 41(11), 3453-3463 (1964)], and previously applied to acetylene by Watson [J. Mol. Spectrosc. 207(2), 276-284 (2001)] in a reduced-dimension calculation. Because the transition involves a large change in the equilibrium geometry of the electronic states, two different types of corrections to the coordinate transformation are considered to first order: corrections for axis-switching between the Cartesian molecular frames and corrections for the curvilinear nature of the normal modes at large amplitude. The angular factor in the wavefunction for the out-of-plane component of the trans bending mode, ν4(″), is treated as a rotation, which results in an Eckart constraint on the polar coordinates of the bending modes. To simplify the calculation, the other degenerate bending mode, ν5(″), is integrated in the Cartesian basis and later transformed to the constrained polar coordinate basis, restoring the conventional v and l quantum numbers. An updated Ã-state harmonic force field obtained recently in the R. W. Field research group is evaluated. The results for transitions involving the gerade vibrational modes are in qualitative agreement with experiment. Calculated results for transitions involving ungerade modes are presented in Paper II of this series [G. B. Park, J. H. Baraban, and R. W. Field, "Full dimensional Franck-Condon factors for the acetylene Ã Au1-X̃ 1Σg+ transition. II. Vibrational overlap factors for levels involving excitation in ungerade modes," J. Chem. Phys. 141, 134305 (2014)].
Stretching and bending dynamics in triatomic ultralong-range Rydberg molecules
Fey, Christian; Schmelcher, Peter
2016-01-01
We investigate polyatomic ultralong-range Rydberg molecules consisting of three ground state atoms bound to a Rydberg atom via $s$- and $p$-wave interactions. By employing the finite basis set representation of the unperturbed Rydberg electron Green's function we reduce the computational effort to solve the electronic problem substantially. This method is subsequently applied to determine the potential energy surfaces of triatomic systems in electronic $s$- and $p$-Rydberg states. Their molecular geometry and resulting vibrational structure are analyzed within an adiabatic approach that separates the vibrational bending and stretching dynamics. This procedure yields information on the radial and angular arrangement of the nuclei and indicates in particular that kinetic couplings between bending and stretching modes induce a linear structure in triatomic $l=0$ ultralong-range Rydberg molecules.
Stretching and bending dynamics in triatomic ultralong-range Rydberg molecules
Fey, Christian; Kurz, Markus; Schmelcher, Peter
2016-07-01
We investigate polyatomic ultralong-range Rydberg molecules consisting of three ground-state atoms bound to a Rydberg atom via s - and p -wave interactions. By employing the finite basis set representation of the unperturbed Rydberg electron Green's function we reduce the computational effort to solve the electronic problem substantially. This method is subsequently applied to determine the potential energy surfaces of triatomic systems in electronic s - and p -Rydberg states. Their molecular geometry and resulting vibrational structure are analyzed within an adiabatic approach that separates the vibrational bending and stretching dynamics. This procedure yields information on the radial and angular arrangement of the nuclei and indicates in particular that kinetic couplings between bending and stretching modes induce a linear structure in triatomic l =0 ultralong-range Rydberg molecules.
Collisions between low-energy electrons and small polyatomic targets of biological relevance
Hargreaves, Leigh
2016-05-01
Over the last decade, cross section measurements and calculations for DNA prototype molecules have received significant attention from the collisions community, due to the potential applications of this data in modelling electron transport through biological matter with a view to improving radiation dosimetry. Such data are additionally interesting from a fundamental aspect, as small carbon-based molecules are ideal targets for considering effects including target conformation, long-range dynamical interactions and coupling effects between the various degrees of freedom on the scattering properties of the target. At the California State University Fullerton, we have made a series of measurements of the elastic, vibrationally inelastic and electronically inelastic cross sections for a variety of small polyatomic targets, including water and the basic alcohols, ethylene, toluene and several fluorinated alkanes. These processes are important in a range of applications, primarily for modelling electron transport and thermalization, and energy deposition to a biological media. The data were obtained using a high resolution electron energy-loss spectrometer, operating in a crossed beam configuration with a moveable aperture gas source. The gas source design facilitates both an expedient and highly accurate method of removing background signal, and removes uncertainties from the data due to uncertainties in the beam profile. We have also performed scattering calculations employing the Schwinger Multichannel method, in collaboration with the California institute of technology, to compare with our measurements. In this talk, I will present an overview of our recent data and future research plans.
Investigations into the origins of polyatomic ions in inductively coupled plasma-mass spectrometry
Energy Technology Data Exchange (ETDEWEB)
McIntyre, Sally M. [Iowa State Univ., Ames, IA (United States)
2010-01-01
An inductively coupled plasma-mass spectrometer (ICP-MS) is an elemental analytical instrument capable of determining nearly all elements in the periodic table at limits of detection in the parts per quadrillion and with a linear analytical range over 8-10 orders of magnitude. Three concentric quartz tubes make up the plasma torch. Argon gas is spiraled through the outer tube and generates the plasma powered by a looped load coil operating at 27.1 or 40.6 MHz. The argon flow of the middle channel is used to keep the plasma above the innermost tube through which solid or aqueous sample is carried in a third argon stream. A sample is progressively desolvated, atomized and ionized. The torch is operated at atmospheric pressure. To reach the reduced pressures of mass spectrometers, ions are extracted through a series of two, approximately one millimeter wide, circular apertures set in water cooled metal cones. The space between the cones is evacuated to approximately one torr. The space behind the second cone is pumped down to, or near to, the pressure needed for the mass spectrometer (MS). The first cone, called the sampler, is placed directly in the plasma plume and its position is adjusted to the point where atomic ions are most abundant. The hot plasma gas expands through the sampler orifice and in this expansion is placed the second cone, called the skimmer. After the skimmer traditional MS designs are employed, i.e. quadrupoles, magnetic sectors, time-of-flight. ICP-MS is the leading trace element analysis technique. One of its weaknesses are polyatomic ions. This dissertation has added to the fundamental understanding of some of these polyatomic ions, their origins and behavior. Although mainly continuing the work of others, certain novel approaches have been introduced here. Chapter 2 includes the first reported efforts to include high temperature corrections to the partition functions of the polyatomic ions in ICP-MS. This and other objections to preceeding
Tscherbul, T V; Grinev, T A; Yu, H-G; Dalgarno, A; Kłos, Jacek; Ma, Lifang; Alexander, Millard H
2012-09-14
We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wave function. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH(2)(X(3)B(1))] with He atoms. To this end, two accurate three-dimensional potential energy surfaces (PESs) of the He-CH(2)(X(3)B(1)) complex are developed using the state-of-the-art coupled-cluster method including single and double excitations along with a perturbative correction for triple excitations and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH(2), CHD, and CD(2) molecules with He atoms occurs at a much slower rate than elastic scattering over a large range of temperatures (1 μK-1 K) and magnetic fields (0.01-1 T), suggesting excellent prospects for cryogenic helium buffer-gas cooling of ground-state ortho-CH(2)(X(3)B(1)) molecules in a magnetic trap. Furthermore, we find that ortho-CH(2) undergoes collision-induced spin relaxation much more slowly than para-CH(2), which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules.
Tscherbul, T. V.; Grinev, T. A.; Yu, H.-G.; Dalgarno, A.; Kłos, Jacek; Ma, Lifang; Alexander, Millard H.
2012-09-01
We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wave function. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH_2(tilde{X}^3B_1)] with He atoms. To this end, two accurate three-dimensional potential energy surfaces (PESs) of the He-CH_2(tilde{X}^3B_1) complex are developed using the state-of-the-art coupled-cluster method including single and double excitations along with a perturbative correction for triple excitations and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH2, CHD, and CD2 molecules with He atoms occurs at a much slower rate than elastic scattering over a large range of temperatures (1 μK-1 K) and magnetic fields (0.01-1 T), suggesting excellent prospects for cryogenic helium buffer-gas cooling of ground-state ortho-CH_2(tilde{X}^3B_1) molecules in a magnetic trap. Furthermore, we find that ortho-CH2 undergoes collision-induced spin relaxation much more slowly than para-CH2, which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules.
Wu, Fangqin; Liu, Wenjian; Zhang, Yong; Li, Zhendong
2011-11-08
To circumvent the cubic scaling and convergence difficulties encountered in the standard top-down localization of the global canonical molecular orbitals (CMOs), a bottom-up localization scheme is proposed based on the idea of "from fragments to molecule". That is, the global localized MOs (LMOs), both occupied and unoccupied, are to be synthesized from the primitive fragment LMOs (pFLMOs) obtained from subsystem calculations. They are orthonormal but are still well localized on the parent fragments of the pFLMOs and can hence be termed as "fragment LMOs" (FLMOs). This has been achieved by making use of two important factors. Physically, it is the transferability of the locality of the fragments that serves as the basis. Mathematically, it is the special block-diagonalization of the Kohn-Sham matrix that allows retention of the locality: The occupied-occupied and virtual-virtual diagonal blocks are only minimally modified when the occupied-virtual off-diagonal blocks are annihilated. Such a bottom-up localization scheme is applicable to systems composed of all kinds of chemical bonds. It is then shown that, by a simple prescreening of the particle-hole pairs, the FLMO-based time-dependent density functional theory (TDDFT) can achieve linear scaling with respect to the system size, with a very small prefactor. As a proof of principle, representative model systems are taken as examples to demonstrate the accuracy and efficiency of the algorithms. As both the orbital picture and integral number of electrons are retained, the FLMO-TDDFT offers a clear characterization of the nature of the excited states in line with chemical/physical intuition.
Garrett, Kerry
Organic electro-optic (OEO) materials integrated into silicon-organic hybrid (SOH) devices afford significant improvements in size, weight, power, and bandwidth (SWAP) performance of integrated electronic/photonic systems critical for current and next generation telecommunication, computer, sensor, transportation, and defense technologies. Improvement in molecular first hyperpolarizability, and in turn electro-optic activity, is crucial to further improvement in the performance of SOH devices. The timely preparation of new chromophores with improved molecular first hyperpolarizability requires theoretical guidance; however, common density functional theory (DFT) methods often perform poorly for optical properties in systems with substantial intramolecular charge transfer character. The first part of this dissertation describes the careful evaluation of popular long-range correction (LC) and range-separated hybrid (RSH) density functional theory (DFT) for definition of structure/function relationships crucial for the optimization of molecular first hyperpolarizability, beta. In particular, a benchmark set of well-characterized OEO chromophores is used to compare calculated results with the corresponding experimentally measured linear and nonlinear optical properties; respectively, the wavelength of the peak one-photon absorption energy, lambdamax, and beta. A goal of this work is to systematically determine the amount of exact exchange in LC/RSH-DFT methods required for accurately computing these properties for a variety OEO chromophores. High-level electron correlation (post-Hartree-Fock) methods are also investigated and compared with DFT. Included are results for the computation of beta using second-order Moller-Plesset perturbation theory (MP2) and the double-hybrid method, B2PLYP. The second part of this work transitions from single-molecule studies to computing bulk electronic and nonlinear optical properties of molecular crystals and isotropic ensembles of a
Long-range effects in electron scattering by polar molecules
Fabrikant, Ilya I.
2016-11-01
We review long-range effects in electron collisions with polar molecules, starting with elastic scattering. We then go to rotationally and vibrationally inelastic processes and dissociative electron attachment. The last two are strongly affected by vibrational Feshbach resonances which have been observed and described theoretically in many systems from simple diatomic molecules to more complex polyatomics, biologically relevant molecules, and van der Waals clusters. We then review environmental effects which include electron interaction with molecules adsorbed on surfaces and molecules in cluster environments. We concentrate on physics rather than on listing results of ab initio calculations. With increasing complexity of targets and processes model approaches become more relevant. We demonstrate their success in the theoretical description of electron attachment to polyatomic molecules and to molecules in complex environments.
Low fragment polyatomic molecular ion source by using permanent magnets.
Takeuchi, Mitsuaki; Hayashi, Kyouhei; Imanaka, Kousuke; Ryuto, Hiromichi; Takaoka, Gikan H
2014-02-01
Electron-ionization-type polyatomic molecular ion source with low fragment was developed by using a pair of ring-shaped Sm-Co magnets. The magnets were placed forward and backward side of ionization part to confine electrons extracted from a thermionic cathode. Calculated electron trajectory of the developed ion source was 20 times longer than that of an ordinary outer filament configuration that has no magnetic confinement. Mass spectra of the molecular ions generated from n-tetradecane (C14H30) gas exhibited 4 times larger intensity than that of the ordinary configuration in a range of mass/charge from 93 to 210 u. This indicates that suppression of fragment ion was obtained by increase of low energy electrons resulted from the electron confinement.
Direct simulation Monte Carlo modeling of relaxation processes in polyatomic gases
Pfeiffer, M.; Nizenkov, P.; Mirza, A.; Fasoulas, S.
2016-02-01
Relaxation processes of polyatomic molecules are modeled and implemented in an in-house Direct Simulation Monte Carlo code in order to enable the simulation of atmospheric entry maneuvers at Mars and Saturn's Titan. The description of rotational and vibrational relaxation processes is derived from basic quantum-mechanics using a rigid rotator and a simple harmonic oscillator, respectively. Strategies regarding the vibrational relaxation process are investigated, where good agreement for the relaxation time according to the Landau-Teller expression is found for both methods, the established prohibiting double relaxation method and the new proposed multi-mode relaxation. Differences and applications areas of these two methods are discussed. Consequently, two numerical methods used for sampling of energy values from multi-dimensional distribution functions are compared. The proposed random-walk Metropolis algorithm enables the efficient treatment of multiple vibrational modes within a time step with reasonable computational effort. The implemented model is verified and validated by means of simple reservoir simulations and the comparison to experimental measurements of a hypersonic, carbon-dioxide flow around a flat-faced cylinder.
Direct simulation Monte Carlo modeling of relaxation processes in polyatomic gases
Energy Technology Data Exchange (ETDEWEB)
Pfeiffer, M., E-mail: mpfeiffer@irs.uni-stuttgart.de; Nizenkov, P., E-mail: nizenkov@irs.uni-stuttgart.de; Mirza, A., E-mail: mirza@irs.uni-stuttgart.de; Fasoulas, S., E-mail: fasoulas@irs.uni-stuttgart.de [Institute of Space Systems, University of Stuttgart, Pfaffenwaldring 29, D-70569 Stuttgart (Germany)
2016-02-15
Relaxation processes of polyatomic molecules are modeled and implemented in an in-house Direct Simulation Monte Carlo code in order to enable the simulation of atmospheric entry maneuvers at Mars and Saturn’s Titan. The description of rotational and vibrational relaxation processes is derived from basic quantum-mechanics using a rigid rotator and a simple harmonic oscillator, respectively. Strategies regarding the vibrational relaxation process are investigated, where good agreement for the relaxation time according to the Landau-Teller expression is found for both methods, the established prohibiting double relaxation method and the new proposed multi-mode relaxation. Differences and applications areas of these two methods are discussed. Consequently, two numerical methods used for sampling of energy values from multi-dimensional distribution functions are compared. The proposed random-walk Metropolis algorithm enables the efficient treatment of multiple vibrational modes within a time step with reasonable computational effort. The implemented model is verified and validated by means of simple reservoir simulations and the comparison to experimental measurements of a hypersonic, carbon-dioxide flow around a flat-faced cylinder.
Mezhevoi, I. N.; Badelin, V. G.
2013-12-01
Integral enthalpies of dissolution Δsol H m of DL-valine are measured via calorimetry of dissolution in aqueous solutions of glycerol, ethylene glycol, and 1,2-propylene glycol. Standard values of the enthalpies of dissolution (Δsol H ○) and transfer (Δtr H ○) of amino acid from water to mixed solvent are calculated from the resulting experimental data. The enthalpy coefficients for pair interactions hxy of amino acid with polyatomic alcohol molecules are calculated using the McMillan-Meyer theory and have positive values. The obtained results are discussed in light of the theory of the predomination of various types of interactions in mixed solutions and the effect of structural features of interacting biomolecules on the thermochemical parameters of the dissolution of amino acids.
Andermatt, Samuel; Cha, Jinwoong; Schiffmann, Florian; VandeVondele, Joost
2016-07-12
In this work, methods for the efficient simulation of large systems embedded in a molecular environment are presented. These methods combine linear-scaling (LS) Kohn-Sham (KS) density functional theory (DFT) with subsystem (SS) DFT. LS DFT is efficient for large subsystems, while SS DFT is linear scaling with a smaller prefactor for large sets of small molecules. The combination of SS and LS, which is an embedding approach, can result in a 10-fold speedup over a pure LS simulation for large systems in aqueous solution. In addition to a ground-state Born-Oppenheimer SS+LS implementation, a time-dependent density functional theory-based Ehrenfest molecular dynamics (EMD) using density matrix propagation is presented that allows for performing nonadiabatic dynamics. Density matrix-based EMD in the SS framework is naturally linear scaling and appears suitable to study the electronic dynamics of molecules in solution. In the LS framework, linear scaling results as long as the density matrix remains sparse during time propagation. However, we generally find a less than exponential decay of the density matrix after a sufficiently long EMD run, preventing LS EMD simulations with arbitrary accuracy. The methods are tested on various systems, including spectroscopy on dyes, the electronic structure of TiO2 nanoparticles, electronic transport in carbon nanotubes, and the satellite tobacco mosaic virus in explicit solution.
Hoshino, Masamitsu; Ishijima, Yohei; Kato, Hidetoshi; Mogi, Daisuke; Takahashi, Yoshinao; Fukae, Katsuya; Limão-Vieira, Paulo; Tanaka, Hiroshi; Shimamura, Isao
2016-04-01
Inelastic and superelastic electron-impact vibrational excitation functions of hot carbonyl sulphide COS (and hot CO2) are measured for electron energies from 0.5 to 3.0 eV (1.5 to 6.0 eV) and at a scattering angle of 90°. Based on the vibrational populations and the principle of detailed balance, these excitation functions are decomposed into contributions from state-to-state vibrational transitions involving up to the second bending overtone (030) in the electronically ground state. Both the 2Π resonance for COS around 1.2 eV and the 2Πu resonance for CO2 around 3.8 eV are shifted to lower energies as the initial vibrational state is excited in the bending mode. The width of the resonance hump for COS changes only little as the molecule bends, whereas that of the overall boomerang resonance for CO2 becomes narrower. The angular distribution of the electrons resonantly scattered by hot COS and hot CO2 is also measured. The different shapes depending on the vibrational transitions and gas temperatures are discussed in terms of the symmetry of the vibrational wave functions. Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.
Gensch, T.; Hofkens, J.; Köhn, F.; Vosch, T.; Herrmann, A.; Müllen, K.; Schryver, F.C. De
2001-01-01
Recently, investigations of the fluorescence properties of a multichromophoric dendritic entity at the single molecule level have revealed multiple fluorescence levels, collective off-states, variations of the polarisation, large shifts in the spectral position and changes in the fluorescence decay
Shao, Zhiyong; Graf, Shannon; Chaga, Oleg Y; Lavrov, Dennis V
2006-10-15
The 16,937-nuceotide sequence of the linear mitochondrial DNA (mt-DNA) molecule of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa) - the first mtDNA sequence from the class Scypozoa and the first sequence of a linear mtDNA from Metazoa - has been determined. This sequence contains genes for 13 energy pathway proteins, small and large subunit rRNAs, and methionine and tryptophan tRNAs. In addition, two open reading frames of 324 and 969 base pairs in length have been found. The deduced amino-acid sequence of one of them, ORF969, displays extensive sequence similarity with the polymerase [but not the exonuclease] domain of family B DNA polymerases, and this ORF has been tentatively identified as dnab. This is the first report of dnab in animal mtDNA. The genes in A. aurita mtDNA are arranged in two clusters with opposite transcriptional polarities; transcription proceeding toward the ends of the molecule. The determined sequences at the ends of the molecule are nearly identical but inverted and lack any obvious potential secondary structures or telomere-like repeat elements. The acquisition of mitochondrial genomic data for the second class of Cnidaria allows us to reconstruct characteristic features of mitochondrial evolution in this animal phylum.
Tscherbul, T V; Yu, H -G; Dalgarno, A; Klos, Jacek; Ma, Lifang; Alexander, Millard H; 10.1063/1.4748258
2012-01-01
We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wavefunction. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH2(X)] with He atoms. To this end, two highly accurate three-dimensional potential energy surfaces (PESs) of the He-CH2(X) complex are developed using the state-of-the-art CCSD(T) method and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH2, CHD, and CD2 molecules with He atoms occu...
Capability of LEP-type surfaces to describe noncollinear reactions 2 - Polyatomic systems
Espinosa-Garcia, Joaquin
2001-01-01
In this second article of the series, the popular LEP-type surface for collinear reaction paths and a "bent" surface, which involves a saddle point geometry with a nonlinear central angle, were used to examine the capacity of LEP-type surfaces to describe the kinetics and dynamics of noncollinear reaction paths in polyatomic systems. Analyzing the geometries, vibrational frequencies, curvature along the reaction path (to estimate the tunneling effect and the reaction coordinate-bound modes coupling), and the variational transition- state theory thermal rate constants for the NH//3 + O(**3P) reaction, we found that the "collinear" LEP-type and the "bent" surfaces for this polyatomic system show similar behavior, thus allowing a considerable saving in time and computational effort. This agreement is especially encouraging for this polyatomic system because in the Cs symmetry the reaction proceeds via two electronic states of symmetries **3A prime and **3A double prime , which had to be independently calibrated....
Institute of Scientific and Technical Information of China (English)
甘慧兰; 丁光涛; 郑贤锋; 崔执凤
2012-01-01
In this paper, based on the model of linear coupled oscillators, the oscillatory differential equations are deduced in three different coordinate representations for linear symmetrical triatomic molecule. Using theory and method of the inverse problem of analytical mechanics, we have established five La-grangians and Hamiltonians, some of which are first reported.%本文以线性耦合振子为模型,导出了三种不同坐标变量表示下线性对称三原子分子的振动微分方程,利用分析力学逆问题理论和方法,构造出了五种对应的Lagrange函数和Hamilton函数,其中有些是新的结果.
Rinkevicius, Zilvinas; Li, Xin; Sandberg, Jaime A R; Ågren, Hans
2014-05-21
We generalize a density functional theory/molecular mechanics approach for heterogeneous environments with an implementation of quadratic response theory. The updated methodology allows us to address a variety of non-linear optical, magnetic and mixed properties of molecular species in complex environments, such as combined metallic, solvent and confined organic environments. Illustrating calculations of para-nitroaniline on gold surfaces and in solution reveals a number of aspects that come into play when analyzing second harmonic generation of such systems--such as surface charge flow, coupled surface-solvent dynamics and induced geometric and electronic structure effects of the adsorbate. Some ramifications of the methodology for applied studies are discussed.
Ghosh, R.; Chandra, N.; Parida, S.
2009-03-01
This paper reports results of a theoretical study of angle- and spin-resolved photo-Auger electron coincident spectroscopy in the form of entanglement between these two particles emitted from a linear molecule. First, we develop an expression for a density matrix needed for studying spin-entanglement between a photoelectron and an Auger electron. In order to properly represent the molecular symmetries, nuclear rotation, and the spin-dependent interactions (SDIs), we have used symmetry adapted wavefunctions in Hund’s coupling scheme (a) for all the species participating in this two-step process. This expression shows that spin-entanglement in a photo-Auger electron pair in the presence of SDIs very strongly depends upon, among other things, polarization of the ionizing radia- tion, directions of motion and of spin polarization of two ejected electrons, and the dynamics of photoionization and of Auger decay. We have applied this expression, as an example, to a generic linear molecule in its J0, M0 = 0 state. This model calculation clearly brings out the salient features of the spin-entanglement of a photo-Auger electron pair in the presence of the SDIs.
Energy Technology Data Exchange (ETDEWEB)
Ghosh, R.; Chandra, N.; Parida, S. [Indian Institute of Technology, Dept. of Physics and Meteorology, Kharagpur (India)
2009-03-15
This paper reports results of a theoretical study of angle- and spin-resolved photo-Auger electron coincident spectroscopy in the form of entanglement between these two particles emitted from a linear molecule. First, we develop an expression for a density matrix needed for studying spin-entanglement between a photoelectron and an Auger electron. In order to properly represent the molecular symmetries, nuclear rotation, and the spin-dependent interactions (SDIs), we have used symmetry adapted wavefunctions in Hund's coupling scheme (a) for all the species participating in this two-step process. This expression shows that spin-entanglement in a photo-Auger electron pair in the presence of SDIs very strongly depends upon, among other things, polarization of the ionizing radiation, directions of motion and of spin polarization of two ejected electrons, and the dynamics of photoionization and of Auger decay. We have applied this expression, as an example, to a generic linear molecule in its J{sub 0}, M{sub 0} = 0 state. This model calculation clearly brings out the salient features of the spin-entanglement of a photo-Auger electron pair in the presence of the SDIs. (authors)
Paschoal, Diego; Santos, Hélio F Dos
2013-05-01
In this paper, we assessed the quantum mechanical level of theory for prediction of linear and nonlinear optical (NLO) properties of push-pull organic molecules. The electric dipole moment (μ), mean polarizability ([Symbol: see text]α[Symbol: see text]) and total static first hyperpolarizability (βt) were calculated for a set of benzene, styrene, biphenyl and stilbene derivatives using HF, MP2 and DFT (31 different functionals) levels and over 71 distinct basis sets. In addition, we propose two new basis sets, NLO-V and aNLO-V, for NLO properties calculations. As the main outcomes it is shown that long-range corrected DFT functionals such as M062X, ωB97, cam-B3LYP, LC-BLYP and LC-ωPBE work satisfactorily for NLO properties when appropriate basis sets such as those proposed here (NLO-V or aNLO-V) are used. For most molecules with β ranging from 0 to 190 esu, the average absolute deviation was 13.2 esu for NLO-V basis sets, compared to 27.2 esu for the standard 6-31 G(2d) basis set. Therefore, we conclude that the new basis sets proposed here (NLO-V and aNLO-V), together with the cam-B3LYP functional, make an affordable calculation scheme to predict NLO properties of large organic molecules.
Watson, James K. G.
1998-03-01
TheQbranch of the 2ν22-00band of the HCN molecule and an intensity asymmetry between thePandRbranches have recently been observed by Maki, Quapp, Klee, Mellau, and Albert (J. Mol. Spectrosc.185,356-369 (1997)). Such intensity effects are associated with a contribution from theM˜22terms of the effective dipole moment operator of Aliev and Watson. The quantum number dependence observed by Makiet al.(cited above) is in agreement with this contribution. A formula is derived for the coefficient of this term, and the value calculated from the anharmonic potential and dipole derivatives is in good agreement with the observed value for a particular choice of signs of the combination-band transition momentsR12andR32. For DCN the second derivatives of the dipole moment are not known, but a comparison with the HCN calculation suggests that the agreement is adequate in view of the relatively large uncertainty of the observed values. Similar intensity effects should occur in the (ν4+ ν5)2-00band of HCCH, for which the coefficient is calculated to be similar in magnitude to that of the 2ν22-00band of HCN. The intensity of the Σ--Σ+component of (ν4+ ν5)-0 of HCCH, which should consist of only aQbranch, is also discussed; from present knowledge of the molecular parameters, it is expected to be much weaker than theQbranch of the Δ-Σ+component.
Anwar, Muhammad U; Tandon, Santokh S; Dawe, Louise N; Habib, Fatemah; Murugesu, Muralee; Thompson, Laurence K
2012-01-16
Tritopic pyridinebis(hydrazone)-based ligands typically produce square M(9) [3 × 3] grid complexes with first-row transition-metal ions (e.g., M = Mn, Fe, Co, Cu, Zn), but with larger lanthanide ions, such coordination motifs are not produced, and instead linear trinuclear complexes appear to be a preferred option. The reaction of 2pomp [derived from pyridine-2,6-bis(hydrazone) and 2-acetylpyridine] with La(III), Gd(III), and Dy(III) salts produces helical linear trinuclear [Ln(3)(2pomp)(2)]-based complexes, where each metal ion occupies one of the three tridentate ligand pockets. Two ligands encompass the three metal ions, and internal connections between metal ions occur through μ-O(hydrazone) bridges. Coligands include benzoate, nitrate, and N,N-dimethylformamide. The linear Dy(III)(3) complex exhibits single-molecule magnet behavior, demonstrated through alternating-current susceptibility measurements. Slow thermal magnetic relaxation was detected in an external field of 1800 Oe, where quantum-tunneling effects were suppressed (U(eff) = 14 K).
Marrero-Ponce, Yovani; Martínez-Albelo, Eugenio R; Casañola-Martín, Gerardo M; Castillo-Garit, Juan A; Echevería-Díaz, Yunaimy; Zaldivar, Vicente Romero; Tygat, Jan; Borges, José E Rodriguez; García-Domenech, Ramón; Torrens, Francisco; Pérez-Giménez, Facundo
2010-11-01
Novel bond-level molecular descriptors are proposed, based on linear maps similar to the ones defined in algebra theory. The kth edge-adjacency matrix (E(k)) denotes the matrix of bond linear indices (non-stochastic) with regard to canonical basis set. The kth stochastic edge-adjacency matrix, ES(k), is here proposed as a new molecular representation easily calculated from E(k). Then, the kth stochastic bond linear indices are calculated using ES(k) as operators of linear transformations. In both cases, the bond-type formalism is developed. The kth non-stochastic and stochastic total linear indices are calculated by adding the kth non-stochastic and stochastic bond linear indices, respectively, of all bonds in molecule. First, the new bond-based molecular descriptors (MDs) are tested for suitability, for the QSPRs, by analyzing regressions of novel indices for selected physicochemical properties of octane isomers (first round). General performance of the new descriptors in this QSPR studies is evaluated with regard to the well-known sets of 2D/3D MDs. From the analysis, we can conclude that the non-stochastic and stochastic bond-based linear indices have an overall good modeling capability proving their usefulness in QSPR studies. Later, the novel bond-level MDs are also used for the description and prediction of the boiling point of 28 alkyl-alcohols (second round), and to the modeling of the specific rate constant (log k), partition coefficient (log P), as well as the antibacterial activity of 34 derivatives of 2-furylethylenes (third round). The comparison with other approaches (edge- and vertices-based connectivity indices, total and local spectral moments, and quantum chemical descriptors as well as E-state/biomolecular encounter parameters) exposes a good behavior of our method in this QSPR studies. Finally, the approach described in this study appears to be a very promising structural invariant, useful not only for QSPR studies but also for similarity
Energy Technology Data Exchange (ETDEWEB)
Kristo, M J
2006-12-12
This work explored the use of pulse height distributions (PHD) from multiplier-type detectors as a means of detecting and eliminating the effects of polyatomic interferences in secondary ion mass spectrometry (SIMS). We explored the behavior of PHD for {sup 235}U{sup +}, {sup 208}Pb{sup 27}Al{sup +} and {sup 207}Pb{sup 28}Si{sup +}, all with a nominal mass-to-charge ratio of 235. In every case, the distribution for the atomic ion ({sup 235}U{sup +}) was clearly shifted relative to the distributions for {sup 208}Pb{sup 27}Al{sup +} and {sup 207}Pb{sup 28}Si{sup +}. When the first surface of the detector is metallic in character, the polyatomic ions are shifted to larger pulse heights relative to the atomic ion. When the first surface of the detector is oxide in character, the atomic ion is shifted to larger pulse heights relative to the polyatomic ions. The relative positioning appear to be stable for a given detector over time at the same secondary ion impact energy. Consequently, it appears to be feasible to use PHD data to detect interfering polyatomic ions and eliminate their deleterious effects using peak deconvolution techniques. Consequently, the updated Ultrafast RAE detector will be designed to make the pulse height information available to the data acquisition system.
A new scaling algorithm for predicting vibrational spectra of polyatomic molecules
Indian Academy of Sciences (India)
M Vijay Madhav; S Manogaran
2009-09-01
We propose here a relationship between the off-diagonal and diagonal force constants which is valid theoretically under harmonic approximation provided the matrix is available from some theoretical calculation using = .
Qin, Yue
Scope and method of study. The tunneling effects in isomerization of HONO and HSiOH have been studied by using classical trajectories with semiclassical tunneling corrections. The potential energy surfaces were constructed by using the available ab initio, spectroscopic and thermodynamic data. A constrained classical trajectory method was employed to study the roles of the various vibrational modes and molecular rotation in intramolecular energy transfer in cis trans HONO. Findings and conclusions. The results show that the rate constants for cisto trans are generally larger than transto cis for HONO isomerizations. Excitations of the OH and N=O stretches yield the smallest rate constants while the N -O stretch excitation gives the largest rate for both cis to trans and transto cis. The rate of energy transfer from bath modes to the torsional mode is found to be a dominant factor for determining the tunneling rate. Similar behaviors are found in the isomerization of HSiOH. The Si-O stretch excitation gives the largest rate constants and the OH stretch excitation yields the smallest rate constants for both cisto trans and transto cis isomerizations. The ratio of the decay rate with tunneling correction to that without tunneling increases with decreasing total energy of the system. Furthermore, the rate difference between the cisto trans and trans to cis decreases with increasing the excitation energy. The values of the effective mass along the tunneling coordinate can facilitate or hinder the tunneling probability. We find that tunneling effects plays an important role in the isomerization of HSiOH. Our results also elucidate that the ONO bending and torsional modes are important for the relaxation of the excited OH stretch. Removing the torsional motion eliminates the influence of rotation on the intramolecular vibrational energy relaxation. The effects of constraining the ONO bending plays a much smaller role than does constraining the HON bending for decreasing the magnitudes of the rate. The interaction between the out-of-plane torsional and HON bending modes is a major factor in causing cis-HONO to isomerize at significantly greater rates than that of trans-HONO.
Fragmentation Control of a Polyatomic Molecule by fully determined Laser-Fields
Directory of Open Access Journals (Sweden)
Varga K.
2013-03-01
Full Text Available Strong-field control of acetylene fragmentation by fully determined few-cycle laser pulses is demonstrated. The control mechanism is shown to be based on electron recollision and inelastic ionization from inner-valence molecular orbitals.
Velizhanin, Kirill A; Kilina, Svetlana; Sewell, Thomas D; Piryatinski, Andrei
2008-10-23
Numerical studies of vibrational energy transport and associated (non)linear infrared and Raman response in polyatomic materials require knowledge of the multidimensional vibrational potential-energy surface and the ability to perform normal-mode analysis on that potential. The presence of translational symmetry, as in crystals, leads to the observed dispersion of the unit cell normal modes and has to be accounted for in calculations of energy transfer rates and other spectroscopic quantities. Here we report on the implementation of a computational approach that combines the generalized supercell method and density functional theory electronic structure calculations to investigate the vibrational structure in translationally symmetric materials containing relatively large numbers of atoms in the unit cell (58 atoms in the present study). The method is applied to calculate the phonon and vibron dispersion relations and the vibrational density of states in pentaerythritol tetranitrate (PETN) molecular crystal which is an important energetic material. The results set the stage for future investigations of vibrational energy transport and associated nonlinear spectroscopic signatures in this class of materials.
Saha, K.; Prabhakaran, A.; Chandrasekaran, V.; Rappaport, M. L.; Heber, O.; Zajfman, D.
2017-05-01
A Velocity Map Imaging (VMI) spectrometer has been designed and integrated with an electrostatic ion beam trap to study delayed electron emission from trapped polyatomic anions upon photodetachment. The VMI spectrometer is small in size and can record a wide range of photoelectron energies, with variable magnification. Delayed electron emission can be recorded in our experimental setup for any time duration after the photoexcitation of the polyatomic anions. Experiments were carried out with trapped O- and C5-ions to demonstrate the capability of the spectrometer. Delayed electron emissions from C5 - as well as prompt photoelectrons from O- were detected by the VMI spectrometer upon photoexcitation. The design and performance of the spectrometer are presented in detail.
Constructing Potential Energy Surfaces for Polyatomic Systems: Recent Progress and New Problems
Directory of Open Access Journals (Sweden)
J. Espinosa-Garcia
2012-01-01
Full Text Available Different methods of constructing potential energy surfaces in polyatomic systems are reviewed, with the emphasis put on fitting, interpolation, and analytical (defined by functional forms approaches, based on quantum chemistry electronic structure calculations. The different approaches are reviewed first, followed by a comparison using the benchmark H + CH4 and the H + NH3 gas-phase hydrogen abstraction reactions. Different kinetics and dynamics properties are analyzed for these reactions and compared with the available experimental data, which permits one to estimate the advantages and disadvantages of each method. Finally, we analyze different problems with increasing difficulty in the potential energy construction: spin-orbit coupling, molecular size, and more complicated reactions with several maxima and minima, which test the soundness and general applicability of each method. We conclude that, although the field of small systems, typically atom-diatom, is mature, there still remains much work to be done in the field of polyatomic systems.
Ivanov, Sergey V.
2016-07-01
Stable bimolecular complexes (tightly bound dimers) in the gas phase are usually created during third body stabilization of their unstable precursors-quasi-bound complexes (QCs). The latter can arise under the condition that at least one of the colliding partners has an internal degree of freedom. In this article, the principal difference between "orbitings" and QCs is demonstrated in the classical nonreactive scattering picture. Additionally, fractions of QCs in binary collisions of different linear molecules are compared. Also in the article the influence of QCs on rotational R-T relaxation and on vibration-rotational spectral line broadening is discussed. Explicit formulae shedding light on the QCs contribution to the R-T relaxation cross section and the line width and shift are presented. The obtained results emphasize the need for including QCs in every theoretical modeling of spectroscopic manifestation of intermolecular interactions. Besides the topics above, the possible manifestation of non-impact effects in the central regions of spectral lines due to QCs is stated. And finally, special consideration is given to the problem of adequate simulation of QCs formation at different pressures.
Arevalo, Ricardo, Jr.; Brinckerhoff, William B.; Pinnick, Veronica T.; van Amerom, Friso H. W.; Danell, Ryan M.; Li, Xiang; Getty, Stephanie; Hovmand, Lars; Atanassova, Martina; Mahaffy, Paul R.; Chu, Zhiping; Goesmann, Fred; Steininger, Harald
2014-01-01
The 2018 ExoMars rover mission includes the Mars Organic Molecule Analyzer (MOMA) investigation. MOMA will examine the chemical composition of samples acquired from depths of up to two meters below the martian surface, where organics may be protected from degradation derived from cosmic radiation and/or oxidative chemical reactions. When combined with the complement of instruments in the rover's Pasteur Payload, MOMA has the potential to reveal the presence of a wide range of organics preserved in a variety of mineralogical environments, and to begin to understand the structural character and potential origin of those compounds. The MOMA investigation is led by the Max Planck Institute for Solar System Research (MPS) with the mass spectrometer subsystem provided by NASA GSFC. MOMA's linear ion trap mass spectrometer (ITMS) is designed to analyze molecular composition of: (i) gas evolved from pyrolyzed powder samples and separated in a gas chromatograph; and, (ii) ions directly desorbed from crushed solid samples at Mars ambient pressure, as enabled by a pulsed UV laser system, fast-actuating aperture valve and capillary ion inlet. Breadboard ITMS and associated electronics have been advanced to high end-to-end fidelity in preparation for flight hardware delivery to Germany in 2015.
van der Wiel, M H D; van der Tak, F F S; Kazmierczak, M; Ceccarelli, C
2013-01-01
We aim to reveal the gas energetics in the circumstellar environment of the prototypical high-mass protostellar object AFGL2591 using space-based far-infrared observations of linear rotor molecules. Rotational spectral line signatures of CO, HCO+, CS, HCN and HNC from a 490-1240 GHz survey with Herschel/HIFI, complemented by ground-based JCMT and IRAM 30m spectra, cover transitions with E(up)/k between 5 and ~300 K (750K for 12C16O, using selected frequency settings up to 1850 GHz). The resolved spectral line profiles are used to separate and study various kinematic components. The line profiles show two emission components, the widest and bluest of which is attributed to an approaching outflow and the other to the envelope. We find evidence for progressively more redshifted and wider line profiles from the envelope gas with increasing energy level, qualitatively explained by residual outflow contribution picked up in the systematically decreasing beam size. Integrated line intensities for each species decrea...
Ma, Q.; Boulet, C.; Tipping, R. H.
2014-01-01
The refinement of the Robert-Bonamy (RB) formalism by considering the line coupling for isotropic Raman Q lines of linear molecules developed in our previous study [Q. Ma, C. Boulet, and R. H. Tipping, J. Chem. Phys. 139, 034305 (2013)] has been extended to infrared P and R lines. In these calculations, the main task is to derive diagonal and off-diagonal matrix elements of the Liouville operator iS1 - S2 introduced in the formalism. When one considers the line coupling for isotropic Raman Q lines where their initial and final rotational quantum numbers are identical, the derivations of off-diagonal elements do not require extra correlation functions of the ^S operator and their Fourier transforms except for those used in deriving diagonal elements. In contrast, the derivations for infrared P and R lines become more difficult because they require a lot of new correlation functions and their Fourier transforms. By introducing two dimensional correlation functions labeled by two tensor ranks and making variable changes to become even functions, the derivations only require the latters' two dimensional Fourier transforms evaluated at two modulation frequencies characterizing the averaged energy gap and the frequency detuning between the two coupled transitions. With the coordinate representation, it is easy to accurately derive these two dimensional correlation functions. Meanwhile, by using the sampling theory one is able to effectively evaluate their two dimensional Fourier transforms. Thus, the obstacles in considering the line coupling for P and R lines have been overcome. Numerical calculations have been carried out for the half-widths of both the isotropic Raman Q lines and the infrared P and R lines of C2H2 broadened by N2. In comparison with values derived from the RB formalism, new calculated values are significantly reduced and become closer to measurements.
Nonadiabatic reaction of energetic molecules.
Bhattacharya, Atanu; Guo, Yuanqing; Bernstein, Elliot R
2010-12-21
Energetic materials store a large amount of chemical energy that can be readily converted into mechanical energy via decomposition. A number of different ignition processes such as sparks, shocks, heat, or arcs can initiate the excited electronic state decomposition of energetic materials. Experiments have demonstrated the essential role of excited electronic state decomposition in the energy conversion process. A full understanding of the mechanisms for the decomposition of energetic materials from excited electronic states will require the investigation and analysis of the specific topography of the excited electronic potential energy surfaces (PESs) of these molecules. The crossing of multidimensional electronic PESs creates a funnel-like topography, known as conical intersections (CIs). CIs are well established as a controlling factor in the excited electronic state decomposition of polyatomic molecules. This Account summarizes our current understanding of the nonadiabatic unimolecular chemistry of energetic materials through CIs and presents the essential role of CIs in the determination of decomposition pathways of these energetic systems. Because of the involvement of more than one PES, a decomposition process involving CIs is an electronically nonadiabatic mechanism. Based on our experimental observations and theoretical calculations, we find that a nonadiabatic reaction through CIs dominates the initial decomposition process of energetic materials from excited electronic states. Although the nonadiabatic behavior of some polyatomic molecules has been well studied, the role of nonadiabatic reactions in the excited electronic state decomposition of energetic molecules has not been well investigated. We use both nanosecond energy-resolved and femtosecond time-resolved spectroscopic techniques to determine the decomposition mechanism and dynamics of energetic species experimentally. Subsequently, we employ multiconfigurational methodologies (such as, CASSCF
Reconstructing Polyatomic Structures from Discrete X-Rays: NP-Completeness Proof for Three Atoms
Durr, Christoph; Chrobak, Marek
1999-01-01
We address a discrete tomography problem that arises in the study of the atomic structure of crystal lattices. A polyatomic structure T can be defined as an integer lattice in dimension D>=2, whose points may be occupied by $c$ distinct types of atoms. To ``analyze'' T, we conduct ell measurements that we call_discrete X-rays_. A discrete X-ray in direction xi determines the number of atoms of each type on each line parallel to xi. Given ell such non-parallel X-rays, we wish to reconstruct T....
An efficient optical biochemical sensor based on a polyatomic photonic crystal ring resonator
Wang, Daobin; Liu, Yanjun; Yuan, Lihua; Lei, Jingli; Li, Xiaoxiao; wu, Gang; Hou, Shanglin
2016-08-01
In this paper, we introduce and investigate a design concept for a polyatomic photonic crystal ring resonator (PCRR). In contrast to conventional sensors, this PCRR comprises two different branching waveguides (WG), which are all oriented in the same lattice direction, but with different optical propagation properties due to the binary nature of the diatomic square lattice. Based on this new scheme, an on-chip biochemical sensor is proposed. Electromagnetic analysis, PWE and FDTD numerical techniques, were used to investigate the sensing performance. Our results show that such a sensor can efficiently detect small changes in the refractive index within the sensing area.
Kinetics and thermochemistry of polyatomic free radicals: New results and new understandings
Gutman, David; Slagle, Irene R.
1990-01-01
An experimental facility for the study of the chemical kinetics of polyatomic free radicals is described which consists of a heatable tubular reactor coupled to a photoionization mass spectrometer. Its use in different kinds of chemical kinetic studies is also discussed. Examples presented include studies of the C2H3 + O2, C2H3 + HC1, CH3 + O, and CH3 + CH3 reactions. The heat of formation of C2H3 was obtained from the results of the study of the C2H3 + HC1 reaction.
Using polyatomic primary ions to probe an amino acid and a nucleic base in water ice
Energy Technology Data Exchange (ETDEWEB)
Conlan, X.A. [Surface Analysis Research Centre, School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Manchester M60 1QD (United Kingdom)]. E-mail: x.conlan@postgrad.manchester.ac.uk; Biddulph, G.X. [Surface Analysis Research Centre, School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Manchester M60 1QD (United Kingdom)]. E-mail: G.Biddulph@postgrad.manchester.ac.uk; Lockyer, N.P. [Surface Analysis Research Centre, School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Manchester M60 1QD (United Kingdom); Vickerman, J.C. [Surface Analysis Research Centre, School of Chemical Engineering and Analytical Science, University of Manchester, P.O. Box 88, Manchester M60 1QD (United Kingdom)]. E-mail: John.Vickerman@manchester.ac.uk
2006-07-30
In this study on pure water ice, we show that protonated water species [H{sub 2}O] {sub n}H{sup +} are more prevalent than (H{sub 2}O) {sub n} {sup +} ions after bombardment by Au{sup +} monoatomic and Au{sub 3} {sup +} and C{sub 60} {sup +} polyatomic projectiles. This data also reveals significant differences in water cluster yields under bombardment by these three projectiles. The amino acid alanine and the nucleic base adenine in solution have been studied and have been shown to have an effect on the water cluster ion yields observed using an Au{sub 3} {sup +} ion beam.
Tripartite entanglement dynamics of vibrations in triatomic molecules.
Zhai, Liangjun; Zheng, Yujun
2016-06-21
In the present study, the dynamical behaviors of tripartite entanglement of vibrations in triatomic molecules are studied based on the Lie algebraic models of molecules. The dynamical behaviors of tripartite entanglement of the local mode molecule H2O and normal mode molecule NO2 are comparatively studied for different initial states by employing the general concurrence. Our results show that the dynamics of tripartite entanglement are relied on the dynamics of intramolecular energy distribution. The local mode molecule is more suitable to construct the tripartite entangled states. Also, the greater degree of tripartite entanglement can be obtained if the stretching vibration is first excited. These results shed new light on the understanding of quantum multipartite entanglement of vibrations in the polyatomic molecules.
Slow light engineering in polyatomic photonic crystal waveguides based on square lattice
Wang, Daobin; Zhang, Jie; Yuan, Lihua; Lei, Jingli; Chen, Sai; Han, Jiawei; Hou, Shanglin
2011-12-01
In this paper, the slow light properties of the polyatomic Photonic Crystal (PhC) which has multiple different air holes in each primitive cell are investigated. A slow light waveguide with "U-type" group index-frequency curve, which results in nearly constant group index over large bandwidth, is achieved using this new photonic crystal geometry based on the square lattice. Also, the radius and position of the innermost rows of small air holes have been modified to investigate the feasibility of controlling the dispersion relation by subtle structural modification. Numerical results demonstrate that decreasing the group velocity effectively and meanwhile maintaining a large Normalized Delay-Bandwidth Product ( NDBP) can be achieved by only modifying the radius of the innermost rows of small air holes. Shifting the innermost rows of small air holes toward the waveguide core is highly beneficial to enlarge the slow light bandwidth, but it contributes nothing to the promotion of NDBP. Our results provide important theoretical basis for the potential application offered by the polyatomic photonic crystal in future optical networks.
Arevalo, R.; Danell, R. M.; Gundersen, C.; Hovmand, L.; Southard, A.; Tan, F.; Grubisic, A.; Brinckerhoff, W. B.; Getty, S. A.; Mahaffy, P.; Cottin, H.; Briois, C.; Colin, F.; Szopa, C.; Vuitton, V.; Makarov, A.; Reinhardt-Szyba, M.
2016-10-01
AROMA combines a linear ion trap and Orbitrap mass analyzer to enable: quantitative measurements of organic and inorganic compounds; selective isolation of targeted mass ranges; tandem mass spectrometry; and, ultrahigh mass resolution and accuracy.
Decelerating and Trapping Large Polar Molecules.
Patterson, David
2016-11-18
Manipulating the motion of large polyatomic molecules, such as benzonitrile (C6 H5 CN), presents significant difficulties compared to the manipulation of diatomic molecules. Although recent impressive results have demonstrated manipulation, trapping, and cooling of molecules as large as CH3 F, no general technique for trapping such molecules has been demonstrated, and cold neutral molecules larger than 5 atoms have not been trapped (M. Zeppenfeld, B. G. U. Englert, R. Glöckner, A. Prehn, M. Mielenz, C. Sommer, L. D. van Buuren, M. Motsch, G. Rempe, Nature 2012, 491, 570-573). In particular, extending Stark deceleration and electrostatic trapping to such species remains challenging. Here, we propose to combine a novel "asymmetric doublet state" Stark decelerator with recently demonstrated slow, cold, buffer-gas-cooled beams of closed-shell volatile molecules to realize a general system for decelerating and trapping samples of a broad range of volatile neutral polar prolate asymmetric top molecules. The technique is applicable to most stable volatile molecules in the 100-500 AMU range, and would be capable of producing trapped samples in a single rotational state and at a motional temperature of hundreds of mK. Such samples would immediately allow for spectroscopy of unprecedented resolution, and extensions would allow for further cooling and direct observation of slow intramolecular processes such as vibrational relaxation and Hertz-level tunneling dynamics.
Positron-molecule interactions: resonant attachment, annihilation, and bound states
Gribakin, G F; Surko, C M; 10.1103/RevModPhys.82.2557
2010-01-01
This article presents an overview of current understanding of the interaction of low-energy positrons with molecules with emphasis on resonances, positron attachment and annihilation. Annihilation rates measured as a function of positron energy reveal the presence of vibrational Feshbach resonances (VFR) for many polyatomic molecules. These resonances lead to strong enhancement of the annihilation rates. They also provide evidence that positrons bind to many molecular species. A quantitative theory of VFR-mediated attachment to small molecules is presented. It is tested successfully for selected molecules (e.g., methyl halides and methanol) where all modes couple to the positron continuum. Combination and overtone resonances are observed and their role is elucidated. In larger molecules, annihilation rates from VFR far exceed those explicable on the basis of single-mode resonances. These enhancements increase rapidly with the number of vibrational degrees of freedom. While the details are as yet unclear, intr...
DEFF Research Database (Denmark)
Kuhlman, Thomas Scheby; Mikkelsen, Kurt V.; Møller, Klaus Braagaard;
2009-01-01
We present a study on the excited states of an ethylene dimer as to investigate the presence of and perturbation from low-lying charge-resonance states calculated by linear response density functional theory (DFT) using the B3LYP and CAM-B3LYP functionals. The calculations are compared to a refer......We present a study on the excited states of an ethylene dimer as to investigate the presence of and perturbation from low-lying charge-resonance states calculated by linear response density functional theory (DFT) using the B3LYP and CAM-B3LYP functionals. The calculations are compared...
Alaofi, Ahmed; On, Ngoc; Kiptoo, Paul; Williams, Todd D; Miller, Donald W; Siahaan, Teruna J
2016-02-01
The aim of this study is to evaluate the effect of peptide cyclization on the blood-brain barrier (BBB) modulatory activity and plasma stability of His-Ala-Val peptides, which are derived from the extracellular 1 domain of human E-cadherin. The activities to modulate the intercellular junctions by linear HAV4 (Ac-SHAVAS-NH2), cyclic cHAVc1 (Cyclo(1,8)Ac-CSHAVASC-NH2), and cyclic cHAVc3 (Cyclo(1,6)Ac-CSHAVC-NH2) were compared in in vitro and in vivo BBB models. Linear HAV4 and cyclic cHAVc1 have the same junction modulatory activities as assessed by in vitro MDCK monolayer model and in situ rat brain perfusion model. In contrast, cyclic cHAVc3 was more effective than linear HAV4 in modulating MDCK cell monolayers and in improving in vivo brain delivery of Gd-DTPA on i.v. administration in Balb/c mice. Cyclic cHAVc3 (t1/2 = 12.95 h) has better plasma stability compared with linear HAV4 (t1/2 = 2.4 h). The duration of the BBB modulation was longer using cHAVc3 (2-4 h) compared with HAV4 (<1 h). Both HAV4 and cHAVc3 peptides also enhanced the in vivo brain delivery of IRdye800cw-PEG (25 kDa) as detected by near IR imaging. The result showed that cyclic cHAVc3 peptide had better activity and plasma stability than linear HAV4 peptide.
A Fokker-Planck Model of the Boltzmann Equation with Correct Prandtl Number for Polyatomic Gases
Mathiaud, J.; Mieussens, L.
2017-09-01
We propose an extension of the Fokker-Planck model of the Boltzmann equation to get a correct Prandtl number in the Compressible Navier-Stokes asymptotics for polyatomic gases. This is obtained by replacing the diffusion coefficient (which is the equilibrium temperature) by a non diagonal temperature tensor, like the Ellipsoidal-Statistical model is obtained from the Bathnagar-Gross-Krook model of the Boltzmann equation, and by adding a diffusion term for the internal energy. Our model is proved to satisfy the properties of conservation and a H-theorem. A Chapman-Enskog analysis shows how to compute the transport coefficients of our model. Some numerical tests are performed to illustrate that a correct Prandtl number can be obtained.
Polyatomic gases with dynamic pressure: Maximum entropy principle and shock structure
Pavić-Čolić, Milana; Simić, Srboljub
2016-01-01
This paper is concerned with the analysis of polyatomic gases within the framework of kinetic theory. Internal degrees of freedom are modeled using a single continuous variable corresponding to the molecular internal energy. Non-equilibrium velocity distribution function, compatible with macroscopic field variables, is constructed using the maximum entropy principle. A proper collision cross section is constructed which obeys the micro-reversibility requirement. The source term and entropy production rate are determined in the form which generalizes the results obtained within the framework of extended thermodynamics. They can be adapted to appropriate physical situations due to the presence of parameters. They are also compared with the results obtained using BGK approximation. For the proposed model the shock structure problem is thoroughly analyzed.
A Fokker-Planck Model of the Boltzmann Equation with Correct Prandtl Number for Polyatomic Gases
Mathiaud, J.; Mieussens, L.
2017-07-01
We propose an extension of the Fokker-Planck model of the Boltzmann equation to get a correct Prandtl number in the Compressible Navier-Stokes asymptotics for polyatomic gases. This is obtained by replacing the diffusion coefficient (which is the equilibrium temperature) by a non diagonal temperature tensor, like the Ellipsoidal-Statistical model is obtained from the Bathnagar-Gross-Krook model of the Boltzmann equation, and by adding a diffusion term for the internal energy. Our model is proved to satisfy the properties of conservation and a H-theorem. A Chapman-Enskog analysis shows how to compute the transport coefficients of our model. Some numerical tests are performed to illustrate that a correct Prandtl number can be obtained.
Institute of Scientific and Technical Information of China (English)
冯海冉; 丁世良
2007-01-01
We have constructed the algebraic vibration Hamiltonian and time evolution operator for the linear triatomic molecule in the intense laser fields by using the quadratic anharmonic model and Magnus approximation.The relations between the multiphoton transition probability of the DCN molecule and the frequency and intensity of the external field are discussed.%使用二次非谐振子模型和Magnus近似方法构造了在强激光场下线型三原子分子的振动哈密顿并推导出时间演化算符的代数形式,在此基础上研究了线型DCN分子的跃迁几率随外场的频率和强度的变化关系,表明了多光子跃迁谱的特点.
Electromagnetically induced transparency of ultra-long-range Rydberg molecules
DEFF Research Database (Denmark)
Mirgorodskiy, Ivan; Christaller, Florian; Braun, Christoph
2017-01-01
We study the impact of Rydberg molecule formation on the storage and retrieval of Rydberg polaritons in an ultracold atomic medium. We observe coherent revivals appearing in the storage and retrieval efficiency of stored photons that originate from simultaneous excitation of Rydberg atoms...... and Rydberg molecules in the system with subsequent interference between the possible storage paths. We show that over a large range of principal quantum numbers the observed results can be described by a two-state model including only the atomic Rydberg state and the Rydberg dimer molecule state. At higher...... principal quantum numbers the influence of polyatomic molecules becomes relevant and the dynamics of the system undergoes a transition from coherent evolution of a few-state system to an effective dephasing into a continuum of molecular states....
Pruemper, G
2007-01-01
In molecular photofragmentation processes by soft X-rays, a number of ionic fragments can be produced, each having a different abundance and correlation with the emitted electron kinetic energy. For investigating these fragmentation processes, electron-ion and electron-ion-ion coincidence experiments, in which the kinetic energy of electrons are analyzed using an electrostatic analyzer while the mass of the ions is analyzed using a pulsed electric field, are very powerful. For such measurements, however, the contribution of random coincidences is substantial and affects the data in a non-trivial way. Simple intuitive subtraction methods cannot be applied. In the present paper, we describe these electron-ion and electron-ion-ion coincidence experiments together with a subtraction method for the contribution from random coincidences. We provide a comprehensive set of equations for the data treatment, including equations for the calculation of error-bars. We demonstrate the method by applying it to the fragmenta...
Energy Technology Data Exchange (ETDEWEB)
Sundberg, K. R.
1976-01-01
A method is developed to optimize the separated-pair independent particle (SPIP) wave function; it is a special case of the separated-pair theory obtained by using two-term natural expansions of the geminals. The orbitals are optimized by a theory based on the generalized Brillouin theorem and iterative configuration interaction (CI) calculations in the space of the SPIP function and its single excitations. The geminal expansion coefficients are optimized by serial 2 x 2 CI calculations. Formulas are derived for the matrix elements. An algorithm to implement the method is presented, and the work needed to evaluate the molecular integrals is discussed. (auth)
Duan, Xiongwei; Xiao, Manjun; Chen, Jianhua; Wang, Xiangdong; Peng, Wenhong; Duan, Linrui; Tan, Hua; Lei, Gangtie; Yang, Renqiang; Zhu, Weiguo
2015-08-26
Two isomeric A-Ar-A-type small molecules of DPP2An(9,10) and DPP2An(2,6), were synthesized with two acceptor arms of diketopyrropyrroles (DPP) and a planar aryl hydrocarbon core of the different substituted anthracene (An), respectively. Their thermal stability, crystallinity, optoelectronic, and photovoltaic performances were investigated. Significantly red-shifted absorption profile and higher HOMO level were observed for the DPP2An(2,6) with 2,6-substituted anthracene relative to the DPP2An(9,10) with 9,10-substituted anthracene, as the former exhibited better planarity and a larger conjugate system. As a result, the solution-processing solar cells based on DPP2An(2,6) and PC71BM (w/w,1:1) displayed remarkably increased power conversion efficiency of 5.44% and short-circuit current density (Jsc) of 11.90 mA/cm(2) under 1% 1,8-diiodooctane additive. The PCE and Jsc values were 3.7 and 2.9 times those of the optimized DPP2An(9,10)-based cells, respectively. This work demonstrates that changing the linkage position of the anthracene core in the A-Ar-A-type SMs can strongly improve the photovoltaic properties in organic solar cells.
Energy Technology Data Exchange (ETDEWEB)
Schmidt, Andre Campos Kersten
1995-12-31
The effects of different vibrational modes on the isomerization process of polyatomic molecules, or solvent`s effects on reaction rates are object of up-to-date interest. In general, such many body phenomena are, in principle, multidimensional, and they first require a reduction of relevant degrees of freedom. In order to investigated, some aspects of the intra-molecular proton tunneling on a malonaldehyde molecule, we use the Generator Coordinate Method. The model used to describe such a process is the so-called System-Bath model, where the system is the reaction coordinate and the bath are the intrinsic degrees of freedom (vibrational modes of the molecule), which are described by a harmonic oscillator set linearly coupled to the system. The reduction of the multidimensional problem to the effective unidimensional one is done using a energy related variational principle on the intrinsic degrees of freedom. we obtained analytically a effective Hamiltonian where the effects of the various degrees of freedom reveal themselves in the appearance of a effective mass and in changes of the shape of the potential barrier. The analyticity of the method was crucial on identifying clearly the roles played by the different physical parameters involved. (author) 17 refs., 29 figs.
Brinckerhoff, W. B.; van Amerom, F.; Danell, R.; Pinnick, V. T.; Arevalo, R. D.; Li, X.; Hovmand, L.; Siljestrom, S.; Mahaffy, P. R.; Goetz, W.; Goesmann, F.; Steininger, H.
2013-12-01
The 2018 ExoMars rover mission includes the Mars Organic Molecule Analyzer (MOMA) investigation. MOMA will examine the chemical composition of samples acquired from depths of up to two meters below the martian surface, where organics may be protected from radiative and oxidative degradation. When combined with the complement of instruments in the rover's Pasteur Payload, MOMA has the potential to reveal the presence of a wide range of organics preserved in a variety of mineralogical environments, and to begin to understand the structural character and potential origin of those compounds. MOMA includes an ion trap mass spectrometer (ITMS) that is designed to analyze molecular composition of (i) gas evolved from pyrolyzed powder samples and separated on a gas chromatograph and (ii) ions directly desorbed from solid samples at Mars ambient pressure using a pulsed laser and a fast-valve capillary ion inlet system. This 'dual source' approach gives MOMA unprecedented breadth of detection over a wide range of molecular weights and volatilities. Analysis of nonvolatile, higher-molecular weight organics such as carboxylic acids and peptides even in the presence of significant perchlorate concentrations is enabled by the extremely short (~1 ns) pulses of the desorption laser. Use of the ion trap's tandem mass spectrometry mode permits selective focus on key species for isolation and controlled fragmentation, providing structural analysis capabilities. The flight-like engineering test unit (ETU) of the ITMS, now under construction, will be used to verify breadboard performance with high fidelity, while simultaneously supporting the development of analytical scripts and spectral libraries using synthetic and natural Mars analog samples guided by current results from MSL. ETU campaign data will strongly advise the specifics of the calibration applied to the MOMA flight model as well as the science operational procedures during the mission.
The method of Gaussian weighted trajectories. V. On the 1GB procedure for polyatomic processes
Bonnet, Laurent
2010-01-01
In recent years, many chemical reactions have been studied by means of the quasi-classical trajectory (QCT) method within the Gaussian binning (GB) procedure. The latter consists in "quantizing" the final vibrational actions in Bohr spirit by putting strong emphasis on the trajectories reaching the products with vibrational actions close to integer values. A major drawback of this procedure is that if N is the number of product vibrational modes, the amount of trajectories necessary to converge the calculations is ~ 10^N larger than with the standard QCT method. Applying it to polyatomic processes is thus problematic. In a recent paper, however, Czako and Bowman propose to quantize the total vibrational energy instead of the vibrational actions [G. Czako and J. M. Bowman, J. Chem. Phys., 131, 244302 (2009)], a procedure called 1GB here. The calculations are then only ~ 10 times more time-consuming than with the standard QCT method, allowing thereby for considerable numerical saving. In this paper, we propose ...
Directory of Open Access Journals (Sweden)
Arindam Chakraborty
2006-03-01
orbital in almost all conformations. One more important result of the present study is that, with the physical process of structural evolution from close angular shape to the linear transition state, the length of the ÃÂƒ (OÃ¢Â€Â“H decreases and its strength increases as a monotone function of reaction coordinates. The bond length is shortest and the strength is largest at the transition state of structural inversion. Result of structural effect of the present study during the evolution of molecular conformations is quite consistent with the result of a very refined calculation that one physically significant feature of force field that the stretching force constants at the linear geometry are considerably larger than their equilibrium counter parts. The variation of bond strength and the hybridization of s and p orbitals on O atom center to form the ÃÂƒ (OÃ¢Â€Â“H bond as a function of evolution of conformations is in accordance with CoulsonÃ¢Â€Â™s prediction. The total dipole moment of all conformations is partitioned into the contribution from bonds and lone pairs and correlated in terms of the computed hybridization in lone pairs. The analysis of the variation of dipole moment as a function of angular to linear structural evolution reveals that the dipole moment of H2O molecule is not due to the bond moments only but a significant contribution comes from a lone pair. It is strongly established that the dipole moment of water molecule at and around the equilibrium geometry is not due to the bond moments only and the major part of the molecular dipole comes from the contribution of lone pair electrons. This necessitates the accommodation of a lone pair of electrons in a hybrid orbital on O atom. The computed LMOÃ¢Â€Â™s webbed with partitioned molecular dipole reveal that one lone pair is in a pure p- type orbital and the other lone pair is in a hybrid of s and p, and not in a pure s type orbital as suggested on the basis of
Hu, Kainan; Zhang, Hongwu
2016-01-01
A lattice Boltzmann scheme associated with flexible Prandtl number and specific heat ratio is proposed, which is based on the polyatomic ellipsoidal statistics model(ES-BGK). The Prandtl number can be modified by a parameter of the Gaussian distribution and the specific heat ratio can be modified by additional free degrees. For the sake of constructing the scheme proposed, the Gaussian distribution is expanded on the Hermite polynomials and the general term formula for the Hermite coefficients of the Gaussian distribution is deduced. Benchmarks are carried out to verify the scheme proposed. The numerical results are in good agreement with the the analytical solutions.
Hutzler, Nicholas R.; Doyle, John M.
2014-06-01
Cryogenic buffer gas cooled beams and cells can be used to study many species, from atoms and polar molecules to biomolecules. We report on recent applications of this technique to improve the limit on the electron electric dipole moment [1], load polar molecules into a magnetic trap through optical pumping [2], perform chirally sensitive microwave spectroscopy on polyatomic molecules [3], progress towards magneto-optical trapping of polar molecules [4], and studies of atom-molecule sticking [5]. [1] The ACME Collaboration: J. Baron et al., Science 343, p. 269 (2014) [2] B. Hemmerling et al., arXiv:1310.2669, to appear in Phys. Rev. Lett. [3] D. Patterson, M. Schnell, & J. M. Doyle, Nature 497, p. 475 (2013) [4] H. Lu et al., arXiv:1310.3239, to appear in New. J. Phys. [5] J. Piskorski et al., under preparation
Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela
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.
Pribil, M.J.; Wanty, R.B.; Ridley, W.I.; Borrok, D.M.
2010-01-01
An increased interest in high precision Cu isotope ratio measurements using multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) has developed recently for various natural geologic systems and environmental applications, these typically contain high concentrations of sulfur, particularly in the form of sulfate (SO42-) and sulfide (S). For example, Cu, Fe, and Zn concentrations in acid mine drainage (AMD) can range from 100??g/L to greater than 50mg/L with sulfur species concentrations reaching greater than 1000mg/L. Routine separation of Cu, Fe and Zn from AMD, Cu-sulfide minerals and other geological matrices usually incorporates single anion exchange resin column chromatography for metal separation. During chromatographic separation, variable breakthrough of SO42- during anion exchange resin column chromatography into the Cu fractions was observed as a function of the initial sulfur to Cu ratio, column properties, and the sample matrix. SO42- present in the Cu fraction can form a polyatomic 32S-14N-16O-1H species causing a direct mass interference with 63Cu and producing artificially light ??65Cu values. Here we report the extent of the mass interference caused by SO42- breakthrough when measuring ??65Cu on natural samples and NIST SRM 976 Cu isotope spiked with SO42- after both single anion column chromatography and double anion column chromatography. A set of five 100??g/L Cu SRM 976 samples spiked with 500mg/L SO42- resulted in an average ??65Cu of -3.50?????5.42??? following single anion column separation with variable SO42- breakthrough but an average concentration of 770??g/L. Following double anion column separation, the average SO42-concentration of 13??g/L resulted in better precision and accuracy for the measured ??65Cu value of 0.01?????0.02??? relative to the expected 0??? for SRM 976. We conclude that attention to SO42- breakthrough on sulfur-rich samples is necessary for accurate and precise measurements of ??65Cu and may require
Directory of Open Access Journals (Sweden)
Gildeberto S. Cardoso
2011-01-01
Full Text Available This paper presents a study of linear control systems based on exact feedback linearization and approximate feedback linearization. As exact feedback linearization is applied, a linear controller can perform the control objectives. The approximate feedback linearization is required when a nonlinear system presents a noninvolutive property. It uses a Taylor series expansion in order to compute a nonlinear transformation of coordinates to satisfy the involutivity conditions.
Energy Technology Data Exchange (ETDEWEB)
Patel, Umang R., E-mail: umangpatel193@yahoo.ca [Gandhinagar Institute of Technology, Moti Bhoyan, Gandhinagar-382721, Gujarat (India); Sardar Patel University, Vallabh Vidyanagar-388120, Gujarat (India); Joshipura, K. N.; Pandya, Siddharth H. [Sardar Patel University, Vallabh Vidyanagar-388120, Gujarat (India); Kothari, Harshit N. [Universal College of Engineering and Technology, Moti Bhoyan, Gandhinagar-382721, Gujarat (India)
2014-01-28
In this paper, we report theoretical electron impact ionization cross sections from threshold to 2000 eV for isocarbonic open chain molecules C{sub 4}H{sub 6}, C{sub 4}H{sub 8}, C{sub 4}F{sub 6} including their isomers, and closed chain molecules c-C{sub 4}H{sub 8} and c-C{sub 4}F{sub 8}. Theoretical formalism employed presently, viz., Complex Scattering Potential-ionization contribution method has been used successfully for a variety of polyatomic molecules. The present ionization calculations are very important since results available for the studied targets are either scarce or none. Our work affords comparison of C{sub 4} containing hydrocarbon versus fluorocarbon molecules. Comparisons of the present ionization cross sections are made wherever possible, and new ionization data are also presented.
Application of the R-matrix method to Photoionization of Molecules
Tashiro, Motomichi
2010-01-01
The R-matrix method has been used for theoretical calculation of electron collision with atoms and molecules for long years. The method was also formulated to treat photoionization process, however, its application has been mostly limited to photoionization of atoms. In this work, we implement the R-matrix method to treat molecular photoionization problem based on the UK R-matrix codes. This method can be used for diatomic as well as polyatomic molecules, with multi-configurational description for electronic states of both target neutral molecule and product molecular ion. Test calculations were performed for valence electron photoionization of nitrogen (N2) as well as nitric oxide (NO) molecules. Calculated photoionization cross sections and asymmetry parameters agree reasonably well with the available experimental results, suggesting usefulness of the method for molecular photoionization.
Energy Technology Data Exchange (ETDEWEB)
Bin Hassan, Oskar Hasdinor
2010-10-21
Materials with Polyatomic anions of [Al{sub 2}O{sub 7}]{sup -8}, [Ti{sub 2}O{sub 8}]{sup -8} and [P{sub 2}O{sub 7}]{sup -4} were investigated with respect to their ionic conductivity properties as well as its thermal expansion properties with the aim to use them as SOFCs electrolytes. The polyatomic anion groups selected from the oxy-cuspidine family of Gd{sub 4}Al{sub 2}O{sub 9} and Gd{sub 4}Ti{sub 2}O{sub 10} as well as from pyrophosphate SnP{sub 2}O{sub 7}. The pure oxy-cuspidine Gd{sub 4}Al{sub 2}O{sub 9}, the series of Gd{sub 4}Al{sub 2-x}Mg{sub x}O{sub 9-x/2} with x=0.10-1.0 and Gd{sub 4-x}M{sub x}Al{sub 2}O{sub 9-x/2} (M=Ca, Sr) with x = 0.05-0.5 were prepared successfully by the citrate complexation method. All samples showed the crystal structure of monoclinic oxycuspidine structure with space group of P2{sub 1/c} and Z=4. No solid solution was observed for Gd{sub 4}Al{sub 2-x}Mg{sub x}O{sub 9-x/2} where additional phases of Gd{sub 2}O{sub 3} and MgO were presence. XRD semiquantitative analysis together with SEM-EDX analysis revealed that Mg{sup 2+} was not able to substitute the Al{sup 3+} ions even at low Mg{sup 2+} concentration. The solid solution limit of Gd{sub 4-x}Ca{sub x}Al{sub 2}O{sub 9-x/2} and Gd{sub 4-x}Sr{sub x}Al{sub 2}O{sub 9-x/2} was determined between 0.05-0.10 and 0.01-0.05 mol for Ca and Sr, respectively. Beyond the substitution limit Gd{sub 4}Al{sub 2}O{sub 9}, GdAlO{sub 3} and SrGd{sub 2}Al{sub 2}O{sub 7} appeared as additional phases. The highest electrical conductivity obtained at 900 C yielded {sigma}= 1.49 x 10{sup -4}Scm{sup -1} for Gd{sub 3.95}Ca{sub 0.05}Al{sub 2}O{sub 8.98}. In comparison, the conductivity of pure Gd{sub 4}Al{sub 2}O{sub 9} was {sigma}= 1.73 x 10{sup -5} Scm{sup -1}. The conductivities determined were in a similar range as those of other cuspidine materials investigated previously. The thermal expansion coefficient of Gd{sub 4}Al{sub 2}O{sub 9} at 1000 C was 7.4 x 10{sup -6}K{sup -1}. The earlier reported
Energy Technology Data Exchange (ETDEWEB)
Bin Hassan, Oskar Hasdinor
2010-10-21
Materials with Polyatomic anions of [Al{sub 2}O{sub 7}]{sup -8}, [Ti{sub 2}O{sub 8}]{sup -8} and [P{sub 2}O{sub 7}]{sup -4} were investigated with respect to their ionic conductivity properties as well as its thermal expansion properties with the aim to use them as SOFCs electrolytes. The polyatomic anion groups selected from the oxy-cuspidine family of Gd{sub 4}Al{sub 2}O{sub 9} and Gd{sub 4}Ti{sub 2}O{sub 10} as well as from pyrophosphate SnP{sub 2}O{sub 7}. The pure oxy-cuspidine Gd{sub 4}Al{sub 2}O{sub 9}, the series of Gd{sub 4}Al{sub 2-x}Mg{sub x}O{sub 9-x/2} with x=0.10-1.0 and Gd{sub 4-x}M{sub x}Al{sub 2}O{sub 9-x/2} (M=Ca, Sr) with x = 0.05-0.5 were prepared successfully by the citrate complexation method. All samples showed the crystal structure of monoclinic oxycuspidine structure with space group of P2{sub 1/c} and Z=4. No solid solution was observed for Gd{sub 4}Al{sub 2-x}Mg{sub x}O{sub 9-x/2} where additional phases of Gd{sub 2}O{sub 3} and MgO were presence. XRD semiquantitative analysis together with SEM-EDX analysis revealed that Mg{sup 2+} was not able to substitute the Al{sup 3+} ions even at low Mg{sup 2+} concentration. The solid solution limit of Gd{sub 4-x}Ca{sub x}Al{sub 2}O{sub 9-x/2} and Gd{sub 4-x}Sr{sub x}Al{sub 2}O{sub 9-x/2} was determined between 0.05-0.10 and 0.01-0.05 mol for Ca and Sr, respectively. Beyond the substitution limit Gd{sub 4}Al{sub 2}O{sub 9}, GdAlO{sub 3} and SrGd{sub 2}Al{sub 2}O{sub 7} appeared as additional phases. The highest electrical conductivity obtained at 900 C yielded {sigma}= 1.49 x 10{sup -4}Scm{sup -1} for Gd{sub 3.95}Ca{sub 0.05}Al{sub 2}O{sub 8.98}. In comparison, the conductivity of pure Gd{sub 4}Al{sub 2}O{sub 9} was {sigma}= 1.73 x 10{sup -5} Scm{sup -1}. The conductivities determined were in a similar range as those of other cuspidine materials investigated previously. The thermal expansion coefficient of Gd{sub 4}Al{sub 2}O{sub 9} at 1000 C was 7.4 x 10{sup -6}K{sup -1}. The earlier reported
Shilov, Georgi E
1977-01-01
Covers determinants, linear spaces, systems of linear equations, linear functions of a vector argument, coordinate transformations, the canonical form of the matrix of a linear operator, bilinear and quadratic forms, Euclidean spaces, unitary spaces, quadratic forms in Euclidean and unitary spaces, finite-dimensional space. Problems with hints and answers.
Directory of Open Access Journals (Sweden)
Agarwalla Arun
2001-01-01
Full Text Available Linear psoriasis, inflammatory linear varrucous epidermal naevus (ILVEN. Lichen straitus, linear lichen planus and invasion of epidermal naevi by psoriasis have clinical and histopathological overlap. We report two young male patients of true linear psoriasis without classical lesions elsewhere which were proved histopathologically. Seasonal variation and good response to topical antipsoriatic treatment supported the diagnosis.
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.
Energy Technology Data Exchange (ETDEWEB)
Visco, Donald Patrick, Jr. (, . Tennessee Technological University, Cookeville, TN); Faulon, Jean-Loup Michel; Roe, Diana C.
2004-04-01
This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.
Das, Animesh; Gieb, Klaus; Krupskaya, Yulia; Demeshko, Serhiy; Dechert, Sebastian; Klingeler, Rüdiger; Kataev, Vladislav; Büchner, Bernd; Müller, Paul; Meyer, Franc
2011-03-16
First members of a new family of heterometallic Mn/Ni complexes [Mn(2)Ni(3)X(2)L(4)(LH)(2)(H(2)O)(2)] (X = Cl: 1; X = Br: 2) with the new ligand 2-{3-(2-hydroxyphenyl)-1H-pyrazol-1-yl}ethanol (H(2)L) have been synthesized, and single crystals obtained from CH(2)Cl(2) solutions have been characterized crystallographically. The molecular structures feature a quasi-linear Mn(III)-Ni(II)-Ni(II)-Ni(II)-Mn(III) core with six-coordinate metal ions, where elongated axes of all the distorted octahedral coordination polyhedra are aligned parallel and are fixed with respect to each other by intramolecular hydrogen bonds. 1 and 2 exhibit quite strong ferromagnetic exchange interactions throughout (J(Mn-Ni) ≈ 40 K (1) or 42 K (2); J(Ni-Ni) ≈ 22 K (1) or 18 K (2)) that lead to an S(tot) = 7 ground state, and a sizable uniaxial magnetoanisotropy with D(mol) values -0.55 K (1) and -0.45 K (2). These values are directly derived also from frequency- and temperature-dependent high-field EPR spectra. Slow relaxation of the magnetization at low temperatures and single-molecule magnet (SMM) behavior are evident from frequency-dependent peaks in the out-of-phase ac susceptibilities and magnetization versus dc field measurements, with significant energy barriers to spin reversal U(eff) = 27 K (1) and 22 K (2). Pronounced quantum tunnelling steps are observed in the hysteresis loops of the temperature- and scan rate-dependent magnetization data, but with the first relaxation step shifted above (1) or below (2) the zero crossing of the magnetic field, despite the very similar molecular structures. The different behavior of 1 and 2 is interpreted in terms of antiferromagnetic (1) or ferromagnetic (2) intermolecular interactions, which are discussed in view of the subtle differences of intermolecular contacts within the crystal lattice.
Energy Technology Data Exchange (ETDEWEB)
Witte, Travis [Iowa State Univ., Ames, IA (United States)
2011-01-01
This dissertation provides a general introduction to Inductively coupled plasma-mass spectrometry (ICP-MS) and laser ablation (LA) sampling, with an examination of analytical challenges in the employment of this technique. It discusses the origin of metal oxide ions (MO+) in LA-ICP-MS, as well as the effect of introducing helium and nitrogen to the aerosol gas flow on the formation of these polyatomic interferences. It extends the study of polyatomic ions in LA-ICP-MS to metal argide (MAr+) species, an additional source of possible significant interferences in the spectrum. It describes the application of fs-LA-ICP-MS to the determination of uranium isotope ratios in particulate samples.
Espinosa-Müller, A. W.; Bravo, A. N.
The force field method developed by Boyd is extended to include molecules containing atoms other than C and H (e.g., N, O, P, S, Cl, Br,…). A new set of force field parameters is determined in order to redefine the potential energy functions that govern the dynamics of the internal (valence coordinates) degrees of freedom of a molecule. It is shown that the minimum of the partial potential energy surface is significantly affected by electrostatic intramolecular interactions. In this regard the non-bonded interactions appears to be less important than the dipole-dipole type interactions for a given interatomic distance when heteroatoms are present in the molecular framework. The reliability of the extended method as regards minimized structure, vibrational spectra and thermodynamic properties has been checked for more than 20 polyatomic molecules. From the correlation between calculated and experimental properties it is concluded that the method has good potential for further applications on polyatomic molecules with increasing size and topological compexities such as adenine and uracil.
Kopylova, T. N.; Svetlichnyi, Valerii A.; Mayer, G. V.; Reznichenko, A. V.; Podgaetskii, Vitalii M.; Ponomareva, O. V.; Samsonova, L. G.; Filinov, D. N.; Pomogaev, V. A.; Tel'minov, E. N.; Lapin, I. N.; Svetlichnaya, N. N.; Sinchenko, E. I.
2003-11-01
Photophysical processes proceeding in polyatomic organic molecules (pyran derivatives and cyanines) excited by high-power laser radiation at 532 nm are studied. Some properties of their changes depending on the structure, solvent, and excitation conditions are determined. The effect of limitation of high-power exciting radiation by the organic molecules is found. The maximum limitation (Kmax = 15.0 at the initial transmission equal to 70%) was observed for the cyanine derivative and is comparable to this effect for fullerenes C60, which are widely used as radiation limiters.
Towards composite spheres as building blocks for structured molecules
Lee, Lloyd L.; Pellicane, Giuseppe
2016-10-01
In order to design a flexible molecular model that mimics the chemical moieties of a polyatomic molecule, we propose the ‘composite-sphere’ model that can assemble the essential elements to produce the structure of the target molecule. This is likened to the polymerization process where monomers assemble to form the polymer. The assemblage is built into the pair interaction potentials which can ‘react’ (figuratively) with selective pieces into various bonds. In addition, we preserve the spherical symmetries of the individual pair potentials so that the isotropic Ornstein-Zernike equation (OZ) for multi-component mixtures can be used as a theoretical framework. We first test our approach on generating a dumbbell molecule. An equimolar binary mixture of hard spheres and square-well spheres are allowed to react to form a dimer. As the bond length shrinks to zero, we create a site-site model of a Janus-like molecule with a repulsive moiety and an attractive moiety. We employ the zero-separation (ZSEP) closure to solve the OZ equations. The structure and thermodynamic properties are calculated at three isotherms and at several densities and the results are compared with Monte Carlo simulations. The close agreement achieved demonstrates that the ZSEP closure is a reliable theory for this composite-sphere fluid model. Contribution to the George Stell Memorial Issue.
Jansen, Paul; Xu, Li-Hong; Ubachs, Wim; Bethlem, Hendrick L
2011-01-01
Recently, methanol was identified as a sensitive target system to probe variations of the proton-to-electron mass ratio $\\mu$ [Jansen \\emph{et al.} Phys. Rev. Lett. \\textbf{106}, 100801 (2011)]. The high sensitivity of methanol originates from the interplay between overall rotation and hindered internal rotation of the molecule -- i.e. transitions that convert internal rotation energy into overall rotation energy, or vice versa, give rise to an enhancement of the sensitivity coefficient, $K_{\\mu}$. As internal rotation is a common phenomenon in polyatomic molecules, it is likely that other molecules display similar or even larger effects. In this paper we generalize the concepts that form the foundation of the high sensitivity in methanol and use this to construct an approximate model which allows to estimate the sensitivities of transitions in internal rotor molecules with $C_{3v}$ symmetry, without performing a full calculation of energy levels. We find that a reliable estimate of transition sensitivities c...
The report documents a series of seminars at Rome Air Development Center with the content equivalent to an intense course in Linear Systems . Material...is slanted toward the practicing engineer and introduces some of the fundamental concepts and techniques for analyzing linear systems . Techniques for
Stoll, R R
1968-01-01
Linear Algebra is intended to be used as a text for a one-semester course in linear algebra at the undergraduate level. The treatment of the subject will be both useful to students of mathematics and those interested primarily in applications of the theory. The major prerequisite for mastering the material is the readiness of the student to reason abstractly. Specifically, this calls for an understanding of the fact that axioms are assumptions and that theorems are logical consequences of one or more axioms. Familiarity with calculus and linear differential equations is required for understand
Simplified generalized-gradient approximation and anharmonicity: Benchmark calculations on molecules
Patton, David C.; Porezag, Dirk V.; Pederson, Mark R.
1997-03-01
Recent implementational improvements of the generalized-gradient approximation (GGA) have led to a simplified version which is parametrized entirely from fundamental constants, easier to use, and possibly easier to improve. We have performed detailed calculations on the geometries, atomization energies, vibrational energies, and infrared and Raman spectra of many first- and second-row dimers as well as some polyatomic molecules. For atomization and vibrational energies, we find that the simplified version of GGA leads to results similar to the original version. We comment on the fact that GGA-induced changes of hydrogenic bonding are different than for the other atoms in the periodic table but still an improvement over the local approximations to density-functional theory. In addition to a harmonic treatment of the vibrational modes we include the contributions of anharmonicity as well. With the exception of the light hydrogen containing molecules anharmonic corrections are quite small.
Application of a Simplified GGA to a Database of Small Molecules
Patton, David C.; Pederson, Mark R.; Porezag, Dirk V.
1997-03-01
Recent implementational improvements of the generalized gradient approximation (GGA) have led to a simplified version.(J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77), 3865 (1996) We have performed detailed calculations on the geometries, atomization energies, vibrational energies, and infrared and Raman spectra of many first- and second- row dimers as well as some polyatomic molecules. For atomization and vibrational energies, we find that the simplified version of GGA leads to results similar to the original version. We explain why the GGA-induced changes of hydrogenic bonding and vibrations are different than for the other atoms in the periodic table but still are an improvement over the local approximations to density-functional theory. Special emphasis on problem cases such as Cr2 and noble gas molecules will be discussed in greater detail.
A new proof of the analyticity of the electronic density of molecules
Jecko, Thierry
2009-01-01
We give a new, short proof of the regularity away from the nuclei of the electronic density of a molecule obtained in [1,2]. The new argument is based on the regularity properties of the Coulomb interactions underlined in [3] and on well-known elliptic technics. [1] S. Fournais, M. Hoffmann-Ostenhof, T. Hoffmann-Ostenhof, T. Oe stergaard Soerensen: The electron density is smooth away from the nuclei. Comm. Math. Phys. 228, no. 3 (2002), 401-415. [2] S. Fournais, M. Hoffmann-Ostenhof, T. Hoffmann-Ostenhof, T. Oestergaard Soerensen: Analyticity of the density of electronic wave functions. Ark. Mat. 42, no. 1 (2004), 87-106. [3] M. Klein, A. Martinez, R. Seiler, X.P. Wang: On the Born-Oppenheimer expansion for polyatomic molecules. Comm. Math. Phys. 143, no. 3, 607-639 (1992).
Searle, Shayle R
2012-01-01
This 1971 classic on linear models is once again available--as a Wiley Classics Library Edition. It features material that can be understood by any statistician who understands matrix algebra and basic statistical methods.
Solow, Daniel
2014-01-01
This text covers the basic theory and computation for a first course in linear programming, including substantial material on mathematical proof techniques and sophisticated computation methods. Includes Appendix on using Excel. 1984 edition.
Berberian, Sterling K
2014-01-01
Introductory treatment covers basic theory of vector spaces and linear maps - dimension, determinants, eigenvalues, and eigenvectors - plus more advanced topics such as the study of canonical forms for matrices. 1992 edition.
Liesen, Jörg
2015-01-01
This self-contained textbook takes a matrix-oriented approach to linear algebra and presents a complete theory, including all details and proofs, culminating in the Jordan canonical form and its proof. Throughout the development, the applicability of the results is highlighted. Additionally, the book presents special topics from applied linear algebra including matrix functions, the singular value decomposition, the Kronecker product and linear matrix equations. The matrix-oriented approach to linear algebra leads to a better intuition and a deeper understanding of the abstract concepts, and therefore simplifies their use in real world applications. Some of these applications are presented in detailed examples. In several ‘MATLAB-Minutes’ students can comprehend the concepts and results using computational experiments. Necessary basics for the use of MATLAB are presented in a short introduction. Students can also actively work with the material and practice their mathematical skills in more than 300 exerc...
Complex organic molecules in protostellar environments in the SKA era
Codella, C; Fontani, F; Jiménez-Serra, I; Caselli, P; Ceccarelli, C; Palumbo, M E; López-Sepulcre, A; Beltrán, M T; Lefloch, B; Brucato, J R; Viti, S; Testi, L
2014-01-01
Molecular complexity builds up at each step of the Sun-like star formation process, starting from simple molecules and ending up in large polyatomic species. Complex organic molecules (COMs; such as methyl formate, HCOOCH$_3$, dymethyl ether, CH$_3$OCH$_3$, formamide, NH$_2$CHO, or glycoaldehyde, HCOCH$_2$OH) are formed in all the components of the star formation recipe (e.g. pre-stellar cores, hot-corinos, circumstellar disks, shocks induced by fast jets), due to ice grain mantle sublimation or sputtering as well as gas-phase reactions. Understanding in great detail the involved processes is likely the only way to predict the ultimate molecular complexity reached in the ISM, as the detection of large molecules is increasingly more difficult with the increase of the number of atoms constituting them. Thanks to the recent spectacular progress of astronomical observations, due to the Herschel (sub-mm and IR), IRAM and SMA (mm and sub-mm), and NRAO (cm) telescopes, an enormous activity is being developed in the ...
Energy Technology Data Exchange (ETDEWEB)
Chu, P.M.Y.
1991-10-01
The vibrational to translational (V{yields}T) energy transfer in collisions between large highly vibrationally excited polyatomics and rare gases was investigated by time-of-flight techniques. Two different methods, UV excitation followed by intemal conversion and infrared multiphoton excitation (IRMPE), were used to form vibrationally excited molecular beams of hexafluorobenzene and sulfur hexafluoride, respectively. The product translational energy was found to be independent of the vibrational excitation. These results indicate that the probability distribution function for V{yields}T energy transfer is peaked at zero. The collisional relaxation of large polyatomic molecules with rare gases most likely occurs through a rotationally mediated process. Photodissociation of nitrobenzene in a molecular beam was studied at 266 nm. Two primary dissociation channels were identified including simple bond rupture to produce nitrogen dioxide and phenyl radical and isomerization to form nitric oxide and phenoxy radical. The time-of-flight spectra indicate that simple bond rupture and isomerization occurs via two different mechanisms. Secondary dissociation of the phenoxy radicals to carbon monoxide and cyclopentadienyl radicals was observed as well as secondary photodissociation of phenyl radical to give H atom and benzyne. A supersonic methyl radical beam source is developed. The beam source configuration and conditions were optimized for CH{sub 3} production from the thermal decomposition of azomethane. Elastic scattering of methyl radical and neon was used to differentiate between the methyl radicals and the residual azomethane in the molecular beam.
Energy Technology Data Exchange (ETDEWEB)
Chu, Pamela Mei-Ying [Univ. of California, Berkeley, CA (United States)
1991-10-01
The vibrational to translational (V→T) energy transfer in collisions between large highly vibrationally excited polyatomics and rare gases was investigated by time-of-flight techniques. Two different methods, UV excitation followed by intemal conversion and infrared multiphoton excitation (IRMPE), were used to form vibrationally excited molecular beams of hexafluorobenzene and sulfur hexafluoride, respectively. The product translational energy was found to be independent of the vibrational excitation. These results indicate that the probability distribution function for V→T energy transfer is peaked at zero. The collisional relaxation of large polyatomic molecules with rare gases most likely occurs through a rotationally mediated process. Photodissociation of nitrobenzene in a molecular beam was studied at 266 nm. Two primary dissociation channels were identified including simple bond rupture to produce nitrogen dioxide and phenyl radical and isomerization to form nitric oxide and phenoxy radical. The time-of-flight spectra indicate that simple bond rupture and isomerization occurs via two different mechanisms. Secondary dissociation of the phenoxy radicals to carbon monoxide and cyclopentadienyl radicals was observed as well as secondary photodissociation of phenyl radical to give H atom and benzyne. A supersonic methyl radical beam source is developed. The beam source configuration and conditions were optimized for CH_{3} production from the thermal decomposition of azomethane. Elastic scattering of methyl radical and neon was used to differentiate between the methyl radicals and the residual azomethane in the molecular beam.
Gutsche, Thomas; Faessler, Amand; Lee, Ian Woo; Lyubovitskij, Valery E
2010-01-01
We discuss a possible interpretation of the open charm mesons $D_{s0}^*(2317)$, $D_{s1}(2460)$ and the hidden charm mesons X(3872), Y(3940) and Y(4140) as hadron molecules. Using a phenomenological Lagrangian approach we review the strong and radiative decays of the $D_{s0}^* (2317)$ and $D_{s1}(2460)$ states. The X(3872) is assumed to consist dominantly of molecular hadronic components with an additional small admixture of a charmonium configuration. Determing the radiative ($\\gamma J/\\psi$ and $\\gamma \\psi(2s)$) and strong ($J/\\psi 2\\pi $ and $ J/\\psi 3\\pi$) decay modes we show that present experimental observation is consistent with the molecular structure assumption of the X(3872). Finally we give evidence for molecular interpretations of the Y(3940) and Y(4140) related to the observed strong decay modes $J/\\psi + \\omega$ or $J/\\psi + \\phi$, respectively.
Olive, David J
2017-01-01
This text covers both multiple linear regression and some experimental design models. The text uses the response plot to visualize the model and to detect outliers, does not assume that the error distribution has a known parametric distribution, develops prediction intervals that work when the error distribution is unknown, suggests bootstrap hypothesis tests that may be useful for inference after variable selection, and develops prediction regions and large sample theory for the multivariate linear regression model that has m response variables. A relationship between multivariate prediction regions and confidence regions provides a simple way to bootstrap confidence regions. These confidence regions often provide a practical method for testing hypotheses. There is also a chapter on generalized linear models and generalized additive models. There are many R functions to produce response and residual plots, to simulate prediction intervals and hypothesis tests, to detect outliers, and to choose response trans...
Sahai, Vivek
2013-01-01
Beginning with the basic concepts of vector spaces such as linear independence, basis and dimension, quotient space, linear transformation and duality with an exposition of the theory of linear operators on a finite dimensional vector space, this book includes the concept of eigenvalues and eigenvectors, diagonalization, triangulation and Jordan and rational canonical forms. Inner product spaces which cover finite dimensional spectral theory and an elementary theory of bilinear forms are also discussed. This new edition of the book incorporates the rich feedback of its readers. We have added new subject matter in the text to make the book more comprehensive. Many new examples have been discussed to illustrate the text. More exercises have been included. We have taken care to arrange the exercises in increasing order of difficulty. There is now a new section of hints for almost all exercises, except those which are straightforward, to enhance their importance for individual study and for classroom use.
Edwards, Harold M
1995-01-01
In his new undergraduate textbook, Harold M Edwards proposes a radically new and thoroughly algorithmic approach to linear algebra Originally inspired by the constructive philosophy of mathematics championed in the 19th century by Leopold Kronecker, the approach is well suited to students in the computer-dominated late 20th century Each proof is an algorithm described in English that can be translated into the computer language the class is using and put to work solving problems and generating new examples, making the study of linear algebra a truly interactive experience Designed for a one-semester course, this text adopts an algorithmic approach to linear algebra giving the student many examples to work through and copious exercises to test their skills and extend their knowledge of the subject Students at all levels will find much interactive instruction in this text while teachers will find stimulating examples and methods of approach to the subject
Institute of Scientific and Technical Information of China (English)
Hu Fei-Fei; Zhou Sheng-Peng; Hu Zhan; Jin Ming-Xing; Zhang Dong-Dong; Wu Di; Cheng Xi-Hui; Jiang Dian-Wu; Diug Da-Jun
2009-01-01
This paper reports that a one-colour fs pump-probe measurement has been carried out for studying photoionization/photodissociation of cyclohexanone(CsH10O)in intense laser field.Two of the fragments from cyclohcxanone,C2H+3 and C3H+3,are studied under 800 nm laser pump-probe and the results obtained show similar time evolutions.It proposes a feasible model for analysing the experimental observations of the one-colour fs pump-probe measurement.The results demonstrate that as an intermediate product,the excited molecular parent ions play a very important role in photionization/photodissociation processes in intense laser field.
Kennedy, Ivan R
2015-01-01
An objective revision of the Laplace barometric formula for isothermal planetary atmospheres is proposed. From Clausius virial theorem equating the root mean square kinetic energy to half the gravitational potential energy, planetary atmospheres are required to have declining temperature with altitude as a consequence of the interaction between thermodynamic heat flow and gravity. The virial action hypothesis predicts non adiabatic lapse rates in temperature yielding a practical means to calculate variations with altitude in atmospheric entropy, free energy, molecular density and pressure. Remarkably, the new formulae derived enable prediction of atmospheric profiles with physical properties closely resembling those observed on Earth, Venus and Mars. These new formulae provide an objective basis for computing the dynamic morphology of the atmosphere. Climate scientists may consider this explanatory hypothesis for self organisation of planetary atmospheres for its possible relevance for predicting global surfa...
Energy Technology Data Exchange (ETDEWEB)
Vasilyev, V.A.; Levay, B.; Minkova, A.; Petrukhin, V.I.; Horvath, D.
1985-12-01
The atomic capture and transfer of stopped negative pions have been studied in binary gas mixtures of H/sub 2/+M, where M is CCl/sub 2/F/sub 2/, CClF/sub 3/, CBrF/sub 3/ or SF/sub 6/. The ..pi../sup 0/ yield, versus relative atomic concentration Csub(A) of M, goes through a maximum at Csub(A)proportional0.1 and levels off at zero at high concentrations. This phenomenon together with other observed characteristics of the atomic capture and transfer of pions in these systems is interpreted in the frame of a phenomenological model. The average transfer coefficients anti ..lambda..sub(Z) exhibit a weak concentration dependence. The estimated average atomic capture ratios anti A(Z/H) are lower than those found for noble gases, probably because of the mutual screening of the constituent atoms in the molecules. The probability of pion capture in an atomic orbit is not proportional to the stopping power of the components of the mixture. (orig.).
Allenby, Reg
1995-01-01
As the basis of equations (and therefore problem-solving), linear algebra is the most widely taught sub-division of pure mathematics. Dr Allenby has used his experience of teaching linear algebra to write a lively book on the subject that includes historical information about the founders of the subject as well as giving a basic introduction to the mathematics undergraduate. The whole text has been written in a connected way with ideas introduced as they occur naturally. As with the other books in the series, there are many worked examples.Solutions to the exercises are available onlin
Karloff, Howard
1991-01-01
To this reviewer’s knowledge, this is the first book accessible to the upper division undergraduate or beginning graduate student that surveys linear programming from the Simplex Method…via the Ellipsoid algorithm to Karmarkar’s algorithm. Moreover, its point of view is algorithmic and thus it provides both a history and a case history of work in complexity theory. The presentation is admirable; Karloff's style is informal (even humorous at times) without sacrificing anything necessary for understanding. Diagrams (including horizontal brackets that group terms) aid in providing clarity. The end-of-chapter notes are helpful...Recommended highly for acquisition, since it is not only a textbook, but can also be used for independent reading and study. —Choice Reviews The reader will be well served by reading the monograph from cover to cover. The author succeeds in providing a concise, readable, understandable introduction to modern linear programming. —Mathematics of Computing This is a textbook intend...
Costes, Jean Pierre; Titos-Padilla, Silvia; Oyarzabal, Itziar; Gupta, Tulika; Duhayon, Carine; Rajaraman, Gopalan; Colacio, Enrique
2015-10-26
Three new Dy complexes have been prepared according to a complex-as-ligand strategy. Structural determinations indicate that the central Dy ion is surrounded by two LZn units (L(2-) is the di-deprotonated form of the N2 O2 compartmental N,N'-2,2-dimethylpropylenedi(3-methoxysalicylideneiminato) Schiff base. The Dy ions are nonacoordinate to eight oxygen atoms from the two L ligands and to a water molecule. The Zn ions are pentacoordinate in all cases, linked to the N2 O2 atoms from L, and the apical position of the Zn coordination sphere is occupied by a water molecule or bromide or chloride ions. These resulting complexes, formulated (LZnX)-Dy-(LZnX), are tricationic with X=H2 O and monocationic with X=Br or Cl. They behave as field-free single-molecule magnets (SMMs) with effective energy barriers (Ueff ) for the reversal of the magnetization of 96.9(6) K with τ0 =2.4×10(-7) s, 146.8(5) K with τ0 =9.2×10(-8) s, and 146.1(10) K with τ0 =9.9×10(-8) s for compounds with ZnOH2 , ZnBr, and ZnCl motifs, respectively. The Cole-Cole plots exhibit semicircular shapes with α parameters in the range of 0.19 to 0.29, which suggests multiple relaxation processes. Under a dc applied magnetic field of 1000 Oe, the quantum tunneling of magnetization (QTM) is partly or fully suppressed and the energy barriers increase to Ueff =128.6(5) K and τ0 =1.8×10(-8) s for 1, Ueff =214.7 K and τ0 =9.8×10(-9) s for 2, and Ueff =202.4 K and τ0 =1.5×10(-8) s for 3. The two pairs of largely negatively charged phenoxido oxygen atoms with short DyO bonds are positioned at opposite sides of the Dy(3+) ion, which thus creates a strong crystal field that stabilizes the axial MJ =±15/2 doublet as the ground Kramers doublet. Although the compound with the ZnOH2 motifs possesses the larger negative charges on the phenolate oxygen atoms, as confirmed by using DFT calculations, it exhibits the larger distortions of the DyO9 coordination
Bourlès, Henri
2013-01-01
Linear systems have all the necessary elements (modeling, identification, analysis and control), from an educational point of view, to help us understand the discipline of automation and apply it efficiently. This book is progressive and organized in such a way that different levels of readership are possible. It is addressed both to beginners and those with a good understanding of automation wishing to enhance their knowledge on the subject. The theory is rigorously developed and illustrated by numerous examples which can be reproduced with the help of appropriate computation software. 60 exe
Meseguer, Carlos; Titos-Padilla, Silvia; Hänninen, Mikko M; Navarrete, R; Mota, A J; Evangelisti, Marco; Ruiz, José; Colacio, Enrique
2014-11-17
New types of linear tetranuclear Ln(III)-Ni(II)-Ni(II)-Ln(III) (Ln(III) = Dy (1), Gd (2)) complexes have been prepared using the multidentate ligand N,N'-bis(3-methoxysalicylidene)-1,3-diaminobenzene, which has two sets of NO and OO' coordination pockets that are able to selectively accommodate Ni(II) and Ln(III) ions, respectively. The X-ray structure analysis reveals that the Ni(II) ions are bridged by phenylenediimine groups forming a 12-membered metallacycle in the central body of the complex, whereas the Ln(III) ions are located at both sides of the metallacycle and linked to the Ni(II) ions by diphenoxo bridging groups. Phenylenediimine and diphenoxo bridging groups transmit ferromagnetic exchange interactions between the two Ni(II) ions and between the Ni(II) and the Ln(III) ions, respectively. Complex 1 shows slow relaxation of the magnetization at zero field and a thermal energy barrier Ueff = 7.4 K with HDC = 1000 Oe, whereas complex 2 exhibits an S = 9 ground state and significant magnetocaloric effect (-ΔSm = 18.5 J kg(-1) K(-1) at T = 3 K and ΔB = 5 T).
Semenov, Alexander; Babikov, Dmitri
2015-12-17
The mixed quantum classical theory, MQCT, for inelastic scattering of two molecules is developed, in which the internal (rotational, vibrational) motion of both collision partners is treated with quantum mechanics, and the molecule-molecule scattering (translational motion) is described by classical trajectories. The resultant MQCT formalism includes a system of coupled differential equations for quantum probability amplitudes, and the classical equations of motion in the mean-field potential. Numerical tests of this theory are carried out for several most important rotational state-to-state transitions in the N2 + H2 system, in a broad range of collision energies. Besides scattering resonances (at low collision energies) excellent agreement with full-quantum results is obtained, including the excitation thresholds, the maxima of cross sections, and even some smaller features, such as slight oscillations of energy dependencies. Most importantly, at higher energies the results of MQCT are nearly identical to the full quantum results, which makes this approach a good alternative to the full-quantum calculations that become computationally expensive at higher collision energies and for heavier collision partners. Extensions of this theory to include vibrational transitions or general asymmetric-top rotor (polyatomic) molecules are relatively straightforward.
High-harmonic spectroscopy of aligned molecules
Yun, Hyeok; Yun, Sang Jae; Lee, Gae Hwang; Nam, Chang Hee
2017-01-01
High harmonics emitted from aligned molecules driven by intense femtosecond laser pulses provide the opportunity to explore the structural information of molecules. The field-free molecular alignment technique is an expedient tool for investigating the structural characteristics of linear molecules. The underlying physics of field-free alignment, showing the characteristic revival structure specific to molecular species, is clearly explained from the quantum-phase analysis of molecular rotational states. The anisotropic nature of molecules is shown from the harmonic polarization measurement performed with spatial interferometry. The multi-orbital characteristics of molecules are investigated using high-harmonic spectroscopy, applied to molecules of N2 and CO2. In the latter case the two-dimensional high-harmonic spectroscopy, implemented using a two-color laser field, is applied to distinguish harmonics from different orbitals. Molecular high-harmonic spectroscopy will open a new route to investigate ultrafast dynamics of molecules.
Visualization of large elongated DNA molecules.
Lee, Jinyong; Kim, Yongkyun; Lee, Seonghyun; Jo, Kyubong
2015-09-01
Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.
Semirigid vibrating rotor target model for atom-polyatom reactions: Application to F+CH4→CH3+HF
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
The semirigid vibrating rotor target (SVRT) model for the polyatomic reaction has been applied to the reaction of F+CH4→HF+CH3. The time-dependent wave packet approach has also been used in the calculation. In the current study, reaction probability, cross-section, and rate constant are calculated for the title reaction on the modified J1 (MJ1) potential energy surface (PES). Numerical calculation shows oscillatory structures in the energy dependence of the calculated reaction probability. Those structures are generally associated with broad dynamical resonance. They are almost washed-out in the energy dependence of integral cross-sections due to summation over partial waves. The calculated rate constant is in good agreement with experimental measurement.
Energy Technology Data Exchange (ETDEWEB)
Holland, D.M.P. E-mail: d.m.p.holland@dl.ac.uk; Shaw, D.A.; Sumner, I.; Hayes, M.A.; Mackie, R.A.; Wannberg, B.; Shpinkova, L.G.; Rennie, E.E.; Cooper, L.; Johnson, C.A.F.; Parker, J.E
2001-08-01
The design, construction and performance of a threshold-photoelectron-photoion coincidence (TPEPICO) spectrometer for the study of unimolecular decomposition in polyatomic ions is described. The spectrometer incorporates a hemispherical electrostatic energy analyser and a time-of-flight (TOF) mass spectrometer. The entrance lens to the hemispherical analyser has been designed to have a high collection efficiency for low energy electrons but to discriminate strongly against energetic electrons. This arrangement has resulted in a resolution of about 3.5 meV being achieved for the threshold electron peak recorded at the krypton {sup 2}P{sub 3/2} ionisation limit. A pulsed electric field is used to extract the ions from the interaction region and propel them towards the TOF analyser. Computer modelling has been used to trace the electron and ion trajectories through their respective analysers. These simulations have enabled the effective interaction volume to be defined, and this has allowed the transmission efficiency of energetic fragment ions, formed through a process which also yielded a threshold electron, to be quantified. The ion TOF peak shape has been examined as a function of initial kinetic energy and as a function of ion residence time. The contribution of energetic fragments, having specific initial spatial and directional properties, to the TOF peak shape has been determined by tracing the paths of individual ions. The actual performance of the spectrometer is illustrated by a TPEPICO spectrum of the krypton isotopes. Experimental breakdown curves for furan are presented as an example of the use of the apparatus to study unimolecular decomposition in polyatomic ions. By introducing a delay between the detection of the threshold electron and the application of the ion extraction field, breakdown curves can be recorded as a function of ion residence time in the source region. The procedure for analysing the data is described, and the experimental factors
LINEAR SYSTEMS AND LINEAR INTERPOLATION I
Institute of Scientific and Technical Information of China (English)
丁立峰
2001-01-01
he linear interpolation of linear system on a family of linear systems is introduced and discussed. Some results and examples on singly generated systems on a finite dimensional vector space are given.
Clouthier, Dennis J.
2011-06-01
One of the important contributions of the science of high resolution molecular spectroscopy has been the identification and characterization of new molecules in the gas phase, whether they exist in the laboratory, in extreme terrestrial environments, or in outer space. Despite the innovative efforts of many dedicated spectroscopists, one can still easily visualize a large number of novel small molecules that remain to be discovered and investigated. In this talk I will review the efforts of our group in recent years to study the electronic spectra of some new, and some not so new but still challenging species, concentrating primarily on those that are made up of main group elements. The target molecules have been produced in a pulsed electric discharge at the exit of a supersonic jet, often using novel precursors which we have had to synthesize in the laboratory. Conventional laser-induced fluorescence as well as wavelength resolved emission, stimulated emission pumping, fluorescence depletion and LIF sync-scan techniques have been used to detect the species of interest. Examples of diatomic and polyatomic transient molecules, free radicals, and ions that we have recently explored will be discussed.
Linear Algebra and Smarandache Linear Algebra
Vasantha, Kandasamy
2003-01-01
The present book, on Smarandache linear algebra, not only studies the Smarandache analogues of linear algebra and its applications, it also aims to bridge the need for new research topics pertaining to linear algebra, purely in the algebraic sense. We have introduced Smarandache semilinear algebra, Smarandache bilinear algebra and Smarandache anti-linear algebra and their fuzzy equivalents. Moreover, in this book, we have brought out the study of linear algebra and ve...
Linear Algebra and Smarandache Linear Algebra
Vasantha, Kandasamy
2003-01-01
The present book, on Smarandache linear algebra, not only studies the Smarandache analogues of linear algebra and its applications, it also aims to bridge the need for new research topics pertaining to linear algebra, purely in the algebraic sense. We have introduced Smarandache semilinear algebra, Smarandache bilinear algebra and Smarandache anti-linear algebra and their fuzzy equivalents. Moreover, in this book, we have brought out the study of linear algebra and ve...
Linear isotherm determination from linear gradient elution experiments.
Pfister, David; Steinebach, Fabian; Morbidelli, Massimo
2015-01-02
A procedure to estimate equilibrium adsorption parameters as a function of the modifier concentration in linear gradient elution chromatography is proposed and its reliability is investigated by comparison with experimental data. Over the past decades, analytical solutions of the so-called equilibrium model under linear gradient elution conditions were derived assuming that proteins and modifier molecules access the same fraction of the pore size distribution of the porous particles. The present approach developed in this work accounts for the size exclusion effect resulting in different exclusions for proteins and modifier. A new analytical solution was derived by applying perturbation theory for differential equations, and the 1st-order approximated solution is presented in this work. Eventually, a turnkey and reliable procedure to efficiently estimate isotherm parameters as a function of modifier concentration from linear gradient elution experiments is proposed.
Linear electric field time-of-flight ion mass spectrometer
Funsten, Herbert O.; Feldman, William C.
2008-06-10
A linear electric field ion mass spectrometer having an evacuated enclosure with means for generating a linear electric field located in the evacuated enclosure and means for injecting a sample material into the linear electric field. A source of pulsed ionizing radiation injects ionizing radiation into the linear electric field to ionize atoms or molecules of the sample material, and timing means determine the time elapsed between ionization of atoms or molecules and arrival of an ion out of the ionized atoms or molecules at a predetermined position.
Institute of Scientific and Technical Information of China (English)
汪明贵; 王宇曦; 唐亚芳; 王正武
2013-01-01
目的评价十二烷基聚氧乙烯聚氧丙烯醚（LSmn）系列表面活性剂与不同类型表面活性剂复配的协同效应。方法测定LS36、LS45、LS54分别与离子型表面活性剂十六烷基三甲基溴化铵（CTAB）、十二烷基磺酸钠（AS）、双-2-乙基己基琥珀酸磺酸钠（AOT）及全氟辛酸钠（OBS）复配的表面张力～浓度对数关系（γ～log c）曲线，计算它们在溶液表面吸附层及胶束中的组成、分子相互作用参数及分子交换能。通过交换能，判断产生的协同效应效果。结果与结论所有混合体系的分子交换能均为负值，与纯组分的表面活性比较，复配后不论是形成胶束的能力，还是降低表面张力的效率和能力均出现显著的协同效应。%Objective To evaluate the synergisms of systems between LSmn surfactants and other types of surfactants. Methods Curves of surface tension vs. the total concentration of the binary system of nonionic surfactants-linear dodecyl polyoxyethylene polyoxypropylene ether C12H25(EO)m(PO)nH, which is also written as LSmn, with different structural ionic surfactants have been measured at 25℃. The series of LSmn are LS36, LS45 and LS54, and the ionic surfactants are cetyltrimethylammonium bromide (CTAB), sodium dodecylesulfonate (AS), sodium of double-2-ethyl hexyl ethylene dicarboxylic acid sulfonic acid (AOT) and sodium perfluorocarylate (OBS). The composition, the parameters of molecule interaction and the molecule-exchanging energies both in the surface phase and in the micelle phase have been obtained from the curves. Results The molecule-exchanging energies are negative. Conclusion All the synergisms in mixed micelle formation and in surface tension reduction efficiency as well as effectiveness remarkably appear in all the studied mixtures.
Prospects for P-bearing molecules in cometary atmospheres
Boice, Daniel; de Almeida, Amaury
Phosphorus is a key element in all known forms of life and phosphorus-bearing compounds have been observed in space. Phosphorus is ubiquitous in meteorites, albeit in small quantities, with phosphates being found in stoney meteorites and phosphides have been identified in iron meteorites. It has been detected as part of the dust component in comet Halley but searches for P-bearing species in the gas phase in comets have been unsuccessful. Based of its moderate cosmic abundance (eighteenth most abundant element, [P]/[N] = 4 x 10-3 ) and the positive identification of P-bearing species in the interstellar medium (such as, PN, PC, HCP and PO), we would expect simple molecules, diatomics (like PH, PO, PC, PS), triatomics (like HCP and PH2 ), and possibly other polyatomics (like phosphine PH3 and diphosphine P2 H4 ), to exist in cometary ices, hence released into the gas phase upon ice sublimation. Our fluid dynamics model with chemistry of cometary comae (SUISEI) has been adapted to study this problem. SUISEI produces cometocentric abundances of the coma gas species; velocities of the bulk gas, light atomic and molecular hydrogen with escape, and electrons; gas and electron temperatures; column densities to facilitate comparison with observations; coma energy budget quantities; attenuation of the solar irradiance; and other quantities that can be related readily to observations. We present results from the first quantitative study of phosphorus-bearing molecules in comets to identify likely species containing phosphorus to aid in future searches for this important element in comets, possibly shedding light on issues of comet formation (time and place) and matters of the prebiotic to biotic evolution of life. Acknowledgements. This work was supported by the NSF Planetary Astronomy Program.
Aligning molecules with intense nonresonant laser fields
DEFF Research Database (Denmark)
Larsen, J.J.; Safvan, C.P.; Sakai, H.
1999-01-01
Molecules in a seeded supersonic beam are aligned by the interaction between an intense nonresonant linearly polarized laser field and the molecular polarizability. We demonstrate the general applicability of the scheme by aligning I2, ICl, CS2, CH3I, and C6H5I molecules. The alignment is probed...... by mass selective two dimensional imaging of the photofragment ions produced by femtosecond laser pulses. Calculations on the degree of alignment of I2 are in good agreement with the experiments. We discuss some future applications of laser aligned molecules....
Madsen, Lars Bojer; Jensen, Frank; Dnestryan, Andrey I.; Tolstikhin, Oleg I.
2017-07-01
In the leading-order approximation of the weak-field asymptotic theory (WFAT), the dependence of the tunneling ionization rate of a molecule in an electric field on its orientation with respect to the field is determined by the structure factor of the ionizing molecular orbital. The WFAT yields an expression for the structure factor in terms of a local property of the orbital in the asymptotic region. However, in general quantum chemistry approaches molecular orbitals are expanded in a Gaussian basis which does not reproduce their asymptotic behavior correctly. This hinders the application of the WFAT to polyatomic molecules, which are attracting increasing interest in strong-field physics. Recently, an integral-equation approach to the WFAT for tunneling ionization of one electron from an arbitrary potential has been developed. The structure factor is expressed in an integral form as a matrix element involving the ionizing orbital. The integral is not sensitive to the asymptotic behavior of the orbital, which resolves the difficulty mentioned above. Here, we extend the integral representation for the structure factor to many-electron systems treated within the Hartree-Fock method and show how it can be implemented on the basis of standard quantum chemistry software packages. We validate the methodology by considering noble-gas atoms and the CO molecule, for which accurate structure factors exist in the literature. We also present benchmark results for CO2 and for NH3 in the pyramidal and planar geometries.
Cui, Jie; Li, Zhiying; Krems, Roman V
2015-10-21
We consider a problem of extrapolating the collision properties of a large polyatomic molecule A-H to make predictions of the dynamical properties for another molecule related to A-H by the substitution of the H atom with a small molecular group X, without explicitly computing the potential energy surface for A-X. We assume that the effect of the -H →-X substitution is embodied in a multidimensional function with unknown parameters characterizing the change of the potential energy surface. We propose to apply the Gaussian Process model to determine the dependence of the dynamical observables on the unknown parameters. This can be used to produce an interval of the observable values which corresponds to physical variations of the potential parameters. We show that the Gaussian Process model combined with classical trajectory calculations can be used to obtain the dependence of the cross sections for collisions of C6H5CN with He on the unknown parameters describing the interaction of the He atom with the CN fragment of the molecule. The unknown parameters are then varied within physically reasonable ranges to produce a prediction uncertainty of the cross sections. The results are normalized to the cross sections for He - C6H6 collisions obtained from quantum scattering calculations in order to provide a prediction interval of the thermally averaged cross sections for collisions of C6H5CN with He.
Mass Spectrometry as a Preparative Tool for the Surface Science of Large Molecules
Rauschenbach, Stephan; Ternes, Markus; Harnau, Ludger; Kern, Klaus
2016-06-01
Measuring and understanding the complexity that arises when nanostructures interact with their environment are one of the major current challenges of nanoscale science and technology. High-resolution microscopy methods such as scanning probe microscopy have the capacity to investigate nanoscale systems with ultimate precision, for which, however, atomic scale precise preparation methods of surface science are a necessity. Preparative mass spectrometry (pMS), defined as the controlled deposition of m/z filtered ion beams, with soft ionization sources links the world of large, biological molecules and surface science, enabling atomic scale chemical control of molecular deposition in ultrahigh vacuum (UHV). Here we explore the application of high-resolution scanning probe microscopy and spectroscopy to the characterization of structure and properties of large molecules. We introduce the fundamental principles of the combined experiments electrospray ion beam deposition and scanning tunneling microscopy. Examples for the deposition and investigation of single particles, for layer and film growth, and for the investigation of electronic properties of individual nonvolatile molecules show that state-of-the-art pMS technology provides a platform analog to thermal evaporation in conventional molecular beam epitaxy. Additionally, it offers additional, unique features due to the use of charged polyatomic particles. This new field is an enormous sandbox for novel molecular materials research and demands the development of advanced molecular ion beam technology.
Energy Technology Data Exchange (ETDEWEB)
Jansen, Paul; Ubachs, Wim; Bethlem, Hendrick L. [Institute for Lasers, Life and Biophotonics, VU University Amsterdam, De Boelelaan 1081, NL-1081 HV Amsterdam (Netherlands); Kleiner, Isabelle [Laboratoire Interuniversitaire des Systemes Atmospheriques (LISA), CNRS UMR 7583 et Universites Paris 7 et Paris Est, 61 avenue du General de Gaulle, FR-94010 Creteil Cedex (France); Xu, Li-Hong [Department of Physics and Centre for Laser, Atomic, and Molecular Sciences, University of New Brunswick, Saint John, New Brunswick, Canada E2L 4L5 (Canada)
2011-12-15
Recently, methanol was identified as a sensitive target system to probe variations of the proton-to-electron mass ratio {mu}[Jansen et al., Phys. Rev. Lett. 106, 100801 (2011)]. The high sensitivity of methanol originates from the interplay between overall rotation and hindered internal rotation of the molecule; that is, transitions that convert internal rotation energy into overall rotation energy, or vice versa, have an enhanced sensitivity coefficient, K{sub {mu}}. As internal rotation is a common phenomenon in polyatomic molecules, it is likely that other molecules display similar or even larger effects. In this paper we generalize the concepts that form the foundation of the high sensitivity in methanol and use this to construct an approximate model which makes it possible to estimate the sensitivities of transitions in internal rotor molecules with C{sub 3v} symmetry, without performing a full calculation of energy levels. We find that a reliable estimate of transition sensitivities can be obtained from the three rotational constants (A, B, and C) and three torsional constants (F, V{sub 3}, and {rho}). This model is verified by comparing obtained sensitivities for methanol, acetaldehyde, acetamide, methyl formate, and acetic acid with a full analysis of the molecular Hamiltonian. Of the molecules considered, methanol is by far the most suitable candidate for laboratory and cosmological tests searching for a possible variation of {mu}.
Zheng, Jingjing; Truhlar, Donald G
2012-01-01
Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.
Johnson, Adam R.
2013-01-01
A molecular orbital (MO) diagram, especially its frontier orbitals, explains the bonding and reactivity for a chemical compound. It is therefore important for students to learn how to construct one. The traditional methods used to derive these diagrams rely on linear algebra techniques to combine ligand orbitals into symmetry-adapted linear…
Park, Jae Woo; Rhee, Young Min
2014-04-28
Simulating molecular dynamics directly on quantum chemically obtained potential energy surfaces is generally time consuming. The cost becomes overwhelming especially when excited state dynamics is aimed with multiple electronic states. The interpolated potential has been suggested as a remedy for the cost issue in various simulation settings ranging from fast gas phase reactions of small molecules to relatively slow condensed phase dynamics with complex surrounding. Here, we present a scheme for interpolating multiple electronic surfaces of a relatively large molecule, with an intention of applying it to studying nonadiabatic behaviors. The scheme starts with adiabatic potential information and its diabatic transformation, both of which can be readily obtained, in principle, with quantum chemical calculations. The adiabatic energies and their derivatives on each interpolation center are combined with the derivative coupling vectors to generate the corresponding diabatic Hamiltonian and its derivatives, and they are subsequently adopted in producing a globally defined diabatic Hamiltonian function. As a demonstration, we employ the scheme to build an interpolated Hamiltonian of a relatively large chromophore, para-hydroxybenzylidene imidazolinone, in reference to its all-atom analytical surface model. We show that the interpolation is indeed reliable enough to reproduce important features of the reference surface model, such as its adiabatic energies and derivative couplings. In addition, nonadiabatic surface hopping simulations with interpolation yield population transfer dynamics that is well in accord with the result generated with the reference analytic surface. With these, we conclude by suggesting that the interpolation of diabatic Hamiltonians will be applicable for studying nonadiabatic behaviors of sizeable molecules.
Linearly constrained minimax optimization
DEFF Research Database (Denmark)
Madsen, Kaj; Schjær-Jacobsen, Hans
1978-01-01
We present an algorithm for nonlinear minimax optimization subject to linear equality and inequality constraints which requires first order partial derivatives. The algorithm is based on successive linear approximations to the functions defining the problem. The resulting linear subproblems...
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.
Foundations of linear and generalized linear models
Agresti, Alan
2015-01-01
A valuable overview of the most important ideas and results in statistical analysis Written by a highly-experienced author, Foundations of Linear and Generalized Linear Models is a clear and comprehensive guide to the key concepts and results of linear statistical models. The book presents a broad, in-depth overview of the most commonly used statistical models by discussing the theory underlying the models, R software applications, and examples with crafted models to elucidate key ideas and promote practical model building. The book begins by illustrating the fundamentals of linear models,
Energy Technology Data Exchange (ETDEWEB)
Seetula, J. [Helsinki Univ. (Finland). Lab. of Physical Chemistry
1996-12-01
The kinetics of the reactions of CH{sub 2}Cl, CHClBr, CH{sub 3}CCl{sub 2} and CCl{sub 3}, with Cl{sub 2} has been investigated in a tubular reactor coupled to a photoionization mass spectrometer. The radicals of interest, R, were generated homogeneously in the reactor by pulse 248 nm exciplex laser photolysis. The decay of R was monitored as a function of Cl{sub 2} concentration under pseudo-first-order condition to determine the rate constant as a function of temperature pressure. The reactions were studied separately over a temperature range up to a temperature of 873 K. The rate constants of CH{sub 2}Cl, CHClBr and CH{sub 3}CCl{sub 2} radicals determined were fitted to three-parameter Arrhenius-type expression (with units of cm{sup 3} molecule{sup -1} s{sup -1}): k(CH{sub 2}Cl) = 1.05x10{sup -16} x (T){sup 1.4} x exp(-357 J mol{sup -1} / RT), k(CHClBr) = 5.83x10{sup -20} x (T){sup 2.3} x exp(-300 J mol{sup -1}/ RT) and k(CH{sub 3}CCl{sub 2}) 1.10x10{sup -}2{sup 6} x (T){sup 4.3} x exp(15000 J mol{sup -1}/ RT). The rate constants CCl{sub 3} radical were fitted to a two-parameter Arrhenius expression (units in cm{sup 3} molecule{sup -1} s{sup -1}): k(CCl{sub 3}) = (8.1 +- 6.7)10{sup -l3} exp[-(25.0 +- 8.7) kJ mol{sup -1}/ RT]. An Arrhenius expression for the reaction of Cl+CCl{sub 4} -> <- CCl{sub 3}+Cl{sub 2} is also obtained from the kinetics of the reaction of CCl{sub 3} radical with Cl{sub 2} combined with the known heat of formation and entropy values of CCl{sub 3} free radical to be as follows (in units cm{sup 3} molecule{sup -1-}5 s{sup -1}): k(Cl+CCl{sub 4}) = (3.9 + 3.2)10{sup -10} exp[-(71 + 9) kJ mol{sup -1}/ RT]. The error limits stated are l{sigma}+Student`s t and base on statistical uncertainties only. (author)
[Endothelial cell adhesion molecules].
Ivanov, A N; Norkin, I A; Puchin'ian, D M; Shirokov, V Iu; Zhdanova, O Iu
2014-01-01
The review presents current data concerning the functional role of endothelial cell adhesion molecules belonging to different structural families: integrins, selectins, cadherins, and the immunoglobulin super-family. In this manuscript the regulatory mechanisms and factors of adhesion molecules expression and distribution on the surface of endothelial cells are discussed. The data presented reveal the importance of adhesion molecules in the regulation of structural and functional state of endothelial cells in normal conditions and in pathology. Particular attention is paid to the importance of these molecules in the processes of physiological and pathological angiogenesis, regulation of permeability of the endothelial barrier and cell transmigration.
Santambrogio, Gabriele
2015-01-01
In the last years, it was demonstrated that neutral molecules can be loaded on a microchip directly from a supersonic beam. The molecules are confined in microscopic traps that can be moved smoothly over the surface of the chip. Once the molecules are trapped, they can be decelerated to a standstill, for instance, or pumped into selected quantum states by laser light or microwaves. Molecules are detected on the chip by time-resolved spatial imaging, which allows for the study of the distribution in the phase space of the molecular ensemble.
Alignment of symmetric top molecules by short laser pulses
DEFF Research Database (Denmark)
Hamilton, Edward; Seideman, Tamar; Ejdrup, Tine
2005-01-01
Nonadiabatic alignment of symmetric top molecules induced by a linearly polarized, moderately intense picosecond laser pulse is studied theoretically and experimentally. Our studies are based on the combination of a nonperturbative solution of the Schrodinger equation with femtosecond time...
Full Alignment of Molecules Using Elliptically Polarized Light
DEFF Research Database (Denmark)
Larsen, Jakob Juul; Hald, Kasper; Seideman, Tamar
When a molecule with an anisotropic polarizability is placed in a strong nonresonant laser field the interaction occurs through the induced dipole moment. The outcome is that the molecule experiences an angular dependent potential energy. It is now well established that a linearly polarized laser...... of the molecule the third axis is also aligned. Experimentally, we investigate the effect by aligning 3,4-dibromothiophene molecules with a strong, nonresonant, nanosecond laser pulse. The alignment is probed by Coulomb exploding the molecules with an intense 20 femtosecond laser pulse. Detection of the emerging...
Császár, Attila G; Furtenbacher, Tibor; Árendás, Péter
2016-11-17
Quantum mechanics builds large-scale graphs (networks): the vertices are the discrete energy levels the quantum system possesses, and the edges are the (quantum-mechanically allowed) transitions. Parts of the complete quantum mechanical networks can be probed experimentally via high-resolution, energy-resolved spectroscopic techniques. The complete rovibronic line list information for a given molecule can only be obtained through sophisticated quantum-chemical computations. Experiments as well as computations yield what we call spectroscopic networks (SN). First-principles SNs of even small, three to five atomic molecules can be huge, qualifying for the big data description. Besides helping to interpret high-resolution spectra, the network-theoretical view offers several ideas for improving the accuracy and robustness of the increasingly important information systems containing line-by-line spectroscopic data. For example, the smallest number of measurements necessary to perform to obtain the complete list of energy levels is given by the minimum-weight spanning tree of the SN and network clustering studies may call attention to "weakest links" of a spectroscopic database. A present-day application of spectroscopic networks is within the MARVEL (Measured Active Rotational-Vibrational Energy Levels) approach, whereby the transitions information on a measured SN is turned into experimental energy levels via a weighted linear least-squares refinement. MARVEL has been used successfully for 15 molecules and allowed to validate most of the transitions measured and come up with energy levels with well-defined and realistic uncertainties. Accurate knowledge of the energy levels with computed transition intensities allows the realistic prediction of spectra under many different circumstances, e.g., for widely different temperatures. Detailed knowledge of the energy level structure of a molecule coming from a MARVEL analysis is important for a considerable number of modeling
How to determine the handedness of single molecules using Coulomb explosion imaging
Pitzer, Martin
2017-08-01
This tutorial is based on a doctoral thesis that was shortlisted for the 2016 AMOP dissertation prize of the German Physical Society (DPG). The principal achievement of the thesis was to use Coulomb explosion imaging (CEI) to determine the microscopic handedness (‘chirality’) of molecular structures on a single-molecule level. It thus shows how a technique developed in atomic physics can address a long-standing problem in chemistry. Owing to these disparate backgrounds, the tutorial has two facets: on the one hand, the history of molecular chirality and recent developments are very briefly reviewed. On the other hand, an account is given of different experimental approaches to CEI, on the physical processes in light-induced Coulomb explosion and—most importantly—on the aspects that are relevant when designing and performing such an experiment. As structural chirality occurs only in polyatomic molecules, special attention will be given to multiple ionization and multi-coincidence measurements. A short discussion of the results presented in earlier papers is given, followed by an outlook on experiments that are under way or can realistically be performed within the next years.
Feedback linearization of piecewise linear systems
Camlibel, Kanat; Ustoglu, Ilker
2005-01-01
One of the classical problems of nonlinear systems and control theory is feedback linearization. Its obvious motivation is that one can utilize linear control theory if the nonlinear system at hand is linearizable by feedback. This problem is well-understood for the smooth nonlinear systems. In the
Iachello, F
1995-01-01
1. The Wave Mechanics of Diatomic Molecules. 2. Summary of Elements of Algebraic Theory. 3. Mechanics of Molecules. 4. Three-Body Algebraic Theory. 5. Four-Body Algebraic Theory. 6. Classical Limit and Coordinate Representation. 8. Prologue to the Future. Appendices. Properties of Lie Algebras; Coupling of Algebras; Hamiltonian Parameters
1992-01-01
In this paper, some results obtained on the formation of isolated molecules of composition SnOx in silver and SnFx in copper-are reviewed. Hyperfine interaction and ion beam interaction techniques were used for the identification of these molecules.
1992-01-01
In this paper, some results obtained on the formation of isolated molecules of composition SnOx in silver and SnFx in copper-are reviewed. Hyperfine interaction and ion beam interaction techniques were used for the identification of these molecules.
Omont, Alain
2007-01-01
The main achievements, current developments and prospects of molecular studies in external galaxies are reviewed. They are put in the context of the results of several decades of studies of molecules in local interstellar medium, their chemistry and their importance for star formation. CO observations have revealed the gross structure of molecular gas in galaxies. Together with other molecules, they are among the best tracers of star formation at galactic scales. Our knowledge about molecular abundances in various local galactic environments is progressing. They trace physical conditions and metallicity, and they are closely related to dust processes and large aromatic molecules. Major recent developments include mega-masers, and molecules in Active Galactic Nuclei; millimetre emission of molecules at very high redshift; and infrared H2 emission as tracer of warm molecular gas, shocks and photodissociation regions. The advent of sensitive giant interferometers from the centimetre to sub-millimetre range, espe...
Impulsive Laser Induced Alignment of Molecules Dissolved in Helium Nanodroplets
DEFF Research Database (Denmark)
Pentlehner, Dominik; H. Nielsen, Jens; Slenczka, Alkwin
2013-01-01
We show that a 450 fs nonresonant, moderately intense, linearly polarized laser pulse can induce field-free molecular axis alignment of methyliodide (CH3I) molecules dissolved in a helium nanodroplet. Time-resolved measurements reveal rotational dynamics much slower than that of isolated molecule...
Impulsive Laser Induced Alignment of Molecules Dissolved in Helium Nanodroplets
DEFF Research Database (Denmark)
Pentlehner, Dominik; H. Nielsen, Jens; Slenczka, Alkwin
2013-01-01
We show that a 450 fs nonresonant, moderately intense, linearly polarized laser pulse can induce field-free molecular axis alignment of methyliodide (CH3I) molecules dissolved in a helium nanodroplet. Time-resolved measurements reveal rotational dynamics much slower than that of isolated molecule...
Cooee bitumen II: Stability of linear asphaltene nanoaggregates
Lemarchand, Claire A; Dyre, Jeppe C; Hansen, Jesper S
2014-01-01
Asphaltene and smaller aromatic molecules tend to form linear nanoaggregates in bitumen.Over the years bitumen undergoes chemical aging and during this process, the size of the nanoaggregate increases. This increase is associated with an increase in viscosity and brittleness of the bitumen, eventually leading to road deterioration. This paper focuses on understanding the mechanisms behind nanoaggregate size and stability. We used molecular dynamics simulations to quantify the probability of having a nanoaggregate of a given size in the stationary regime. To model this complicated behavior, we chose first to consider the simple case where only asphaltene molecules are counted in a nanoaggregate. We used a master equation approach and a related statistical mechanics model. The linear asphaltene nanoaggregates behave as a rigid linear chain. The most complicated case where all aromatic molecules are counted in a nanoaggregate is then discussed. The linear aggregates where all aromatic molecules are counted seem ...
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.
Light-controllable linear dichroism in nematics.
Petriashvili, Gia; Hamdi, Ridha; De Santo, Maria Penelope; Gary, Ramla; Barberi, Riccardo
2015-10-01
We report a method to obtain a light-controllable dichroism. The main effect is achieved using spiropyran-doped (SP-doped) nematic liquid crystal mixtures. SP molecules exhibit a high solubility in the liquid crystal host, which can vary between 1% and 4% in weight, without destroying the liquid crystalline phase. Due to their elongated shape, SP molecules are oriented along the nematic liquid crystal director. The obtained linear dichroism was measured to be 1.08 with a dichroic ratio of 7.12. Further, a two-direction linear dichroism was obtained by adding a dichroic dye to the mixture. The angle between the two dichroic axes was found to be 11°. Two-direction linear dichroism is also light controllable and can be switched back to one-direction dichroism.
Liu, Yizhuang
2016-01-01
We briefly review the formation of pion-mediated heavy-light exotic molecules with both charm and bottom, under the general strictures of chiral and heavy quark symmetries. The charm isosinglet exotic molecules with $J^{PC}=1^{++}$ binds, which we identify as the reported neutral $X(3872)$. The bottom isotriplet exotic with $J^{PC}=1^{+-}$ binds, and is identified as a mixed state of the reported charged exotics $Z^+_b(10610)$ and $Z^+_b(10650)$. The bound bottom isosinglet molecule with $J^{PC}=1^{++}$ is a possible neutral $X_b(10532)$ to be observed.
Liu, Yizhuang; Zahed, Ismail
We briefly review the formation of pion-mediated heavy-light exotic molecules with both charm and bottom, under the general structures of chiral and heavy quark symmetries. The charm isosinglet exotic molecules with JPC = 1++ binds, which we identify as the reported neutral X(3872). The bottom isotriplet exotic with JPC = 1+1 binds, and is identified as a mixed state of the reported charged exotics Zb+(10610) and Zb-(10650). The bound bottom isosinglet molecule with JPC = 1++ is a possible neutral Xb(10532) to be observed.
Electron correlation in molecules
Wilson, S
2007-01-01
Electron correlation effects are of vital significance to the calculation of potential energy curves and surfaces, the study of molecular excitation processes, and in the theory of electron-molecule scattering. This text describes methods for addressing one of theoretical chemistry's central problems, the study of electron correlation effects in molecules.Although the energy associated with electron correlation is a small fraction of the total energy of an atom or molecule, it is of the same order of magnitude as most energies of chemical interest. If the solution of quantum mechanical equatio
Comprehensive mass spectrometric analysis of novel organic semiconductor molecules
Prada, Svitlana
implemented. The contribution of the quadrupole RF field to the drift dynamics also was taken into consideration. The IMR was successfully employed in the ion-molecule reactions study of four functionalized pentacene derivatives such as TIPS, o-TIPS, 6,13-bis-[(triisopropylsilyl)-ethynyl]-pentacene-2,3-dicarbonitrile (TIPS(CN)2), and 6,13-bis-[(triisopropylsilyl)-ethynyl]-pentacene-2,3,9,10-tetracarbonitrile (TIPS(CN)4). Details of the IMR operation in this mode are extensively discussed. The purity of the starting material is one of the most important parameters for the fabrication of a molecular electronic device. We report the method of determination of trace elemental impurities (Li, Na, Al, Mg, Be, Pb, Mn, Co, Ti, Sn, Cu, Cr, V, Zn, Fe, Ca, K and Ni) in organic semiconductor materials, such as Tetracene, Anthracene, Pentacene, TIPS and Rubrene, using an inductively coupled plasma quadrupole mass spectrometer (ICP-MS) fitted with a dynamic reaction cell (DRC). The determination of Fe, Ca, K and Ni in the organic semiconductor materials was carried out using NH3 as a reaction gas in the DRC mode to obviate the effect of polyatomic isobaric interferences. The other trace elements such as Li, Na, Al, Mg, Be, Pb, Mn, Co, Ti, Sn, Cu, Cr, V and Zn have been determined under standard operating conditions.
Tuey, R. C.
1972-01-01
Computer solutions of linear programming problems are outlined. Information covers vector spaces, convex sets, and matrix algebra elements for solving simultaneous linear equations. Dual problems, reduced cost analysis, ranges, and error analysis are illustrated.
Single molecules and nanotechnology
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.
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...
Wu, Jiang
2014-01-01
This book reviews recent advances in the exciting and rapidly growing field of quantum dot molecules (QDMs). It offers state-of-the-art coverage of novel techniques and connects fundamental physical properties with device design.
Al-Malah, Kamal I
2011-05-01
The aqueous solubility of a single-carbon organic molecule as a function of its size & dipole moment was investigated. The molecular dipole moment was chosen to represent the polar character of a poly-atomic molecule. It is hypothesized here that at a given pH, temperature, and pressure, the solubility of a single-carbon organic molecule in water will be a function of its polar character; namely, dipole moment and of its molecular size. Different forms of the solubility function were tested; it was found that the solubility model, given by Eq. 1, which is based on the polar character and the molecular volume, adequately described the aqueous solubility of single-carbon organic moieties. The aqueous solubility of single-carbon organic solutes exhibits maximum at the condition of high polar character (large dipole moment) and low molecular volume. The general trend of the solubility of single-carbon organic solutes, based on the proposed model (Eq. 1) could be explained in terms of the trade-off between the driving force (degree of polar character of the solute) for solubilization versus the resistance to be solubilized as a result of the entropic effects which increase with increasing molecular volume of the organic moiety.
Classifying Linear Canonical Relations
Lorand, Jonathan
2015-01-01
In this Master's thesis, we consider the problem of classifying, up to conjugation by linear symplectomorphisms, linear canonical relations (lagrangian correspondences) from a finite-dimensional symplectic vector space to itself. We give an elementary introduction to the theory of linear canonical relations and present partial results toward the classification problem. This exposition should be accessible to undergraduate students with a basic familiarity with linear algebra.
Energy Technology Data Exchange (ETDEWEB)
Peterson, David; Stofleth, Jerome H.; Saul, Venner W.
2017-07-11
Linear shaped charges are described herein. In a general embodiment, the linear shaped charge has an explosive with an elongated arrowhead-shaped profile. The linear shaped charge also has and an elongated v-shaped liner that is inset into a recess of the explosive. Another linear shaped charge includes an explosive that is shaped as a star-shaped prism. Liners are inset into crevices of the explosive, where the explosive acts as a tamper.
Institute of Scientific and Technical Information of China (English)
T. (A)LVAREZ
2012-01-01
For a closed linear relation in a Banach space the concept of regularity is introduced and studied.It is shown that many of the results of Mbekhta and other authors for operators remain valid in the context of multivalued linear operators.We also extend the punctured neighbourhood theorem for operators to linear relations and as an application we obtain a characterization of semiFredholm linear relations which are regular.
Lawson, C. L.; Krogh, F. T.; Gold, S. S.; Kincaid, D. R.; Sullivan, J.; Williams, E.; Hanson, R. J.; Haskell, K.; Dongarra, J.; Moler, C. B.
1982-01-01
The Basic Linear Algebra Subprograms (BLAS) library is a collection of 38 FORTRAN-callable routines for performing basic operations of numerical linear algebra. BLAS library is portable and efficient source of basic operations for designers of programs involving linear algebriac computations. BLAS library is supplied in portable FORTRAN and Assembler code versions for IBM 370, UNIVAC 1100 and CDC 6000 series computers.
Lawson, C. L.; Krogh, F. T.; Gold, S. S.; Kincaid, D. R.; Sullivan, J.; Williams, E.; Hanson, R. J.; Haskell, K.; Dongarra, J.; Moler, C. B.
1982-01-01
The Basic Linear Algebra Subprograms (BLAS) library is a collection of 38 FORTRAN-callable routines for performing basic operations of numerical linear algebra. BLAS library is portable and efficient source of basic operations for designers of programs involving linear algebriac computations. BLAS library is supplied in portable FORTRAN and Assembler code versions for IBM 370, UNIVAC 1100 and CDC 6000 series computers.
Cooperstein, Bruce
2010-01-01
Vector SpacesFieldsThe Space FnVector Spaces over an Arbitrary Field Subspaces of Vector SpacesSpan and IndependenceBases and Finite Dimensional Vector SpacesBases and Infinite Dimensional Vector SpacesCoordinate VectorsLinear TransformationsIntroduction to Linear TransformationsThe Range and Kernel of a Linear TransformationThe Correspondence and Isomorphism TheoremsMatrix of a Linear TransformationThe Algebra of L(V, W) and Mmn(F)Invertible Transformations and MatricesPolynomialsThe Algebra of PolynomialsRoots of PolynomialsTheory of a Single Linear OperatorInvariant Subspaces of an Operator
Soliton molecules for advanced optical telecommunications
Mitschke, Fedor; Hause, Alexander; Mahnke, Christoph
2016-11-01
Recent developments in the technology of optical telecommunications are pushed forward by the rapidly growing demand for data-carrying capacity. Current approaches are discussed; most lines of investigation are limited to the linear (i.e. low power) regime. It is shown how this restriction poses a limit for further evolution. If, on the other hand, the nonlinear regime is entered, recent developments about soliton molecules offer a possibility to advance further.
Cardelli, Luca
Molecular biology investigates the structure and function of biochemical systems starting from their basic building blocks: macromolecules. A macromolecule is a large, complex molecule (a protein or a nucleic acid) that usually has inner mutable state and external activity. Informal explanations of biochemical events trace individual macromolecules through their state changes and their interaction histories: a macromolecule is endowed with an identity that is retained through its transformations, even through changes in molecular energy and mass. A macromolecule, therefore, is qualitatively different from the small molecules of inorganic chemistry. Such molecules are stateless: in the standard notation for chemical reactions they are seemingly created and destroyed, and their atomic structure is used mainly for the bookkeeping required by the conservation of mass.
Cherchneff, Isabelle
2011-01-01
The first molecules detected at infrared wavelengths in the ejecta of a Type II supernova, namely SN1987A, consisted of CO and SiO. Since then, confirmation of the formation of these two species in several other supernovae a few hundred days after explosion has been obtained. However, supernova environments appear to hamper the synthesis of large, complex species due to the lack of microscopically-mixed hydrogen deep in supernova cores. Because these environments also form carbon and silicate dust, it is of importance to understand the role played by molecules in the depletion of elements and how chemical species get incorporated into dust grains. In the present paper, we review our current knowledge of the molecular component of supernova ejecta, and present new trends and results on the synthesis of molecules in these harsh, explosive events.
Energy Technology Data Exchange (ETDEWEB)
Loinard, Laurent; Menten, Karl M.; Guesten, Rolf [Max-Planck Institut fuer Radioastronomie, Auf dem Huegel 69, 53121 Bonn (Germany); Zapata, Luis A.; Rodriguez, Luis F. [Centro de Radioastronomia y Astrofisica, Universidad Nacional Autonoma de Mexico, Apartado Postal 3-72, 58090 Morelia, Michoacan (Mexico)
2012-04-10
We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.
Loinard, Laurent; Guesten, Rolf; Zapata, Luis A; Rodriguez, Luis F
2012-01-01
We report the detection toward \\eta\\ Carinae of six new molecules, CO, CN, HCO+, HCN, HNC, and N2H+, and of two of their less abundant isotopic counterparts, 13CO and H13CN. The line profiles are moderately broad (about 100 km /s) indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO+ do not appear to be under-abundant in \\eta\\ Carinae. On the other hand, molecules containing nitrogen or the 13C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of eta Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.
Non linear system become linear system
Directory of Open Access Journals (Sweden)
Petre Bucur
2007-01-01
Full Text Available The present paper refers to the theory and the practice of the systems regarding non-linear systems and their applications. We aimed the integration of these systems to elaborate their response as well as to highlight some outstanding features.
Enzyme molecules as nanomotors.
Sengupta, Samudra; Dey, Krishna K; Muddana, Hari S; Tabouillot, Tristan; Ibele, Michael E; Butler, Peter J; Sen, Ayusman
2013-01-30
Using fluorescence correlation spectroscopy, we show that the diffusive movements of catalase enzyme molecules increase in the presence of the substrate, hydrogen peroxide, in a concentration-dependent manner. Employing a microfluidic device to generate a substrate concentration gradient, we show that both catalase and urease enzyme molecules spread toward areas of higher substrate concentration, a form of chemotaxis at the molecular scale. Using glucose oxidase and glucose to generate a hydrogen peroxide gradient, we induce the migration of catalase toward glucose oxidase, thereby showing that chemically interconnected enzymes can be drawn together.
Multicolor Bound Soliton Molecule
Luo, Rui; Lin, Qiang
2015-01-01
We show a new class of bound soliton molecule that exists in a parametrically driven nonlinear optical cavity with appropriate dispersion characteristics. The composed solitons exhibit distinctive colors but coincide in time and share a common phase, bound together via strong inter-soliton four-wave mixing and Cherenkov radiation. The multicolor bound soliton molecule shows intriguing spectral locking characteristics and remarkable capability of spectrum management to tailor soliton frequencies, which may open up a great avenue towards versatile generation and manipulation of multi-octave spanning phase-locked Kerr frequency combs, with great potential for applications in frequency metrology, optical frequency synthesis, and spectroscopy.
Institute of Scientific and Technical Information of China (English)
LIU Fang; WANG Hao; HOUK K. N.
2011-01-01
Donald J.Cram,the great UCLA chemist,received the Nobel Prize for his discoveries about host-guest complexes [1].Both theoretical and experimental studies have been conducted about the nature and strength of interactions between the host and guest molecules.The concepts of constrictive binding (the activation energy of the binding process) and intrinsic binding (the free energy difference between the complex and the free host and guest molecules) were introduced to characterize different binding properties (Figure 1)[2].
Energy Technology Data Exchange (ETDEWEB)
Wiedemann, H.
1981-11-01
Since no linear colliders have been built yet it is difficult to know at what energy the linear cost scaling of linear colliders drops below the quadratic scaling of storage rings. There is, however, no doubt that a linear collider facility for a center of mass energy above say 500 GeV is significantly cheaper than an equivalent storage ring. In order to make the linear collider principle feasible at very high energies a number of problems have to be solved. There are two kinds of problems: one which is related to the feasibility of the principle and the other kind of problems is associated with minimizing the cost of constructing and operating such a facility. This lecture series describes the problems and possible solutions. Since the real test of a principle requires the construction of a prototype I will in the last chapter describe the SLC project at the Stanford Linear Accelerator Center.
Blyth, T S
2002-01-01
Basic Linear Algebra is a text for first year students leading from concrete examples to abstract theorems, via tutorial-type exercises. More exercises (of the kind a student may expect in examination papers) are grouped at the end of each section. The book covers the most important basics of any first course on linear algebra, explaining the algebra of matrices with applications to analytic geometry, systems of linear equations, difference equations and complex numbers. Linear equations are treated via Hermite normal forms which provides a successful and concrete explanation of the notion of linear independence. Another important highlight is the connection between linear mappings and matrices leading to the change of basis theorem which opens the door to the notion of similarity. This new and revised edition features additional exercises and coverage of Cramer's rule (omitted from the first edition). However, it is the new, extra chapter on computer assistance that will be of particular interest to readers:...
Linearity in Process Languages
DEFF Research Database (Denmark)
Nygaard, Mikkel; Winskel, Glynn
2002-01-01
The meaning and mathematical consequences of linearity (managing without a presumed ability to copy) are studied for a path-based model of processes which is also a model of affine-linear logic. This connection yields an affine-linear language for processes, automatically respecting open-map bisi......The meaning and mathematical consequences of linearity (managing without a presumed ability to copy) are studied for a path-based model of processes which is also a model of affine-linear logic. This connection yields an affine-linear language for processes, automatically respecting open......-map bisimulation, in which a range of process operations can be expressed. An operational semantics is provided for the tensor fragment of the language. Different ways to make assemblies of processes lead to different choices of exponential, some of which respect bisimulation....
On the theoretical description of nuclear quadrupole coupling in Π states of small molecules
Energy Technology Data Exchange (ETDEWEB)
Fišer, J. [Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2 (Czech Republic); Polák, R., E-mail: rudolf.polak@jh-inst.cas.cz [J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i, Dolejškova 3, 182 23 Prague 8 (Czech Republic)
2013-11-08
Highlights: • Nuclear quadrupole coupling (NQC) in Π states of small molecules was investigated. • The many-electron modification of the orbital method of Western et al. was used. • The calculated NQC constants were compared with available corresponding data. - Abstract: Axial (eQq{sub 0}) and perpendicular (eQq{sub 2}) nuclear quadrupole coupling constants were evaluated from the electric field gradient at the quadrupolar nuclei ({sup 7}Li, {sup 14}N, {sup 17}O, {sup 33}S, {sup 35}Cl) in diatomic (LiO, CN, NH{sup +}, NH, N{sub 2}{sup +}, NO, OH, HCl{sup +}, CCl, OCl, NS) and polyatomic (C{sub 2}N, C{sub 4}N, NCO, N{sub 3}) Π states. For diatomics the nuclear quadrupole coupling constants (NQCCs) were determined as a function of the vibrational quantum number. The calculations were performed using the internally contracted multireference configuration interaction and single-configuration coupled-cluster approaches with large correlation-consistent basis sets. The overall quality of the wave functions was tested by comparing the calculated electric dipole moments and diatomic spectroscopic constants with external data. The calculated NQCCs were discussed and compared with previous experimental and theoretical studies.
Kostko, Oleg; Kim, Sang Kyu; Leone, Stephen R; Ahmed, Musahid
2009-12-31
Mass-analyzed threshold ionization (MATI) spectroscopy using synchrotron radiation (Advanced Light Source, Lawrence Berkeley National Laboratory) has been performed for Ar, N(2), O(2), N(2)O, H(2)O, C(2)H(2), and C(6)H(6). MATI allows for a better determination of ionization energies compared to those derived from photoionization efficiency curves traditionally used in synchrotron photoionization mass spectrometry. The separation of the long-lived Rydberg state from the directly formed prompt ion, essential for a meaningful MATI spectrum, has been accomplished by employing an arrangement of ion optics coupled to unique electric field pulsing schemes. For Ar, a number of resolved bands below the ionization energy are observed, and these are ascribed to high-n,l Rydberg states prepared in the MATI scheme. The first vibrational state resolved MATI spectra of N(2) and O(2) are reported, and spectral characteristics are discussed in comparison with previously reported threshold photoelectron spectroscopic studies. Although MATI performed with synchrotron radiation is intrinsically less sensitive compared to laser-based sources, this work demonstrates that MATI spectroscopy performed with widely tunable vacuum ultraviolet (VUV) radiation is a complementary technique for studying the ionization spectroscopy of polyatomic molecules.
Matrices and linear transformations
Cullen, Charles G
1990-01-01
""Comprehensive . . . an excellent introduction to the subject."" - Electronic Engineer's Design Magazine.This introductory textbook, aimed at sophomore- and junior-level undergraduates in mathematics, engineering, and the physical sciences, offers a smooth, in-depth treatment of linear algebra and matrix theory. The major objects of study are matrices over an arbitrary field. Contents include Matrices and Linear Systems; Vector Spaces; Determinants; Linear Transformations; Similarity: Part I and Part II; Polynomials and Polynomial Matrices; Matrix Analysis; and Numerical Methods. The first
Shelah, Saharon
2011-01-01
We address the following question: Can we expand an NIP theory by adding a linear order such that the expansion is still NIP? Easily, if acl(A)=A for all A, then this is true. Otherwise, we give counterexamples. More precisely, there is a totally categorical theory for which every expansion by a linear order has IP. There is also an \\omega-stable NDOP theory for which every expansion by a linear order interprets bounded arithmetic.
Efficient Non Linear Loudspeakers
DEFF Research Database (Denmark)
Petersen, Bo R.; Agerkvist, Finn T.
2006-01-01
Loudspeakers have traditionally been designed to be as linear as possible. However, as techniques for compensating non linearities are emerging, it becomes possible to use other design criteria. This paper present and examines a new idea for improving the efficiency of loudspeakers at high levels...... by changing the voice coil layout. This deliberate non-linear design has the benefit that a smaller amplifier can be used, which has the benefit of reducing system cost as well as reducing power consumption....
On the Mass of Atoms in Molecules: Beyond the Born-Oppenheimer Approximation
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
Carr, Joseph
1996-01-01
The linear IC market is large and growing, as is the demand for well trained technicians and engineers who understand how these devices work and how to apply them. Linear Integrated Circuits provides in-depth coverage of the devices and their operation, but not at the expense of practical applications in which linear devices figure prominently. This book is written for a wide readership from FE and first degree students, to hobbyists and professionals.Chapter 1 offers a general introduction that will provide students with the foundations of linear IC technology. From chapter 2 onwa
Charges for linearized gravity
Aksteiner, Steffen
2013-01-01
Maxwell test fields as well as solutions of linearized gravity on the Kerr exterior admit non-radiating modes, i.e. non-trivial time-independent solutions. These are closely related to conserved charges. In this paper we discuss the non-radiating modes for linearized gravity, which may be seen to correspond to the Poincare Lie-algebra. The 2-dimensional isometry group of Kerr corresponds to a 2-parameter family of gauge-invariant non-radiating modes representing infinitesimal perturbations of mass and azimuthal angular momentum. We calculate the linearized mass charge in terms of linearized Newman-Penrose scalars.
Chen, Qingwen; Narayanan, Kumaran
2015-01-01
Recombineering is a powerful genetic engineering technique based on homologous recombination that can be used to accurately modify DNA independent of its sequence or size. One novel application of recombineering is the assembly of linear BACs in E. coli that can replicate autonomously as linear plasmids. A circular BAC is inserted with a short telomeric sequence from phage N15, which is subsequently cut and rejoined by the phage protelomerase enzyme to generate a linear BAC with terminal hairpin telomeres. Telomere-capped linear BACs are protected against exonuclease attack both in vitro and in vivo in E. coli cells and can replicate stably. Here we describe step-by-step protocols to linearize any BAC clone by recombineering, including inserting and screening for presence of the N15 telomeric sequence, linearizing BACs in vivo in E. coli, extracting linear BACs, and verifying the presence of hairpin telomere structures. Linear BACs may be useful for functional expression of genomic loci in cells, maintenance of linear viral genomes in their natural conformation, and for constructing innovative artificial chromosome structures for applications in mammalian and plant cells.
Fault tolerant linear actuator
Tesar, Delbert
2004-09-14
In varying embodiments, the fault tolerant linear actuator of the present invention is a new and improved linear actuator with fault tolerance and positional control that may incorporate velocity summing, force summing, or a combination of the two. In one embodiment, the invention offers a velocity summing arrangement with a differential gear between two prime movers driving a cage, which then drives a linear spindle screw transmission. Other embodiments feature two prime movers driving separate linear spindle screw transmissions, one internal and one external, in a totally concentric and compact integrated module.
Faraway, Julian J
2014-01-01
A Hands-On Way to Learning Data AnalysisPart of the core of statistics, linear models are used to make predictions and explain the relationship between the response and the predictors. Understanding linear models is crucial to a broader competence in the practice of statistics. Linear Models with R, Second Edition explains how to use linear models in physical science, engineering, social science, and business applications. The book incorporates several improvements that reflect how the world of R has greatly expanded since the publication of the first edition.New to the Second EditionReorganiz
Reinhoudt, D.N.; Crego-Calama, M.
2002-01-01
Weak, noncovalent interactions between molecules control many biological functions. In chemistry, noncovalent interactions are now exploited for the synthesis in solution of large supramolecular aggregates. The aim of these syntheses is not only the creation of a particular structure, but also the i
Vologodskii, Alexander
2016-09-01
The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.
Vologodskii, Alexander
2016-09-01
The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.
Diversity in Biological Molecules
Newbury, H. John
2010-01-01
One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…
Diversity in Biological Molecules
Newbury, H. John
2010-01-01
One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…
Atoms, Molecules, and Compounds
Manning, Phillip
2007-01-01
Explores the atoms that govern chemical processes. This book shows how the interactions between simple substances such as salt and water are crucial to life on Earth and how those interactions are predestined by the atoms that make up the molecules.
Properties of entanglement molecules
Energy Technology Data Exchange (ETDEWEB)
Huang Yanxia [Department of Physics, Hubei Normal University, Huangshi 435002 (China); Zhan Mingsheng [State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China)
2004-09-14
We propose a scheme to prepare a certain kind of N-atom entangled state that allows us to construct some possible types of entanglement molecules via cavity QED. The entanglement properties of entanglement molecules vertical bar {psi}{sub N}){sub {alpha}} are studied with respect to bipartite entanglement that is robust against the disposal of particles and are compared with entanglement molecules {rho}{sub I} introduced in Dur (2001 Phys. Rev. A 63 020303). We also give the maximal amount of entanglement achievable for two particular situations in two possible configurations. Meanwhile, we investigate the entanglement properties of entanglement molecules vertical bar {psi}{sub N}){sub {alpha}} in terms of local measurement using the maximum connectedness and persistency and compare them with other kinds of N-atom entangled states such as |GHZ), vertical bar W{sub N}) and vertical bar {phi}{sub N}). We show that the maximal value N - 1 of the persistency of the state vertical bar {psi}{sub N}){sub {alpha}} corresponds to the case that all atoms are pairwise entangled. If any pair of atoms {rho}{sub ij} is disentangled, the entanglement of the state vertical bar {psi}{sub N}){sub {alpha}} is very easy to destroy by a single local measurement.
Properties of entanglement molecules
Huang, Yan-Xia; Zhan, Ming-Sheng
2004-09-01
We propose a scheme to prepare a certain kind of N-atom entangled state that allows us to construct some possible types of entanglement molecules via cavity QED. The entanglement properties of entanglement molecules |psgrNrangagr are studied with respect to bipartite entanglement that is robust against the disposal of particles and are compared with entanglement molecules rgrI introduced in Dur (2001 Phys. Rev. A 63 020303). We also give the maximal amount of entanglement achievable for two particular situations in two possible configurations. Meanwhile, we investigate the entanglement properties of entanglement molecules |psgrNrangagr in terms of local measurement using the maximum connectedness and persistency and compare them with other kinds of N-atom entangled states such as |GHZrang, |WNrang and |phgrNrang. We show that the maximal value N - 1 of the persistency of the state |psgrNrangagr corresponds to the case that all atoms are pairwise entangled. If any pair of atoms rgrij is disentangled, the entanglement of the state |psgrNrangagr is very easy to destroy by a single local measurement.
Capillary condensation of short-chain molecules.
Bryk, Paweł; Pizio, Orest; Sokolowski, Stefan
2005-05-15
A density-functional study of capillary condensation of fluids of short-chain molecules confined to slitlike pores is presented. The molecules are modeled as freely jointed tangent spherical segments with a hard core and with short-range attractive interaction between all the segments. We investigate how the critical parameters of capillary condensation of the fluid change when the pore width decreases and eventually becomes smaller than the nominal linear dimension of the single-chain molecule. We find that the dependence of critical parameters for a fluid of dimers and of tetramers on pore width is similar to that of the monomer fluid. On the other hand, for a fluid of chains consisting of a larger number of segments we observe an inversion effect. Namely, the critical temperature of capillary condensation decreases with increasing pore width for a certain interval of values of the pore width. This anomalous behavior is also influenced by the interaction between molecules and pore walls. We attribute this behavior to the effect of conformational changes of molecules upon confinement.
Energy Technology Data Exchange (ETDEWEB)
Herbert, John M. [Kansas State Univ., Manhattan, KS (United States). Dept. of Chemistry
1997-01-01
Rayleigh-Schroedinger perturbation theory is an effective and popular tool for describing low-lying vibrational and rotational states of molecules. This method, in conjunction with ab initio techniques for computation of electronic potential energy surfaces, can be used to calculate first-principles molecular vibrational-rotational energies to successive orders of approximation. Because of mathematical complexities, however, such perturbation calculations are rarely extended beyond the second order of approximation, although recent work by Herbert has provided a formula for the nth-order energy correction. This report extends that work and furnishes the remaining theoretical details (including a general formula for the Rayleigh-Schroedinger expansion coefficients) necessary for calculation of energy corrections to arbitrary order. The commercial computer algebra software Mathematica is employed to perform the prohibitively tedious symbolic manipulations necessary for derivation of generalized energy formulae in terms of universal constants, molecular constants, and quantum numbers. As a pedagogical example, a Hamiltonian operator tailored specifically to diatomic molecules is derived, and the perturbation formulae obtained from this Hamiltonian are evaluated for a number of such molecules. This work provides a foundation for future analyses of polyatomic molecules, since it demonstrates that arbitrary-order perturbation theory can successfully be applied with the aid of commercially available computer algebra software.
Bacterial invasion reconstructed molecule by molecule
Energy Technology Data Exchange (ETDEWEB)
Werner, James H [Los Alamos National Laboratory
2009-01-01
We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the
Yuce, C
2015-01-01
We predict the existence of linear discrete rogue waves. We discuss that Josephson effect is the underlying reason for the formation of such waves. We study linear rogue waves in continuous system and present an exact analytical rogue wave solution of the Schrodinger-like equation.
2014-01-01
© 2015 Elsevier B.V. Motivated by recent extensive studies on Wenger graphs, we introduce a new infinite class of bipartite graphs of a similar type, called linearized Wenger graphs. The spectrum, diameter and girth of these linearized Wenger graphs are determined.
Efficient Non Linear Loudspeakers
DEFF Research Database (Denmark)
Petersen, Bo R.; Agerkvist, Finn T.
2006-01-01
Loudspeakers have traditionally been designed to be as linear as possible. However, as techniques for compensating non linearities are emerging, it becomes possible to use other design criteria. This paper present and examines a new idea for improving the efficiency of loudspeakers at high levels...... by changing the voice coil layout. This deliberate non-linear design has the benefit that a smaller amplifier can be used, which has the benefit of reducing system cost as well as reducing power consumption.......Loudspeakers have traditionally been designed to be as linear as possible. However, as techniques for compensating non linearities are emerging, it becomes possible to use other design criteria. This paper present and examines a new idea for improving the efficiency of loudspeakers at high levels...
Axler, Sheldon
2015-01-01
This best-selling textbook for a second course in linear algebra is aimed at undergrad math majors and graduate students. The novel approach taken here banishes determinants to the end of the book. The text focuses on the central goal of linear algebra: understanding the structure of linear operators on finite-dimensional vector spaces. The author has taken unusual care to motivate concepts and to simplify proofs. A variety of interesting exercises in each chapter helps students understand and manipulate the objects of linear algebra. The third edition contains major improvements and revisions throughout the book. More than 300 new exercises have been added since the previous edition. Many new examples have been added to illustrate the key ideas of linear algebra. New topics covered in the book include product spaces, quotient spaces, and dual spaces. Beautiful new formatting creates pages with an unusually pleasant appearance in both print and electronic versions. No prerequisites are assumed other than the ...
Berdyugina, Svetlana
2015-08-01
Molecules probe cool matter in the Universe and various astrophysical objects. Their ability to sense magnetic fields provides new insights into magnetic properties of these objects. During the past fifteen years we have carried out a theoretical study of molecular magnetic effects such as the Zeeman, Paschen-Back and Hanle effects and their applications for inferring magnetic structures and spatial inhomogeneities on the Sun, cool stars, brown dwarfs, and exoplanets from molecular spectro-polarimetry (e.g., Berdyugina 2011). Here, we present an overview of this study and compare our theoretical predictions with recent laboratory measurements of magnetic properties of some molecules. We present also a new web-based tool to compute molecular magnetic effects and polarized spectra which is supported by the ERC Advanced Grant HotMol.
Graybill, George
2007-01-01
Young scientists will be thrilled to explore the invisible world of atoms, molecules and elements. Our resource provides ready-to-use information and activities for remedial students using simplified language and vocabulary. Students will label each part of the atom, learn what compounds are, and explore the patterns in the periodic table of elements to find calcium (Ca), chlorine (Cl), and helium (He) through hands-on activities.
Model molecules mimicking asphaltenes.
Sjöblom, Johan; Simon, Sébastien; Xu, Zhenghe
2015-04-01
Asphalthenes are typically defined as the fraction of petroleum insoluble in n-alkanes (typically heptane, but also hexane or pentane) but soluble in toluene. This fraction causes problems of emulsion formation and deposition/precipitation during crude oil production, processing and transport. From the definition it follows that asphaltenes are not a homogeneous fraction but is composed of molecules polydisperse in molecular weight, structure and functionalities. Their complexity makes the understanding of their properties difficult. Proper model molecules with well-defined structures which can resemble the properties of real asphaltenes can help to improve this understanding. Over the last ten years different research groups have proposed different asphaltene model molecules and studied them to determine how well they can mimic the properties of asphaltenes and determine the mechanisms behind the properties of asphaltenes. This article reviews the properties of the different classes of model compounds proposed and present their properties by comparison with fractionated asphaltenes. After presenting the interest of developing model asphaltenes, the composition and properties of asphaltenes are presented, followed by the presentation of approaches and accomplishments of different schools working on asphaltene model compounds. The presentation of bulk and interfacial properties of perylene-based model asphaltene compounds developed by Sjöblom et al. is the subject of the next part. Finally the emulsion-stabilization properties of fractionated asphaltenes and model asphaltene compounds is presented and discussed.
Hydrogen molecules in semiconductors
Energy Technology Data Exchange (ETDEWEB)
Weber, Joerg [Technische Universitaet Dresden, 01062 Dresden (Germany)], E-mail: joerg.weber@tu-dresden.de; Hiller, Martin; Lavrov, Edward V. [Technische Universitaet Dresden, 01062 Dresden (Germany)
2007-12-15
Molecular hydrogen, the simplest of all molecules, allows a direct insight into the fundamental properties of quantum mechanics. In the case of H{sub 2}, the Pauli principle leads to two different species, para-H{sub 2} and ortho-H{sub 2}. A conversion between these species is prohibited. Vibrational mode spectra reflect the fundamental properties and allow an unambiguous identification of the H{sub 2} molecules. Today, we have experimental evidence for the trapping of hydrogen molecules in the semiconductors Si, Ge and GaAs at the interstitial sites, within hydrogen-induced platelets, in voids and at impurities (interstitial oxygen in Si). Interstitial H{sub 2} is a nearly free rotor with a surprisingly simple behavior. We review on interstitial H{sub 2} in semiconductors and report on the unexpected preferential disappearance of the para-H{sub 2} or ortho-D{sub 2} species. The origin of the detected ortho-para conversion will be discussed.
Photonic Molecule Lasers Revisited
Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.
2014-05-01
Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.
Schneider, Hans
1989-01-01
Linear algebra is one of the central disciplines in mathematics. A student of pure mathematics must know linear algebra if he is to continue with modern algebra or functional analysis. Much of the mathematics now taught to engineers and physicists requires it.This well-known and highly regarded text makes the subject accessible to undergraduates with little mathematical experience. Written mainly for students in physics, engineering, economics, and other fields outside mathematics, the book gives the theory of matrices and applications to systems of linear equations, as well as many related t
Weisberg, Sanford
2013-01-01
Praise for the Third Edition ""...this is an excellent book which could easily be used as a course text...""-International Statistical Institute The Fourth Edition of Applied Linear Regression provides a thorough update of the basic theory and methodology of linear regression modeling. Demonstrating the practical applications of linear regression analysis techniques, the Fourth Edition uses interesting, real-world exercises and examples. Stressing central concepts such as model building, understanding parameters, assessing fit and reliability, and drawing conclusions, the new edition illus
Amir-Moez, A R; Sneddon, I N
1962-01-01
Elements of Linear Space is a detailed treatment of the elements of linear spaces, including real spaces with no more than three dimensions and complex n-dimensional spaces. The geometry of conic sections and quadric surfaces is considered, along with algebraic structures, especially vector spaces and transformations. Problems drawn from various branches of geometry are given.Comprised of 12 chapters, this volume begins with an introduction to real Euclidean space, followed by a discussion on linear transformations and matrices. The addition and multiplication of transformations and matrices a
Weisberg, Sanford
2005-01-01
Master linear regression techniques with a new edition of a classic text Reviews of the Second Edition: ""I found it enjoyable reading and so full of interesting material that even the well-informed reader will probably find something new . . . a necessity for all of those who do linear regression."" -Technometrics, February 1987 ""Overall, I feel that the book is a valuable addition to the now considerable list of texts on applied linear regression. It should be a strong contender as the leading text for a first serious course in regression analysis."" -American Scientist, May-June 1987
Abian, Alexander
1973-01-01
Linear Associative Algebras focuses on finite dimensional linear associative algebras and the Wedderburn structure theorems.The publication first elaborates on semigroups and groups, rings and fields, direct sum and tensor product of rings, and polynomial and matrix rings. The text then ponders on vector spaces, including finite dimensional vector spaces and matrix representation of vectors. The book takes a look at linear associative algebras, as well as the idempotent and nilpotent elements of an algebra, ideals of an algebra, total matrix algebras and the canonical forms of matrices, matrix
Unsupervised Linear Discriminant Analysis
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
An algorithm for unsupervised linear discriminant analysis was presented. Optimal unsupervised discriminant vectors are obtained through maximizing covariance of all samples and minimizing covariance of local k-nearest neighbor samples. The experimental results show our algorithm is effective.
Isolated linear blaschkoid psoriasis.
Nasimi, M; Abedini, R; Azizpour, A; Nikoo, A
2016-10-01
Linear psoriasis (LPs) is considered a rare clinical presentation of psoriasis, which is characterized by linear erythematous and scaly lesions along the lines of Blaschko. We report the case of a 20-year-old man who presented with asymptomatic linear and S-shaped erythematous, scaly plaques on right side of his trunk. The plaques were arranged along the lines of Blaschko with a sharp demarcation at the midline. Histological examination of a skin biopsy confirmed the diagnosis of psoriasis. Topical calcipotriol and betamethasone dipropionate ointments were prescribed for 2 months. A good clinical improvement was achieved, with reduction in lesion thickness and scaling. In patients with linear erythematous and scaly plaques along the lines of Blaschko, the diagnosis of LPs should be kept in mind, especially in patients with asymptomatic lesions of late onset. © 2016 British Association of Dermatologists.
Linear systems theory revisited
Willigenburg, van L.G.; Koning, de W.L.
2008-01-01
This paper investigates and clarifies how different definitions of reachability, observability, controllability, reconstructability and minimality that appear in the control literature, may be equivalent or different, depending on the type of linear system. The differences are caused by (1) whether
Machine Learning for Quantum Mechanical Properties of Atoms in Molecules
Rupp, Matthias; von Lilienfeld, O Anatole
2015-01-01
We introduce machine learning models of quantum mechanical observables of atoms in molecules. Instant out-of-sample predictions for proton and carbon nuclear chemical shifts, atomic core level excitations, and forces on atoms reach accuracies on par with density functional theory reference. Locality is exploited within non-linear regression via local atom-centered coordinate systems. The approach is validated on a diverse set of 9k small organic molecules. Linear scaling is demonstrated for saturated polymers with up to sub-mesoscale lengths.
Andrilli, Stephen
2010-01-01
Elementary Linear Algebra develops and explains in careful detail the computational techniques and fundamental theoretical results central to a first course in linear algebra. This highly acclaimed text focuses on developing the abstract thinking essential for further mathematical study. The authors give early, intensive attention to the skills necessary to make students comfortable with mathematical proofs. The text builds a gradual and smooth transition from computational results to general theory of abstract vector spaces. It also provides flexbile coverage of practical applications, expl
Callier, Frank M.; Desoer, Charles A.
1991-01-01
The aim of this book is to provide a systematic and rigorous access to the main topics of linear state-space system theory in both the continuous-time case and the discrete-time case; and the I/O description of linear systems. The main thrusts of the work are the analysis of system descriptions and derivations of their properties, LQ-optimal control, state feedback and state estimation, and MIMO unity-feedback systems.
1985-04-01
7.0 % % o the testing of an experimental linear motor driven expander using a standard production 1/4W split Stirling Common Module compressor. . - o...3 2.2 Expander Design CTI-CRYOGENICS has long recognized the potential of employing a linear drive motor to assist regenerator displacement and...assessment of the expander’s performance with lip seals and clearance seals for a regenerator comprised of nickel balls. Further comparison of a stainless
DEFF Research Database (Denmark)
Høskuldsson, Agnar
1996-01-01
Determination of the proper dimension of a given linear model is one of the most important tasks in the applied modeling work. We consider here eight criteria that can be used to determine the dimension of the model, or equivalently, the number of components to use in the model. Four...... the basic problems in determining the dimension of linear models. Then each of the eight measures are treated. The results are illustrated by examples....
Spackman, Mark A.
2013-04-01
Hirshfeld surface analysis has developed from the serendipitous discovery of a novel partitioning of the crystal electron density into discrete molecular fragments, to a suite of computational tools used widely for the identification, analysis and discussion of intermolecular interactions in molecular crystals. The relationship between the Hirshfeld surface and very early ideas on the internal structure of crystals is outlined, and applications of Hirshfeld surface analysis are presented for three molecules of historical importance in the development of modern x-ray crystallography: hexamethylbenzene, hexamethylenetetramine and diketopiperazine.
Periodic tables of diatomic and triatomic molecules%二原子分子和三原子分子的周期表
Institute of Scientific and Technical Information of China (English)
孔繁敖; 吴为强
2012-01-01
The Mendeleev periodic table of atoms is one of the most important principles in natural science. However, there is shortage of analog for molecules. Here we propose two periodic tables, one for diatomic molecules and one for triatomic molecules. The form of the molecular periodic tables is analogous to that of Mendeleev periodic table of atoms. In the table, molecules are classified and arranged by their group number G, which is the number of valence electrons, and the periodic number P, which represents the size of the molecules. The basic molecular properties, including bond length, binding energy, force constant, ionization potential, spin multiplicity, chemical reactivity, and bond angle, change periodically within the tables. The periodicities of diatomic and triatomic molecules are thus revealed. We also demonstrate that the periodicity originates from the shell-like electronic configurations of the molecules. The periodic tables not only contain free molecules, but also the "virtual" molecules present in polyatomic molecules. The periodic tables can be used to classify molecules, to predict unknown molecular properties, to understand the role of virtual molecules in polyatomic molecules, and to initiate new research fields, such as the periodicities of aromatic species, clusters, or nanoparticles. The tables should be of interest not only to scientists in a variety of disciplines, but also to undergraduates studying natural sciences.%门捷列夫元素周期表是自然科学中最重要的原则之一.然而,对于分子而言,却缺乏类似的表格.本文提出两个分别对应于二原子分子和三原子分子的周期表.这些分子周期表的格式和门捷列夫原子周期表相似,在这些表格中,分子依照它们各自的族数G和周期数P分类排列,G是价电子的数目而P则表示分子的尺寸,分子的基本性质,包括键长、结合能、力常数、电离势、自旋多重度、化学反应活性以及键角等等,都随
Multiorbital tunneling ionization of the CO molecule
Wu, J; Kunitski, M; Meckel, M; Voss, S; Sann, H; Kim, H; Jahnke, T; Czasch, A; Dörner, R
2012-01-01
We coincidently measure the molecular frame photoelectron angular distribution and the ion sum-momentum distribution of single and double ionization of CO molecules by using circularly and elliptically polarized femtosecond laser pulses, respectively. The orientation dependent ionization rates for various kinetic energy releases allow us to individually identify the ionizations of multiple orbitals, ranging from the highest occupied to the next two lower-lying molecular orbitals for various channels observed in our experiments. Not only the emission of a single electron, but also the sequential tunneling dynamics of two electrons from multiple orbitals are traced step by step. Our results confirm that the shape of the ionizing orbitals determine the strong laser field tunneling ionization in the CO molecule, whereas the linear Stark effect plays a minor role.
Effective interaction between helical bio-molecules
Allahyarov, E
1999-01-01
The effective interaction between two parallel strands of helicalbio-molecules, such as deoxyribose nucleic acids (DNA), is calculated usingcomputer simulations of the "primitive" model of electrolytes. In particular westudy a simple model for B-DNA incorporating explicitly its charge pattern as adouble-helix structure. The effective force and the effective torque exertedonto the molecules depend on the central distance and on the relativeorientation. The contributions of nonlinear screening by monovalent counterionsto these forces and torques are analyzed and calculated for different saltconcentrations. As a result, we find that the sign of the force dependssensitively on the relative orientation. For intermolecular distances smallerthan $6\\AA$ it can be both attractive and repulsive. Furthermore we report anonmonotonic behaviour of the effective force for increasing saltconcentration. Both features cannot be described within linear screeningtheories. For large distances, on the other hand, the results agree...
Ultra-cold molecule production.
Energy Technology Data Exchange (ETDEWEB)
Ramirez-Serrano, Jamie; Chandler, David W.; Strecker, Kevin; Rahn, Larry A.
2005-12-01
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.
Entanglement Dynamics in Typical Local- and Normal-Mode Molecules
Institute of Scientific and Technical Information of China (English)
HOU Xi-Wen; WAN Ming-Fang; MA Zhong-Qi
2007-01-01
The entanglement dynamics of two stretching vibrations in theoretically typical local- and normal-mode molecules and realistic molecules H2O and SO2 in an algebraic model is studied in terms of the reduced-density linear entropy with initial entangled states taken to be two-mode squeezed vacuum states. It is shown that the behaviour of the entropy in theoretically typical molecules appears to be more regular than that in realistic ones, and that the entropy becomes irregular as the amplitude of two-mode squeezed vacuum states increases. For initial states with a small amplitude, it is demonstrated that the periodicity and the "classical" beat phenomenon of the entropy occur with the beat in theoretically typical molecules being more regular than that in realistic molecules H2O and SO2.
Visualization of DNA molecules in time during electrophoresis
Lubega, Seth
1991-01-01
For several years individual DNA molecules have been observed and photographed during agarose gel electrophoresis. The DNA molecule is clearly the largest molecule known. Nevertheless, the largest molecule is still too small to be seen using a microscope. A technique developed by Morikawa and Yanagida has made it possible to visualize individual DNA molecules. When these long molecules are labeled with appropriate fluorescence dyes and observed under a fluorescence microscope, although it is not possible to directly visualize the local ultrastructure of the molecules, yet because they are long light emitting chains, their microscopic dynamical behavior can be observed. This visualization works in the same principle that enables one to observe a star through a telescope because it emits light against a dark background. The dynamics of individual DNA molecules migrating through agarose matrix during electrophoresis have been described by Smith et al. (1989), Schwartz and Koval (1989), and Bustamante et al. (1990). DNA molecules during agarose gel electrophoresis advance lengthwise thorough the gel in an extended configuration. They display an extension-contraction motion and tend to bunch up in their leading ends as the 'heads' find new pores through the gel. From time to time they get hooked on obstacles in the gel to form U-shaped configurations before they resume their linear configuration.
Covalent bonding from alchemical linear response density functional theory
Chang, K Y Samuel; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole
2015-01-01
We assess the predictive accuracy of linear response based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated single bonds to hydrogen, as well as single, double, and triple bonds between main-group elements, occurring in small iso-electronic molecular spaces with atomic elements drawn from rows 2-3 in the $p$-block of the periodic table. Numerical evidence suggests that first order estimates of bonding potentials can achieve chemical accuracy if the alchemical interpolation connects molecules containing late elements in the periodic table (3$^{rd}$ and 4$^{th}$ row) and identical number of atoms and molecular geometries. For these interpolations, changes in bonding potential are near-linear in the coupling parameter, resulting in accurate Hellmann-Feynman predictions. Second order estimates for such interpolations yield worse predictions. The predictions become substantially worse if initial and final molecules differ not only in composition...
Blyth, T S
2002-01-01
Most of the introductory courses on linear algebra develop the basic theory of finite dimensional vector spaces, and in so doing relate the notion of a linear mapping to that of a matrix. Generally speaking, such courses culminate in the diagonalisation of certain matrices and the application of this process to various situations. Such is the case, for example, in our previous SUMS volume Basic Linear Algebra. The present text is a continuation of that volume, and has the objective of introducing the reader to more advanced properties of vector spaces and linear mappings, and consequently of matrices. For readers who are not familiar with the contents of Basic Linear Algebra we provide an introductory chapter that consists of a compact summary of the prerequisites for the present volume. In order to consolidate the student's understanding we have included a large num ber of illustrative and worked examples, as well as many exercises that are strategi cally placed throughout the text. Solutions to the ex...
Directory of Open Access Journals (Sweden)
Sinan AYDIN
2009-04-01
Full Text Available Linear algebra is a basic course followed in mathematics, science, and engineering university departments.Generally, this course is taken in either the first or second year but there have been difficulties in teachingand learning. This type of active algebra has resulted in an increase in research by mathematics educationresearchers. But there is insufficient information on this subject in Turkish and therefore it has not beengiven any educational status. This paper aims to give a general overview of this subject in teaching andlearning. These education studies can be considered quadruple: a the history of linear algebra, b formalismobstacles of linear algebra and cognitive flexibility to improve teaching and learning, c the relation betweenlinear algebra and geometry, d using technology in the teaching and learning linear algebra.Mathematicseducation researchers cannot provide an absolute solution to overcome the teaching and learning difficultiesof linear algebra. Epistemological analyses and experimental teaching have shown the learning difficulties.Given these results, further advice and assistance can be offered locally.
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...
Molecules Best Paper Award 2013.
McPhee, Derek J
2013-02-05
Molecules has started to institute a "Best Paper" award to recognize the most outstanding papers in the area of natural products, medicinal chemistry and molecular diversity published in Molecules. We are pleased to announce the second "Molecules Best Paper Award" for 2013.
Banach, S
1987-01-01
This classic work by the late Stefan Banach has been translated into English so as to reach a yet wider audience. It contains the basics of the algebra of operators, concentrating on the study of linear operators, which corresponds to that of the linear forms a1x1 + a2x2 + ... + anxn of algebra.The book gathers results concerning linear operators defined in general spaces of a certain kind, principally in Banach spaces, examples of which are: the space of continuous functions, that of the pth-power-summable functions, Hilbert space, etc. The general theorems are interpreted in various mathematical areas, such as group theory, differential equations, integral equations, equations with infinitely many unknowns, functions of a real variable, summation methods and orthogonal series.A new fifty-page section (``Some Aspects of the Present Theory of Banach Spaces'''') complements this important monograph.
Hogben, Leslie
2013-01-01
With a substantial amount of new material, the Handbook of Linear Algebra, Second Edition provides comprehensive coverage of linear algebra concepts, applications, and computational software packages in an easy-to-use format. It guides you from the very elementary aspects of the subject to the frontiers of current research. Along with revisions and updates throughout, the second edition of this bestseller includes 20 new chapters.New to the Second EditionSeparate chapters on Schur complements, additional types of canonical forms, tensors, matrix polynomials, matrix equations, special types of
Linear Algebra Thoroughly Explained
Vujičić, Milan
2008-01-01
Linear Algebra Thoroughly Explained provides a comprehensive introduction to the subject suitable for adoption as a self-contained text for courses at undergraduate and postgraduate level. The clear and comprehensive presentation of the basic theory is illustrated throughout with an abundance of worked examples. The book is written for teachers and students of linear algebra at all levels and across mathematics and the applied sciences, particularly physics and engineering. It will also be an invaluable addition to research libraries as a comprehensive resource book for the subject.
Cooperstein, Bruce
2015-01-01
Advanced Linear Algebra, Second Edition takes a gentle approach that starts with familiar concepts and then gradually builds to deeper results. Each section begins with an outline of previously introduced concepts and results necessary for mastering the new material. By reviewing what students need to know before moving forward, the text builds a solid foundation upon which to progress. The new edition of this successful text focuses on vector spaces and the maps between them that preserve their structure (linear transformations). Designed for advanced undergraduate and beginning graduate stud
Institute of Scientific and Technical Information of China (English)
SHEN Guo-quan; XIAO Yuan-chun
2003-01-01
@@ Linear-rubbing is a characteristic technique in the academic school of internal exercise massage in Shanghai. It was known as "flat pushing method" in the past times. The academic school of internal exercise Tuina finds, in the clinical practice of flat pushing, that if the internal exercise accumuhtes in the palm and one-way movement is replaced by two-way movement, the kinetic energy may be transformed into heat energy, bringing about a new unique manipulating technique, which is rather different from the usual flat pushing no longer and now called linear-rubbing therapy.
Linear Logical Voting Protocols
DEFF Research Database (Denmark)
DeYoung, Henry; Schürmann, Carsten
2012-01-01
. In response, we promote linear logic as a high-level language for both specifying and implementing voting protocols. Our linear logical specifications of the single-winner first-past-the-post (SW- FPTP) and single transferable vote (STV) protocols demonstrate that this approach leads to concise......Current approaches to electronic implementations of voting protocols involve translating legal text to source code of an imperative programming language. Because the gap between legal text and source code is very large, it is difficult to trust that the program meets its legal specification...... implementations that closely correspond to their legal specification, thereby increasing trust....
POLYMER TOPOLOGY AND DIFFUSION - A COMPARISON OF DIFFUSION IN LINEAR AND CYCLIC MACROMOLECULES
TEAD, SF; KRAMER, EJ; HADZIIOANNOU, G; ANTONIETTI, M; SILLESCU, H; LUTZ, P; STRAZIELLE, C
1992-01-01
Diffusion experiments using polystyrene (PS) molecules of three different topologies, linear, ring, and microgel, were performed. Tracer diffusion of linear PS in ring matrices was found to be nearly identical to that in linear matrices, a surprising result in view of current theories for
Analysis of exact linearization and aproximate feedback linearization techniques
Schnitman, Leizer; Cardoso, Gildeberto de Souza
2011-01-01
p. 1-17 This paper presents a study of linear control systems based on exact feedback linearization and approximate feedback linearization. As exact feedback linearization is applied, a linear controller can perform the control objectives. The approximate feedback linearization is required when a nonlinear system presents a noninvolutive property. It uses a Taylor series expansion in order to compute a nonlinear transformation of coordinates to satisfy the involutivity conditions.
Analysis of Exact Linearization and Aproximate Feedback Linearization Techniques
Cardoso, Gildeberto S.; Leizer Schnitman
2011-01-01
This paper presents a study of linear control systems based on exact feedback linearization and approximate feedback linearization. As exact feedback linearization is applied, a linear controller can perform the control objectives. The approximate feedback linearization is required when a nonlinear system presents a noninvolutive property. It uses a Taylor series expansion in order to compute a nonlinear transformation of coordinates to satisfy the involutivity conditions.
Lanthanide single molecule magnets
Energy Technology Data Exchange (ETDEWEB)
Tang, Jinkui; Zhang, Peng [Chinese Academy of Sciences, Changchun (China). Changchun Inst. of Applied Chemistry
2015-10-01
This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures - an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and explore new directions.
Astrochemistry and Interstellar Molecules
Minh, Y. C.
2010-03-01
Astrochemistry provides powerful tools to understand various cosmic phenomena, including those in our solar system to the large-scale structure of the universe. In addition, the chemical property of an astronomical body is a crucial factor which governs the evolution of the system. Recent progress in astrophysical theories, computational modelings, and observational techniques requires a detailed understanding of the interactions between the constituents of an astronomical system, which are atoms and molecules within the system. Especially the far-infrared/sub-millimeter wave range, which is called as the last frontier in astronomical observations, contains numerous molecular lines, which may provide a huge amount of new information. However, we need an astrochemical understanding to use this information fully. Although this review is very limited, I would like to stress the importance of astrochemical approach in this overview for the field, which is getting much more attention than ever before.
Lanthanide single molecule magnets
Tang, Jinkui
2015-01-01
This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs, and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures – an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and...
Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W
2007-01-01
Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another?
Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics
Alizadehheidari, M; Noble, C; Reiter-Schad, M; Nyberg, L K; Fritzsche, J; Mehlig, B; Tegenfeldt, J O; Ambjörnsson, T; Persson, F; Westerlund, F
2016-01-01
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA....
Linear Projective Program Syntax
Bergstra, J.A.; Bethke, I.
2004-01-01
Based on an extremely simple program notation more advanced program features can be developed in linear projective program syntax such as conditional statements, while loops, recursion, use of an evaluation stack, object classes, method calls etc. Taking care of a cumulative and bottom up
Directory of Open Access Journals (Sweden)
Ovidiu T. Pop
2007-01-01
Full Text Available Using the method of Jakimovski and Leviatan from their work in 1969, we construct a general class of linear positive operators. We study the convergence, the evaluation for the rate of convergence in terms of the first modulus of smoothness and we give a Voronovskaja-type theorem for these operators.
Linear Mappings of Quaternion Algebra
Kleyn, Aleks
2011-01-01
In the paper I considered linear and antilinear automorphisms of quaternion algebra. I proved the theorem that there is unique expansion of R-linear mapping of quaternion algebra relative to the given set of linear and antilinear automorphisms.
Unidirectional Rotation of Molecules Measured by the Rotational Doppler Effect
Directory of Open Access Journals (Sweden)
Prior Yehiam
2013-03-01
Full Text Available A pair of linearly polarized pump pulses induce field-free unidirectional molecular rotation, which is detected by a delayed circularly polarized probe. The polarization and spectrum of the probe are modified by the interaction with the molecules, in accordance with the Rotational Doppler Effect.
Kinetics of hydrogen molecules in MAGNUM-PSI
Baeva, M.; W. J. Goedheer,; Cardozo, N. J. L.
2008-01-01
Results from simulations of plasma and neutrals under conditions predictively characterizing the detached plasma regime in the linear machine MAGNUM-PSI are presented. The relaxation of the vibrationally excited hydrogen molecules is investigated in order to establish a relation between their relaxa
Finite-dimensional linear algebra
Gockenbach, Mark S
2010-01-01
Some Problems Posed on Vector SpacesLinear equationsBest approximationDiagonalizationSummaryFields and Vector SpacesFields Vector spaces Subspaces Linear combinations and spanning sets Linear independence Basis and dimension Properties of bases Polynomial interpolation and the Lagrange basis Continuous piecewise polynomial functionsLinear OperatorsLinear operatorsMore properties of linear operatorsIsomorphic vector spaces Linear operator equations Existence and uniqueness of solutions The fundamental theorem; inverse operatorsGaussian elimination Newton's method Linear ordinary differential eq
Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same
Croteau, Rodney Bruce; Burke, Charles Cullen
2008-06-24
In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.
Mechanical response of collagen molecule under hydrostatic compression
Energy Technology Data Exchange (ETDEWEB)
Saini, Karanvir, E-mail: karans@iitrpr.ac.in; Kumar, Navin
2015-04-01
Proteins like collagen are the basic building blocks of various body tissues (soft and hard). Collagen molecules find their presence in the skeletal system of the body where they bear mechanical loads from different directions, either individually or along with hydroxy-apatite crystals. Therefore, it is very important to understand the mechanical behavior of the collagen molecule which is subjected to multi-axial state of loading. The estimation of strains of collagen molecule along different directions resulting from the changes in hydrostatic pressure magnitude, can provide us new insights into its mechanical behavior. In the present work, full atomistic simulations have been used to study global (volumetric) as well as local (along different directions) mechanical properties of the hydrated collagen molecule which is subjected to different hydrostatic pressure magnitudes. To estimate the local mechanical properties, the strains of collagen molecule along its longitudinal and transverse directions have been acquired at different hydrostatic pressure magnitudes. In spite of non-homogeneous distribution of atoms within the collagen molecule, the calculated values of local mechanical properties have been found to carry the same order of magnitude along the longitudinal and transverse directions. It has been demonstrated that the values of global mechanical properties like compressibility, bulk modulus, etc. as well as local mechanical properties like linear compressibility, linear elastic modulus, etc. are functions of magnitudes of applied hydrostatic pressures. The mechanical characteristics of collagen molecule based on the atomistic model have also been compared with that of the continuum model in the present work. The comparison showed up orthotropic material behavior for the collagen molecule. The information on collagen molecule provided in the present study can be very helpful in designing the future bio-materials.
Structure and dynamics of water molecules confined in triglyceride oils.
Groot, Carien C M; Velikov, Krassimir P; Bakker, Huib J
2016-10-26
Though it is commonly known that a small amount of water can be present in triglyceride oil, a molecular picture of how water molecules organize in the oil phase is lacking. We investigate the hydrogen-bond configuration and dynamics of water in triacetin, tributyrin and trioctanoin using linear infrared and time-resolved two-dimensional infrared (2DIR) spectroscopy of the water hydroxyl stretch vibration. We identify water molecules with a single strong hydrogen bond to the triglyceride, water molecules with two weaker hydrogen bonds to the triglycerides, and water clusters. These species do not interconvert on the 20 ps timescale of the experiment, as evidenced by the absence of cross-peaks in the 2DIR spectrum. The vibrational response of water molecules with a single strong hydrogen bond to the triglyceride depends strongly on the excitation frequency, revealing the presence of different subspecies of singly-bound water molecules that correspond to different hydrogen-bond locations. In contrast, the water molecules with two weaker hydrogen bonds to the triglyceride correspond to a single, specific hydrogen-bond configuration; these molecules likely bridge the carbonyl groups of adjacent triglyceride molecules, which can have considerable influence on liquid triglyceride properties.
Floppy Molecules with Internal Rotation and Inversion
Kreglewski, Marek
2016-06-01
There are different ways to analyze rovibrational structure of molecules having several large amplitude motions of different type, like internal rotation and inversion or ring-puckering. In my research group we have developed and used methods starting from potential surfaces for large amplitude motions but also applied purely effective Hamiltonians, where tunneling splittings were key parameters. Whatever is the method the following problems must be solved when addressing a rovibrational problem with large amplitude vibrations: 1) a definition of the permutation-inversion molecular symmetry group, 2) a choice of the internal coordinates and their transformation in the symmetry group, 3) derivation of the Hamiltonian in chosen coordinates, 4) calculation of the Hamiltonian matrix elements in a symmetrized basis set. These points will be discussed. The advantage of methods which start from the geometry and potential surface for large amplitude vibrations give much clearer picture of internal dynamics of molecules but generally the fit to experimental data is much poorer. The fitting procedure is strongly non-linear and the iteration procedure much longer. The effective Hamiltonians the fit is generally much better since almost all optimized parameters are linear but the parameters have no clear physical meaning. This method is very useful in the assignment of experimental spectra. Results of the application of both method to methylamine and hydrazine will be presented.
Indian Academy of Sciences (India)
J V Yakhmi
2009-06-01
The conventional magnetic materials used in current technology, such as, Fe, Fe2O3, Cr2O3, SmCo5, Nd2Fe14B etc are all atom-based, and their preparation/processing require high temperature routes. Employing self-assembly methods, it is possible to engineer a bulk molecular material with long-range magnetic order, mainly because one can play with the weak intermolecular interactions. Since the first successful synthesis of molecular magnets in 1986, a large variety of them have been synthesized, which can be categorized on the basis of the chemical nature of the magnetic units involved: organic-, metal-based systems, heterobimetallic assemblies, or mixed organic–inorganic systems. The design of molecule-based magnets has also been extended to the design of poly-functional molecular magnets, such as those exhibiting second-order optical nonlinearity, liquid crystallinity, or chirality simultaneously with long-range magnetic order. Solubility, low density and biocompatibility are attractive features of molecular magnets. Being weakly coloured, unlike their opaque classical magnet ‘cousins’ listed above, possibilities of photomagnetic switching exist. Persistent efforts also continue to design the ever-elusive polymer magnets towards applications in industry. While providing a brief overview of the field of molecular magnetism, this article highlights some recent developments in it, with emphasis on a few studies from the author’s own lab.
Topics in computational linear optimization
DEFF Research Database (Denmark)
Hultberg, Tim Helge
2000-01-01
. Linear optimization problems covers both linear programming problems, which are polynomially solvable, and mixed integer linear programming problems, which belong to the class of NP-hard problems. The three main reasons for the practical succes of linear optimization are: wide applicability, availabilty...... of high quality solvers and the use of algebraic modelling systems to handle the communication between the modeller and the solver. This dissertation features four topics in computational linear optimization: A) automatic reformulation of mixed 0/1 linear programs, B) direct solution of sparse unsymmetric...... systems of linear equations, C) reduction of linear programs and D) integration of algebraic modelling of linear optimization problems in C++. Each of these topics is treated in a separate paper included in this dissertation. The efficiency of solving mixed 0-1 linear programs by linear programming based...
Partially dark optical molecule via phase control
Wang, Z. H.; Xu, Xun-Wei; Li, Yong
2017-01-01
We study the tunable photonic distribution in an optical molecule consisting of two linearly coupled single-mode cavities. With the intercavity coupling and two driving fields, the energy levels of the optical-molecule system form a closed cyclic energy-level diagram, and the phase difference between the driving fields serves as a sensitive controller on the dynamics of the system. Due to the quantum interference effect, we can realize a partially dark optical molecule, where the steady-state mean photon number in one of the cavities achieves zero even under the external driving. And the dark cavity can be changed from one of the cavities to the other by only adjusting the phase difference. We also show that our proposal is robust to the noise at zero temperature. Furthermore, we show that when one of the cavities couples with an atomic ensemble, it will be dark under the same condition as that in the case without atoms, but the condition for the other cavity to be dark is modified.
Schmidt, Bruno E; Ernotte, Guilmot; Clerici, Matteo; Morandotti, Roberto; Ibrahim, Heide; Legare, Francois
2016-01-01
In the framework of linear optics, light fields do not interact with each other in a medium. Yet, when their field amplitude becomes comparable to the electron binding energies of matter, the nonlinear motion of these electrons emits new dipole radiation whose amplitude, frequency and phase differ from the incoming fields. Such high fields are typically achieved with ultra-short, femtosecond (1fs = 10-15 sec.) laser pulses containing very broad frequency spectra. Here, the matter not only couples incoming and outgoing fields but also causes different spectral components to interact and mix through a convolution process. In this contribution, we describe how frequency domain nonlinear optics overcomes the shortcomings arising from this convolution in conventional time domain nonlinear optics1. We generate light fields with previously inaccessible properties because the uncontrolled coupling of amplitudes and phases is turned off. For example, arbitrary phase functions are transferred linearly to the second har...
Extended linear chain compounds
Linear chain substances span a large cross section of contemporary chemistry ranging from covalent polymers, to organic charge transfer com plexes to nonstoichiometric transition metal coordination complexes. Their commonality, which coalesced intense interest in the theoretical and exper imental solid state physics/chemistry communities, was based on the obser vation that these inorganic and organic polymeric substrates exhibit striking metal-like electrical and optical properties. Exploitation and extension of these systems has led to the systematic study of both the chemistry and physics of highly and poorly conducting linear chain substances. To gain a salient understanding of these complex materials rich in anomalous aniso tropic electrical, optical, magnetic, and mechanical properties, the conver gence of diverse skills and talents was required. The constructive blending of traditionally segregated disciplines such as synthetic and physical organic, inorganic, and polymer chemistry, crystallog...
Linear recursive distributed representations.
Voegtlin, Thomas; Dominey, Peter F
2005-09-01
Connectionist networks have been criticized for their inability to represent complex structures with systematicity. That is, while they can be trained to represent and manipulate complex objects made of several constituents, they generally fail to generalize to novel combinations of the same constituents. This paper presents a modification of Pollack's Recursive Auto-Associative Memory (RAAM), that addresses this criticism. The network uses linear units and is trained with Oja's rule, in which it generalizes PCA to tree-structured data. Learned representations may be linearly combined, in order to represent new complex structures. This results in unprecedented generalization capabilities. Capacity is orders of magnitude higher than that of a RAAM trained with back-propagation. Moreover, regularities of the training set are preserved in the new formed objects. The formation of new structures displays developmental effects similar to those observed in children when learning to generalize about the argument structure of verbs.
Van der Veken, Frederik F
2014-01-01
Wilson lines, being comparators that render non-local operator products gauge invariant, are extensively used in QCD calculations, especially in small-$x$ calculations, calculations concerning validation of factorisation schemes and in calculations for constructing or modelling parton density functions. We develop an algorithm to express piecewise path ordered exponentials as path ordered integrals over the separate segments, and apply it on linear segments, reducing the number of diagrams needed to be calculated. We show how different linear path topologies can be related using their colour structure. This framework allows one to easily switch results between different Wilson line structures, which is especially useful when testing different structures against each other, e.g. when checking universality properties of non-perturbative objects.
Scaled Sparse Linear Regression
Sun, Tingni
2011-01-01
Scaled sparse linear regression jointly estimates the regression coefficients and noise level in a linear model. It chooses an equilibrium with a sparse regression method by iteratively estimating the noise level via the mean residual squares and scaling the penalty in proportion to the estimated noise level. The iterative algorithm costs nearly nothing beyond the computation of a path of the sparse regression estimator for penalty levels above a threshold. For the scaled Lasso, the algorithm is a gradient descent in a convex minimization of a penalized joint loss function for the regression coefficients and noise level. Under mild regularity conditions, we prove that the method yields simultaneously an estimator for the noise level and an estimated coefficient vector in the Lasso path satisfying certain oracle inequalities for the estimation of the noise level, prediction, and the estimation of regression coefficients. These oracle inequalities provide sufficient conditions for the consistency and asymptotic...
Sander, K F
1964-01-01
Linear Network Theory covers the significant algebraic aspect of network theory, with minimal reference to practical circuits. The book begins the presentation of network analysis with the exposition of networks containing resistances only, and follows it up with a discussion of networks involving inductance and capacity by way of the differential equations. Classification and description of certain networks, equivalent networks, filter circuits, and network functions are also covered. Electrical engineers, technicians, electronics engineers, electricians, and students learning the intricacies
Danto, L A; Wolfman, E F
1976-03-01
Three cases of blunt abdominal trauma are presented to exemplify the mechanism of trauma and the problems of diagnosis associated with any linear blow to the abdomen. The mechanisms of visceral injury are reviewed, and special attention is directed to the abdominal wall injury that can be present in these patients. This injury has special implications in directing the operative approach and repair. An unusual aortic occlusion is described which is peculiar to this type of injury.
Redesigning linear algebra algorithms
Energy Technology Data Exchange (ETDEWEB)
Dongarra, J.J.
1983-01-01
Many of the standard algorithms in linear algebra as implemented in FORTRAN do not achieve maximum performance on today's large-scale vector computers. The author examines the problem and constructs alternative formulations of algorithms that do not lose the clarity of the original algorithm or sacrifice the FORTRAN portable environment, but do gain the performance attainable on these supercomputers. The resulting implementation not only performs well on vector computers but also increases performance on conventional sequential computers. 13 references.
Redesigning linear algebra algorithms
Energy Technology Data Exchange (ETDEWEB)
Dongarra, J.J.
1983-01-01
Many of the standard algorithms in linear algebra as implemented in FORTRAN do not achieve maximum performance on today's large-scale vector computers. In this paper we examine the problem and construct alternative formulations of algorithms that do not lose the clarity of the original algorithm or sacrifice the Fortran portable environment, but do gain the performance attainable on these supercomputers. The resulting implementation not only performs well on vector computers but also increases performance on conventional sequential computers.
Fundamentals of linear algebra
Dash, Rajani Ballav
2008-01-01
FUNDAMENTALS OF LINEAR ALGEBRA is a comprehensive Text Book, which can be used by students and teachers of All Indian Universities. The Text has easy, understandable form and covers all topics of UGC Curriculum. There are lots of worked out examples which helps the students in solving the problems without anybody's help. The Problem sets have been designed keeping in view of the questions asked in different examinations.
Relativistic Linear Restoring Force
Clark, D.; Franklin, J.; Mann, N.
2012-01-01
We consider two different forms for a relativistic version of a linear restoring force. The pair comes from taking Hooke's law to be the force appearing on the right-hand side of the relativistic expressions: d"p"/d"t" or d"p"/d["tau"]. Either formulation recovers Hooke's law in the non-relativistic limit. In addition to these two forces, we…
Strongly interacting ultracold polar molecules
Gadway, Bryce
2016-01-01
This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole-dipole interactions. Ultracold samples of dipolar molecules with long-range interactions offer a unique platform for quantum simulations and the study of correlated many-body physics. We provide an introduction to the physics of dipolar quantum gases, both electric and magnetic, and summarize the multipronged efforts to bring dipolar molecules into the quantum regime. We discuss in detail the recent experimental progress in realizing and studying strongly interacting systems of polar molecules trapped in optical lattices, with particular emphasis on the study of interacting spin systems and non-equilibrium quantum magnetism. Finally, we conclude with a brief discussion of the future prospects for studies of strongly interacting dipolar molecules.
Kroonblawd, Matthew P; Sewell, Thomas D; Maillet, Jean-Bernard
2016-02-14
In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.
Energy Technology Data Exchange (ETDEWEB)
Kroonblawd, Matthew P.; Sewell, Thomas D., E-mail: sewellt@missouri.edu [Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211-7600 (United States); Maillet, Jean-Bernard, E-mail: jean-bernard.maillet@cea.fr [CEA, DAM, DIF, F-91297 Arpajon (France)
2016-02-14
In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.
Springer, T A
1998-01-01
"[The first] ten chapters...are an efficient, accessible, and self-contained introduction to affine algebraic groups over an algebraically closed field. The author includes exercises and the book is certainly usable by graduate students as a text or for self-study...the author [has a] student-friendly style… [The following] seven chapters... would also be a good introduction to rationality issues for algebraic groups. A number of results from the literature…appear for the first time in a text." –Mathematical Reviews (Review of the Second Edition) "This book is a completely new version of the first edition. The aim of the old book was to present the theory of linear algebraic groups over an algebraically closed field. Reading that book, many people entered the research field of linear algebraic groups. The present book has a wider scope. Its aim is to treat the theory of linear algebraic groups over arbitrary fields. Again, the author keeps the treatment of prerequisites self-contained. The material of t...
The International Linear Collider
Barish, Barry
2013-01-01
In this article, we describe the key features of the recently completed technical design for the International Linear Collider (ILC), a 200-500 GeV linear electron-positron collider (expandable to 1 TeV) that is based on 1.3 GHz superconducting radio-frequency (SCRF) technology. The machine parameters and detector characteristics have been chosen to complement the Large Hadron Collider physics, including the discovery of the Higgs boson, and to further exploit this new particle physics energy frontier with a precision instrument. The linear collider design is the result of nearly twenty years of R&D, resulting in a mature conceptual design for the ILC project that reflects an international consensus. We summarize the physics goals and capability of the ILC, the enabling R&D and resulting accelerator design, as well as the concepts for two complementary detectors. The ILC is technically ready to be proposed and built as a next generation lepton collider, perhaps to be built in stages beginning as a Hig...
Linearized Kernel Dictionary Learning
Golts, Alona; Elad, Michael
2016-06-01
In this paper we present a new approach of incorporating kernels into dictionary learning. The kernel K-SVD algorithm (KKSVD), which has been introduced recently, shows an improvement in classification performance, with relation to its linear counterpart K-SVD. However, this algorithm requires the storage and handling of a very large kernel matrix, which leads to high computational cost, while also limiting its use to setups with small number of training examples. We address these problems by combining two ideas: first we approximate the kernel matrix using a cleverly sampled subset of its columns using the Nystr\\"{o}m method; secondly, as we wish to avoid using this matrix altogether, we decompose it by SVD to form new "virtual samples," on which any linear dictionary learning can be employed. Our method, termed "Linearized Kernel Dictionary Learning" (LKDL) can be seamlessly applied as a pre-processing stage on top of any efficient off-the-shelf dictionary learning scheme, effectively "kernelizing" it. We demonstrate the effectiveness of our method on several tasks of both supervised and unsupervised classification and show the efficiency of the proposed scheme, its easy integration and performance boosting properties.
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...
Linear optical response of finite systems using multishift linear system solvers.
Hübener, Hannes; Giustino, Feliciano
2014-07-28
We discuss the application of multishift linear system solvers to linear-response time-dependent density functional theory. Using this technique the complete frequency-dependent electronic density response of finite systems to an external perturbation can be calculated at the cost of a single solution of a linear system via conjugate gradients. We show that multishift time-dependent density functional theory yields excitation energies and oscillator strengths in perfect agreement with the standard diagonalization of the response matrix (Casida's method), while being computationally advantageous. We present test calculations for benzene, porphin, and chlorophyll molecules. We argue that multishift solvers may find broad applicability in the context of excited-state calculations within density-functional theory and beyond.
Linear optical response of finite systems using multishift linear system solvers
Energy Technology Data Exchange (ETDEWEB)
Hübener, Hannes; Giustino, Feliciano [Department of Materials, University of Oxford, Oxford OX1 3PH (United Kingdom)
2014-07-28
We discuss the application of multishift linear system solvers to linear-response time-dependent density functional theory. Using this technique the complete frequency-dependent electronic density response of finite systems to an external perturbation can be calculated at the cost of a single solution of a linear system via conjugate gradients. We show that multishift time-dependent density functional theory yields excitation energies and oscillator strengths in perfect agreement with the standard diagonalization of the response matrix (Casida's method), while being computationally advantageous. We present test calculations for benzene, porphin, and chlorophyll molecules. We argue that multishift solvers may find broad applicability in the context of excited-state calculations within density-functional theory and beyond.
Plesa, Calin; Cornelissen, Ludo; Tuijtel, Maarten W.; Dekker, Cees
2013-01-01
We investigate translocation of linear and circular double-stranded DNA molecules through solid state nanopores where each molecule is recaptured and re-translocated many times. Single molecules can be recaptured by switching voltage polarity for hundreds or even thousands of times. The large number
STM investigation of surfactant molecules
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
Adsorption and self-organization of sodium alkyl sulfonates (STS and SHS) have been studied on HOPG by using the in situ scanning tunneling microscopy (STM). Both SHS and STS molecules adsorb on the HOPG surface and form long-range well-ordered monolayers. The neighboring molecules in different rows form a "head to head" configuration. In the high-resolution images of STS and SHS molecules, one end of the molecules shows bright spots which are attributed to the SO3- groups.
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...
Quantum Monte Carlo for vibrating molecules
Energy Technology Data Exchange (ETDEWEB)
Brown, W.R. [Univ. of California, Berkeley, CA (United States). Chemistry Dept.]|[Lawrence Berkeley National Lab., CA (United States). Chemical Sciences Div.
1996-08-01
Quantum Monte Carlo (QMC) has successfully computed the total electronic energies of atoms and molecules. The main goal of this work is to use correlation function quantum Monte Carlo (CFQMC) to compute the vibrational state energies of molecules given a potential energy surface (PES). In CFQMC, an ensemble of random walkers simulate the diffusion and branching processes of the imaginary-time time dependent Schroedinger equation in order to evaluate the matrix elements. The program QMCVIB was written to perform multi-state VMC and CFQMC calculations and employed for several calculations of the H{sub 2}O and C{sub 3} vibrational states, using 7 PES`s, 3 trial wavefunction forms, two methods of non-linear basis function parameter optimization, and on both serial and parallel computers. In order to construct accurate trial wavefunctions different wavefunctions forms were required for H{sub 2}O and C{sub 3}. In order to construct accurate trial wavefunctions for C{sub 3}, the non-linear parameters were optimized with respect to the sum of the energies of several low-lying vibrational states. In order to stabilize the statistical error estimates for C{sub 3} the Monte Carlo data was collected into blocks. Accurate vibrational state energies were computed using both serial and parallel QMCVIB programs. Comparison of vibrational state energies computed from the three C{sub 3} PES`s suggested that a non-linear equilibrium geometry PES is the most accurate and that discrete potential representations may be used to conveniently determine vibrational state energies.
Adiabatic field-free alignment of asymmetric top molecules with an optical centrifuge
Korobenko, A
2015-01-01
We use an optical centrifuge to align asymmetric top $\\mathrm{SO_2}$ molecules by adiabatically spinning their most polarizable O-O axis. The effective centrifugal potential in the rotating frame confines sulfur atoms to the plane of the laser-induced rotation, leading to the planar molecular alignment which persists after the molecules are released from the centrifuge. Periodic appearance of the full three-dimensional alignment, typically observed only with linear and symmetric top molecules, is also detected. Together with strong in-plane centrifugal forces, which bend the molecules by up to 10 degrees, permanent field-free alignment offers new ways of controlling molecules with laser light.
A model for positron binding to polar molecules
Gribakin, G F
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 polarization potential via perturbation theory. The improved model enables reliable predictions of binding energies to be made for a range of polar organic molecules and hydrogen cyanide, whose binding energy is known from accurate quantum chemistry calculations. The model explains 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].
Deflection of Rotating Symmetric Molecules by Inhomogeneous Fields
Gershnabel, Erez
2011-01-01
We consider deflection of rotating symmetric molecules by inhomogeneous optical and static electric fields, compare results with the case of linear molecules, and find new singularities in the distribution of the scattering angle. Scattering of the prolate/oblate molecules is analyzed in detail, and it is shown that the process can be efficiently controlled by means of short and strong femtosecond laser pulses. In particular, the angular dispersion of the deflected molecules may be dramatically reduced by laser-induced molecular pre-alignment. We first study the problem by using a simple classical model, and then find similar results by means of more sophisticated methods, including the formalism of adiabatic invariants and direct numerical simulation of the Euler-Lagrange equations of motion. The suggested control scheme opens new ways for many applications involving molecular focusing, guiding, and trapping by optical and static fields.
DEFF Research Database (Denmark)
Markussen, Troels; Stadler, Robert; Thygesen, Kristian Sommer
2011-01-01
with tight-binding and density functional theory calculations to investigate QI in linear molecular chains and aromatic molecules with different side groups. For the molecular chains we find a linear relation between the position of the transmission nodes and the side group π orbital energy. In contrast......, the transmission functions of functionalized aromatic molecules generally display a rather complex nodal structure due to the interplay between molecular topology and the energy of the side group orbital....
Differential Equations with Linear Algebra
Boelkins, Matthew R; Potter, Merle C
2009-01-01
Linearity plays a critical role in the study of elementary differential equations; linear differential equations, especially systems thereof, demonstrate a fundamental application of linear algebra. In Differential Equations with Linear Algebra, we explore this interplay between linear algebra and differential equations and examine introductory and important ideas in each, usually through the lens of important problems that involve differential equations. Written at a sophomore level, the text is accessible to students who have completed multivariable calculus. With a systems-first approach, t
Cooee bitumen. II. Stability of linear asphaltene nanoaggregates
DEFF Research Database (Denmark)
Lemarchand, Claire; Schrøder, Thomas; Dyre, J. C.;
2014-01-01
Asphaltene and smaller aromatic molecules tend to form linear nanoaggregates in bitumen. Over the years bitumen undergoes chemical aging and during this process, the size of the nanoaggregate increases. This increase is associated with an increase in viscosity and brittleness of the bitumen...
Lopez, Cesar
2014-01-01
MATLAB is a high-level language and environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java. MATLAB Linear Algebra introduces you to the MATLAB language with practical hands-on instructions and results, allowing you to quickly achieve your goals. In addition to giving an introduction to
Directory of Open Access Journals (Sweden)
Kenneth D. Magill
2001-01-01
Full Text Available We determine, up to isomorphism, all those topological nearrings n whose additive groups are the n-dimensional Euclidean groups, n>1, and which contain n one-dimensional linear subspaces {Ji}i=1n which are also right ideals of the nearring satisfying several additional properties. Specifically, for each w∈n, we require that there exist wi∈Ji, 1≤i≤n, such that w=w1+w2+⋯+wn and multiplication on the left of w yields the same result as multiplication by the same element on the left of wn. That is, vw=vwn for each v∈n.
Energy Technology Data Exchange (ETDEWEB)
Casasent, D.; Ghosh, A.
1983-01-01
Many of the linear algebra operations and algorithms possible on optical matrix-vector processors are reviewed. Emphasis is given to the use of direct solutions and their realization on systolic optical processors. As an example, implicit and explicit solutions to partial differential equations are considered. The matrix-decomposition required is found to be the major operation recommended for optical realization. The pipelining and flow of data and operations are noted to be key issues in the realization of any algorithm on an optical systolic array processor. A realization of the direct solution by householder qr decomposition is provided as a specific case study. 19 references.
Energy Technology Data Exchange (ETDEWEB)
Strecker, Kevin E.; Chandler, David W.
2009-10-01
We have developed a novel experimental technique for direct production of cold molecules using a combination of techniques from atomic optical and molecular physics and physical chemistry. The ability to produce samples of cold molecules has application in a broad spectrum of technical fields high-resolution spectroscopy, remote sensing, quantum computing, materials simulation, and understanding fundamental chemical dynamics. Researchers around the world are currently exploring many techniques for producing samples of cold molecules, but to-date these attempts have offered only limited success achieving milli-Kelvin temperatures with low densities. This Laboratory Directed Research and Development project is to develops a new experimental technique for producing micro-Kelvin temperature molecules via collisions with laser cooled samples of trapped atoms. The technique relies on near mass degenerate collisions between the molecule of interest and a laser cooled (micro-Kelvin) atom. A subset of collisions will transfer all (nearly all) of the kinetic energy from the 'hot' molecule, cooling the molecule at the expense of heating the atom. Further collisions with the remaining laser cooled atoms will thermally equilibrate the molecules to the micro-Kelvin temperature of the laser-cooled atoms.
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...
Triatomic molecules laser-cooled
2017-06-01
Molecules containing three atoms have been laser-cooled to ultracold temperatures for the first time. John Doyle and colleagues at Harvard University in the US used a technique called Sisyphus cooling to chill an ensemble of about a million strontium-monohydroxide molecules to 750 μK.
Kinetics of Hydrogen Molecules in MAGNUM-PSI
Institute of Scientific and Technical Information of China (English)
M.BAEVA; W.J.GOEDHEER; N.J.LOPES CARDOZO
2008-01-01
Results from simulations of plasma and neutrals under conditions predictively characterizing the detached plasma regime in the linear machine MAGNUM-PSI are presented. The relaxation of the vibrationally excited hydrogen molecules is investigated in order to establish a relation between their relaxation and dwell times, and the role of the various mechanisms of the molecular vibrational kinetics. The results obtained show that the individual vibrational states have to be included in the transport code for neutrals as distinct species, since the relaxation time of the vibrational states is sufficiently longer than the typical dwell time of hydrogen molecules in the detached plasma region. The parameters of plasma and neutrals are affected by the transport of the vibrationally excited hydrogen molecules. Furthermore, the rate of molecular recombination is overestimated by a factor of～5 provided that the transport of hydrogen molecules only in their ground vibrational state is considered. The role of the various processes of vibrational kinetics is studied. The vibrational excitation through singlet electronic states has a strong influence on the molecular densities for levels with vibrational quantum numbers v≥ 5. Vibration-vibration (V-V) collisions between vibrationally excited hydrogen molecules and vibration-translation (V-T) collisions between vibrationally excited hydrogen molecules and ground state molecules and atoms are of minor importance in MAGNUM-PSI.
Kinetics of Hydrogen Molecules in MAGNUM-PSI
Baeva, M.; J. Goedheer, W.; J. Lopes Cardozo, N.
2008-04-01
Results from simulations of plasma and neutrals under conditions predictively characterizing the detached plasma regime in the linear machine MAGNUM-PSI are presented. The relaxation of the vibrationally excited hydrogen molecules is investigated in order to establish a relation between their relaxation and dwell times, and the role of the various mechanisms of the molecular vibrational kinetics. The results obtained show that the individual vibrational states have to be included in the transport code for neutrals as distinct species, since the relaxation time of the vibrational states is sufficiently longer than the typical dwell time of hydrogen molecules in the detached plasma region. The parameters of plasma and neutrals are affected by the transport of the vibrationally excited hydrogen molecules. Furthermore, the rate of molecular recombination is overestimated by a factor of ~ 5 provided that the transport of hydrogen molecules only in their ground vibrational state is considered. The role of the various processes of vibrational kinetics is studied. The vibrational excitation through singlet electronic states has a strong influence on the molecular densities for levels with vibrational quantum numbers v 5. Vibration-vibration (V-V) collisions between vibrationally excited hydrogen molecules and vibration-translation (V-T) collisions between vibrationally excited hydrogen molecules and ground state molecules and atoms are of minor importance in MAGNUM-PSI.
Enzyme molecules in solitary confinement.
Liebherr, Raphaela B; Gorris, Hans H
2014-09-12
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.
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.
Study on Non-Sequential Double Ionization of Aligned Diatomic Molecules in Strong Laser Fields
Institute of Scientific and Technical Information of China (English)
LI Yan; CHEN Jing; YANG Shi-Ping; LIU Jie
2007-01-01
We develop a semiclassical model to describe the non-sequential double ionization of aligned diatomic molecules in an intense linearly polarized field. It is found that in the tunnelling regime, the oriented molecule shows geometric effects on double ionization process when aligned parallel and perpendicular to the external Geld. Our results are qualitatively consistent with the recent experimental observations.
El-Orany, Faisal A A
2009-01-01
In this paper, we develop the notion of the linear atomic quantum coupler. This device consists of two modes propagating into two waveguides, each of them includes a localized and/or a trapped atom. These waveguides are placed close enough to allow exchanging energy between them via evanescent waves. Each mode interacts with the atom in the same waveguide in the standard way, i.e. as the Jaynes-Cummings model (JCM), and with the atom-mode in the second waveguide via evanescent wave. We present the Hamiltonian for the system and deduce the exact form for the wavefunction. We investigate the atomic inversions and the second-order correlation function. In contrast to the conventional linear coupler, the atomic quantum coupler is able to generate nonclassical effects. The atomic inversions can exhibit long revival-collapse phenomenon as well as subsidiary revivals based on the competition among the switching mechanisms in the system. Finally, under certain conditions, the system can yield the results of the two-m...
Topics in computational linear optimization
DEFF Research Database (Denmark)
Hultberg, Tim Helge
2000-01-01
of high quality solvers and the use of algebraic modelling systems to handle the communication between the modeller and the solver. This dissertation features four topics in computational linear optimization: A) automatic reformulation of mixed 0/1 linear programs, B) direct solution of sparse unsymmetric...... systems of linear equations, C) reduction of linear programs and D) integration of algebraic modelling of linear optimization problems in C++. Each of these topics is treated in a separate paper included in this dissertation. The efficiency of solving mixed 0-1 linear programs by linear programming based...... reductions. In the fourth and last paper, a prototype implementation of a C++ class library, FLOPC++, for formulating linear optimization problems is presented. Using FLOPC++, linear optimization models can be specified in a declarative style, similar to algebraic modelling languages such as GAMS and AMPL...
2001-05-01
Third Nucleus Observed with the VLT Summary New images from the VLT show that one of the two nuclei of Comet LINEAR (C/2001 A2), now about 100 million km from the Earth, has just split into at least two pieces . The three fragments are now moving through space in nearly parallel orbits while they slowly drift apart. This comet will pass through its perihelion (nearest point to the Sun) on May 25, 2001, at a distance of about 116 million kilometres. It has brightened considerably due to the splitting of its "dirty snowball" nucleus and can now be seen with the unaided eye by observers in the southern hemisphere as a faint object in the southern constellation of Lepus (The Hare). PR Photo 18a/01 : Three nuclei of Comet LINEAR . PR Photo 18b/01 : The break-up of Comet LINEAR (false-colour). Comet LINEAR splits and brightens ESO PR Photo 18a/01 ESO PR Photo 18a/01 [Preview - JPEG: 400 x 438 pix - 55k] [Normal - JPEG: 800 x 875 pix - 136k] ESO PR Photo 18b/01 ESO PR Photo 18b/01 [Preview - JPEG: 367 x 400 pix - 112k] [Normal - JPEG: 734 x 800 pix - 272k] Caption : ESO PR Photo 18a/01 shows the three nuclei of Comet LINEAR (C/2001 A2). It is a reproduction of a 1-min exposure in red light, obtained in the early evening of May 16, 2001, with the 8.2-m VLT YEPUN (UT4) telescope at Paranal. ESO PR Photo 18b/01 shows the same image, but in a false-colour rendering for more clarity. The cometary fragment "B" (right) has split into "B1" and "B2" (separation about 1 arcsec, or 500 km) while fragment "A" (upper left) is considerably fainter. Technical information about these photos is available below. Comet LINEAR was discovered on January 3, 2001, and designated by the International Astronomical Union (IAU) as C/2001 A2 (see IAU Circular 7564 [1]). Six weeks ago, it was suddenly observed to brighten (IAUC 7605 [1]). Amateurs all over the world saw the comparatively faint comet reaching naked-eye magnitude and soon thereafter, observations with professional telescopes indicated
On the linear programming bound for linear Lee codes.
Astola, Helena; Tabus, Ioan
2016-01-01
Based on an invariance-type property of the Lee-compositions of a linear Lee code, additional equality constraints can be introduced to the linear programming problem of linear Lee codes. In this paper, we formulate this property in terms of an action of the multiplicative group of the field [Formula: see text] on the set of Lee-compositions. We show some useful properties of certain sums of Lee-numbers, which are the eigenvalues of the Lee association scheme, appearing in the linear programming problem of linear Lee codes. Using the additional equality constraints, we formulate the linear programming problem of linear Lee codes in a very compact form, leading to a fast execution, which allows to efficiently compute the bounds for large parameter values of the linear codes.
Linear algebra, geometry and transformation
Solomon, Bruce
2014-01-01
Vectors, Mappings and Linearity Numeric Vectors Functions Mappings and Transformations Linearity The Matrix of a Linear Transformation Solving Linear Systems The Linear SystemThe Augmented Matrix and RRE Form Homogeneous Systems in RRE Form Inhomogeneous Systems in RRE Form The Gauss-Jordan Algorithm Two Mapping Answers Linear Geometry Geometric Vectors Geometric/Numeric Duality Dot-Product Geometry Lines, Planes, and Hyperplanes System Geometry and Row/Column Duality The Algebra of Matrices Matrix Operations Special Matrices Matrix Inversion A Logical Digression The Logic of the Inversion Alg
Single Molecule Electronics and Devices
Directory of Open Access Journals (Sweden)
Makusu Tsutsui
2012-05-01
Full Text Available The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule.
Byron, S.
1985-03-01
The low pressure gas-filled thyratron is scalable in the long dimension. Internally the tube is formed as a tetrode, with an auxiliary grid placed between the cathode and the control grid. A dc or pulsed power source drives the auxiliary grid both to insure uniform cathode emission and to provide a grid-cathode plasma prior to commutation. The high voltage holdoff structure consists of the anode, the control grid and its electrostatic shielding baffles, and a main quartz insulator. A small gas flow supply and exhaust system is used that eliminates the need for a hydrogen reservoir and permits other gases, such as helium, to be used. The thyratron provides a low inductance, high current, long lifetime switch configuration: useful for switch-on applications involving large scale lasers and other similar loads that are distributed in a linear geometry.
Introduction to linear elasticity
Gould, Phillip L
2013-01-01
Introduction to Linear Elasticity, 3rd Edition, provides an applications-oriented grounding in the tensor-based theory of elasticity for students in mechanical, civil, aeronautical, and biomedical engineering, as well as materials and earth science. The book is distinct from the traditional text aimed at graduate students in solid mechanics by introducing the subject at a level appropriate for advanced undergraduate and beginning graduate students. The author's presentation allows students to apply the basic notions of stress analysis and move on to advanced work in continuum mechanics, plasticity, plate and shell theory, composite materials, viscoelasticity and finite method analysis. This book also: Emphasizes tensor-based approach while still distilling down to explicit notation Provides introduction to theory of plates, theory of shells, wave propagation, viscoelasticity and plasticity accessible to advanced undergraduate students Appropriate for courses following emerging trend of teaching solid mechan...
Hsie, Cho-Shuen; Campen, R. Kramer; Verde, Ana Vila; Bolhuis, Peter; Nienhuys, Han-Kwang; Bonn, Mischa
2012-01-01
About 70% of our planet is covered in water. Most of that water exists as water in the bulk – the neighbors of water molecules are other water molecules – and only a small fraction of molecules are at the air-water interface. Despite the small relative abundance of interfacial water, it is of the utmost importance: it governs the chemistry involving the surface of oceans and seawater aerosols, or the small water droplets forming clouds. Reactions at the air-water interface are directly releva...
Recursive Algorithm For Linear Regression
Varanasi, S. V.
1988-01-01
Order of model determined easily. Linear-regression algorithhm includes recursive equations for coefficients of model of increased order. Algorithm eliminates duplicative calculations, facilitates search for minimum order of linear-regression model fitting set of data satisfactory.
Computer Program For Linear Algebra
Krogh, F. T.; Hanson, R. J.
1987-01-01
Collection of routines provided for basic vector operations. Basic Linear Algebra Subprogram (BLAS) library is collection from FORTRAN-callable routines for employing standard techniques to perform basic operations of numerical linear algebra.
Linear connections on matrix geometries
Madore, J; Mourad, J; Madore, John; Masson, Thierry; Mourad, Jihad
1994-01-01
A general definition of a linear connection in noncommutative geometry has been recently proposed. Two examples are given of linear connections in noncommutative geometries which are based on matrix algebras. They both possess a unique metric connection.
Computer Program For Linear Algebra
Krogh, F. T.; Hanson, R. J.
1987-01-01
Collection of routines provided for basic vector operations. Basic Linear Algebra Subprogram (BLAS) library is collection from FORTRAN-callable routines for employing standard techniques to perform basic operations of numerical linear algebra.
Coupled Cluster Theory for Large Molecules
DEFF Research Database (Denmark)
Baudin, Pablo
2017-01-01
This thesis describes the development of local approximations to coupled cluster (CC) theory for large molecules. Two different methods are presented, the divide–expand–consolidate scheme (DEC), for the calculation of ground state energies, and a local framework denoted LoFEx, for the calculation...... of electronic excitation energies and oscillator strengths. After an introduction to the relevant notions of electronic-structure theory, the principal aspects of DEC and LoFEx are summarized. For comparison, a selected review of the state-of-the-art is presented for each domain. This thesis should serve...... as an introduction to the work developed and presented in the scientific articles collected as appendices. The DEC scheme has been applied successfully to the calculation of MP2, CCSD and CCSD(T) ground state energies. The intrinsic structure of DEC allows for a linear-scaling (with system size) and massively...
Discrete energy transport in collagen molecules
Alain, Mvogo; Germain, H. Ben-Bolie; Timoléon, C. Kofané
2014-09-01
The modulational instability in the three coupled α-polypeptide chains of a collagen molecule is investigated. Choosing symmetric and asymmetric solutions, and applying the so-called rotating-wave approximation, we describe the dynamics of the system by the discrete nonlinear Schrödinger (DNLS) equation. The linear stability analysis of the continuous wave solution is performed. The numerical simulations show the generation of trains of solitonic structures in the lattice with increasing amplitude as time progresses. The effect of damping and noise forces of the physiological temperature (T = 300 K) introduces an erratic behavior to the formed patterns, reinforcing the idea that the energy used in metabolic processes is confined to specific regions for efficiency.
Monahan, John F
2008-01-01
Preface Examples of the General Linear Model Introduction One-Sample Problem Simple Linear Regression Multiple Regression One-Way ANOVA First Discussion The Two-Way Nested Model Two-Way Crossed Model Analysis of Covariance Autoregression Discussion The Linear Least Squares Problem The Normal Equations The Geometry of Least Squares Reparameterization Gram-Schmidt Orthonormalization Estimability and Least Squares Estimators Assumptions for the Linear Mean Model Confounding, Identifiability, and Estimability Estimability and Least Squares Estimators F
Jensen, L; van Duijnen, PT; Snijders, JG
2003-01-01
A discrete solvent reaction field model for calculating frequency-dependent molecular linear response properties of molecules in solution is presented. The model combines a time-dependent density functional theory (QM) description of the solute molecule with a classical (MM) description of the discr
Templates for Linear Algebra Problems
Bai, Z.; Day, D.; Demmel, J.; Dongarra, J.; Gu, M.; Ruhe, A.; Vorst, H.A. van der
2001-01-01
The increasing availability of advanced-architecture computers is having a very signicant eect on all spheres of scientic computation, including algorithm research and software development in numerical linear algebra. Linear algebra {in particular, the solution of linear systems of equations and eig
DEFF Research Database (Denmark)
Engberg, Uffe Henrik; Winskel, Glynn
This article shows how individual Petri nets form models of Girard's intuitionistic linear logic. It explores questions of expressiveness and completeness of linear logic with respect to this interpretation. An aim is to use Petri nets to give an understanding of linear logic and give some apprai...
Absorption characteristics of bacteriorhodopsin molecules
Indian Academy of Sciences (India)
H K T Kumar; K Appaji Gowda
2000-03-01
The bacteriorhodopsin molecule absorbs light and undergoes a series of structural transformation following a well-deﬁned photocycle. The complex photocycle is transformed to an equivalent level diagram by considering the lifetime of the intermediate states. Assuming that only and states are appreciably populated at any instant of time, the level diagram is further simpliﬁed to two-level system. Based on the rate equations for two-level system, an analytic expression for the absorption coefﬁcient of bacteriorhodopsin molecule is derived. It is applied to study the behaviour of absorption coefﬁcient of bacteriorhodopsin ﬁlm in the visible wavelength region of 514 nm. The dependence of absorption coefﬁcient of bacteriorhodopsin ﬁlm on the thickness of the ﬁlm, total number density of active molecules and initial number density of molecules in -state is presented in the graphical form.
Cell adhesion molecules and sleep.
O'Callaghan, Emma Kate; Ballester Roig, Maria Neus; Mongrain, Valérie
2017-03-01
Cell adhesion molecules (CAMs) play essential roles in the central nervous system, where some families are involved in synaptic development and function. These synaptic adhesion molecules (SAMs) are involved in the regulation of synaptic plasticity, and the formation of neuronal networks. Recent findings from studies examining the consequences of sleep loss suggest that these molecules are candidates to act in sleep regulation. This review highlights the experimental data that lead to the identification of SAMs as potential sleep regulators, and discusses results supporting that specific SAMs are involved in different aspects of sleep regulation. Further, some potential mechanisms by which SAMs may act to regulate sleep are outlined, and the proposition that these molecules may serve as molecular machinery in the two sleep regulatory processes, the circadian and homeostatic components, is presented. Together, the data argue that SAMs regulate the neuronal plasticity that underlies sleep and wakefulness. Copyright © 2016 Elsevier Ireland Ltd and Japan Neuroscience Society. All rights reserved.
Special Issue: Single Molecule Techniques
Directory of Open Access Journals (Sweden)
Hans H. Gorris
2015-04-01
Full Text Available Technological advances in the detection and manipulation of single molecules have enabled new insights into the function, structure and interactions of biomolecules. This Special Issue was launched to account for the rapid progress in the field of “Single Molecule Techniques”. Four original research articles and seven review articles provide an introduction, as well as an in-depth discussion, of technical developments that are indispensable for the characterization of individual biomolecules. Fluorescence microscopy takes center stage in this Special Issue because it is one of the most sensitive and flexible techniques, which has been adapted in many variations to the specific demands of single molecule analysis. Two additional articles are dedicated to single molecule detection based on atomic force microscopy.
Quantum Transport Through Heterocyclic Molecules
Maiti, Santanu K.; Karmakar, S. N.
We explore electron transport properties in molecular wires made of heterocyclic molecules (pyrrole, furan and thiophene) by using the Green's function technique. Parametric calculations are given based on the tight-binding model to describe the electron transport in these wires. It is observed that the transport properties are significantly influenced by (a) the heteroatoms in the heterocyclic molecules and (b) the molecule-to-electrodes coupling strength. Conductance (g) shows sharp resonance peaks associated with the molecular energy levels in the limit of weak molecular coupling, while they get broadened in the strong molecular coupling limit. These resonances get shifted with the change of the heteroatoms in these heterocyclic molecules. All the essential features of the electron transfer through these molecular wires become much more clearly visible from the study of our current-voltage (I-V) characteristics, and they provide several key information in the study of molecular transport.
Guidance molecules in lung cancer
Nasarre, Patrick; Potiron, Vincent; Drabkin, Harry; Roche, Joëlle
2010-01-01
Guidance molecules were first described in the nervous system to control axon outgrowth direction. They are also widely expressed outside the nervous system where they control cell migration, tissue development and establishment of the vascular network. In addition, they are involved in cancer development, tumor angiogenesis and metastasis. This review is primarily focused on their functions in lung cancer and their involvement in lung development is also presented. Five guidance molecule fam...
Plasmonic atoms and plasmonic molecules
Klimov, V V
2007-01-01
The proposed paradigm of plasmonic atoms and plasmonic molecules allows one to describe and predict the strongly localized plasmonic oscillations in the clusters of nanoparticles and some other nanostructures in uniform way. Strongly localized plasmonic molecules near the contacting surfaces might become the fundamental elements (by analogy with Lego bricks) for a construction of fully integrated opto-electronic nanodevices of any complexity and scale of integration.
Plasmonic atoms and plasmonic molecules
Klimov, V. V.; Guzatov, D. V.
2007-11-01
The proposed paradigm of plasmonic atoms and plasmonic molecules allows one to describe and predict the strongly localized plasmonic oscillations in the clusters of nanoparticles and some other nanostructures in uniform way. Strongly localized plasmonic molecules near the contacting surfaces might become the fundamental elements (by analogy with Lego bricks) for the construction of fully integrated opto-electronic nanodevices of any complexity and scale of integration.
Optofluidic single molecule flow proteometry
Jing, Nan; Chou, Chao-Kai; Hung, Mien-Chie; Kameoka, Jun
2009-02-01
A microfluidic single molecule fluorescence-based detection scheme is developed to identify target protein direct from cell lysate by using polyclonal antibody. Relative concentration of target protein in solution is determined by twodimensional (2D) photon burst analysis. Compared to conventional ensemble measurement assays, this microfluidic single molecule approach combines the advantages of higher sensitivity, fast processing time, small sample consumption and high resolution quantitative analysis.
Evolution of linear mitochondrial genomes in medusozoan cnidarians.
Kayal, Ehsan; Bentlage, Bastian; Collins, Allen G; Kayal, Mohsen; Pirro, Stacy; Lavrov, Dennis V
2012-01-01
In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans.
Clément, G; Leygnac, C; Clement, Gerard; Gal'tsov, Dmitri; Leygnac, Cedric
2003-01-01
We present new solutions to Einstein-Maxwell-dilaton-axion (EMDA) gravity in four dimensions describing black holes which asymptote to the linear dilaton background. In the non-rotating case they can be obtained as the limiting geometry of dilaton black holes. The rotating solutions (possibly endowed with a NUT parameter) are constructed using a generating technique based on the Sp(4,R) duality of the EMDA system. In a certain limit (with no event horizon present) our rotating solutions coincide with supersymmetric Israel-Wilson-Perjes type dilaton-axion solutions. In presence of an event horizon supersymmetry is broken. The temperature of the static black holes is constant, and their mass does not depend on it, so the heat capacity is zero. We investigate geodesics and wave propagation in these spacetimes and find superradiance in the rotating case. Because of the non-asymptotically flat nature of the geometry, certain modes are reflected from infinity, in particular, all superradiant modes are confined. Thi...
Generalized Linear Covariance Analysis
Carpenter, James R.; Markley, F. Landis
2014-01-01
This talk presents a comprehensive approach to filter modeling for generalized covariance analysis of both batch least-squares and sequential estimators. We review and extend in two directions the results of prior work that allowed for partitioning of the state space into solve-for'' and consider'' parameters, accounted for differences between the formal values and the true values of the measurement noise, process noise, and textita priori solve-for and consider covariances, and explicitly partitioned the errors into subspaces containing only the influence of the measurement noise, process noise, and solve-for and consider covariances. In this work, we explicitly add sensitivity analysis to this prior work, and relax an implicit assumption that the batch estimator's epoch time occurs prior to the definitive span. We also apply the method to an integrated orbit and attitude problem, in which gyro and accelerometer errors, though not estimated, influence the orbit determination performance. We illustrate our results using two graphical presentations, which we call the variance sandpile'' and the sensitivity mosaic,'' and we compare the linear covariance results to confidence intervals associated with ensemble statistics from a Monte Carlo analysis.
Nassisi, V.; Delle Side, D.
2017-02-01
Nowadays, the employment and development of fast current pulses require sophisticated systems to perform measurements. Rogowski coils are used to diagnose cylindrical shaped beams; therefore, they are designed and built with a toroidal structure. Recently, to perform experiments of radiofrequency biophysical stresses, flat transmission lines have been developed. Therefore, in this work we developed a linear Rogowski coil to detect current pulses inside flat conductors. The system is first approached by means of transmission line theory. We found that, if the pulse width to be diagnosed is comparable with the propagation time of the signal in the detector, it is necessary to impose a uniform current as input pulse, or to use short coils. We further analysed the effect of the resistance of the coil and the influence of its magnetic properties. As a result, the device we developed is able to record pulses lasting for some hundreds of nanoseconds, depending on the inductance, load impedance, and resistance of the coil. Furthermore, its response is characterized by a sub-nanosecond rise time (˜100 ps). The attenuation coefficient depends mainly on the turn number of the coil, while the fidelity of the response depends both on the magnetic core characteristics and on the current distribution along the plane conductors.
Berkeley Proton Linear Accelerator
Alvarez, L. W.; Bradner, H.; Franck, J.; Gordon, H.; Gow, J. D.; Marshall, L. C.; Oppenheimer, F. F.; Panofsky, W. K. H.; Richman, C.; Woodyard, J. R.
1953-10-13
A linear accelerator, which increases the energy of protons from a 4 Mev Van de Graaff injector, to a final energy of 31.5 Mev, has been constructed. The accelerator consists of a cavity 40 feet long and 39 inches in diameter, excited at resonance in a longitudinal electric mode with a radio-frequency power of about 2.2 x 10{sup 6} watts peak at 202.5 mc. Acceleration is made possible by the introduction of 46 axial "drift tubes" into the cavity, which is designed such that the particles traverse the distance between the centers of successive tubes in one cycle of the r.f. power. The protons are longitudinally stable as in the synchrotron, and are stabilized transversely by the action of converging fields produced by focusing grids. The electrical cavity is constructed like an inverted airplane fuselage and is supported in a vacuum tank. Power is supplied by 9 high powered oscillators fed from a pulse generator of the artificial transmission line type.
Random linear codes in steganography
Directory of Open Access Journals (Sweden)
Kamil Kaczyński
2016-12-01
Full Text Available Syndrome coding using linear codes is a technique that allows improvement in the steganographic algorithms parameters. The use of random linear codes gives a great flexibility in choosing the parameters of the linear code. In parallel, it offers easy generation of parity check matrix. In this paper, the modification of LSB algorithm is presented. A random linear code [8, 2] was used as a base for algorithm modification. The implementation of the proposed algorithm, along with practical evaluation of algorithms’ parameters based on the test images was made.[b]Keywords:[/b] steganography, random linear codes, RLC, LSB
On constructing disjoint linear codes
Institute of Scientific and Technical Information of China (English)
ZHANG Weiguo; CAI Mian; XIAO Guozhen
2007-01-01
To produce a highly nonlinear resilient function,the disjoint linear codes were originally proposed by Johansson and Pasalic in IEEE Trans.Inform.Theory,2003,49(2):494-501.In this paper,an effective method for finding a set of such disjoint linear codes is presented.When n≥2k,we can find a set of[n,k] disjoint linear codes with joint linear codes exists with cardinality at least 2.We also describe a result on constructing a set of [n,k] disjoint linear codes with minimum distance at least some fixed positive integer.
Bond length variation in hydronitride molecules and nitride crystals
Buterakos, L. A.; Gibbs, G. V.; Boisen, M. B.
1992-08-01
Bond lengths calculated for the coordination polyhedra in hydronitride molecules match average values observed for XN bonds involving main group X-cations in nitride crystals to within ˜0.04 Å. As suggested for oxide and sulfide molecules and crystals, the forces that determine the average bond lengths recorded for coordinated polyhedra in hydronitride molecules and nitride crystals appear to be governed in large part by the atoms that comprise the polyhedra and those that induce local charge balance. The forces exerted on the coordinated polyhedra by other parts of the structure seem to play a small if not an insignificant role in governing bond length variations. Bonded radii for the nitride ion obtained from theoretical electron density maps calculated for the molecules increase linearly with bond length as observed for nitride crystals with the rock salt structure. Promolecule radii calculated for the molecules correlate with bonded and ionic radii, indicating that the electron density distributions in hydronitride molecules possess a significant atomic component, despite bond type.
Signaling Molecules and Pulp Regeneration.
Schmalz, Gottfried; Widbiller, Matthias; Galler, Kerstin M
2017-09-01
Signaling molecules play an essential role in tissue engineering because they regulate regenerative processes. Evidence exists from animal studies that single molecules such as members of the transforming growth factor beta superfamily and factors that induce the growth of blood vessels (vascular endothelial growth factor), nerves (brain-derived neurotrophic factor), or fibroblasts (fibroblast growth factor) may induce reparative dentin formation. Mainly the formation of atubular dentin (osteodentin) has been described after the application of single molecules or combinations of recombinant growth factors on healthy exposed pulps or in pulp regeneration. Generally, such preparations have not received regulatory approval on the market so far. Only the use of granulocyte colony-stimulating factors together with cell transplantation is presently tested clinically. Besides approaches with only 1 or few combined molecules, the exploitation of tissue-derived growth factors depicts a third promising way in dental pulp tissue engineering. Preparations such as platelet-rich plasma or platelet-rich fibrin provide a multitude of endogenous signaling molecules, and special regulatory approval for the market does not seem necessary. Furthermore, dentin is a perfect reservoir of signaling molecules that can be mobilized by treatment with demineralizing agents such as EDTA. This conditions the dentin surface and allows for contact differentiation of pulp stem cells into odontoblastlike cells, protects dentin from resorption, and enhances cell growth as well as attachment to dentin. By ultrasonic activation, signaling molecules can be further released from EDTA pretreated dentin into saline, thus avoiding cytotoxic EDTA in the final preparation. The use of dentin-derived growth factors offers a number of advantages because they are locally available and presumably are most fit to induce signaling processes in dental pulp. However, better characterization and standardization of the
PbCNN: A molecule containing Pb≡C bonding
Institute of Scientific and Technical Information of China (English)
ZHANG Wen-Bin; SHI Guo-Sheng; DING Yi-Hong; SUN Chia-Chung
2009-01-01
In order to predict potential molecules with Pb≡C bonding, we investigated the potential energy sur-face of a tetra-atomic system [PbCN2] at the CCSD(T)//B3LYP level. We found that the linear isomer PbCNN possesses good thermodynamic and kinetic stability. The combined molecular orbital analysis, hydrogenation heat, bond energy and bond dissociation energy all proved that PbCNN is composed of Pb≡C triple bonding.
PbCNN: A molecule containing Pb≡C bonding
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
In order to predict potential molecules with Pb≡C bonding, we investigated the potential energy sur-face of a tetra-atomic system [PbCN2] at the CCSD(T)//B3LYP level. We found that the linear isomer PbCNN possesses good thermodynamic and kinetic stability. The combined molecular orbital analysis, hydrogenation heat, bond energy and bond dissociation energy all proved that PbCNN is composed of Pb≡ C triple bonding.
Jovan Jose, K V; Raghavachari, Krishnan
2016-02-09
We present an efficient method for the calculation of the Raman optical activity (ROA) spectra for large molecules through the molecules-in-molecules (MIM) fragment-based method. The relevant higher energy derivatives from smaller fragments are used to build the property tensors of the parent molecule to enable the extension of the MIM method for evaluating ROA spectra (MIM-ROA). Two factors were found to be particularly important in yielding accurate results. First, the link-atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, yielding a mathematically rigorous method. Second, the long-range interactions between fragments are taken into account by using a less computationally expensive lower level of theory. The performance of the MIM-ROA model is calibrated on the enantiomeric pairs of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and ROA intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-ROA method is employed to predict the ROA spectra of d-maltose, α-D-cyclodextrin, and cryptophane-A, yielding spectra in excellent agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-ROA model for exploring ROA spectra of large molecules.
The Molecule Cloud - compact visualization of large collections of molecules.
Ertl, Peter; Rohde, Bernhard
2012-07-06
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. 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. 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 data sets, including PubChem, ChEMBL and ZINC databases using
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
Linear Algebraic Method for Non-Linear Map Analysis
Energy Technology Data Exchange (ETDEWEB)
Yu,L.; Nash, B.
2009-05-04
We present a newly developed method to analyze some non-linear dynamics problems such as the Henon map using a matrix analysis method from linear algebra. Choosing the Henon map as an example, we analyze the spectral structure, the tune-amplitude dependence, the variation of tune and amplitude during the particle motion, etc., using the method of Jordan decomposition which is widely used in conventional linear algebra.
Electronic Single Molecule Identification of Carbohydrate Isomers by Recognition Tunneling
Im, JongOne; Liu, Hao; Zhao, Yanan; Sen, Suman; Biswas, Sudipta; Ashcroft, Brian; Borges, Chad; Wang, Xu; Lindsay, Stuart; Zhang, Peiming
2016-01-01
Glycans play a central role as mediators in most biological processes, but their structures are complicated by isomerism. Epimers and anomers, regioisomers, and branched sequences contribute to a structural variability that dwarfs those of nucleic acids and proteins, challenging even the most sophisticated analytical tools, such as NMR and mass spectrometry. Here, we introduce an electron tunneling technique that is label-free and can identify carbohydrates at the single-molecule level, offering significant benefits over existing technology. It is capable of analyzing sub-picomole quantities of sample, counting the number of individual molecules in each subset in a population of coexisting isomers, and is quantitative over more than four orders of magnitude of concentration. It resolves epimers not well separated by ion-mobility and can be implemented on a silicon chip. It also provides a readout mechanism for direct single-molecule sequencing of linear oligosaccharides.
Few-photon coherent nonlinear optics with a single molecule
Maser, Andreas; Utikal, Tobias; Götzinger, Stephan; Sandoghdar, Vahid
2015-01-01
The pioneering experiments of linear spectroscopy were performed using flames in the 1800s, but nonlinear optical measurements had to wait until lasers became available in the twentieth century. Because the nonlinear cross section of materials is very small, usually macroscopic bulk samples and pulsed lasers are used. Numerous efforts have explored coherent nonlinear signal generation from individual nanoparticles or small atomic ensembles with millions of atoms. Experiments on a single semiconductor quantum dot have also been reported, albeit with a very small yield. Here, we report on coherent nonlinear spectroscopy of a single molecule under continuous-wave single-pass illumination, where efficient photon-molecule coupling in a tight focus allows switching of a laser beam by less than a handful of pump photons nearly resonant with the sharp molecular transition. Aside from their fundamental importance, our results emphasize the potential of organic molecules for applications such as quantum information pro...
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
on graphene can be followed molecule-by-molecule with FEBID. The results show that mechanisms that are inherent to the process inhibit a further increase in control over the process. Hence, our results present the resolution limit of (electron) optical lithography techniques. The writing of isolated...... atoms also be written with an electron beam? We verify this with focused electron-beam-induced deposition (FEBID), a direct-write technique that has the current record for the smallest feature written by (electron) optical lithography. We show that the deposition of an organometallic precursor...
Fast Arc-Annotated Subsequence Matching in Linear Space
DEFF Research Database (Denmark)
Bille, Philip; Gørtz, Inge Li
2010-01-01
for investigating the function of RNA molecules. Gramm et al. [ACM Trans. Algorithms 2006] gave an algorithm for this problem using O(nm) time and space, where m and n are the lengths of P and Q, respectively. In this paper we present; a new algorithm using O(nm) time and O(n+m,) space, thereby matching...... the previous time bound while significantly reducing the space from a quadratic term to linear. This is essential to process large RNA molecules where the space is a likely to be a bottleneck. To obtain our result we introduce several novel ideas which may be of independent interest for related problems on arc...
Exploiting micelle-driven coordination to evaluate the lipophilicity of molecules.
Fernandez, Yuri A Diaz; Pasotti, Luca; Pallavicini, Piersandro; Hechavarria, Jose M Fernandez
2012-07-03
We present a systematic study based on the calculation of complexation constants between a Zn-complex solubilized in Triton X-100 micellar solutions and a series of linear mono- and dicarboxylic acids, under physiological pH conditions, that allowed the evaluation of the lipophilicity of these molecules. This empirical lipophilicity parameter describes conveniently the partition of organic molecules between hydrophobic microdomains and water. The results can be used to predict the lipophilicity of molecules with similar structure and allows the distinction of intrinsic contributions of the carboxylates and of the methylene groups to the lipophilicity of the molecule.
Small molecule fluoride toxicity agonists.
Nelson, James W; Plummer, Mark S; Blount, Kenneth F; Ames, Tyler D; Breaker, Ronald R
2015-04-23
Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here, we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride. Copyright © 2015 Elsevier Ltd. All rights reserved.
Electric Deflection of Rotating Molecules
Gershnabel, E
2010-01-01
We provide a theory of the deflection of polar and non-polar rotating molecules by inhomogeneous static electric field. Rainbow-like features in the angular distribution of the scattered molecules are analyzed in detail. Furthermore, we demonstrate that one may efficiently control the deflection process with the help of short and strong femtosecond laser pulses. In particular the deflection process may by turned-off by a proper excitation, and the angular dispersion of the deflected molecules can be substantially reduced. We study the problem both classically and quantum mechanically, taking into account the effects of strong deflecting field on the molecular rotations. In both treatments we arrive at the same conclusions. The suggested control scheme paves the way for many applications involving molecular focusing, guiding, and trapping by inhomogeneous fields.
Small Molecule Fluoride Toxicity Agonists
Nelson1, James W.; Plummer, Mark S.; Blount, Kenneth F.; Ames, Tyler D.; Breaker, Ronald R.
2015-01-01
SUMMARY Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch-reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride. PMID:25910244
Laser spectroscopy of cold molecules
Borri, Simone
2016-01-01
This paper reviews the recent results in high-resolution spectroscopy on cold molecules. Laser spectroscopy of cold molecules addresses issues of symmetry violation, like in the search for the electric dipole moment of the electron and the studies on energy differences in enantiomers of chiral species; tries to improve the precision to which fundamental physical constants are known and tests for their possible variation in time and space; tests quantum electrodynamics, and searches for a fifth force. Further, we briefly review the recent technological progresses in the fields of cold molecules and mid-infrared lasers, which are the tools that mainly set the limits for the resolution that is currently attainable in the measurements.
Feature-Weighted Linear Stacking
Sill, Joseph; Mackey, Lester; Lin, David
2009-01-01
Ensemble methods, such as stacking, are designed to boost predictive accuracy by blending the predictions of multiple machine learning models. Recent work has shown that the use of meta-features, additional inputs describing each example in a dataset, can boost the performance of ensemble methods, but the greatest reported gains have come from nonlinear procedures requiring significant tuning and training time. Here, we present a linear technique, Feature-Weighted Linear Stacking (FWLS), that incorporates meta-features for improved accuracy while retaining the well-known virtues of linear regression regarding speed, stability, and interpretability. FWLS combines model predictions linearly using coefficients that are themselves linear functions of meta-features. This technique was a key facet of the solution of the second place team in the recently concluded Netflix Prize competition. Significant increases in accuracy over standard linear stacking is demonstrated on the Netflix Prize collaborative filtering da...
Linearization of CIF Through SOS
Agut, Damian Nadales; 10.4204/EPTCS.64.6
2011-01-01
Linearization is the procedure of rewriting a process term into a linear form, which consist only of basic operators of the process language. This procedure is interesting both from a theoretical and a practical point of view. In particular, a linearization algorithm is needed for the Compositional Interchange Format (CIF), an automaton based modeling language. The problem of devising efficient linearization algorithms is not trivial, and has been already addressed in literature. However, the linearization algorithms obtained are the result of an inventive process, and the proof of correctness comes as an afterthought. Furthermore, the semantic specification of the language does not play an important role on the design of the algorithm. In this work we present a method for obtaining an efficient linearization algorithm, through a step-wise refinement of the SOS rules of CIF. As a result, we show how the semantic specification of the language can guide the implementation of such a procedure, yielding a simple ...
Linear Programming and Network Flows
Bazaraa, Mokhtar S; Sherali, Hanif D
2011-01-01
The authoritative guide to modeling and solving complex problems with linear programming-extensively revised, expanded, and updated The only book to treat both linear programming techniques and network flows under one cover, Linear Programming and Network Flows, Fourth Edition has been completely updated with the latest developments on the topic. This new edition continues to successfully emphasize modeling concepts, the design and analysis of algorithms, and implementation strategies for problems in a variety of fields, including industrial engineering, management science, operations research