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Sample records for accurate molecular constants

  1. Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure.

    PubMed

    Lippert, Ross A; Predescu, Cristian; Ierardi, Douglas J; Mackenzie, Kenneth M; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2013-10-28

    In molecular dynamics simulations, control over temperature and pressure is typically achieved by augmenting the original system with additional dynamical variables to create a thermostat and a barostat, respectively. These variables generally evolve on timescales much longer than those of particle motion, but typical integrator implementations update the additional variables along with the particle positions and momenta at each time step. We present a framework that replaces the traditional integration procedure with separate barostat, thermostat, and Newtonian particle motion updates, allowing thermostat and barostat updates to be applied infrequently. Such infrequent updates provide a particularly substantial performance advantage for simulations parallelized across many computer processors, because thermostat and barostat updates typically require communication among all processors. Infrequent updates can also improve accuracy by alleviating certain sources of error associated with limited-precision arithmetic. In addition, separating the barostat, thermostat, and particle motion update steps reduces certain truncation errors, bringing the time-average pressure closer to its target value. Finally, this framework, which we have implemented on both general-purpose and special-purpose hardware, reduces software complexity and improves software modularity.

  2. Accurate CO{sub 2} laser frequencies and molecular constants of regular and new hot-band lines

    SciTech Connect

    Chou, Che-Chung; Shy, Jow-Tsong; Maki, A.G.

    1994-12-31

    A new, high-resolution, highly efficient, cw, CO{sub 2} laser oscillating on more than 250 lines including over 40 lines in the new 9 {mu}m hot band has been built at NIST, Boulder. The frequencies of the 9 and 10 {mu}m hot band lines and high J (to J=66) regular band lines of {sup 12}C{sup 16}O{sub 2} , which now fill the gap between the 9 and 10 {mu}m regions, have been locked to saturated fluorescence signals in CO{sub 2}, and measured. New molecular constants and more accurate frequencies of the four common isotopes of CO{sub 2} have been obtained.

  3. Accurate lineshape spectroscopy and the Boltzmann constant

    PubMed Central

    Truong, G.-W.; Anstie, J. D.; May, E. F.; Stace, T. M.; Luiten, A. N.

    2015-01-01

    Spectroscopy has an illustrious history delivering serendipitous discoveries and providing a stringent testbed for new physical predictions, including applications from trace materials detection, to understanding the atmospheres of stars and planets, and even constraining cosmological models. Reaching fundamental-noise limits permits optimal extraction of spectroscopic information from an absorption measurement. Here, we demonstrate a quantum-limited spectrometer that delivers high-precision measurements of the absorption lineshape. These measurements yield a very accurate measurement of the excited-state (6P1/2) hyperfine splitting in Cs, and reveals a breakdown in the well-known Voigt spectral profile. We develop a theoretical model that accounts for this breakdown, explaining the observations to within the shot-noise limit. Our model enables us to infer the thermal velocity dispersion of the Cs vapour with an uncertainty of 35 p.p.m. within an hour. This allows us to determine a value for Boltzmann's constant with a precision of 6 p.p.m., and an uncertainty of 71 p.p.m. PMID:26465085

  4. History and progress on accurate measurements of the Planck constant.

    PubMed

    Steiner, Richard

    2013-01-01

    The measurement of the Planck constant, h, is entering a new phase. The CODATA 2010 recommended value is 6.626 069 57 × 10(-34) J s, but it has been a long road, and the trip is not over yet. Since its discovery as a fundamental physical constant to explain various effects in quantum theory, h has become especially important in defining standards for electrical measurements and soon, for mass determination. Measuring h in the International System of Units (SI) started as experimental attempts merely to prove its existence. Many decades passed while newer experiments measured physical effects that were the influence of h combined with other physical constants: elementary charge, e, and the Avogadro constant, N(A). As experimental techniques improved, the precision of the value of h expanded. When the Josephson and quantum Hall theories led to new electronic devices, and a hundred year old experiment, the absolute ampere, was altered into a watt balance, h not only became vital in definitions for the volt and ohm units, but suddenly it could be measured directly and even more accurately. Finally, as measurement uncertainties now approach a few parts in 10(8) from the watt balance experiments and Avogadro determinations, its importance has been linked to a proposed redefinition of a kilogram unit of mass. The path to higher accuracy in measuring the value of h was not always an example of continuous progress. Since new measurements periodically led to changes in its accepted value and the corresponding SI units, it is helpful to see why there were bumps in the road and where the different branch lines of research joined in the effort. Recalling the bumps along this road will hopefully avoid their repetition in the upcoming SI redefinition debates. This paper begins with a brief history of the methods to measure a combination of fundamental constants, thus indirectly obtaining the Planck constant. The historical path is followed in the section describing how the

  5. Accurate Molecular Polarizabilities Based on Continuum Electrostatics

    PubMed Central

    Truchon, Jean-François; Nicholls, Anthony; Iftimie, Radu I.; Roux, Benoît; Bayly, Christopher I.

    2013-01-01

    A novel approach for representing the intramolecular polarizability as a continuum dielectric is introduced to account for molecular electronic polarization. It is shown, using a finite-difference solution to the Poisson equation, that the Electronic Polarization from Internal Continuum (EPIC) model yields accurate gas-phase molecular polarizability tensors for a test set of 98 challenging molecules composed of heteroaromatics, alkanes and diatomics. The electronic polarization originates from a high intramolecular dielectric that produces polarizabilities consistent with B3LYP/aug-cc-pVTZ and experimental values when surrounded by vacuum dielectric. In contrast to other approaches to model electronic polarization, this simple model avoids the polarizability catastrophe and accurately calculates molecular anisotropy with the use of very few fitted parameters and without resorting to auxiliary sites or anisotropic atomic centers. On average, the unsigned error in the average polarizability and anisotropy compared to B3LYP are 2% and 5%, respectively. The correlation between the polarizability components from B3LYP and this approach lead to a R2 of 0.990 and a slope of 0.999. Even the F2 anisotropy, shown to be a difficult case for existing polarizability models, can be reproduced within 2% error. In addition to providing new parameters for a rapid method directly applicable to the calculation of polarizabilities, this work extends the widely used Poisson equation to areas where accurate molecular polarizabilities matter. PMID:23646034

  6. Molecular dynamics at constant Cauchy stress

    NASA Astrophysics Data System (ADS)

    Miller, Ronald E.; Tadmor, Ellad B.; Gibson, Joshua S.; Bernstein, Noam; Pavia, Fabio

    2016-05-01

    The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress.

  7. Quick and accurate estimation of the elastic constants using the minimum image method

    NASA Astrophysics Data System (ADS)

    Tretiakov, Konstantin V.; Wojciechowski, Krzysztof W.

    2015-04-01

    A method for determining the elastic properties using the minimum image method (MIM) is proposed and tested on a model system of particles interacting by the Lennard-Jones (LJ) potential. The elastic constants of the LJ system are determined in the thermodynamic limit, N → ∞, using the Monte Carlo (MC) method in the NVT and NPT ensembles. The simulation results show that when determining the elastic constants, the contribution of long-range interactions cannot be ignored, because that would lead to erroneous results. In addition, the simulations have revealed that the inclusion of further interactions of each particle with all its minimum image neighbors even in case of small systems leads to results which are very close to the values of elastic constants in the thermodynamic limit. This enables one for a quick and accurate estimation of the elastic constants using very small samples.

  8. An analytic model for accurate spring constant calibration of rectangular atomic force microscope cantilevers.

    PubMed

    Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang

    2015-10-29

    Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.

  9. An analytic model for accurate spring constant calibration of rectangular atomic force microscope cantilevers

    PubMed Central

    Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang

    2015-01-01

    Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson’s ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers. PMID:26510769

  10. Radiometer for accurate (+ or - 1%) measurement of solar irradiance equal to 10,000 solar constants

    NASA Technical Reports Server (NTRS)

    Kendall, J. M., Sr.

    1981-01-01

    The 10,000 solar constant radiometer was developed for the accurate (+ or - 1%) measurement of the irradiance produced in the image formed by a parabolic reflector or by a multiple mirror solar installation. This radiometer is water cooled, weighs about 1 kg, and is 5 cm (2 in.) in diameter by 10 cm (4 in.) long. A sting is provided for mounting the radiometer in the solar installation capable of measuring irradiances as high as 20,000 solar constants, the instrument is self calibrating. Its accuracy depends on the accurate determination of the cavity aperture, and absorptivity of the cavity, and accurate electrical measurements. The spectral response is flat over the entire spectrum from far UV to far IR. The radiometer responds to a measurement within 99.7% of the final value within 8 s. During a measurement of the 10,000 solar constant irradiance, the temperature rise of the water is about 20 C. The radiometer has perfect cosine response up to 60 deg off the radiometer axis.

  11. Accurate and precise calibration of AFM cantilever spring constants using laser Doppler vibrometry.

    PubMed

    Gates, Richard S; Pratt, Jon R

    2012-09-21

    Accurate cantilever spring constants are important in atomic force microscopy both in control of sensitive imaging and to provide correct nanomechanical property measurements. Conventional atomic force microscope (AFM) spring constant calibration techniques are usually performed in an AFM. They rely on significant handling and often require touching the cantilever probe tip to a surface to calibrate the optical lever sensitivity of the configuration. This can damage the tip. The thermal calibration technique developed for laser Doppler vibrometry (LDV) can be used to calibrate cantilevers without handling or touching the tip to a surface. Both flexural and torsional spring constants can be measured. Using both Euler-Bernoulli modeling and an SI traceable electrostatic force balance technique as a comparison we demonstrate that the LDV thermal technique is capable of providing rapid calibrations with a combination of ease, accuracy and precision beyond anything previously available.

  12. Accurate flexural spring constant calibration of colloid probe cantilevers using scanning laser Doppler vibrometry.

    PubMed

    Gates, Richard S; Osborn, William A; Shaw, Gordon A

    2015-06-12

    Calibration of the flexural spring constant for atomic force microscope (AFM) colloid probe cantilevers provides significant challenges. The presence of a large attached spherical added mass complicates many of the more common calibration techniques such as reference cantilever, Sader, and added mass. Even the most promising option, AFM thermal calibration, can encounter difficulties during the optical lever sensitivity measurement due to strong adhesion and friction between the sphere and a surface. This may cause buckling of the end of the cantilever and hysteresis in the approach-retract curves resulting in increased uncertainty in the calibration. Most recently, a laser Doppler vibrometry thermal method has been used to accurately calibrate the normal spring constant of a wide variety of tipped and tipless commercial cantilevers. This paper describes a variant of the technique, scanning laser Doppler vibrometry, optimized for colloid probe cantilevers and capable of spring constant calibration uncertainties near ±1%.

  13. Accurate quantum thermal rate constants for the three-dimensional H+H2 reaction

    NASA Astrophysics Data System (ADS)

    Park, Tae Jun; Light, J. C.

    1989-07-01

    The rate constants for the three-dimensional H+H2 reaction on the Liu-Siegbahn-Truhlar-Horowitz (LSTH) surface are calculated using Pack-Parker hyperspherical (APH) coordinates and a C2v symmetry adapted direct product discrete variable representation (DVR). The C2v symmetry decomposition and the parity decoupling on the basis are performed for the internal coordinate χ. The symmetry decomposition results in a block diagonal representation of the flux and Hamiltonian operators. The multisurface flux is introduced to represent the multichannel reactive flux. The eigenvalues and eigenvectors of the J=0 internal Hamiltonian are obtained by sequential diagonalization and truncation. The individual symmetry blocks of the flux operator are propagated by the corresponding blocks of the Hamiltonian, and the J=0 rate constant k0(T) is obtained as a sum of the rate constants calculated for each block. k0(T) is compared with the exact k0(T) obtained from thermal averaging of the J=0 reaction probabilities; the errors are within 5%-20% up to T=1500 K. The sequential diagonalization-truncation method reduces the size of the Hamiltonian greatly, but the resulting Hamiltonian matrix still describes the time evolution very accurately. For the J≠0 rate constant calculations, the truncated internal Hamiltonian eigenvector basis is used to construct reduced (JKJ) blocks of the Hamiltonian. The individual (JKJ) blocks are diagonalized neglecting Coriolis coupling and treating the off-diagonal KJ±2 couplings by second order perturbation theory. The full wave function is parity decoupled. The rate constant is obtained as a sum over J of (2J+1)kJ(T). The time evolution of the flux for J≠0 is again very accurately described to give a well converged rate constant.

  14. Accurate Measurements of the Dielectric Constant of Seawater at L Band

    NASA Technical Reports Server (NTRS)

    Lang, Roger; Zhou, Yiwen; Utku, Cuneyt; Le Vine, David

    2016-01-01

    This paper describes measurements of the dielectric constant of seawater at a frequency of 1.413 GHz, the center of the protected band (i.e., passive use only) used in the measurement of sea surface salinity from space. The objective of the measurements is to accurately determine the complex dielectric constant of seawater as a function of salinity and temperature. A resonant cylindrical microwave cavity in transmission mode has been employed to make the measurements. The measurements are made using standard seawater at salinities of 30, 33, 35, and 38 practical salinity units over a range of temperatures from 0 degree C to 35 degree C in 5 degree C intervals. Repeated measurements have been made at each temperature and salinity. Mean values and standard deviations are then computed. The total error budget indicates that the real and imaginary parts of the dielectric constant have a combined standard uncertainty of about 0.3 over the range of salinities and temperatures considered. The measurements are compared with the dielectric constants obtained from the model functions of Klein and Swift and those of Meissner and Wentz. The biggest differences occur at low and high temperatures.

  15. Developing accurate molecular mechanics force fields for conjugated molecular systems.

    PubMed

    Do, Hainam; Troisi, Alessandro

    2015-10-14

    A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed by electronic structure methods, because it is possible to build force fields that are consistent with electronic structure calculations that follow classical simulations. Such applications are commonly encountered in organic electronics, spectroscopy of complex systems and photobiology (e.g. photosynthetic systems). We illustrate the method by parameterizing the force fields of a molecule used in molecular semiconductors (2,2-dicyanovinyl-capped S,N-heteropentacene or DCV-SN5), a polymeric semiconductor (thieno[3,2-b]thiophene-diketopyrrolopyrrole TT-DPP) and a chromophore embedded in a protein environment (15,16-dihydrobiliverdin or DBV) where several hundreds of parameters need to be optimized in parallel.

  16. Accurate Measurements of the Dielectric Constant of Seawater at L Band

    NASA Technical Reports Server (NTRS)

    Lang, Roger H.; Utku, Cuneyt; Tarkocin, Yalcin; LeVine, David M.

    2010-01-01

    This report describes measurements of the dielectric constant of seawater at a frequency of 1.413 GHz that is at the center of the L-Sand radiometric protected frequency spectrum. Aquarius will be sensing the sea surface salinity from space in this band. The objective of the project is to refine the model function for the dielectric constant as a function of salinity and temperature so that remote sensing measurements can be made with the accuracy needed to meet the measurement goals (0.2 psu) of the Aquarius mission. The measurements were made, using a microwave cavity operated in the transmission configuration. The cavity's temperature was accurately regulated to 0.02 C by immersing it in a temperature controlled bath of distilled water and ethanol glycol. Seawater had been purchased from Ocean Scientific International Limited (OS1L) at salinities of 30, 35 and 38 psu. Measurements of these seawater samples were then made over a range of temperatures, from l0 C to 35 C in 5 C intervals. Repeated measurements were made at each temperature and salinity, Mean values and standard deviations were then computed. Total error budgets indicated that the real and imaginary parts of the dielectric constant had a relative accuracy of about l%.

  17. Reliable Spectroscopic Constants for CCH-, NH2- and Their Isotopomers from an Accurate Potential Energy Function

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.; Schwenke, David W.; Chaban, Galina M.

    2005-01-01

    Accurate quartic force fields have been determined for the CCH- and NH2- molecular anions using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, CCSD(T). Very large one-particle basis sets have been used including diffuse functions and up through g-type functions. Correlation of the nitrogen and carbon core electrons has been included, as well as other "small" effects, such as the diagonal Born-Oppenheimer correction, and basis set extrapolation, and corrections for higher-order correlation effects and scalar relativistic effects. Fundamental vibrational frequencies have been computed using standard second-order perturbation theory as well as variational methods. Comparison with the available experimental data is presented and discussed. The implications of our research for the astronomical observation of molecular anions will be discussed.

  18. Effect of molecular orientation on the elastic constants of polypropylene.

    SciTech Connect

    Kumar, S. R.; Renusch, D. P.; Grimsditch, M.; Materials Science Division; Amoco Polymers Research & Development

    2000-03-07

    The Brillouin spectroscopic measurements of elastic properties of polypropylene films fabricated by different processing techniques are described. We find that the elastic symmetry and the associated elastic constants are dependent on the molecular orientation brought about by the processing conditions used to produce the films. We have shown that Brillouin scattering techniques can successfully be used to track the molecular orientation induced by uniaxial stretching. We find a direct correspondence between the Brillouin measurements and optical birefringence measurements, illustrating that molecular orientation plays a dominant role in determining the mechanical anisotropy in these materials.

  19. Highly Accurate Quartic Force Fields, Vibrational Frequencies, and Spectroscopic Constants for Cyclic and Linear C3H3(+)

    NASA Technical Reports Server (NTRS)

    Huang, Xinchuan; Taylor, Peter R.; Lee, Timothy J.

    2011-01-01

    High levels of theory have been used to compute quartic force fields (QFFs) for the cyclic and linear forms of the C H + molecular cation, referred to as c-C H + and I-C H +. Specifically the 33 3333 singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations, CCSD(T), has been used in conjunction with extrapolation to the one-particle basis set limit and corrections for scalar relativity and core correlation have been included. The QFFs have been used to compute highly accurate fundamental vibrational frequencies and other spectroscopic constants using both vibrational 2nd-order perturbation theory and variational methods to solve the nuclear Schroedinger equation. Agreement between our best computed fundamental vibrational frequencies and recent infrared photodissociation experiments is reasonable for most bands, but there are a few exceptions. Possible sources for the discrepancies are discussed. We determine the energy difference between the cyclic and linear forms of C H +, 33 obtaining 27.9 kcal/mol at 0 K, which should be the most reliable available. It is expected that the fundamental vibrational frequencies and spectroscopic constants presented here for c-C H + 33 and I-C H + are the most reliable available for the free gas-phase species and it is hoped that 33 these will be useful in the assignment of future high-resolution laboratory experiments or astronomical observations.

  20. Highly accurate quartic force fields, vibrational frequencies, and spectroscopic constants for cyclic and linear C3H3(+).

    PubMed

    Huang, Xinchuan; Taylor, Peter R; Lee, Timothy J

    2011-05-19

    High levels of theory have been used to compute quartic force fields (QFFs) for the cyclic and linear forms of the C(3)H(3)(+) molecular cation, referred to as c-C(3)H(3)(+) and l-C(3)H(3)(+). Specifically, the singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations, CCSD(T), has been used in conjunction with extrapolation to the one-particle basis set limit, and corrections for scalar relativity and core correlation have been included. The QFFs have been used to compute highly accurate fundamental vibrational frequencies and other spectroscopic constants by use of both vibrational second-order perturbation theory and variational methods to solve the nuclear Schrödinger equation. Agreement between our best computed fundamental vibrational frequencies and recent infrared photodissociation experiments is reasonable for most bands, but there are a few exceptions. Possible sources for the discrepancies are discussed. We determine the energy difference between the cyclic and linear forms of C(3)H(3)(+), obtaining 27.9 kcal/mol at 0 K, which should be the most reliable available. It is expected that the fundamental vibrational frequencies and spectroscopic constants presented here for c-C(3)H(3)(+) and l-C(3)H(3)(+) are the most reliable available for the free gas-phase species, and it is hoped that these will be useful in the assignment of future high-resolution laboratory experiments or astronomical observations. PMID:21510653

  1. A robust and accurate formulation of molecular and colloidal electrostatics

    NASA Astrophysics Data System (ADS)

    Sun, Qiang; Klaseboer, Evert; Chan, Derek Y. C.

    2016-08-01

    This paper presents a re-formulation of the boundary integral method for the Debye-Hückel model of molecular and colloidal electrostatics that removes the mathematical singularities that have to date been accepted as an intrinsic part of the conventional boundary integral equation method. The essence of the present boundary regularized integral equation formulation consists of subtracting a known solution from the conventional boundary integral method in such a way as to cancel out the singularities associated with the Green's function. This approach better reflects the non-singular physical behavior of the systems on boundaries with the benefits of the following: (i) the surface integrals can be evaluated accurately using quadrature without any need to devise special numerical integration procedures, (ii) being able to use quadratic or spline function surface elements to represent the surface more accurately and the variation of the functions within each element is represented to a consistent level of precision by appropriate interpolation functions, (iii) being able to calculate electric fields, even at boundaries, accurately and directly from the potential without having to solve hypersingular integral equations and this imparts high precision in calculating the Maxwell stress tensor and consequently, intermolecular or colloidal forces, (iv) a reliable way to handle geometric configurations in which different parts of the boundary can be very close together without being affected by numerical instabilities, therefore potentials, fields, and forces between surfaces can be found accurately at surface separations down to near contact, and (v) having the simplicity of a formulation that does not require complex algorithms to handle singularities will result in significant savings in coding effort and in the reduction of opportunities for coding errors. These advantages are illustrated using examples drawn from molecular and colloidal electrostatics.

  2. A robust and accurate formulation of molecular and colloidal electrostatics.

    PubMed

    Sun, Qiang; Klaseboer, Evert; Chan, Derek Y C

    2016-08-01

    This paper presents a re-formulation of the boundary integral method for the Debye-Hückel model of molecular and colloidal electrostatics that removes the mathematical singularities that have to date been accepted as an intrinsic part of the conventional boundary integral equation method. The essence of the present boundary regularized integral equation formulation consists of subtracting a known solution from the conventional boundary integral method in such a way as to cancel out the singularities associated with the Green's function. This approach better reflects the non-singular physical behavior of the systems on boundaries with the benefits of the following: (i) the surface integrals can be evaluated accurately using quadrature without any need to devise special numerical integration procedures, (ii) being able to use quadratic or spline function surface elements to represent the surface more accurately and the variation of the functions within each element is represented to a consistent level of precision by appropriate interpolation functions, (iii) being able to calculate electric fields, even at boundaries, accurately and directly from the potential without having to solve hypersingular integral equations and this imparts high precision in calculating the Maxwell stress tensor and consequently, intermolecular or colloidal forces, (iv) a reliable way to handle geometric configurations in which different parts of the boundary can be very close together without being affected by numerical instabilities, therefore potentials, fields, and forces between surfaces can be found accurately at surface separations down to near contact, and (v) having the simplicity of a formulation that does not require complex algorithms to handle singularities will result in significant savings in coding effort and in the reduction of opportunities for coding errors. These advantages are illustrated using examples drawn from molecular and colloidal electrostatics. PMID:27497538

  3. Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency

    NASA Astrophysics Data System (ADS)

    Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao

    2008-05-01

    Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.

  4. Molecular dynamics simulations of solutions at constant chemical potential

    NASA Astrophysics Data System (ADS)

    Perego, C.; Salvalaglio, M.; Parrinello, M.

    2015-04-01

    Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

  5. Ab Initio Simulation Beryllium in Solid Molecular Hydrogen: Elastic Constant

    NASA Astrophysics Data System (ADS)

    Guerrero, Carlo L.; Perlado, Jose M.

    2016-03-01

    In systems of inertial confinement fusion targets Deuterium-Tritium are manufactured with a solid layer, it must have specific properties to increase the efficiency of ignition. Currently there have been some proposals to model the phases of hydrogen isotopes and hence their high pressure, but these works do not allow explaining some of the structures present at the solid phase change effect of increased pressure. By means of simulation with first principles methods and Quantum Molecular Dynamics, we compare the structural difference of solid molecular hydrogen pure and solid molecular hydrogen with beryllium, watching beryllium inclusion in solid hydrogen matrix, we obtain several differences in mechanical properties, in particular elastic constants. For C11 the difference between hydrogen and hydrogen with beryllium is 37.56%. This may produce a non-uniform initial compression and decreased efficiency of ignition.

  6. Towards Accurate Molecular Modeling of Plastic Bonded Explosives

    NASA Astrophysics Data System (ADS)

    Chantawansri, T. L.; Andzelm, J.; Taylor, D.; Byrd, E.; Rice, B.

    2010-03-01

    There is substantial interest in identifying the controlling factors that influence the susceptibility of polymer bonded explosives (PBXs) to accidental initiation. Numerous Molecular Dynamics (MD) simulations of PBXs using the COMPASS force field have been reported in recent years, where the validity of the force field in modeling the solid EM fill has been judged solely on its ability to reproduce lattice parameters, which is an insufficient metric. Performance of the COMPASS force field in modeling EMs and the polymeric binder has been assessed by calculating structural, thermal, and mechanical properties, where only fair agreement with experimental data is obtained. We performed MD simulations using the COMPASS force field for the polymer binder hydroxyl-terminated polybutadiene and five EMs: cyclotrimethylenetrinitramine, 1,3,5,7-tetranitro-1,3,5,7-tetra-azacyclo-octane, 2,4,6,8,10,12-hexantirohexaazazisowurzitane, 2,4,6-trinitro-1,3,5-benzenetriamine, and pentaerythritol tetranitate. Predicted EM crystallographic and molecular structural parameters, as well as calculated properties for the binder will be compared with experimental results for different simulation conditions. We also present novel simulation protocols, which improve agreement between experimental and computation results thus leading to the accurate modeling of PBXs.

  7. Accurate calibration and uncertainty estimation of the normal spring constant of various AFM cantilevers.

    PubMed

    Song, Yunpeng; Wu, Sen; Xu, Linyan; Fu, Xing

    2015-03-10

    Measurement of force on a micro- or nano-Newton scale is important when exploring the mechanical properties of materials in the biophysics and nanomechanical fields. The atomic force microscope (AFM) is widely used in microforce measurement. The cantilever probe works as an AFM force sensor, and the spring constant of the cantilever is of great significance to the accuracy of the measurement results. This paper presents a normal spring constant calibration method with the combined use of an electromagnetic balance and a homemade AFM head. When the cantilever presses the balance, its deflection is detected through an optical lever integrated in the AFM head. Meanwhile, the corresponding bending force is recorded by the balance. Then the spring constant can be simply calculated using Hooke's law. During the calibration, a feedback loop is applied to control the deflection of the cantilever. Errors that may affect the stability of the cantilever could be compensated rapidly. Five types of commercial cantilevers with different shapes, stiffness, and operating modes were chosen to evaluate the performance of our system. Based on the uncertainty analysis, the expanded relative standard uncertainties of the normal spring constant of most measured cantilevers are believed to be better than 2%.

  8. Recent Results on the Accurate Measurements of the Dielectric Constant of Seawater at 1.413GHZ

    NASA Technical Reports Server (NTRS)

    Lang, R.H.; Tarkocin, Y.; Utku, C.; Le Vine, D.M.

    2008-01-01

    Measurements of the complex. dielectric constant of seawater at 30.00 psu, 35.00 psu and 38.27 psu over the temperature range from 5 C to 3 5 at 1.413 GHz are given and compared with the Klein-Swift results. A resonant cavity technique is used. The calibration constant used in the cavity perturbation formulas is determined experimentally using methanol and ethanediol (ethylene glycol) as reference liquids. Analysis of the data shows that the measurements are accurate to better than 1.0% in almost all cases studied.

  9. Highly accurate analytical energy of a two-dimensional exciton in a constant magnetic field

    NASA Astrophysics Data System (ADS)

    Hoang, Ngoc-Tram D.; Nguyen, Duy-Anh P.; Hoang, Van-Hung; Le, Van-Hoang

    2016-08-01

    Explicit expressions are given for analytically describing the dependence of the energy of a two-dimensional exciton on magnetic field intensity. These expressions are highly accurate with the precision of up to three decimal places for the whole range of the magnetic field intensity. The results are shown for the ground state and some excited states; moreover, we have all formulae to obtain similar expressions of any excited state. Analysis of numerical results shows that the precision of three decimal places is maintained for the excited states with the principal quantum number of up to n=100.

  10. Accurate AB Initio Calculation of Anharmonic Force Fields and Spectroscopic Constants of Small Polyatomic Molecules

    NASA Astrophysics Data System (ADS)

    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.

  11. Constant pressure and temperature discrete-time Langevin molecular dynamics

    SciTech Connect

    Grønbech-Jensen, Niels; Farago, Oded

    2014-11-21

    We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are built on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems—a one-dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three-dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb and Dünweg [J. Chem. Phys. 111, 4453 (1999)], show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation.

  12. Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting

    PubMed Central

    Khan, Tarik A.; Friedensohn, Simon; de Vries, Arthur R. Gorter; Straszewski, Jakub; Ruscheweyh, Hans-Joachim; Reddy, Sai T.

    2016-01-01

    High-throughput antibody repertoire sequencing (Ig-seq) provides quantitative molecular information on humoral immunity. However, Ig-seq is compromised by biases and errors introduced during library preparation and sequencing. By using synthetic antibody spike-in genes, we determined that primer bias from multiplex polymerase chain reaction (PCR) library preparation resulted in antibody frequencies with only 42 to 62% accuracy. Additionally, Ig-seq errors resulted in antibody diversity measurements being overestimated by up to 5000-fold. To rectify this, we developed molecular amplification fingerprinting (MAF), which uses unique molecular identifier (UID) tagging before and during multiplex PCR amplification, which enabled tagging of transcripts while accounting for PCR efficiency. Combined with a bioinformatic pipeline, MAF bias correction led to measurements of antibody frequencies with up to 99% accuracy. We also used MAF to correct PCR and sequencing errors, resulting in enhanced accuracy of full-length antibody diversity measurements, achieving 98 to 100% error correction. Using murine MAF-corrected data, we established a quantitative metric of recent clonal expansion—the intraclonal diversity index—which measures the number of unique transcripts associated with an antibody clone. We used this intraclonal diversity index along with antibody frequencies and somatic hypermutation to build a logistic regression model for prediction of the immunological status of clones. The model was able to predict clonal status with high confidence but only when using MAF error and bias corrected Ig-seq data. Improved accuracy by MAF provides the potential to greatly advance Ig-seq and its utility in immunology and biotechnology. PMID:26998518

  13. Computational study of the reactions of methanol with the hydroperoxyl and methyl radicals. 2. Accurate thermal rate constants.

    PubMed

    Alecu, I M; Truhlar, Donald G

    2011-12-29

    Multistructural canonical variational-transition-state theory with multidimensional tunneling (MS-CVT/MT) is employed to calculate thermal rate constants for the abstraction of hydrogen atoms from both positions of methanol by the hydroperoxyl and methyl radicals over the temperature range 100-3000 K. The M08-HX hybrid meta-generalized gradient approximation density functional and M08-HX with specific reaction parameters, both with the maug-cc-pVTZ basis set, were validated in part 1 of this study (Alecu, I. M.; Truhlar, D. G. J. Phys. Chem. A2011, 115, 2811) against highly accurate CCSDT(2)(Q)/CBS calculations for the energetics of these reactions, and they are used here to compute the properties of all stationary points and the energies, gradients, and Hessians of nonstationary points along each considered reaction path. The internal rotations in some of the transition states are found to be highly anharmonic and strongly coupled to each other, and they generate multiple structures (conformations) whose contributions are included in the partition function. It is shown that the previous estimates for these rate constants used to build kinetic models for the combustion of methanol, some of which were based on transition state theory calculations with one-dimensional tunneling corrections and harmonic-oscillator approximations or separable one-dimensional hindered rotor treatments of torsions, are appreciably different than the ones presently calculated using MS-CVT/MT. The rate constants obtained from the best MS-CVT/MT calculations carried out in this study, in which the important effects of corner cutting due to small and large reaction path curvature are captured via a microcanonical optimized multidimensional tunneling (μOMT) treatment, are recommended for future refinement of the kinetic model for methanol combustion. PMID:22059377

  14. Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

    PubMed Central

    Baele, Guy; Li, Wai Lok Sibon; Drummond, Alexei J.; Suchard, Marc A.; Lemey, Philippe

    2013-01-01

    Recent implementations of path sampling (PS) and stepping-stone sampling (SS) have been shown to outperform the harmonic mean estimator (HME) and a posterior simulation-based analog of Akaike’s information criterion through Markov chain Monte Carlo (AICM), in Bayesian model selection of demographic and molecular clock models. Almost simultaneously, a Bayesian model averaging approach was developed that avoids conditioning on a single model but averages over a set of relaxed clock models. This approach returns estimates of the posterior probability of each clock model through which one can estimate the Bayes factor in favor of the maximum a posteriori (MAP) clock model; however, this Bayes factor estimate may suffer when the posterior probability of the MAP model approaches 1. Here, we compare these two recent developments with the HME, stabilized/smoothed HME (sHME), and AICM, using both synthetic and empirical data. Our comparison shows reassuringly that MAP identification and its Bayes factor provide similar performance to PS and SS and that these approaches considerably outperform HME, sHME, and AICM in selecting the correct underlying clock model. We also illustrate the importance of using proper priors on a large set of empirical data sets. PMID:23090976

  15. Analyzing and Interpreting NMR Spin-Spin Coupling Constants Using Molecular Orbital Calculations

    ERIC Educational Resources Information Center

    Autschbach, Jochen; Le Guennic, Boris

    2007-01-01

    Molecular orbital plots are used to analyze and interpret NMR spin-spin coupling constants, also known as J coupling constants. Students have accepted the concept of contributions to molecular properties from individual orbitals without the requirement to provide explicit equations.

  16. A Simple and Convenient Method of Multiple Linear Regression to Calculate Iodine Molecular Constants

    ERIC Educational Resources Information Center

    Cooper, Paul D.

    2010-01-01

    A new procedure using a student-friendly least-squares multiple linear-regression technique utilizing a function within Microsoft Excel is described that enables students to calculate molecular constants from the vibronic spectrum of iodine. This method is advantageous pedagogically as it calculates molecular constants for ground and excited…

  17. Microcomputer Calculation of Equilibrium Constants from Molecular Parameters of Gases.

    ERIC Educational Resources Information Center

    Venugopalan, Mundiyath

    1989-01-01

    Lists a BASIC program which computes the equilibrium constant as a function of temperature. Suggests use by undergraduates taking a one-year calculus-based physical chemistry course. Notes the program provides for up to four species, typically two reactants and two products. (MVL)

  18. Accurate rotational constant and bond lengths of hexafluorobenzene by femtosecond rotational Raman coherence spectroscopy and ab initio calculations

    SciTech Connect

    Den, Takuya S.; Frey, Hans-Martin; Leutwyler, Samuel

    2014-11-21

    The gas-phase rotational motion of hexafluorobenzene has been measured in real time using femtosecond (fs) time-resolved rotational Raman coherence spectroscopy (RR-RCS) at T = 100 and 295 K. This four-wave mixing method allows to probe the rotation of non-polar gas-phase molecules with fs time resolution over times up to ∼5 ns. The ground state rotational constant of hexafluorobenzene is determined as B{sub 0} = 1029.740(28) MHz (2σ uncertainty) from RR-RCS transients measured in a pulsed seeded supersonic jet, where essentially only the v = 0 state is populated. Using this B{sub 0} value, RR-RCS measurements in a room temperature gas cell give the rotational constants B{sub v} of the five lowest-lying thermally populated vibrationally excited states ν{sub 7/8}, ν{sub 9}, ν{sub 11/12}, ν{sub 13}, and ν{sub 14/15}. Their B{sub v} constants differ from B{sub 0} by between −1.02 MHz and +2.23 MHz. Combining the B{sub 0} with the results of all-electron coupled-cluster CCSD(T) calculations of Demaison et al. [Mol. Phys. 111, 1539 (2013)] and of our own allow to determine the C-C and C-F semi-experimental equilibrium bond lengths r{sub e}(C-C) = 1.3866(3) Å and r{sub e}(C-F) = 1.3244(4) Å. These agree with the CCSD(T)/wCVQZ r{sub e} bond lengths calculated by Demaison et al. within ±0.0005 Å. We also calculate the semi-experimental thermally averaged bond lengths r{sub g}(C-C)=1.3907(3) Å and r{sub g}(C-F)=1.3250(4) Å. These are at least ten times more accurate than two sets of experimental gas-phase electron diffraction r{sub g} bond lengths measured in the 1960s.

  19. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

    PubMed

    Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L

    2014-07-01

    pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible.

  20. Efficient implementation of constant pH molecular dynamics on modern graphics processors.

    PubMed

    Arthur, Evan J; Brooks, Charles L

    2016-09-15

    The treatment of pH sensitive ionization states for titratable residues in proteins is often omitted from molecular dynamics (MD) simulations. While static charge models can answer many questions regarding protein conformational equilibrium and protein-ligand interactions, pH-sensitive phenomena such as acid-activated chaperones and amyloidogenic protein aggregation are inaccessible to such models. Constant pH molecular dynamics (CPHMD) coupled with the Generalized Born with a Simple sWitching function (GBSW) implicit solvent model provide an accurate framework for simulating pH sensitive processes in biological systems. Although this combination has demonstrated success in predicting pKa values of protein structures, and in exploring dynamics of ionizable side-chains, its speed has been an impediment to routine application. The recent availability of low-cost graphics processing unit (GPU) chipsets with thousands of processing cores, together with the implementation of the accurate GBSW implicit solvent model on those chipsets (Arthur and Brooks, J. Comput. Chem. 2016, 37, 927), provide an opportunity to improve the speed of CPHMD and ionization modeling greatly. Here, we present a first implementation of GPU-enabled CPHMD within the CHARMM-OpenMM simulation package interface. Depending on the system size and nonbonded force cutoff parameters, we find speed increases of between one and three orders of magnitude. Additionally, the algorithm scales better with system size than the CPU-based algorithm, thus allowing for larger systems to be modeled in a cost effective manner. We anticipate that the improved performance of this methodology will open the door for broad-spread application of CPHMD in its modeling pH-mediated biological processes. © 2016 Wiley Periodicals, Inc. PMID:27405884

  1. A multireference configuration interaction study of CuB and CuAl molecular constants and photoionization spectra.

    PubMed

    Ferrão, Luiz F A; Spada, Rene F K; Roberto-Neto, Orlando; Machado, Francisco B C

    2013-09-28

    Accurate potential energy curves and molecular constants for the low-lying electronic states of CuX(y) (X = B, Al; y = 0, +1) were investigated using the complete active space self-consistent field/multireference configuration interaction (MRCI) methodology with aug-cc-pV5Z basis set. The photoionization spectra of CuX were computed, showing electron detachment in the region of far ultraviolet. The results complement the previous theoretical characterizations and the few experimental studies. A comparative analysis was carried out concerning the different choices of reference configuration state functions in the MRCI calculations with and without the contribution of scalar relativistic effects. The results obtained with a small reference set adequately constructed are competitive to those using a much larger number of configuration state functions, and also the scalar relativistic effects improve significantly the molecular constants in this kind of system containing a 3d metal atom.

  2. Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates

    NASA Astrophysics Data System (ADS)

    Yogurtcu, Osman N.; Johnson, Margaret E.

    2015-08-01

    The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute

  3. Modified Nose-Hoover thermostat for solid state for constant temperature molecular dynamics simulation

    SciTech Connect

    Chen, Wen-Hwa; Wu, Chun-Hung; Cheng, Hsien-Chie

    2011-07-10

    Nose-Hoover (NH) thermostat methods incorporated with molecular dynamics (MD) simulation have been widely used to simulate the instantaneous system temperature and feedback energy in a canonical ensemble. The method simply relates the kinetic energy to the system temperature via the particles' momenta based on the ideal gas law. However, when used in a tightly bound system such as solids, the method may suffer from deriving a lower system temperature and potentially inducing early breaking of atomic bonds at relatively high temperature due to the neglect of the effect of the potential energy of atoms based on solid state physics. In this paper, a modified NH thermostat method is proposed for solid system. The method takes into account the contribution of phonons by virtue of the vibrational energy of lattice and the zero-point energy, derived based on the Debye theory. Proof of the equivalence of the method and the canonical ensemble is first made. The modified NH thermostat is tested on different gold nanocrystals to characterize their melting point and constant volume specific heat, and also their size and temperature dependence. Results show that the modified NH method can give much more comparable results to both the literature experimental and theoretical data than the standard NH. Most importantly, the present model is the only one, among the six thermostat algorithms under comparison, that can accurately reproduce the experimental data and also the T{sup 3}-law at temperature below the Debye temperature, where the specific heat of a solid at constant volume is proportional to the cube of temperature.

  4. Modified Nosé-Hoover thermostat for solid state for constant temperature molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Chen, Wen-Hwa; Wu, Chun-Hung; Cheng, Hsien-Chie

    2011-07-01

    Nosé-Hoover (NH) thermostat methods incorporated with molecular dynamics (MD) simulation have been widely used to simulate the instantaneous system temperature and feedback energy in a canonical ensemble. The method simply relates the kinetic energy to the system temperature via the particles' momenta based on the ideal gas law. However, when used in a tightly bound system such as solids, the method may suffer from deriving a lower system temperature and potentially inducing early breaking of atomic bonds at relatively high temperature due to the neglect of the effect of the potential energy of atoms based on solid state physics. In this paper, a modified NH thermostat method is proposed for solid system. The method takes into account the contribution of phonons by virtue of the vibrational energy of lattice and the zero-point energy, derived based on the Debye theory. Proof of the equivalence of the method and the canonical ensemble is first made. The modified NH thermostat is tested on different gold nanocrystals to characterize their melting point and constant volume specific heat, and also their size and temperature dependence. Results show that the modified NH method can give much more comparable results to both the literature experimental and theoretical data than the standard NH. Most importantly, the present model is the only one, among the six thermostat algorithms under comparison, that can accurately reproduce the experimental data and also the T 3-law at temperature below the Debye temperature, where the specific heat of a solid at constant volume is proportional to the cube of temperature.

  5. Frictional Response of Molecularly Thin Liquid Polymer Films Subject to Constant Shear Stress

    NASA Astrophysics Data System (ADS)

    Tschirhart, Charles; Troian, Sandra

    2014-03-01

    Measurements of the frictional response of nanoscale viscous films are typically obtained using the surface force apparatus in which a fluid layer is confined between smooth solid substrates approaching at constant speed or force. The squeezing pressure causes lateral flow from which the shear viscosity can be deduced. Under these conditions however, molecularly thin films tend to solidify wholly or partially and estimates of the shear viscosity can exceed those in macroscale films by many orders of magnitude. This problem can be avoided altogether by examining the response of an initially flat, supported, free surface film subject to comparable values of surface shear stress by application of an external inert gas stream. This method was first conceived by Derjaguin in 1944; more recent studies by Mate et al. at IBM Almaden on complex polymeric systems have uncovered fluid layering and other interesting behaviors. The only drawback is that this alternative technique requires an accurate model for interface distortion. We report on ellipsometric measurements of ultrathin polymeric films in efforts to determine whether the usual interface equations for free surface films based purely on continuum models can be properly extended to nanoscale films. Supported by a Fred and Jean Felberg Fellowship and G. W. Housner Student Discovery Fund.

  6. Low temperature rate constants for the N + CN → N2 + C reaction: two-dimensional quantum capture calculations on an accurate potential energy surface.

    PubMed

    Ma, Jianyi; Guo, Hua; Dawes, Richard

    2012-09-21

    The title reaction is thought to be responsible for the production of molecular nitrogen in interstellar clouds. In this work, we report quantum capture calculations on a new two-dimensional potential energy surface determined by interpolating high-level ab initio data. The low-temperature rate constant calculated using a capture model is quite large and has a positive temperature dependence, in agreement with a recent experiment. The origin of the aforementioned behaviors of the rate constant is analyzed.

  7. Accurate Prediction of Hyperfine Coupling Constants in Muoniated and Hydrogenated Ethyl Radicals: Ab Initio Path Integral Simulation Study with Density Functional Theory Method.

    PubMed

    Yamada, Kenta; Kawashima, Yukio; Tachikawa, Masanori

    2014-05-13

    We performed ab initio path integral molecular dynamics (PIMD) simulations with a density functional theory (DFT) method to accurately predict hyperfine coupling constants (HFCCs) in the ethyl radical (CβH3-CαH2) and its Mu-substituted (muoniated) compound (CβH2Mu-CαH2). The substitution of a Mu atom, an ultralight isotope of the H atom, with larger nuclear quantum effect is expected to strongly affect the nature of the ethyl radical. The static conventional DFT calculations of CβH3-CαH2 find that the elongation of one Cβ-H bond causes a change in the shape of potential energy curve along the rotational angle via the imbalance of attractive and repulsive interactions between the methyl and methylene groups. Investigation of the methyl-group behavior including the nuclear quantum and thermal effects shows that an unbalanced CβH2Mu group with the elongated Cβ-Mu bond rotates around the Cβ-Cα bond in a muoniated ethyl radical, quite differently from the CβH3 group with the three equivalent Cβ-H bonds in the ethyl radical. These rotations couple with other molecular motions such as the methylene-group rocking motion (inversion), leading to difficulties in reproducing the corresponding barrier heights. Our PIMD simulations successfully predict the barrier heights to be close to the experimental values and provide a significant improvement in muon and proton HFCCs given by the static conventional DFT method. Further investigation reveals that the Cβ-Mu/H stretching motion, methyl-group rotation, methylene-group rocking motion, and HFCC values deeply intertwine with each other. Because these motions are different between the radicals, a proper description of the structural fluctuations reflecting the nuclear quantum and thermal effects is vital to evaluate HFCC values in theory to be comparable to the experimental ones. Accordingly, a fundamental difference in HFCC between the radicals arises from their intrinsic molecular motions at a finite temperature, in

  8. A benchmark study of molecular structure by experimental and theoretical methods: Equilibrium structure of thymine from microwave rotational constants and coupled-cluster computations

    NASA Astrophysics Data System (ADS)

    Vogt, Natalja; Demaison, Jean; Ksenafontov, Denis N.; Rudolph, Heinz Dieter

    2014-11-01

    Accurate equilibrium, re, structures of thymine have been determined using two different, and to some extent complementary techniques. The composite ab initio Born-Oppenheimer, re(best ab initio), structural parameters are obtained from the all-electron CCSD(T) and MP2 geometry optimizations using Gaussian basis sets up to quadruple-zeta quality. The semi-experimental mixed estimation method, where internal coordinates are fitted concurrently to equilibrium rotational constants and geometry parameters obtained from a high level of electronic structure theory. The equilibrium rotational constants are derived from experimental effective ground-state rotational constants and rovibrational corrections based on a quantum-chemical cubic force field. Equilibrium molecular structures accurate to 0.002 Å and 0.2° have been determined. This work is one of a few accurate equilibrium structure determinations for large molecules. The poor behavior of Kraitchman's equations is discussed.

  9. Finite-temperature elastic constants of paramagnetic materials within the disordered local moment picture from ab initio molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Mozafari, E.; Shulumba, N.; Steneteg, P.; Alling, B.; Abrikosov, Igor A.

    2016-08-01

    We present a theoretical scheme to calculate the elastic constants of magnetic materials in the high-temperature paramagnetic state. Our approach is based on a combination of disordered local moments picture and ab initio molecular dynamics (DLM-MD). Moreover, we investigate a possibility to enhance the efficiency of the simulations of elastic properties using the recently introduced method: symmetry imposed force constant temperature-dependent effective potential (SIFC-TDEP). We have chosen cubic paramagnetic CrN as a model system. This is done due to its technological importance and its demonstrated strong coupling between magnetic and lattice degrees of freedom. We have studied the temperature-dependent single-crystal and polycrystalline elastic constants of paramagentic CrN up to 1200 K. The obtained results at T = 300 K agree well with the experimental values of polycrystalline elastic constants as well as the Poisson ratio at room temperature. We observe that the Young's modulus is strongly dependent on temperature, decreasing by ˜14 % from T = 300 K to 1200 K. In addition we have studied the elastic anisotropy of CrN as a function of temperature and we observe that CrN becomes substantially more isotropic as the temperature increases. We demonstrate that the use of Birch law may lead to substantial errors for calculations of temperature induced changes of elastic moduli. The proposed methodology can be used for accurate predictions of mechanical properties of magnetic materials at temperatures above their magnetic order-disorder phase transition.

  10. Use of hydrophobic constants of molecular fragments for characterizing analytical systems

    SciTech Connect

    Tselik, E.I.; Polvektov, N.S.

    1985-06-10

    The authors attempt to clarify the applicability of the proposed hydrophobicity parameters to a description of the behavior of complex compounds with organic ligands in extractional systems, and to establish quantitative relationships between the properties of the complex and hydrophobicity of the ligand. It was found that the stability constants of the ionic associates of lanthanum, neodymium, and erbium with certain derivatives of salicylic acid, dihalogenated derivatives of 8-hydroxyquinoline, and Rhodamine B correlate with the hydrophobicity of the ligands. The quantitative expressions of these serve as empirical hydrophobic constants of molecular fragments of organic compounds.

  11. Molecular dynamics calculation of elastic constants in Gay-Berne nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Allen, Michael P.; Warren, Mark A.; Wilson, Mark R.; Sauron, Alain; Smith, William

    1996-08-01

    In this paper we present a molecular dynamics calculation of the Frank elastic constants of a nematic liquid crystal. We study two well-known variants of the Gay-Berne potential, and determine the elastic constants by measuring orientational fluctuations as a function of wave vector, using reasonably large system sizes in the range 1000-8000 molecules. For some of the simulations, a set of Lagrangian constraints was applied in order to keep the director fixed along one of the box axes, facilitating the measurement of fluctuations in components of the reciprocal-space order tensor Q̂(k) in the director frame.

  12. A simple method for the accurate determination of the Henry's law constant for highly sorptive, semivolatile organic compounds.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2016-01-01

    A novel technique is developed to determine the Henry's law constants (HLCs) of seven volatile fatty acids (VFAs) with significantly high solubility using a combined application of thermal desorber/gas chromatography/mass spectrometry (TD/GC/MS). In light of the strong sorptive properties of these semi-volatile organic compounds (SVOCs), their HLCs were determined by properly evaluating the fraction lost on the surface of the materials used to induce equilibrium (vial, gas-tight syringe, and sorption tube). To this end, a total of nine repeated experiments were conducted in a closed (static) system at three different gas/liquid volume ratios. The best estimates for HLCs (M/atm) were thus 7,200 (propionic acid), 4,700 (i-butyric acid), 4,400 (n-butyric acid), 2,700 (i-valeric acid), 2,400 (n-valeric acid), 1,000 (hexanoic acid), and 1,500 (heptanoic acid). The differences in the HLC values between this study and previous studies, if assessed in terms of the percent difference, ranged from 9.2% (n-valeric acid) to 55.7% (i-valeric acid). We overcame the main cause of errors encountered in previous studies by performing the proper correction of the sorptive losses of the SVOCs that inevitably took place, particularly on the walls of the equilibration systems (mainly the headspace vial and/or the glass tight syringe). PMID:26577086

  13. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space.

    PubMed

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O Anatole; Müller, Klaus-Robert; Tkatchenko, Alexandre

    2015-06-18

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  14. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    SciTech Connect

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  15. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    DOE PAGES

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

  16. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

    PubMed Central

    2015-01-01

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

  17. Application of potential constants: Empirical determination of molecular energy components for diatomic molecules—II

    NASA Astrophysics Data System (ADS)

    Ohwada, Ken

    The harmonic and anharmonic potential (force) constants which are usually available from a normal coordinate analysis for a diatomic molecule are applied to determine the molecular energy components such as the electronic kinetic energy, the total electrostatic potential energy, the electron—nuclear attraction energy, the electron—electron repulsion energy, the nuclear—nuclear repulsion energy, and the Hartree—Fock eigen-value sum. The method developed here is based on an inhomogeneous linear third-order differential equation derived from the quantum mechanical virial theorem, and a homogeneity hypothesis of the molecular energy with respect to the atomic number. To confirm the utility of the method, the calculated molecular energy components of diatomic molecules are compared with available Hartree—Fock data. It is concluded from this data that the present method is simple and useful for evaluating the molecular energy components of various diatomic molecules.

  18. Accurate determination of the nuclear quadrupole moment of xenon from the molecular method

    NASA Astrophysics Data System (ADS)

    Canella, Guilherme A.; Santiago, Régis T.; Haiduke, Roberto L. A.

    2016-09-01

    This study provides a new determination of the nuclear electric quadrupole moment (NQM) for 131Xe, which is achieved by the molecular method. Dirac-Coulomb Coupled Cluster calculations with a Gaunt correction (DC+G-CC) of electric field gradients (EFGs) and experimental nuclear quadrupole coupling constants of six molecular systems (XeH+, XeCuF, XeCuCl, XeAgF, XeAgCl and XeAuF) were considered. The best NQM obtained by our DC+G-CCSD-T EFGs was -114.6(1.1) mbarn, which is recommended as the new reference value for this nuclide given the high level electron structure calculations done here.

  19. Molecular Simulation of Carbon Dioxide Capture by Montmorillonite Using an Accurate and Flexible Force Field

    SciTech Connect

    Romanov, V N; Cygan, R T; Myshakin, E M

    2012-06-21

    Naturally occurring clay minerals provide a distinctive material for carbon capture and carbon dioxide sequestration. Swelling clay minerals, such as the smectite variety, possess an aluminosilicate structure that is controlled by low-charge layers that readily expand to accommodate water molecules and, potentially, CO2. Recent experimental studies have demonstrated the efficacy of intercalating CO2 in the interlayer of layered clays, but little is known about the molecular mechanisms of the process and the extent of carbon capture as a function of clay charge and structure. A series of molecular dynamics simulations and vibrational analyses have been completed to assess the molecular interactions associated with incorporation of CO2 and H2O in the interlayer of montmorillonite clay and to help validate the models with experimental observation. An accurate and fully flexible set of interatomic potentials for CO2 is developed and combined with Clayff potentials to help evaluate the intercalation mechanism and examine the effect of molecular flexibility onthe diffusion rate of CO2 in water.

  20. Accurate static and dynamic properties of liquid electrolytes for Li-ion batteries from ab initio molecular dynamics.

    PubMed

    Ganesh, P; Jiang, De-en; Kent, P R C

    2011-03-31

    Lithium-ion batteries have the potential to revolutionize the transportation industry, as they did for wireless communication. A judicious choice of the liquid electrolytes used in these systems is required to achieve a good balance among high-energy storage, long cycle life and stability, and fast charging. Ethylene-carbonate (EC) and propylene-carbonate (PC) are popular electrolytes. However, to date, almost all molecular-dynamics simulations of these fluids rely on classical force fields, while a complete description of the functionality of Li-ion batteries will eventually require quantum mechanics. We perform accurate ab initio molecular-dynamics simulations of ethylene- and propylene-carbonate with LiPF(6) at experimental concentrations to build solvation models which explain available neutron scattering and nuclear magnetic resonance (NMR) results and to compute Li-ion solvation energies and diffusion constants. Our results suggest some similarities between the two liquids as well as some important differences. Simulations also provide useful insights into formation of solid-electrolyte interphases in the presence of electrodes in conventional Li-ion batteries.

  1. Accurate determination of one-bond heteronuclear coupling constants with “pure shift” broadband proton-decoupled CLIP/CLAP-HSQC experiments

    NASA Astrophysics Data System (ADS)

    Timári, István; Kaltschnee, Lukas; Kolmer, Andreas; Adams, Ralph W.; Nilsson, Mathias; Thiele, Christina M.; Morris, Gareth A.; Kövér, Katalin E.

    2014-02-01

    We report broadband proton-decoupled CLIP/CLAP-HSQC experiments for the accurate determination of one-bond heteronuclear couplings and, by extension, for the reliable measurement of small residual dipolar coupling constants. The combination of an isotope-selective BIRD(d) filter module with a non-selective 1H inversion pulse is employed to refocus proton-proton coupling evolution prior to the acquisition of brief chunks of free induction decay that are subsequently assembled to reconstruct the fully-decoupled signal evolution. As a result, the cross-peaks obtained are split only by the heteronuclear one-bond coupling along the F2 dimension, allowing coupling constants to be extracted by measuring simple frequency differences between singlet maxima. The proton decoupling scheme presented has also been utilized in standard HSQC experiments, resulting in a fully-decoupled pure shift correlation map with significantly improved resolution.

  2. Molecular Simulation of the Free Energy for the Accurate Determination of Phase Transition Properties of Molecular Solids

    NASA Astrophysics Data System (ADS)

    Sellers, Michael; Lisal, Martin; Brennan, John

    2015-06-01

    Investigating the ability of a molecular model to accurately represent a real material is crucial to model development and use. When the model simulates materials in extreme conditions, one such property worth evaluating is the phase transition point. However, phase transitions are often overlooked or approximated because of difficulty or inaccuracy when simulating them. Techniques such as super-heating or super-squeezing a material to induce a phase change suffer from inherent timescale limitations leading to ``over-driving,'' and dual-phase simulations require many long-time runs to seek out what frequently results in an inexact location of phase-coexistence. We present a compilation of methods for the determination of solid-solid and solid-liquid phase transition points through the accurate calculation of the chemical potential. The methods are applied to the Smith-Bharadwaj atomistic potential's representation of cyclotrimethylene trinitramine (RDX) to accurately determine its melting point (Tm) and the alpha to gamma solid phase transition pressure. We also determine Tm for a coarse-grain model of RDX, and compare its value to experiment and atomistic counterpart. All methods are employed via the LAMMPS simulator, resulting in 60-70 simulations that total 30-50 ns. Approved for public release. Distribution is unlimited.

  3. A large catalog of accurate distances to molecular clouds from PS1 photometry

    SciTech Connect

    Schlafly, E. F.; Rix, H.-W.; Martin, N. F.; Green, G.; Finkbeiner, D. P.; Bell, E. F.; Burgett, W. S.; Chambers, K. C.; Hodapp, K. W.; Kaiser, N.; Magnier, E. A.; Tonry, J. L.; Draper, P. W.; Metcalfe, N.; Price, P. A.

    2014-05-01

    Distance measurements to molecular clouds are important but are often made separately for each cloud of interest, employing very different data and techniques. We present a large, homogeneous catalog of distances to molecular clouds, most of which are of unprecedented accuracy. We determine distances using optical photometry of stars along lines of sight toward these clouds, obtained from PanSTARRS-1. We simultaneously infer the reddenings and distances to these stars, tracking the full probability distribution function using a technique presented in Green et al. We fit these star-by-star measurements using a simple dust screen model to find the distance to each cloud. We thus estimate the distances to almost all of the clouds in the Magnani et al. catalog, as well as many other well-studied clouds, including Orion, Perseus, Taurus, Cepheus, Polaris, California, and Monoceros R2, avoiding only the inner Galaxy. Typical statistical uncertainties in the distances are 5%, though the systematic uncertainty stemming from the quality of our stellar models is about 10%. The resulting catalog is the largest catalog of accurate, directly measured distances to molecular clouds. Our distance estimates are generally consistent with available distance estimates from the literature, though in some cases the literature estimates are off by a factor of more than two.

  4. Indirect Terahertz Spectroscopy of Molecular Ions Using Highly Accurate and Precise Mid-Ir Spectroscopy

    NASA Astrophysics Data System (ADS)

    Mills, Andrew A.; Ford, Kyle B.; Kreckel, Holger; Perera, Manori; Crabtree, Kyle N.; McCall, Benjamin J.

    2009-06-01

    With the advent of Herschel and SOFIA, laboratory methods capable of providing molecular rest frequencies in the terahertz and sub-millimeter regime are increasingly important. As of yet, it has been difficult to perform spectroscopy in this wavelength region due to the limited availability of radiation sources, optics, and detectors. Our goal is to provide accurate THz rest frequencies for molecular ions by combining previously recorded microwave transitions with combination differences obtained from high precision mid-IR spectroscopy. We are constructing a Sensitive Resolved Ion Beam Spectroscopy setup which will harness the benefits of kinematic compression in a molecular ion beam to enable very high resolution spectroscopy. This ion beam is interrogated by continuous-wave cavity ringdown spectroscopy using a home-made widely tunable difference frequency laser that utilizes two near-IR lasers and a periodically-poled lithium niobate crystal. Here, we report our efforts to optimize our ion beam spectrometer and to perform high-precision and high-accuracy frequency measurements using an optical frequency comb. footnote

  5. Local Elastic Constants for Epoxy-Nanotube Composites from Molecular Dynamics Simulation

    NASA Technical Reports Server (NTRS)

    Frankland, S. J. V.; Gates, T. S.

    2007-01-01

    A method from molecular dynamics simulation is developed for determining local elastic constants of an epoxy/nanotube composite. The local values of C11, C33, K12, and K13 elastic constants are calculated for an epoxy/nanotube composite as a function of radial distance from the nanotube. While the results possess a significant amount of statistical uncertainty resulting from both the numerical analysis and the molecular fluctuations during the simulation, the following observations can be made. If the size of the region around the nanotube is increased from shells of 1 to 6 in thickness, then the scatter in the data reduces enough to observe trends. All the elastic constants determined are at a minimum 20 from the center of the nanotube. The C11, C33, and K12 follow similar trends as a function of radial distance from the nanotube. The K13 decreases greater distances from the nanotube and becomes negative which may be a symptom of the statistical averaging.

  6. Measurement of State-Specific Association Constants in Allosteric Sensors through Molecular Stapling and NMR.

    PubMed

    Moleschi, Kody J; Akimoto, Madoka; Melacini, Giuseppe

    2015-08-26

    Allostery is a ubiquitous mechanism to control biological function and arises from the coupling of inhibitory and binding equilibria. The extent of coupling reflects the inactive vs active state selectivity of the allosteric effector. Hence, dissecting allosteric determinants requires quantification of state-specific association constants. However, observed association constants are typically population-averages, reporting on overall affinities but not on allosteric coupling. Here we propose a general method to measure state-specific association constants in allosteric sensors based on three key elements, i.e., state-selective molecular stapling through disulfide bridges, competition binding saturation transfer experiments and chemical shift correlation analyses to gauge state populations. The proposed approach was applied to the prototypical cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA-RIα), for which the structures of the inactive and active states are available, as needed to design the state-selective disulfide bridges. Surprisingly, the PKA-RIα state-specific association constants are comparable to those of a structurally homologous domain with ∼10(3)-fold lower cAMP-affinity, suggesting that the affinity difference arises primarily from changes in the position of the dynamic apo inhibitory equilibrium.

  7. Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes

    DOE PAGES

    Sjostrom, Travis; Daligault, Jerome

    2014-10-10

    Here, we develop and implement a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory. The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) density functional theory and path integral Monte Carlo calculations for microscopic features such as the electron density as well as the equation of state. The present approach does not scale with temperature and hence extends to higher temperatures than is accessible in the Kohn-Sham method and lowermore » temperatures than is accessible by path integral Monte Carlo calculations, while being significantly less computationally expensive than either of those two methods.« less

  8. Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes

    SciTech Connect

    Sjostrom, Travis; Daligault, Jerome

    2014-10-10

    Here, we develop and implement a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory. The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) density functional theory and path integral Monte Carlo calculations for microscopic features such as the electron density as well as the equation of state. The present approach does not scale with temperature and hence extends to higher temperatures than is accessible in the Kohn-Sham method and lower temperatures than is accessible by path integral Monte Carlo calculations, while being significantly less computationally expensive than either of those two methods.

  9. Accurate force fields and methods for modelling organic molecular crystals at finite temperatures.

    PubMed

    Nyman, Jonas; Pundyke, Orla Sheehan; Day, Graeme M

    2016-06-21

    We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy.

  10. Simple, rapid and accurate molecular diagnosis of acute promyelocytic leukemia by loop mediated amplification technology.

    PubMed

    Spinelli, Orietta; Rambaldi, Alessandro; Rigo, Francesca; Zanghì, Pamela; D'Agostini, Elena; Amicarelli, Giulia; Colotta, Francesco; Divona, Mariadomenica; Ciardi, Claudia; Coco, Francesco Lo; Minnucci, Giulia

    2015-01-01

    The diagnostic work-up of acute promyelocytic leukemia (APL) includes the cytogenetic demonstration of the t(15;17) translocation and/or the PML-RARA chimeric transcript by RQ-PCR or RT-PCR. This latter assays provide suitable results in 3-6 hours. We describe here two new, rapid and specific assays that detect PML-RARA transcripts, based on the RT-QLAMP (Reverse Transcription-Quenching Loop-mediated Isothermal Amplification) technology in which RNA retrotranscription and cDNA amplification are carried out in a single tube with one enzyme at one temperature, in fluorescence and real time format. A single tube triplex assay detects bcr1 and bcr3 PML-RARA transcripts along with GUS housekeeping gene. A single tube duplex assay detects bcr2 and GUSB. In 73 APL cases, these assays detected in 16 minutes bcr1, bcr2 and bcr3 transcripts. All 81 non-APL samples were negative by RT-QLAMP for chimeric transcripts whereas GUSB was detectable. In 11 APL patients in which RT-PCR yielded equivocal breakpoint type results, RT-QLAMP assays unequivocally and accurately defined the breakpoint type (as confirmed by sequencing). Furthermore, RT-QLAMP could amplify two bcr2 transcripts with particularly extended PML exon 6 deletions not amplified by RQ-PCR. RT-QLAMP reproducible sensitivity is 10(-3) for bcr1 and bcr3 and 10(-)2 for bcr2 thus making this assay particularly attractive at diagnosis and leaving RQ-PCR for the molecular monitoring of minimal residual disease during the follow up. In conclusion, PML-RARA RT-QLAMP compared to RT-PCR or RQ-PCR is a valid improvement to perform rapid, simple and accurate molecular diagnosis of APL. PMID:25815362

  11. Simple, rapid and accurate molecular diagnosis of acute promyelocytic leukemia by loop mediated amplification technology

    PubMed Central

    Spinelli, Orietta; Rambaldi, Alessandro; Rigo, Francesca; Zanghì, Pamela; D'Agostini, Elena; Amicarelli, Giulia; Colotta, Francesco; Divona, Mariadomenica; Ciardi, Claudia; Coco, Francesco Lo; Minnucci, Giulia

    2015-01-01

    The diagnostic work-up of acute promyelocytic leukemia (APL) includes the cytogenetic demonstration of the t(15;17) translocation and/or the PML-RARA chimeric transcript by RQ-PCR or RT-PCR. This latter assays provide suitable results in 3-6 hours. We describe here two new, rapid and specific assays that detect PML-RARA transcripts, based on the RT-QLAMP (Reverse Transcription-Quenching Loop-mediated Isothermal Amplification) technology in which RNA retrotranscription and cDNA amplification are carried out in a single tube with one enzyme at one temperature, in fluorescence and real time format. A single tube triplex assay detects bcr1 and bcr3 PML-RARA transcripts along with GUS housekeeping gene. A single tube duplex assay detects bcr2 and GUSB. In 73 APL cases, these assays detected in 16 minutes bcr1, bcr2 and bcr3 transcripts. All 81 non-APL samples were negative by RT-QLAMP for chimeric transcripts whereas GUSB was detectable. In 11 APL patients in which RT-PCR yielded equivocal breakpoint type results, RT-QLAMP assays unequivocally and accurately defined the breakpoint type (as confirmed by sequencing). Furthermore, RT-QLAMP could amplify two bcr2 transcripts with particularly extended PML exon 6 deletions not amplified by RQ-PCR. RT-QLAMP reproducible sensitivity is 10−3 for bcr1 and bcr3 and 10−2 for bcr2 thus making this assay particularly attractive at diagnosis and leaving RQ-PCR for the molecular monitoring of minimal residual disease during the follow up. In conclusion, PML-RARA RT-QLAMP compared to RT-PCR or RQ-PCR is a valid improvement to perform rapid, simple and accurate molecular diagnosis of APL. PMID:25815362

  12. Surface electron density models for accurate ab initio molecular dynamics with electronic friction

    NASA Astrophysics Data System (ADS)

    Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.

    2016-06-01

    Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.

  13. PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

    NASA Astrophysics Data System (ADS)

    Sibaev, Marat; Crittenden, Deborah L.

    2016-06-01

    The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).

  14. Constant-pH Molecular Dynamics Study of Kyotorphin in an Explicit Bilayer.

    PubMed

    Magalhães, Pedro R; Machuqueiro, Miguel; Baptista, António M

    2015-05-01

    To our knowledge, we present the first constant-pH molecular dynamics study of the neuropeptide kyotorphin in the presence of an explicit lipid bilayer. The overall conformation freedom of the peptide was found to be affected by the interaction with the membrane, in accordance with previous results using different methodologies. Analysis of the interactions between the N-terminus amine group of the peptide and several lipid atoms shows that the membrane is able to stabilize both ionized and neutral forms of kyotorphin, resulting in a pKa value that is similar to the one obtained in water. This illustrates how a detailed molecular model of the membrane leads to rather different results than would be expected from simply regarding it as a low-dielectric slab. PMID:25954885

  15. Constant-pH Molecular Dynamics Study of Kyotorphin in an Explicit Bilayer

    PubMed Central

    Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.

    2015-01-01

    To our knowledge, we present the first constant-pH molecular dynamics study of the neuropeptide kyotorphin in the presence of an explicit lipid bilayer. The overall conformation freedom of the peptide was found to be affected by the interaction with the membrane, in accordance with previous results using different methodologies. Analysis of the interactions between the N-terminus amine group of the peptide and several lipid atoms shows that the membrane is able to stabilize both ionized and neutral forms of kyotorphin, resulting in a pKa value that is similar to the one obtained in water. This illustrates how a detailed molecular model of the membrane leads to rather different results than would be expected from simply regarding it as a low-dielectric slab. PMID:25954885

  16. The Importance of Accurate Atomic and Molecular Line-lists for Characterizing Exoplanetary Atmospheres

    NASA Astrophysics Data System (ADS)

    Madhusudhan, Nikku; Freedman, R.; Tennyson, J.

    2013-06-01

    Recent advancements in exoplanet observations are placing unprecedented constraints on the physical and chemical properties of exoplanetary atmospheres. Statistically significant constraints have been placed on the abundances of atomic and molecular species, elemental abundance ratios, temperature profiles, energy circulation, presence of hazes/clouds, and non-equilibrium chemistry, in several exoplanetary atmospheres, including gas giants, ice giants, as well as super-Earths, over a wide temperature range. The chemical constraints have also motivated new paradigms for classifying exoplanets and new efforts to constraint their formation conditions. Central to all interpretations of exoplanet spectra, however, is the accuracy of fundamental inputs in the models, primarily, the atomic and molecular opacities, which are derived from laboratory experiments and/or ab initio numerical calculations. In this talk, we will review the state-of-the-art in atomic and molecular line-lists as applied to studies of exoplanetary atmospheres. We will discuss examples where advances in laboratory astrophysics, experimental and computational, have addressed important problems in the area of exoplanetary atmospheres, as well as outstanding questions requiring new experiments and/or theoretical calculations. For example, recent studies are suggesting that high-temperature line-lists of hydrocarbons (CH4, C2H2, HCN, etc.), and several metal hydrides, in addition to refined line-lists of several well-studied molecules, are important to accurately interpret exoplanetary spectra. We will highlight several fundamental questions in the area that require new efforts in laboratory astrophysics. Besides their importance in interpreting observations with current instruments, the refined parameters are also critical in the assessment of future facilities for exoplanet characterization, such as JWST, GMT, etc.

  17. Molecular dynamics simulations to calculate glass transition temperature and elastic constants of novel polyethers.

    PubMed

    Sarangapani, Radhakrishnan; Reddy, Sreekantha T; Sikder, Arun K

    2015-04-01

    Molecular dynamics simulations studies are carried out on hydroxyl terminated polyethers that are useful in energetic polymeric binder applications. Energetic polymers derived from oxetanes with heterocyclic side chains with different energetic substituents are designed and simulated under the ensembles of constant particle number, pressure, temperature (NPT) and constant particle number, volume, temperature (NVT). Specific volume of different amorphous polymeric models is predicted using NPT-MD simulations as a function of temperature. Plots of specific volume versus temperature exhibited a characteristic change in slope when amorphous systems change from glassy to rubbery state. Several material properties such as Young's, shear, and bulk modulus, Poisson's ratio, etc. are predicted from equilibrated structures and established the structure-property relations among designed polymers. Energetic performance parameters of these polymers are calculated and results reveal that the performance of the designed polymers is comparable to the benchmark energetic polymers like polyNIMMO, polyAMMO and polyBAMO. Overall, it is worthy remark that this molecular simulations study on novel energetic polyethers provides a good guidance on mastering the design principles and allows us to design novel polymers of tailored properties.

  18. Partial hessian fitting for determining force constant parameters in molecular mechanics.

    PubMed

    Wang, Ruixing; Ozhgibesov, Mikhail; Hirao, Hajime

    2016-10-01

    We present a new protocol for deriving force constant parameters that are used in molecular mechanics (MM) force fields to describe the bond-stretching, angle-bending, and dihedral terms. A 3 × 3 partial matrix is chosen from the MM Hessian matrix in Cartesian coordinates according to a simple rule and made as close as possible to the corresponding partial Hessian matrix computed using quantum mechanics (QM). This partial Hessian fitting (PHF) is done analytically and thus rapidly in a least-squares sense, yielding force constant parameters as the output. We herein apply this approach to derive force constant parameters for the AMBER-type energy expression. Test calculations on several different molecules show good performance of the PHF parameter sets in terms of how well they can reproduce QM-calculated frequencies. When soft bonds are involved in the target molecule as in the case of secondary building units of metal-organic frameworks, the MM-optimized geometry sometimes deviates significantly from the QM-optimized one. We show that this problem is rectified effectively by use of a simple procedure called Katachi that modifies the equilibrium bond distances and angles in bond-stretching and angle-bending terms. © 2016 Wiley Periodicals, Inc. PMID:27497261

  19. Partial hessian fitting for determining force constant parameters in molecular mechanics.

    PubMed

    Wang, Ruixing; Ozhgibesov, Mikhail; Hirao, Hajime

    2016-10-01

    We present a new protocol for deriving force constant parameters that are used in molecular mechanics (MM) force fields to describe the bond-stretching, angle-bending, and dihedral terms. A 3 × 3 partial matrix is chosen from the MM Hessian matrix in Cartesian coordinates according to a simple rule and made as close as possible to the corresponding partial Hessian matrix computed using quantum mechanics (QM). This partial Hessian fitting (PHF) is done analytically and thus rapidly in a least-squares sense, yielding force constant parameters as the output. We herein apply this approach to derive force constant parameters for the AMBER-type energy expression. Test calculations on several different molecules show good performance of the PHF parameter sets in terms of how well they can reproduce QM-calculated frequencies. When soft bonds are involved in the target molecule as in the case of secondary building units of metal-organic frameworks, the MM-optimized geometry sometimes deviates significantly from the QM-optimized one. We show that this problem is rectified effectively by use of a simple procedure called Katachi that modifies the equilibrium bond distances and angles in bond-stretching and angle-bending terms. © 2016 Wiley Periodicals, Inc.

  20. Lattice constants of pure methane and carbon dioxide hydrates at low temperatures. Implementing quantum corrections to classical molecular dynamics studies

    NASA Astrophysics Data System (ADS)

    Costandy, Joseph; Michalis, Vasileios K.; Tsimpanogiannis, Ioannis N.; Stubos, Athanassios K.; Economou, Ioannis G.

    2016-03-01

    We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies.

  1. Molecular properties in the Tamm-Dancoff approximation: indirect nuclear spin-spin coupling constants

    NASA Astrophysics Data System (ADS)

    Cheng, Chi Y.; Ryley, Matthew S.; Peach, Michael J. G.; Tozer, David J.; Helgaker, Trygve; Teale, Andrew M.

    2015-07-01

    The Tamm-Dancoff approximation (TDA) can be applied to the computation of excitation energies using time-dependent Hartree-Fock (TD-HF) and time-dependent density-functional theory (TD-DFT). In addition to simplifying the resulting response equations, the TDA has been shown to significantly improve the calculation of triplet excitation energies in these theories, largely overcoming issues associated with triplet instabilities of the underlying reference wave functions. Here, we examine the application of the TDA to the calculation of another response property involving triplet perturbations, namely the indirect nuclear spin-spin coupling constant. Particular attention is paid to the accuracy of the triplet spin-dipole and Fermi-contact components. The application of the TDA in HF calculations leads to vastly improved results. For DFT calculations, the TDA delivers improved stability with respect to geometrical variations but does not deliver higher accuracy close to equilibrium geometries. These observations are rationalised in terms of the ground- and excited-state potential energy surfaces and, in particular, the severity of the triplet instabilities associated with each method. A notable feature of the DFT results within the TDA is their similarity across a wide range of different functionals. The uniformity of the TDA results suggests that some conventional evaluations may exploit error cancellations between approximations in the functional forms and those arising from triplet instabilities. The importance of an accurate treatment of correlation for evaluating spin-spin coupling constants is highlighted by this comparison.

  2. Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

    PubMed Central

    Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee

    2012-01-01

    Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular “linear response” model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution). PMID:23020318

  3. Accurate calculation of binding energies for molecular clusters - Assessment of different models

    NASA Astrophysics Data System (ADS)

    Friedrich, Joachim; Fiedler, Benjamin

    2016-06-01

    In this work we test different strategies to compute high-level benchmark energies for medium-sized molecular clusters. We use the incremental scheme to obtain CCSD(T)/CBS energies for our test set and carefully validate the accuracy for binding energies by statistical measures. The local errors of the incremental scheme are <1 kJ/mol. Since they are smaller than the basis set errors, we obtain higher total accuracy due to the applicability of larger basis sets. The final CCSD(T)/CBS benchmark values are ΔE = - 278.01 kJ/mol for (H2O)10, ΔE = - 221.64 kJ/mol for (HF)10, ΔE = - 45.63 kJ/mol for (CH4)10, ΔE = - 19.52 kJ/mol for (H2)20 and ΔE = - 7.38 kJ/mol for (H2)10 . Furthermore we test state-of-the-art wave-function-based and DFT methods. Our benchmark data will be very useful for critical validations of new methods. We find focal-point-methods for estimating CCSD(T)/CBS energies to be highly accurate and efficient. For foQ-i3CCSD(T)-MP2/TZ we get a mean error of 0.34 kJ/mol and a standard deviation of 0.39 kJ/mol.

  4. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    USGS Publications Warehouse

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  5. An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

    PubMed Central

    Füsti-Molnár, László; Merz, Kenneth M.

    2008-01-01

    An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

  6. A survey of factors contributing to accurate theoretical predictions of atomization energies and molecular structures

    NASA Astrophysics Data System (ADS)

    Feller, David; Peterson, Kirk A.; Dixon, David A.

    2008-11-01

    High level electronic structure predictions of thermochemical properties and molecular structure are capable of accuracy rivaling the very best experimental measurements as a result of rapid advances in hardware, software, and methodology. Despite the progress, real world limitations require practical approaches designed for handling general chemical systems that rely on composite strategies in which a single, intractable calculation is replaced by a series of smaller calculations. As typically implemented, these approaches produce a final, or "best," estimate that is constructed from one major component, fine-tuned by multiple corrections that are assumed to be additive. Though individually much smaller than the original, unmanageable computational problem, these corrections are nonetheless extremely costly. This study presents a survey of the widely varying magnitude of the most important components contributing to the atomization energies and structures of 106 small molecules. It combines large Gaussian basis sets and coupled cluster theory up to quadruple excitations for all systems. In selected cases, the effects of quintuple excitations and/or full configuration interaction were also considered. The availability of reliable experimental data for most of the molecules permits an expanded statistical analysis of the accuracy of the approach. In cases where reliable experimental information is currently unavailable, the present results are expected to provide some of the most accurate benchmark values available.

  7. Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method.

    PubMed

    Chen, Yunjie; Roux, Benoît

    2015-08-11

    A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys. 2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD-MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD-MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems. PMID:26300709

  8. Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method

    PubMed Central

    2016-01-01

    A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys.2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD–MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD–MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems. PMID:26300709

  9. NMR J-coupling constants in cisplatin derivatives studied by molecular dynamics and relativistic DFT.

    PubMed

    Sutter, Kiplangat; Truflandier, Lionel A; Autschbach, Jochen

    2011-06-01

    Solvent effects on J((195)Pt-(15)N) one-bond nuclear spin-spin coupling constants (J(PtN)) of cisplatin [cis-diamminedichloroplatinum(II)] and three cisplatin derivatives are investigated using a combination of density functional theory (DFT) based ab initio molecular dynamics (aiMD) and all-electron relativistic DFT NMR calculations employing the two-component relativistic zeroth-order regular approximation (ZORA). Good agreement with experiment is obtained when explicit solvent molecules are considered and when the computations are performed with a hybrid functional. Spin-orbit coupling causes only small effects on J(PtN) . Key factors contributing to the magnitude of coupling constants are elucidated, with the most significant being the presence of solvent as well as the quality of the density functional and basis set combination. The solvent effects are of the same magnitude as J(PtN) calculated for gas-phase geometries. However, the trends of J(PtN) among the complexes are already present in the gas phase. Results obtained with a continuum solvent model agree quite well with the aiMD results, provided that the Pt solvent-accessible radius is carefully chosen. The aiMD results support the existence of a partial hydrogen-bond-like inverse-hydration-type interaction affording a weak (1)J(Pt⋅⋅⋅H(w)) coupling between the complexes and the coordinating water molecule.

  10. Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations.

    PubMed

    Soares, Rosemberg O; Torres, Pedro H M; da Silva, Manuela L; Pascutti, Pedro G

    2016-08-01

    The active site of HIV protease (HIV-PR) is covered by two flaps. These flaps are known to be essential for the catalytic activity of the HIV-PR, but their exact conformations at the different stages of the enzymatic pathway remain subject to debate. Understanding the correct functional dynamics of the flaps might aid the development of new HIV-PR inhibitors. It is known that, the HIV-PR catalytic efficiency is pH-dependent, likely due to the influence of processes such as charge transfer and protonation/deprotonation of ionizable residues. Several Molecular Dynamics (MD) simulations have reported information about the HIV-PR flaps. However, in MD simulations the protonation of a residue is fixed and thus it is not possible to study the correlation between conformation and protonation state. To address this shortcoming, this work attempts to capture, through Constant pH Molecular Dynamics (CpHMD), the conformations of the apo, substrate-bound and inhibitor-bound HIV-PR, which differ drastically in their flap arrangements. The results show that the HIV-PR flaps conformations are defined by the protonation of the catalytic residues Asp25/Asp25' and that these residues are sensitive to pH changes. This study suggests that the catalytic aspartates can modulate the opening of the active site and substrate binding. PMID:27291071

  11. Accurate molecular structure and spectroscopic properties for nucleobases: A combined computational - microwave investigation of 2-thiouracil as a case study

    PubMed Central

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2015-01-01

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739

  12. Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

    PubMed Central

    2015-01-01

    We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The pKa values estimated with the EDS-HREX method agree well with the experimental pKa values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 pKa units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 pKa units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated pKa values. PMID:25061443

  13. A Pure-Phase Homonuclear J-Modulated HMQC Experiment with Tilted Cross-Peak Patterns for an Accurate Determination of Homonuclear Coupling Constants

    NASA Astrophysics Data System (ADS)

    Koź Miń Ski, Wiktor

    1999-11-01

    A new HMQC-based experiment is presented which allows for an efficient determination of accurate homonuclear coupling-constant values. Pure absorption lineshapes with tilted cross-peak patterns are obtained by a combination of the active-coupling-pattern tilting (ACT) scheme with J-scaling. Characteristic features include separate heteronuclear echo and antiecho acquisition with a BIRDy pulse positioned before or after the t1 period, respectively, to refocus I-spin homonuclear coupling evolution. Additionally, due to the incorporation of J-scaling the relative spacing of the S-spin chemical-shift differences and I-spin homonuclear coupling splittings in the F1 domain is largely under experimental control. The most important advantage of the proposed method is that the I-spin homonuclear coupling evolution occurs simultaneously with the evolution of the heteronuclear zero and double-quantum coherences, which exhibit a slower transverse relaxation than I-spin single-quantum coherences. The effectiveness of the new sequence is demonstrated by a determination of the 3JHN,Hα couplings in a peptide sample. Additionally, the broadband property of the new sequence is verified with a sucrose sample.

  14. The calculation of accurate 17O hyperfine coupling constants in the hydroxyl radical: A difficult problem for current quantum chemical methods

    NASA Astrophysics Data System (ADS)

    Wetmore, Stacey D.; Eriksson, Leif A.; Boyd, Russell J.

    1998-12-01

    The hyperfine coupling constants (HFCCs) in the hydroxyl radical are investigated through comparison of results obtained from a variety of quantum chemical methods. The couplings obtained from the multi-reference configuration interaction (MRCI) wave function, built upon the restricted open-shell Hartree-Fock (ROHF) reference determinant, are investigated in terms of the basis set, the configuration selection energy threshold, and the size of the reference space. Overall results which converge to the experimental couplings are obtained for hydrogen, but not for oxygen. In particular, the MRCI method shows no improvement over density functional theory (the B3LYP functional), for the calculation of Aiso(17O). On the other hand, results in excellent agreement with experiment are obtained through the use of the quadratic configuration interaction (QCISD) method based on the unrestricted HF (UHF) reference determinant with the identical basis sets. Examination of UHF and ROHF based coupled-cluster methods, CCSD and CCSD(T), indicates that once a high enough level of electron correlation is included, the oxygen HFCC is independent of the form of the reference determinant. Unlike the ROHF-CCSD method, which yields reliable results once the effects of triple excitations have been taken into account, the MRCI wave function cannot easily be adjusted to account for the inadequacies of the ROHF reference determinant in order to accurately predict 17O HFCCs.

  15. Capturing molten globule state of α-lactalbumin through constant pH molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, Nicholus; Rani, Pooja; Biswas, Parbati

    2013-03-01

    The recently developed methods of constant pH molecular dynamics directly captures the correlation between protonation and conformation to probe protein structure, function, and dynamics. In this work, we investigate the effect of pH on the conformational properties of the protein human α-lactalbumin. Constant pH simulations at both acidic and alkaline medium indicate the formation of the molten globule state, which is in accordance with the previous experimental observations (especially, in acidic medium). The size of the protein measured by its radius of gyration (RG) exhibits a marked increase in both acidic and alkaline medium, which matches with the corresponding experimentally observed value of RG found in the molten globule. The probability of native contacts is also considerably reduced at acidic and basic pH as compared to that of native structure crystallized at neutral pH. The mean fractal dimension D2 of the protein records a sharp increase in basic medium as compared to those in neutral and acidic solutions implying a significant pH induced conformational change. The mean square fluctuations of all residues of the entire protein are found to increase by several folds in both acidic and basic medium, which may be correlated with the normalized solvent accessibility of the residues indicating role of solvent accessible surface area on protein internal dynamics. The helices comprising the α-domain of the protein are moderately preserved in the acidic and alkaline pH. However, the β-sheet structures present in the β-domain are completely disrupted in both acidic as well as basic pH.

  16. Interpolation constants for calculation of transmittance and rate of dissociation of molecular oxygen in the mesosphere and lower thermosphere

    NASA Technical Reports Server (NTRS)

    Hudson, R. D.; Mahle, S. H.

    1972-01-01

    Values of band oscillator strengths and rotational line widths for the Schumann-Runge band system have been used to derive interpolation constants from which the transmittance and rate of dissociation of molecular oxygen can be calculated. These constants, valid for temperatures between 150 and 300 K and for column densities between 1 x 10 to the 17th power/cm sq and 7 x 10 to the 24th power/cm sq, cover the wavelength range 1750 and 2050A.

  17. Perspective: Tipping the scales: Search for drifting constants from molecular spectra

    SciTech Connect

    Jansen, Paul; Bethlem, Hendrick L.; Ubachs, Wim

    2014-01-07

    Transitions in atoms and molecules provide an ideal test ground for constraining or detecting a possible variation of the fundamental constants of nature. In this perspective, we review molecular species that are of specific interest in the search for a drifting proton-to-electron mass ratio μ. In particular, we outline the procedures that are used to calculate the sensitivity coefficients for transitions in these molecules and discuss current searches. These methods have led to a rate of change in μ bounded to 6 × 10{sup −14}/yr from a laboratory experiment performed in the present epoch. On a cosmological time scale, the variation is limited to |Δμ/μ| < 10{sup −5} for look-back times of 10–12× 10{sup 9} years and to |Δμ/μ| < 10{sup −7} for look-back times of 7× 10{sup 9} years. The last result, obtained from high-redshift observation of methanol, translates into μ{sup .}/μ=(1.4±1.4)×10{sup −17}/yr if a linear rate of change is assumed.

  18. Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer.

    PubMed Central

    Tu, K; Tobias, D J; Klein, M L

    1995-01-01

    We report a constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal (L alpha) phase bilayer of dipalmitoylphosphatidylcholine at 50 degrees C and 28 water molecules/lipid. We have shown that the bilayer is stable throughout the 1550-ps simulation and have demonstrated convergence of the system dimensions. Several important aspects of the bilayer structure have been investigated and compared favorably with experimental results. For example, the average positions of specific carbon atoms along the bilayer normal agree well with neutron diffraction data, and the electron density profile is in accord with x-ray diffraction results. The hydrocarbon chain deuterium order parameters agree reasonably well with NMR results for the middles of the chains, but the simulation predicts too much order at the chain ends. In spite of the deviations in the order parameters, the hydrocarbon chain packing density appears to be essentially correct, inasmuch as the area/lipid and bilayer thickness are in agreement with the most refined experimental estimates. The deuterium order parameters for the glycerol and choline groups, as well as the phosphorus chemical shift anisotropy, are in qualitative agreement with those extracted from NMR measurements. PMID:8599662

  19. Lattice constants of pure methane and carbon dioxide hydrates at low temperatures. Implementing quantum corrections to classical molecular dynamics studies.

    PubMed

    Costandy, Joseph; Michalis, Vasileios K; Tsimpanogiannis, Ioannis N; Stubos, Athanassios K; Economou, Ioannis G

    2016-03-28

    We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies. PMID:27036466

  20. Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

    NASA Astrophysics Data System (ADS)

    Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

    2016-06-01

    In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH• radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH• radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

  1. Communication: Rate coefficients of the H + CH4 → H2 + CH3 reaction from ring polymer molecular dynamics on a highly accurate potential energy surface.

    PubMed

    Meng, Qingyong; Chen, Jun; Zhang, Dong H

    2015-09-14

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.

  2. Communication: Rate coefficients of the H + CH4 → H2 + CH3 reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    NASA Astrophysics Data System (ADS)

    Meng, Qingyong; Chen, Jun; Zhang, Dong H.

    2015-09-01

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.

  3. Studies on the Vibrational and Rovibrational Energies and Vibrational Force Constants of Diatomic Molecular States Using Algebraic and Variational Methods

    NASA Astrophysics Data System (ADS)

    Sun, Weiguo; Hou, Shilin; Feng, Hao; Ren, Weiyi

    2002-09-01

    Alternative expressions for vibrational and rotational spectrum constants and energies of diatomic molecular electronic states based on perturbation theory are suggested. An algebraic method (AM) is proposed to generate a converged full vibrational spectrum from limited energy data, and a potential variational method (PVM) is suggested to produce the vibrational force constants fn and rotational spectrum constants using the perturbation formulae and the AM vibrational constants. The AM and PVM have been applied to study 10 diatomic electronic states: the X1Σ g+ and C1Π u- states of H 2; the X1Σ g+, A3Σ u+, B' 3Σ u-, and B3Π g states of N 2; the X3Σ g-, A3Σ u+, and c1Σ u- states of O 2; and the X1Σ g+ state of Br 2. Calculations show that (1) the AM Eυ max converges to the correct molecular dissociation energy; (2) the AM not only reproduce the input energies, but also generate the Eυ's of high vibrational excited states which may be difficult to obtain experimentally or theoretically; (3) the PVM vibrational force constants fn may be used to measure the relative chemical bondstrengths of different diatomic electronic states for a molecule quantitatively.

  4. Comparison of one-particle basis set extrapolation to explicitly correlated methods for the calculation of accurate quartic force fields, vibrational frequencies, and spectroscopic constants: application to H2O, N2H+, NO2+, and C2H2.

    PubMed

    Huang, Xinchuan; Valeev, Edward F; Lee, Timothy J

    2010-12-28

    One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H(2)O, N(2)H(+), NO(2)(+), and C(2)H(2) molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N(2)H(+) where it is concluded that basis set extrapolation is still preferred. The differences for H(2)O and NO(2)(+) are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C(2)H(2), however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)(R12), incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N(2)H(+) and NO(2)(+) were computed, including basis set extrapolation, core-correlation, scalar

  5. Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations.

    PubMed

    Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

    2015-03-14

    Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online. PMID:25770527

  6. Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations

    SciTech Connect

    Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

    2015-03-14

    Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10{sup 3}-10{sup 5} molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

  7. Liquid-Liquid Phase Transitions of Phosphorus via Constant-Pressure First-Principles Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Morishita, Tetsuya

    2001-09-01

    Pressure-induced phase transitions in liquid phosphorus have been studied by constant-pressure first-principles molecular dynamics simulations. By compressing a low-pressure liquid which consists of the tetrahedral P4 molecules, a structural phase transition from the molecular to polymeric liquid (a high-pressure phase) observed in the recent experiment by Katayama et al. [Nature (London) 403, 170 (2000)] was successfully realized. It is found that this transition is caused by a breakup of the tetrahedral molecules with large volume contraction. The same transition is also realized by heating. This indicates that only the polymeric liquid can stably exist at high temperature.

  8. Determination of association constant of host-guest supramolecular complex (molecular recognition of carbamazepine, antiseizure drug, with calix(4)arene).

    PubMed

    Meenakshi, C; Jayabal, P; Ramakrishnan, V

    2015-12-01

    The thermodynamic property of the host-guest, inclusion complex formed between p-t-butyl calix(4)arene which is a supramolecule, and the antiseizure drug, carbamazepine was studied. p-t-Butyl calix(4)arene has been used as a host molecule and carbamazepine as a guest molecule. Optical absorption spectral studies were carried out to investigate the molecular recognition properties of p-t-butyl calix(4)arene with carbamazepine. The stochiometry of the host-guest complexes formed and the association constant were determined. An interesting 1:2 stochiometric host-guest complex was formed. Job's continuous method of variation and Benesi-Hildebrand expression were used for the determination of binding constant and the stochiometry of the host-guest complex formed. Molecular dimension of the host molecule plays a vital role in the formation of the host-guest stochiometric complexes.

  9. Molecular Detection of Foodborne Pathogens: A Rapid and Accurate Answer to Food Safety.

    PubMed

    Mangal, Manisha; Bansal, Sangita; Sharma, Satish K; Gupta, Ram K

    2016-07-01

    Food safety is a global health concern. For the prevention and recognition of problems related to health and safety, detection of foodborne pathogen is of utmost importance at all levels of food production chain. For several decades, a lot of research has been targeted at the development of rapid methodology as reducing the time needed to complete pathogen detection tests has been the primary goal of food microbiologists. With the result, food microbiology laboratories now have a wide array of detection methods and automated technologies such as enzyme immunoassay, polymerase chain reaction, and microarrays, which can cut test times considerably. Nucleic acid amplification strategies and advances in amplicon detection methodologies have been the key factors in the progress of molecular microbiology. A comprehensive literature survey has been carried out to give an overview in the field of foodborne pathogen detection. In this paper, we describe the conventional methods, as well as recent developments in food pathogen detection, identification, and quantification, with a major emphasis on molecular detection methods.

  10. Fully Coriolis-coupled quantum studies of the H + O2 (upsilon i = 0-2, j i = 0,1) --> OH + O reaction on an accurate potential energy surface: integral cross sections and rate constants.

    PubMed

    Lin, Shi Ying; Sun, Zhigang; Guo, Hua; Zhang, Dong Hui; Honvault, Pascal; Xie, Daiqian; Lee, Soo-Y

    2008-01-31

    We present accurate quantum calculations of the integral cross section and rate constant for the H + O2 --> OH + O combustion reaction on a recently developed ab initio potential energy surface using parallelized time-dependent and Chebyshev wavepacket methods. Partial wave contributions up to J = 70 were computed with full Coriolis coupling, which enabled us to obtain the initial state-specified integral cross sections up to 2.0 eV of the collision energy and thermal rate constants up to 3000 K. The integral cross sections show a large reaction threshold due to the quantum endothermicity of the reaction, and they monotonically increase with the collision energy. As a result, the temperature dependence of the rate constant is of the Arrhenius type. In addition, it was found that reactivity is enhanced by reactant vibrational excitation. The calculated thermal rate constant shows a significant improvement over that obtained on the DMBE IV potential, but it still underestimates the experimental consensus.

  11. Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations

    NASA Astrophysics Data System (ADS)

    Hepburn, I.; Chen, W.; De Schutter, E.

    2016-08-01

    Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.

  12. Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations.

    PubMed

    Hepburn, I; Chen, W; De Schutter, E

    2016-08-01

    Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification. PMID:27497550

  13. Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations.

    PubMed

    Hepburn, I; Chen, W; De Schutter, E

    2016-08-01

    Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.

  14. A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat.

    PubMed

    Liu, Jian; Li, Dezhang; Liu, Xinzijian

    2016-07-14

    We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.

  15. A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat

    NASA Astrophysics Data System (ADS)

    Liu, Jian; Li, Dezhang; Liu, Xinzijian

    2016-07-01

    We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.

  16. A rapid and accurate method for calculation of stratospheric photolysis rates with molecular scattering

    NASA Technical Reports Server (NTRS)

    Boughner, Robert E.

    1986-01-01

    A method for calculating the photodissociation rates needed for photochemical modeling of the stratosphere, which includes the effects of molecular scattering, is described. The procedure is based on Sokolov's method of averaging functional correction. The radiation model and approximations used to calculate the radiation field are examined. The approximated diffuse fields and photolysis rates are compared with exact data. It is observed that the approximate solutions differ from the exact result by 10 percent or less at altitudes above 15 km; the photolysis rates differ from the exact rates by less than 5 percent for altitudes above 10 km and all zenith angles, and by less than 1 percent for altitudes above 15 km.

  17. Estimation of Henry's Law Constant for a Diverse Set of Organic Compounds from Molecular Structure

    EPA Science Inventory

    The SPARC (SPARC Performs Automated Reasoning in Chemistry) vapor pressure and activity coefficient models were coupled to estimate Henry’s Law Constant (HLC) in water and in hexadecane for a wide range of non-polar and polar organic compounds without modification or additional p...

  18. Predicting accurate fluorescent spectra for high molecular weight polycyclic aromatic hydrocarbons using density functional theory

    NASA Astrophysics Data System (ADS)

    Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.

    2016-10-01

    The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.

  19. The effects of molecular weight on the single lap shear creep and constant strain rate behavior of thermoplastic polyimidesulfone adhesive

    NASA Technical Reports Server (NTRS)

    Dembosky, Stanley K.; Sancaktar, Erol

    1985-01-01

    The bonded shear creep and constant strain rate behaviors of zero, one, and three percent endcapped thermoplastic polyimidesulfone adhesive were examined at room and elevated temperatures. Endcapping was accomplished by the addition of phthalic anhydrides. The primary objective was to determine the effects of molecular weight on the mechanical properties of the adhesive. Viscoelastic and nonlinear elastic constitutive equations were utilized to model the adhesive. Ludwik's and Crochet's relations were used to describe the experimental failure data. The effects of molecular weight changes on the above mentioned mechanical behavior were assessed. The viscoelastic Chase-Goldsmith and elastic nonlinear relations gave a good fit to the experimental stress strain behavior. Crochet's relations based on Maxwell and Chase-Goldsmith models were fit to delayed failure data. Ludwik's equations revealed negligible rate dependence. Ultimate stress levels and the safe levels for creep stresses were found to decrease as molecular weight was reduced.

  20. Structure of liquid phosphorus: A liquid-liquid phase transition via constant-pressure first-principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Morishita, Tetsuya

    2001-12-01

    Constant-pressure first-principles molecular dynamics simulations have been carried out to study structural phase transitions of liquid black phosphorus. By compressing the tetrahedral molecular liquid (a low-pressure phase), a structural phase transition from the molecular to polymeric liquid (a high-pressure phase) was successfully realized just as observed in the recent experiment by Katayama et al. [Nature 170 (2000) 403]. Structural properties in the polymeric liquid were investigated and it is found that the covalent p-state bonds are dominant within the first nearest neighbors of each atom. However, further compression of the polymeric liquid shows that the covalent bonding is weakened as pressure is increased. As a result, liquid phosphorus becomes similar to the simple liquid in which atoms form a close-packed structure at very high pressure.

  1. Accurate Gaussian basis sets for atomic and molecular calculations obtained from the generator coordinate method with polynomial discretization.

    PubMed

    Celeste, Ricardo; Maringolo, Milena P; Comar, Moacyr; Viana, Rommel B; Guimarães, Amanda R; Haiduke, Roberto L A; da Silva, Albérico B F

    2015-10-01

    Accurate Gaussian basis sets for atoms from H to Ba were obtained by means of the generator coordinate Hartree-Fock (GCHF) method based on a polynomial expansion to discretize the Griffin-Wheeler-Hartree-Fock equations (GWHF). The discretization of the GWHF equations in this procedure is based on a mesh of points not equally distributed in contrast with the original GCHF method. The results of atomic Hartree-Fock energies demonstrate the capability of these polynomial expansions in designing compact and accurate basis sets to be used in molecular calculations and the maximum error found when compared to numerical values is only 0.788 mHartree for indium. Some test calculations with the B3LYP exchange-correlation functional for N2, F2, CO, NO, HF, and HCN show that total energies within 1.0 to 2.4 mHartree compared to the cc-pV5Z basis sets are attained with our contracted bases with a much smaller number of polarization functions (2p1d and 2d1f for hydrogen and heavier atoms, respectively). Other molecular calculations performed here are also in very good accordance with experimental and cc-pV5Z results. The most important point to be mentioned here is that our generator coordinate basis sets required only a tiny fraction of the computational time when compared to B3LYP/cc-pV5Z calculations.

  2. Spectroscopic Constants and Vibrational Frequencies for l-C3H+ and Isotopologues from Highly-Accurate Quartic Force Fields: The Detection of l-C3H+ in the Horsehead Nebula PDR Questioned

    NASA Technical Reports Server (NTRS)

    Huang, Xinchuan; Fortenberry, Ryan Clifton; Lee, Timothy J.

    2013-01-01

    Very recently, molecular rotational transitions observed in the photon-dominated region of the Horsehead nebula have been attributed to l-C3H+. In an effort to corroborate this finding, we employed state-of-the art and proven high-accuracy quantum chemical techniques to compute spectroscopic constants for this cation and its isotopologues. Even though the B rotational constant from the fit of the observed spectrum and our computations agree to within 20 MHz, a typical level of accuracy, the D rotational constant differs by more than 40%, while the H rotational constant differs by three orders of magnitude. With the likely errors in the rotational transition energies resulting from this difference in D on the order of 1 MHz for the lowest observed transition (J = 4 yields 3) and growing as J increases, the assignment of the observed rotational lines from the Horsehead nebula to l-C3H+ is questionable.

  3. SPECTROSCOPIC CONSTANTS AND VIBRATIONAL FREQUENCIES FOR l-C{sub 3}H{sup +} AND ISOTOPOLOGUES FROM HIGHLY ACCURATE QUARTIC FORCE FIELDS: THE DETECTION OF l-C{sub 3}H{sup +} IN THE HORSEHEAD NEBULA PDR QUESTIONED

    SciTech Connect

    Huang Xinchuan; Fortenberry, Ryan C.; Lee, Timothy J.

    2013-05-10

    Very recently, molecular rotational transitions observed in the photon-dominated region of the Horsehead nebula have been attributed to l-C{sub 3}H{sup +}. In an effort to corroborate this finding, we employed state-of-the-art and proven high-accuracy quantum chemical techniques to compute spectroscopic constants for this cation and its isotopologues. Even though the B rotational constant from the fit of the observed spectrum and our computations agree to within 20 MHz, a typical level of accuracy, the D rotational constant differs by more than 40%, while the H rotational constant differs by three orders of magnitude. With the likely errors in the rotational transition energies resulting from this difference in D on the order of 1 MHz for the lowest observed transition (J = 4 {yields} 3) and growing as J increases, the assignment of the observed rotational lines from the Horsehead nebula to l-C{sub 3}H{sup +} is questionable.

  4. Beyond transition state theory: accurate description of nuclear quantum effects on the rate and equilibrium constants of chemical reactions using Feynman path integrals.

    PubMed

    Vanícek, Jirí

    2011-01-01

    Nuclear tunneling and other nuclear quantum effects have been shown to play a significant role in molecules as large as enzymes even at physiological temperatures. I discuss how these quantum phenomena can be accounted for rigorously using Feynman path integrals in calculations of the equilibrium and kinetic isotope effects as well as of the temperature dependence of the rate constant. Because these calculations are extremely computationally demanding, special attention is devoted to increasing the computational efficiency by orders of magnitude by employing efficient path integral estimators.

  5. Towards more accurate molecular dynamics calculation of thermal conductivity: Case study of GaN bulk crystals

    NASA Astrophysics Data System (ADS)

    Zhou, X. W.; Aubry, S.; Jones, R. E.; Greenstein, A.; Schelling, P. K.

    2009-03-01

    Significant differences exist among literature for thermal conductivity of various systems computed using molecular dynamics simulation. In some cases, unphysical results, for example, negative thermal conductivity, have been found. Using GaN as an example case and the direct nonequilibrium method, extensive molecular dynamics simulations and Monte Carlo analysis of the results have been carried out to quantify the uncertainty level of the molecular dynamics methods and to identify the conditions that can yield sufficiently accurate calculations of thermal conductivity. We found that the errors of the calculations are mainly due to the statistical thermal fluctuations. Extrapolating results to the limit of an infinite-size system tend to magnify the errors and occasionally lead to unphysical results. The error in bulk estimates can be reduced by performing longer time averages using properly selected systems over a range of sample lengths. If the errors in the conductivity estimates associated with each of the sample lengths are kept below a certain threshold, the likelihood of obtaining unphysical bulk values becomes insignificant. Using a Monte Carlo approach developed here, we have determined the probability distributions for the bulk thermal conductivities obtained using the direct method. We also have observed a nonlinear effect that can become a source of significant errors. For the extremely accurate results presented here, we predict a [0001] GaN thermal conductivity of 185W/Km at 300 K, 102W/Km at 500 K, and 74W/Km at 800 K. Using the insights obtained in the work, we have achieved a corresponding error level (standard deviation) for the bulk (infinite sample length) GaN thermal conductivity of less than 10W/Km , 5W/Km , and 15W/Km at 300 K, 500 K, and 800 K, respectively.

  6. Development of an accurate molecular mechanics model for buckling behavior of multi-walled carbon nanotubes under axial compression.

    PubMed

    Safaei, B; Naseradinmousavi, P; Rahmani, A

    2016-04-01

    In the present paper, an analytical solution based on a molecular mechanics model is developed to evaluate the elastic critical axial buckling strain of chiral multi-walled carbon nanotubes (MWCNTs). To this end, the total potential energy of the system is calculated with the consideration of the both bond stretching and bond angular variations. Density functional theory (DFT) in the form of generalized gradient approximation (GGA) is implemented to evaluate force constants used in the molecular mechanics model. After that, based on the principle of molecular mechanics, explicit expressions are proposed to obtain elastic surface Young's modulus and Poisson's ratio of the single-walled carbon nanotubes corresponding to different types of chirality. Selected numerical results are presented to indicate the influence of the type of chirality, tube diameter, and number of tube walls in detailed. An excellent agreement is found between the present numerical results and those found in the literature which confirms the validity as well as the accuracy of the present closed-form solution. It is found that the value of critical axial buckling strain exhibit significant dependency on the type of chirality and number of tube walls.

  7. Molecular Dynamics Evaluation of Dielectric-Constant Mixing Rules for H2O-CO2 at Geologic Conditions

    PubMed Central

    Mountain, Raymond D.; Harvey, Allan H.

    2015-01-01

    Modeling of mineral reaction equilibria and aqueous-phase speciation of C-O-H fluids requires the dielectric constant of the fluid mixture, which is not known from experiment and is typically estimated by some rule for mixing pure-component values. In order to evaluate different proposed mixing rules, we use molecular dynamics simulation to calculate the dielectric constant of a model H2O–CO2 mixture at temperatures of 700 K and 1000 K at pressures up to 3 GPa. We find that theoretically based mixing rules that depend on combining the molar polarizations of the pure fluids systematically overestimate the dielectric constant of the mixture, as would be expected for mixtures of nonpolar and strongly polar components. The commonly used semiempirical mixing rule due to Looyenga works well for this system at the lower pressures studied, but somewhat underestimates the dielectric constant at higher pressures and densities, especially at the water-rich end of the composition range. PMID:26664009

  8. Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation.

    PubMed

    Swails, Jason M; York, Darrin M; Roitberg, Adrian E

    2014-03-11

    By utilizing Graphics Processing Units, we show that constant pH molecular dynamics simulations (CpHMD) run in Generalized Born (GB) implicit solvent for long time scales can yield poor pKa predictions as a result of sampling unrealistic conformations. To address this shortcoming, we present a method for performing constant pH molecular dynamics simulations (CpHMD) in explicit solvent using a discrete protonation state model. The method involves standard molecular dynamics (MD) being propagated in explicit solvent followed by protonation state changes being attempted in GB implicit solvent at fixed intervals. Replica exchange along the pH-dimension (pH-REMD) helps to obtain acceptable titration behavior with the proposed method. We analyzed the effects of various parameters and settings on the titration behavior of CpHMD and pH-REMD in explicit solvent, including the size of the simulation unit cell and the length of the relaxation dynamics following protonation state changes. We tested the method with the amino acid model compounds, a small pentapeptide with two titratable sites, and hen egg white lysozyme (HEWL). The proposed method yields superior predicted pKa values for HEWL over hundreds of nanoseconds of simulation relative to corresponding predicted values from simulations run in implicit solvent.

  9. The protective effect of a constant magnetic field. [reduction of molecular cell pathology

    NASA Technical Reports Server (NTRS)

    Sosunov, A. V.; Tripuzov, A. N.

    1974-01-01

    The protective effect of a constant magnetic field sharply reduced spontaneous lysis of E. coli cells when subjected to ultraviolet radiation. A protective effect of a CMF was found in a study of tissue cultures of normally growing cells (kidney epithelium) and cancer cells (cells from a cancer of the larynx). The protective effect of a CMF is also seen in a combined exposure of tissue cultures to X-rays and CMF energy (strength of the CMF was 2000 oersteds with a gradient of 500 oersteds/cm). The data obtained are of interest to experimental oncology (development of new methods of treating malignant tumors).

  10. Linear transformation of anharmonic molecular force constants between normal and Cartesian coordinates.

    PubMed

    Mackie, Cameron J; Candian, Alessandra; Huang, Xinchuan; Lee, Timothy J; Tielens, Alexander G G M

    2015-06-28

    A full derivation of the analytic transformation of the quadratic, cubic, and quartic force constants from normal coordinates to Cartesian coordinates is given. Previous attempts at this transformation have resulted in non-linear transformations; however, for the first time, a simple linear transformation is presented here. Two different approaches have been formulated and implemented, one of which does not require prior knowledge of the translation-rotation eigenvectors from diagonalization of the Hessian matrix. The validity of this method is tested using two molecules H2O and c-C3H2D(+). PMID:26133410

  11. Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC

    NASA Astrophysics Data System (ADS)

    Lee, Hsing; Darden, Thomas; Pedersen, Lee

    1995-09-01

    Long molecular dynamics (MD) simulations for two crystal RNA dinucleotides ApU (2.0 ns) and GpC (1.5 ns) were performed, starting from the crystallographic positions of all heavy atoms in the crystals. By employing the particle-mesh-Ewald algorithm [Darden et al., J. Chem. Phys. 98 (1993) 10089] to accommodate the long-range Coulomb interactions, highly accurate MD structures were obtained for both crystals. The instantaneous root-mean-square positional deviations of the heavy atoms equilibrate at approximately 0.4 Å for both systems, while the experimental and calculated temperature factors are comparable in size. These results describe the first successful crystal MD simulation of RNA molecules.

  12. L-DNA molecular beacon: a safe, stable, and accurate intracellular nano-thermometer for temperature sensing in living cells.

    PubMed

    Ke, Guoliang; Wang, Chunming; Ge, Yun; Zheng, Nanfeng; Zhu, Zhi; Yang, Chaoyong James

    2012-11-21

    Noninvasive and accurate measurement of intracellular temperature is of great significance in biology and medicine. This paper describes a safe, stable, and accurate intracellular nano-thermometer based on an L-DNA molecular beacon (L-MB), a dual-labeled hairpin oligonucleotide built from the optical isomer of naturally occurring d-DNA. Relying on the temperature-responsive hairpin structure and the FRET signaling mechanism of MBs, the fluorescence of L-MBs is quenched below the melting temperature and enhanced with increasing temperature. Because of the excellent reversibility and tunable response range, L-MBs are very suitable for temperature sensing. More importantly, the non-natural L-DNA backbone prevents the L-MBs from binding to cellular nucleic acids and proteins as well as from being digested by nucleases inside the cells, thus ensuring excellent stability and accuracy of the nano-thermometer in a complex cellular environment. The L-MB nano-thermometer was used for the photothermal study of Pd nanosheets in living cells, establishing the nano-thermometer as a useful tool for intracellular temperature measurement.

  13. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    SciTech Connect

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-28

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.

  14. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    NASA Astrophysics Data System (ADS)

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-01

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.

  15. Extending the molecular size in accurate quantum-chemical calculations: the equilibrium structure and spectroscopic properties of uracil.

    PubMed

    Puzzarini, Cristina; Barone, Vincenzo

    2011-04-21

    The equilibrium structure of uracil has been investigated using both theoretical and experimental data. With respect to the former, quantum-chemical calculations at the coupled-cluster level in conjunction with a triple-zeta basis set have been carried out. Extrapolation to the basis set limit, performed employing the second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections have also been considered. Based on the available rotational constants for various isotopic species together with corresponding computed vibrational corrections, the semi-experimental equilibrium structure of uracil has been determined for the first time. Theoretical and semi-experimental structures have been found in remarkably good agreement, thus pointing out the limitations of previous experimental determinations. Molecular and spectroscopic properties of uracil have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the revision of the dipole moment. On the whole, it has been proved that the computational procedure presented is able to provide parameters with the proper accuracy to support experimental investigations of large molecules of biological interest.

  16. Accurate path integral molecular dynamics simulation of ab-initio water at near-zero added cost

    NASA Astrophysics Data System (ADS)

    Elton, Daniel; Fritz, Michelle; Soler, José; Fernandez-Serra, Marivi

    It is now established that nuclear quantum motion plays an important role in determining water's structure and dynamics. These effects are important to consider when evaluating DFT functionals and attempting to develop better ones for water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads, which is typically 32. Here we introduce a method whereby PIMD can be incorporated into a DFT molecular dynamics simulation at virtually zero cost. The method is based on the cluster (many body) expansion of the energy. We first subtract the DFT monomer energies, using a custom DFT-based monomer potential energy surface. The evolution of the PIMD beads is then performed using only the more-accurate Partridge-Schwenke monomer energy surface. The DFT calculations are done using the centroid positions. Various bead thermostats can be employed to speed up the sampling of the quantum ensemble. The method bears some resemblance to multiple timestep algorithms and other schemes used to speed up PIMD with classical force fields. We show that our method correctly captures some of key effects of nuclear quantum motion on both the structure and dynamics of water. We acknowledge support from DOE Award No. DE-FG02-09ER16052 (D.E.) and DOE Early Career Award No. DE-SC0003871 (M.V.F.S.).

  17. Improved constraints on possible variation of physical constants from H i 21-cm and molecular QSO absorption lines

    NASA Astrophysics Data System (ADS)

    Murphy, M. T.; Webb, J. K.; Flambaum, V. V.; Drinkwater, M. J.; Combes, F.; Wiklind, T.

    2001-11-01

    Quasar (QSO) absorption spectra provide an extremely useful probe of possible cosmological variation in various physical constants. Comparison of Hi 21-cm absorption with corresponding molecular (rotational) absorption spectra allows us to constrain variation in [formmu2]y≡α2gp, where α is the fine-structure constant and gp is the proton g-factor. We analyse spectra of two QSOs, PKS 1413+135 and TXS 0218+357, and derive values of [formmu3]Δy/y at absorption redshifts of [formmu4]z=0.2467 and 0.6847 by simultaneous fitting of the Hi 21-cm and molecular lines. We find [formmu5]Δy/y=(-0.20+/-0.44)×10-5 and [formmu6]Δy/y=(-0.16+/-0.54)×10-5 respectively, indicating an insignificantly smaller y in the past. We compare our results with other constraints from the same two QSOs given recently by Drinkwater et al. and Carilli et al., and with our recent optical constraints, which indicated a smaller α at higher redshifts.

  18. ESTIMATION OF HYDROLYSIS RATE CONSTANTS OF CARBOXYLIC ACID ESTER AND PHOSPHATE ESTER COMPOUNDS IN AQUEOUS SYSTEMS FROM MOLECULAR STRUCTURE BY SPARC

    EPA Science Inventory

    SPARC (SPARC Performs Automated Reasoning in Chemistry) chemical reactivity models were extended to calculate hydrolysis rate constants for carboxylic acid ester and phosphate ester compounds in aqueous non- aqueous and systems strictly from molecular structure. The energy diffe...

  19. Rate Constant Change of Photo Reaction of Bacteriorhodopsin Observed in Trimeric Molecular System.

    PubMed

    Tsujiuchi, Yutaka; Masumoto, Hiroshi; Goto, Takashi

    2016-04-01

    To elucidate the time evolution of photo reaction of bacteriorhodopsin in glycerol mixed purple membrane at around 196 K under irradiation by red light, a kinetic model was constructed. The change of absorption with irradiation at times of 560 nm and 412 nm was analyzed for the purpose of determining reaction rates of photo reaction of bacteriorhodopsin and its product M intermediate. In this study it is shown that reaction rates of conversion from bacteriorhodopsin to the M intermediate can be explained by a set of linear differential equations. This model analysis concludes that bacteriorhodopsin in which constitutes a trimer unit with other two bacteriorhodopsin molecules changes into M intermediates in the 1.73 of reaction rate, in the initial step, and according to the number of M intermediate in a trimer unit, from three to one, the reaction rate of bacteriorhodopsin into M intermediates smaller as 1.73, 0.80, 0.19 which caused by influence of inter-molecular interaction between bacteriorhodopsin.

  20. Rate Constant Change of Photo Reaction of Bacteriorhodopsin Observed in Trimeric Molecular System.

    PubMed

    Tsujiuchi, Yutaka; Masumoto, Hiroshi; Goto, Takashi

    2016-04-01

    To elucidate the time evolution of photo reaction of bacteriorhodopsin in glycerol mixed purple membrane at around 196 K under irradiation by red light, a kinetic model was constructed. The change of absorption with irradiation at times of 560 nm and 412 nm was analyzed for the purpose of determining reaction rates of photo reaction of bacteriorhodopsin and its product M intermediate. In this study it is shown that reaction rates of conversion from bacteriorhodopsin to the M intermediate can be explained by a set of linear differential equations. This model analysis concludes that bacteriorhodopsin in which constitutes a trimer unit with other two bacteriorhodopsin molecules changes into M intermediates in the 1.73 of reaction rate, in the initial step, and according to the number of M intermediate in a trimer unit, from three to one, the reaction rate of bacteriorhodopsin into M intermediates smaller as 1.73, 0.80, 0.19 which caused by influence of inter-molecular interaction between bacteriorhodopsin. PMID:27451646

  1. The Effect of Approximating Some Molecular Integrals in Coupled-Cluster Calculations: Fundamental Frequencies and Rovibrational Spectroscopic Constants of Cyclopropenylidene

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.

    2005-01-01

    The singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations, denoted CCSD(T), has been used, in conjunction with approximate integral techniques, to compute highly accurate rovibrational spectroscopic constants of cyclopropenylidene, C3H2. The approximate integral technique was proposed in 1994 by Rendell and Lee in order to avoid disk storage and input/output bottlenecks, and today it will also significantly aid in the development of algorithms for distributed memory, massively parallel computer architectures. It is shown in this study that use of approximate integrals does not impact the accuracy of CCSD(T) calculations. In addition, the most accurate spectroscopic data yet for C3H2 is presented based on a CCSD(T)/cc-pVQZ quartic force field that is modified to include the effects of core-valence electron correlation. Cyclopropenylidene is of great astronomical and astrobiological interest because it is the smallest aromatic ringed compound to be positively identified in the interstellar medium, and is thus involved in the prebiotic processing of carbon and hydrogen. The singles and doubles coupled-cluster method that includes a perturbational estimate of

  2. A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes.

    PubMed

    Ovchinnikov, Victor; Nam, Kwangho; Karplus, Martin

    2016-08-25

    A method is developed to obtain simultaneously free energy profiles and diffusion constants from restrained molecular simulations in diffusive systems. The method is based on low-order expansions of the free energy and diffusivity as functions of the reaction coordinate. These expansions lead to simple analytical relationships between simulation statistics and model parameters. The method is tested on 1D and 2D model systems; its accuracy is found to be comparable to or better than that of the existing alternatives, which are briefly discussed. An important aspect of the method is that the free energy is constructed by integrating its derivatives, which can be computed without need for overlapping sampling windows. The implementation of the method in any molecular simulation program that supports external umbrella potentials (e.g., CHARMM) requires modification of only a few lines of code. As a demonstration of its applicability to realistic biomolecular systems, the method is applied to model the α-helix ↔ β-sheet transition in a 16-residue peptide in implicit solvent, with the reaction coordinate provided by the string method. Possible modifications of the method are briefly discussed; they include generalization to multidimensional reaction coordinates [in the spirit of the model of Ermak and McCammon (Ermak, D. L.; McCammon, J. A. J. Chem. Phys. 1978, 69, 1352-1360)], a higher-order expansion of the free energy surface, applicability in nonequilibrium systems, and a simple test for Markovianity. In view of the small overhead of the method relative to standard umbrella sampling, we suggest its routine application in the cases where umbrella potential simulations are appropriate.

  3. An accurate metalloprotein-specific scoring function and molecular docking program devised by a dynamic sampling and iteration optimization strategy.

    PubMed

    Bai, Fang; Liao, Sha; Gu, Junfeng; Jiang, Hualiang; Wang, Xicheng; Li, Honglin

    2015-04-27

    Metalloproteins, particularly zinc metalloproteins, are promising therapeutic targets, and recent efforts have focused on the identification of potent and selective inhibitors of these proteins. However, the ability of current drug discovery and design technologies, such as molecular docking and molecular dynamics simulations, to probe metal-ligand interactions remains limited because of their complicated coordination geometries and rough treatment in current force fields. Herein we introduce a robust, multiobjective optimization algorithm-driven metalloprotein-specific docking program named MpSDock, which runs on a scheme similar to consensus scoring consisting of a force-field-based scoring function and a knowledge-based scoring function. For this purpose, in this study, an effective knowledge-based zinc metalloprotein-specific scoring function based on the inverse Boltzmann law was designed and optimized using a dynamic sampling and iteration optimization strategy. This optimization strategy can dynamically sample and regenerate decoy poses used in each iteration step of refining the scoring function, thus dramatically improving both the effectiveness of the exploration of the binding conformational space and the sensitivity of the ranking of the native binding poses. To validate the zinc metalloprotein-specific scoring function and its special built-in docking program, denoted MpSDockZn, an extensive comparison was performed against six universal, popular docking programs: Glide XP mode, Glide SP mode, Gold, AutoDock, AutoDock4Zn, and EADock DSS. The zinc metalloprotein-specific knowledge-based scoring function exhibited prominent performance in accurately describing the geometries and interactions of the coordination bonds between the zinc ions and chelating agents of the ligands. In addition, MpSDockZn had a competitive ability to sample and identify native binding poses with a higher success rate than the other six docking programs.

  4. Accurate Treatment of Electrostatics during Molecular Adsorption in Nanoporous Crystals without Assigning Point Charges to Framework Atoms

    SciTech Connect

    Watanabe, T; Manz, TA; Sholl, DS

    2011-03-24

    Molecular simulations have become an important complement to experiments for studying gas adsorption and separation in crystalline nanoporous materials. Conventionally, these simulations use force fields that model adsorbate-pore interactions by assigning point charges to the atoms of the adsorbent. The assignment of framework charges always introduces ambiguity because there are many different choices for defining point charges, even when the true electron density of a material is known. We show how to completely avoid such ambiguity by using the electrostatic potential energy surface (EPES) calculated from plane wave density functional theory (DFT). We illustrate this approach by simulating CO(2) adsorption in four metal-organic frameworks (MOFs): IRMOF-1, ZIE-8, ZIE-90, and Zn(nicotinate)(2). The resulting CO(2) adsorption isotherms are insensitive to the exchange-correlation functional used in the DFT calculation of the EPES but are sensitive to changes in the crystal structure and lattice parameters. Isotherms computed from the DFT EPES are compared to those computed from several point charge models. This comparison makes possible, for the first time, an unbiased assessment of the accuracy of these point charge models for describing adsorption in MOFs. We find an unusually high Henry's constant (109 mmol/g.bar) and intermediate isosteric heat of adsorption (34.9 kJ/mol) for Zn(nicotinate)(2), which makes it a potentially attractive mateiial for CO(2) adsorption applications.

  5. Accurate Treatment of Electrostatics during Molecular Adsorption in Nanoporous Crystals without Assigning Point Charges to Framework Atoms

    SciTech Connect

    Watanabe, Taku; Manz, Thomas A.; Sholl, David S.

    2011-02-28

    Molecular simulations have become an important complement to experiments for studying gas adsorption and separation in crystalline nanoporous materials. Conventionally, these simulations use force fields that model adsorbate-pore interactions by assigning point charges to the atoms of the adsorbent. The assignment of framework charges always introduces ambiguity because there are many different choices for defining point charges, even when the true electron density of a material is known. We show how to completely avoid such ambiguity by using the electrostatic potential energy surface (EPES) calculated from plane wave density functional theory (DFT). We illustrate this approach by simulating CO2 adsorption in four metal-organic frameworks (MOFs): IRMOF-1, ZIF-8, ZIF-90, and Zn(nicotinate)2. The resulting CO2 adsorption isotherms are insensitive to the exchange-correlation functional used in the DFT calculation of the EPES but are sensitive to changes in the crystal structure and lattice parameters. Isotherms computed from the DFT EPES are compared to those computed from several point charge models. This comparison makes possible, for the first time, an unbiased assessment of the accuracy of these point charge models for describing adsorption in MOFs. We find an unusually high Henry’s constant (109 mmol/g·bar) and intermediate isosteric heat of adsorption (34.9 kJ/mol) for Zn(nicotinate)2, which makes it a potentially attractive material for CO2 adsorption applications.

  6. Calculations of hyperfine coupling constant of copper(II) in aqueous environment. Finite temperature molecular dynamics and relativistic effects.

    PubMed

    Malček, Michal; Bučinský, Lukáš; Valko, Marián; Biskupič, Stanislav

    2015-09-01

    The presented paper is focused on the calculation of hyperfine coupling constants (HFCC) of Cu (2+) ion in water environment. To simulate the conditions of the electron paramagnetic resonance (EPR) experiment in aqueous phase, molecular dynamics using the density functional theory (DFT) was employed. In total three different functionals (BLYP, B3LYP, M06) were employed for studying their suitability in describing coordination of Cu (2+) by water molecules. The system of our interest was composed of one Cu (2+) cation surrounded by a selected number (between thirty and fifty) of water molecules. Besides the non-relativistic HFCCs (Fermi contact terms) of Cu (2+) also the four-component relativistic HFCC calculations are presented. The importance of the proper evaluation of HFCCs, the inclusion of spin-orbit term, for Cu (2+) containing systems (Neese, J. Chem. Phys. 118, 3939 2003; Almeida et al., Chem. Phys. 332, 176 2007) is confirmed at the relativistic four-component level of theory.

  7. Nonlinear Optical Properties of Fluorescent Dyes Allow for Accurate Determination of Their Molecular Orientations in Phospholipid Membranes.

    PubMed

    Timr, Štěpán; Brabec, Jiří; Bondar, Alexey; Ryba, Tomáš; Železný, Miloš; Lazar, Josef; Jungwirth, Pavel

    2015-07-30

    Several methods based on single- and two-photon fluorescence detected linear dichroism have recently been used to determine the orientational distributions of fluorescent dyes in lipid membranes. However, these determinations relied on simplified descriptions of nonlinear anisotropic properties of the dye molecules, using a transition dipole-moment-like vector instead of an absorptivity tensor. To investigate the validity of the vector approximation, we have now carried out a combination of computer simulations and polarization microscopy experiments on two representative fluorescent dyes (DiI and F2N12S) embedded in aqueous phosphatidylcholine bilayers. Our results indicate that a simplified vector-like treatment of the two-photon transition tensor is applicable for molecular geometries sampled in the membrane at ambient conditions. Furthermore, our results allow evaluation of several distinct polarization microscopy techniques. In combination, our results point to a robust and accurate experimental and computational treatment of orientational distributions of DiI, F2N12S, and related dyes (including Cy3, Cy5, and others), with implications to monitoring physiologically relevant processes in cellular membranes in a novel way.

  8. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

    PubMed Central

    Flynn, Jullien M; Brown, Emily A; Chain, Frédéric J J; MacIsaac, Hugh J; Cristescu, Melania E

    2015-01-01

    Metabarcoding has the potential to become a rapid, sensitive, and effective approach for identifying species in complex environmental samples. Accurate molecular identification of species depends on the ability to generate operational taxonomic units (OTUs) that correspond to biological species. Due to the sometimes enormous estimates of biodiversity using this method, there is a great need to test the efficacy of data analysis methods used to derive OTUs. Here, we evaluate the performance of various methods for clustering length variable 18S amplicons from complex samples into OTUs using a mock community and a natural community of zooplankton species. We compare analytic procedures consisting of a combination of (1) stringent and relaxed data filtering, (2) singleton sequences included and removed, (3) three commonly used clustering algorithms (mothur, UCLUST, and UPARSE), and (4) three methods of treating alignment gaps when calculating sequence divergence. Depending on the combination of methods used, the number of OTUs varied by nearly two orders of magnitude for the mock community (60–5068 OTUs) and three orders of magnitude for the natural community (22–22191 OTUs). The use of relaxed filtering and the inclusion of singletons greatly inflated OTU numbers without increasing the ability to recover species. Our results also suggest that the method used to treat gaps when calculating sequence divergence can have a great impact on the number of OTUs. Our findings are particularly relevant to studies that cover taxonomically diverse species and employ markers such as rRNA genes in which length variation is extensive. PMID:26078860

  9. Absorption spectroscopy of the rubidium dimer in an overheated vapor: An accurate check of molecular structure and dynamics

    SciTech Connect

    Beuc, R.; Movre, M.; Horvatic, V.; Vadla, C.; Dulieu, O.; Aymar, M.

    2007-03-15

    Experimental studies of the absorption spectrum of the Rb{sub 2} dimer are performed in the 600-1100 nm wavelength range for temperatures between 615 and 745 K. The reduced absorption coefficient is measured by spatially resolved white light absorption in overheated rubidium vapor with a radial temperature gradient, which enables simultaneous measurements at different temperatures. Semiclassical and quantum spectral simulations are obtained by taking into account all possible transitions involving the potential curves stemming from the 5 {sup 2}S+5 {sup 2}S and 5 {sup 2}S+5 {sup 2}P asymptotes. The most accurate experimental potential curves are used where available, and newly calculated potential curves and transition dipole moments otherwise. The overall consistency of the theoretical model with the experimental interpretation is obtained only if the radial dependence of both the calculated transition dipole moments and the spin-orbit coupling is taken into account. This highlights the low-resolution absorption spectroscopy as a valuable tool for checking the accuracy of molecular electronic structure calculations.

  10. Molecular dynamics and analytical Langevin equation approach for the self-diffusion constant of an anisotropic fluid.

    PubMed

    Colmenares, Pedro J; López, Floralba; Olivares-Rivas, Wilmer

    2009-12-01

    We carried out a molecular-dynamics (MD) study of the self-diffusion tensor of a Lennard-Jones-type fluid, confined in a slit pore with attractive walls. We developed Bayesian equations, which modify the virtual layer sampling method proposed by Liu, Harder, and Berne (LHB) [P. Liu, E. Harder, and B. J. Berne, J. Phys. Chem. B 108, 6595 (2004)]. Additionally, we obtained an analytical solution for the corresponding nonhomogeneous Langevin equation. The expressions found for the mean-squared displacement in the layers contain naturally a modification due to the mean force in the transverse component in terms of the anisotropic diffusion constants and mean exit time. Instead of running a time consuming dual MD-Langevin simulation dynamics, as proposed by LHB, our expression was used to fit the MD data in the entire survival time interval not only for the parallel but also for the perpendicular direction. The only fitting parameter was the diffusion constant in each layer. PMID:20365134

  11. Molecular dynamics and analytical Langevin equation approach for the self-diffusion constant of an anisotropic fluid

    NASA Astrophysics Data System (ADS)

    Colmenares, Pedro J.; López, Floralba; Olivares-Rivas, Wilmer

    2009-12-01

    We carried out a molecular-dynamics (MD) study of the self-diffusion tensor of a Lennard-Jones-type fluid, confined in a slit pore with attractive walls. We developed Bayesian equations, which modify the virtual layer sampling method proposed by Liu, Harder, and Berne (LHB) [P. Liu, E. Harder, and B. J. Berne, J. Phys. Chem. B 108, 6595 (2004)]. Additionally, we obtained an analytical solution for the corresponding nonhomogeneous Langevin equation. The expressions found for the mean-squared displacement in the layers contain naturally a modification due to the mean force in the transverse component in terms of the anisotropic diffusion constants and mean exit time. Instead of running a time consuming dual MD-Langevin simulation dynamics, as proposed by LHB, our expression was used to fit the MD data in the entire survival time interval not only for the parallel but also for the perpendicular direction. The only fitting parameter was the diffusion constant in each layer.

  12. Molecular dynamics and analytical Langevin equation approach for the self-diffusion constant of an anisotropic fluid.

    PubMed

    Colmenares, Pedro J; López, Floralba; Olivares-Rivas, Wilmer

    2009-12-01

    We carried out a molecular-dynamics (MD) study of the self-diffusion tensor of a Lennard-Jones-type fluid, confined in a slit pore with attractive walls. We developed Bayesian equations, which modify the virtual layer sampling method proposed by Liu, Harder, and Berne (LHB) [P. Liu, E. Harder, and B. J. Berne, J. Phys. Chem. B 108, 6595 (2004)]. Additionally, we obtained an analytical solution for the corresponding nonhomogeneous Langevin equation. The expressions found for the mean-squared displacement in the layers contain naturally a modification due to the mean force in the transverse component in terms of the anisotropic diffusion constants and mean exit time. Instead of running a time consuming dual MD-Langevin simulation dynamics, as proposed by LHB, our expression was used to fit the MD data in the entire survival time interval not only for the parallel but also for the perpendicular direction. The only fitting parameter was the diffusion constant in each layer.

  13. [Effect of low molecular weight organic acids on Pb2+ adsorption and desorption by constant charge soil colloids].

    PubMed

    Yang, Yati; Wang, Xudong; Zhang, Yiping; Qu, Aihua

    2003-11-01

    The isothermal curves of Pb2+ adsorption-desorption by soil colloids followed Freundlich and Langmuir equation. The adsorption constant Ka showed the trend of old manured loessal soil > yellow loessal soil > dark cultivated loessal soil > yellow cinamon soil, which was consistent with surface charge density sigma 0, an indicator of the strength of Pb2+ adsorption by each soil colloid. Low molecular-weight organic acids (LMWOAs) made Pb2+ adsorbed amount decreased and adsorption affinity increased, and the effect of citric acid was larger than that of oxalic acid. The constant Kd of residual Pb2+ adsorption after desorption showed the trend of old manured loessal soil > yellow cinamon soil > dark cultivated loessal soil > yellow loessal soil, which reflected the adsorption strength of residual Pb2+ after desorption, and was related to the contents of organic matter and free ferric oxide. The isothermal curves of Pb2+ desorption from soil colloids were obvious higher than those of Pb2+ adsorption. In NaNO3 and oxalic acid background solution, the isothermal curves of Pb2+ adsorption were far away from those of Pb2+ desorption, showing that the hysteretic degree between adsorption and desorption was very large. The isothermal curves of Pb2+ desorption from soil colloids were closed to those of Pb2+ adsorption in citric acid background solution, which showed that the Pb adsorption and desorption was reversible.

  14. Prediction of the dissociation constant pKa of organic acids from local molecular parameters of their electronic ground state.

    PubMed

    Yu, Haiying; Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit

    2011-09-26

    A quantum chemical method has been developed to estimate the dissociation constant pK(a) of organic acids from their neutral molecular structures by employing electronic structure properties. The data set covers 219 phenols (including 29 phenols with intramolecular H-bonding), 150 aromatic carboxylic acids, 190 aliphatic carboxylic acids, and 138 alcohols, with pK(a) varying by 16 units (0.38-16.80). Optimized ground-state geometries employing the semiempirical AM1 Hamiltonian have been used to quantify the site-specific molecular readiness to donate or accept electron charge in terms of both charge-associated energies and energy-associated charges, augmented by an ortho substitution indicator for aromatic compounds. The resultant regression models yield squared correlation coefficients (r(2)) from 0.82 to 0.90 and root-mean-square errors (rms) from 0.39 to 0.70 pK(a) units, corresponding to an overall (subset-weighted) r(2) of 0.86. Simulated external validation, leave-10%-out cross-validation and target value scrambling demonstrate the statistical robustness and prediction power of the derived model suite. The low intercorrelation with prediction errors from the commercial ACD package provides opportunity for a consensus model approach, offering a pragmatic way for further increasing the confidence in prediction significantly. Interestingly, inclusion of calculated free energies of aqueous solvation does not improve the prediction performance, probably because of the limited precision provided by available continuum-solvation models.

  15. A path integral molecular dynamics study of the hyperfine coupling constants of the muoniated and hydrogenated acetone radicals

    NASA Astrophysics Data System (ADS)

    Oba, Yuki; Kawatsu, Tsutomu; Tachikawa, Masanori

    2016-08-01

    The on-the-fly ab initio density functional path integral molecular dynamics (PIMD) simulations, which can account for both the nuclear quantum effect and thermal effect, were carried out to evaluate the structures and "reduced" isotropic hyperfine coupling constants (HFCCs) for muoniated and hydrogenated acetone radicals (2-muoxy-2-propyl and 2-hydoxy-2-propyl) in vacuo. The reduced HFCC value from a simple geometry optimization calculation without both the nuclear quantum effect and thermal effect is -8.18 MHz, and that by standard ab initio molecular dynamics simulation with only the thermal effect and without the nuclear quantum effect is 0.33 MHz at 300 K, where these two methods cannot distinguish the difference between muoniated and hydrogenated acetone radicals. In contrast, the reduced HFCC value of the muoniated acetone radical by our PIMD simulation is 32.1 MHz, which is about 8 times larger than that for the hydrogenated radical of 3.97 MHz with the same level of calculation. We have found that the HFCC values are highly correlated with the local molecular structures; especially, the Mu—O bond length in the muoniated acetone radical is elongated due to the large nuclear quantum effect of the muon, which makes the expectation value of the HFCC larger. Although our PIMD result calculated in vacuo is about 4 times larger than the measured experimental value in aqueous solvent, the ratio of these HFCC values between muoniated and hydrogenated acetone radicals in vacuo is in reasonable agreement with the ratio of the experimental values in aqueous solvent (8.56 MHz and 0.9 MHz); the explicit presence of solvent molecules has a major effect on decreasing the reduced muon HFCC of in vacuo calculations for the quantitative reproduction.

  16. Accurate molecular structure and spectroscopic properties of nucleobases: a combined computational-microwave investigation of 2-thiouracil as a case study.

    PubMed

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L

    2013-10-21

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier transform microwave spectrometers. The joint experimental-computational study allowed us to determine the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.

  17. Finite-Perturbation Intermediate - Neglect - of - Differential - Overlap Molecular Orbital Calculations of Nuclear Magnetic Resonance Spin-Spin Coupling Constants for Polycyclic Aromatic Hydrocarbons and Aromatic Nitrogen Heterocyclics

    NASA Astrophysics Data System (ADS)

    Long, Sheila Ann Thibeault

    The H-H, C-H, and C-C spin-spin coupling constants were calculated by the finite-perturbation, intermediate -neglect-of-differential-overlap method using the Fermi contact interaction for benzene, naphthalene, biphenyl, anthracene, phenanthrene, and pyrene. The calculations were made using both the actual and the average molecular geometries. For all six of these molecules, the agreements between the calculated and the experimental coupling constants were comparable to those previously reported for other, predominantly smaller, molecules. The actual molecular geometries always gave the correct relative order of values for the H-H coupling constants, whereas the average molecular geometries did not always do so. The magnitudes, but not the signs, of the calculated coupling constants were sensitive to small changes in molecular geometry. The results were the best (next best) for the H-H (C-H) coupling constants. In addition the H-H, C-H, N-H, C-C, and N-C spin -spin coupling constants were calculated in a similar manner for pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, quinoline, quinoxaline, phthalazine, benzo g quinoxaline, and benzo b phenazine. The agreements between the theoretical and the experimental values were comparable to those for the polycyclic aromatic hydrocarbons.

  18. Excited vibrational level rotational constants for SiC2: A sensitive molecular diagnostic for astrophysical conditions

    NASA Astrophysics Data System (ADS)

    Fortenberry, Ryan C.; Lee, Timothy J.; Müller, Holger S. P.

    2015-11-01

    Silacyclopropynylidene, SiC2, is a known and highly abundant circumstellar molecule. Its spectrum has been established as a major component of lines observed toward the carbon-rich star IRC +10216 (CW Leonis). It has been detected in its low-lying v3 = 1 and 2 vibrational states as well as in various isotopic compositions. Increasing sensitivity and spatial resolution will enable many more emission or absorption lines to be detected. In order to detect new molecular species, unassigned lines of known species must be identified. This work uses established ab initio quartic force fields to produce data necessary for this classification of lines related to SiC2. Agreement between the theoretical vibrational frequencies and known rotational and spectroscopic constants is quite good, as good as 5 cm-1 and 3 MHz, respectively in some cases. In addition, experimentally unknown vibrational frequencies and rotational constants are provided for the first overtones and combination bands in addition to 3ν3, the second overtone of the low-lying antisymmetric stretch/carbide rotation mode. Frequencies of v3 = 3 low-J rotational transitions of the main isotopic species are also estimated from published data for v3 ≤ 2. Further, we determine rotational and centrifugal distortion parameters for which in most cases vibrational effects due to the ν3 mode were reduced to first, and in several cases also to second order. These values may approximate equilibrium values better than the ground state values. The data produced herein will aid in the experimental and observational characterization of this known astromolecule in order to identify some of the unassigned lines for a known entity.

  19. Recent advances in thermal desorption-gas chromatography-mass spectrometery method to eliminate the matrix effect between air and water samples: application to the accurate determination of Henry's law constant.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2014-05-16

    Accurate values for the Henry's law constants are essential to describe the environmental dynamics of a solute, but substantial errors are recognized in many reported data due to practical difficulties in measuring solubility and/or vapor pressure. Despite such awareness, validation of experimental approaches has scarcely been made. An experimental approach based on thermal desorption-gas chromatography-mass spectrometery (TD-GC-MS) method was developed to concurrently allow the accurate determination of target compounds from the headspace and aqueous samples in closed equilibrated system. The analysis of six aromatics and eight non-aromatic oxygenates was then carried out in a static headspace mode. An estimation of the potential bias and mass balance (i.e., sum of mass measured individually from gas and liquid phases vs. the mass initially added to the system) demonstrates compound-specific phase dependency so that the best results are obtained by aqueous (less soluble aromatics) and headspace analysis (more soluble non-aromatics). Accordingly, we were able to point to the possible sources of biases in previous studies and provide the best estimates for the Henry's constants (Matm(-1)): benzene (0.17), toluene (0.15), p-xylene (0.13), m-xylene (0.13), o-xylene (0.19), styrene (0.27); propionaldehyde (9.26), butyraldehyde (6.19), isovaleraldehyde (2.14), n-valeraldehyde (3.98), methyl ethyl ketone (10.5), methyl isobutyl ketone (3.93), n-butyl acetate (2.41), and isobutyl alcohol (22.2).

  20. Recent advances in thermal desorption-gas chromatography-mass spectrometery method to eliminate the matrix effect between air and water samples: application to the accurate determination of Henry's law constant.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2014-05-16

    Accurate values for the Henry's law constants are essential to describe the environmental dynamics of a solute, but substantial errors are recognized in many reported data due to practical difficulties in measuring solubility and/or vapor pressure. Despite such awareness, validation of experimental approaches has scarcely been made. An experimental approach based on thermal desorption-gas chromatography-mass spectrometery (TD-GC-MS) method was developed to concurrently allow the accurate determination of target compounds from the headspace and aqueous samples in closed equilibrated system. The analysis of six aromatics and eight non-aromatic oxygenates was then carried out in a static headspace mode. An estimation of the potential bias and mass balance (i.e., sum of mass measured individually from gas and liquid phases vs. the mass initially added to the system) demonstrates compound-specific phase dependency so that the best results are obtained by aqueous (less soluble aromatics) and headspace analysis (more soluble non-aromatics). Accordingly, we were able to point to the possible sources of biases in previous studies and provide the best estimates for the Henry's constants (Matm(-1)): benzene (0.17), toluene (0.15), p-xylene (0.13), m-xylene (0.13), o-xylene (0.19), styrene (0.27); propionaldehyde (9.26), butyraldehyde (6.19), isovaleraldehyde (2.14), n-valeraldehyde (3.98), methyl ethyl ketone (10.5), methyl isobutyl ketone (3.93), n-butyl acetate (2.41), and isobutyl alcohol (22.2). PMID:24704185

  1. Molecular-genetic analysis is essential for accurate classification of renal carcinoma resembling Xp11.2 translocation carcinoma.

    PubMed

    Hayes, Malcolm; Peckova, Kvetoslava; Martinek, Petr; Hora, Milan; Kalusova, Kristyna; Straka, Lubomir; Daum, Ondrej; Kokoskova, Bohuslava; Rotterova, Pavla; Pivovarčikova, Kristyna; Branzovsky, Jindrich; Dubova, Magdalena; Vesela, Pavla; Michal, Michal; Hes, Ondrej

    2015-03-01

    tumours can only be sub-classified accurately by multi-parameter molecular-genetic analysis. PMID:25544614

  2. Ab initio molecular dynamics study of water at constant pressure using converged basis sets and empirical dispersion corrections

    NASA Astrophysics Data System (ADS)

    Ma, Zhonghua; Zhang, Yanli; Tuckerman, Mark E.

    2012-07-01

    It is generally believed that studies of liquid water using the generalized gradient approximation to density functional theory require dispersion corrections in order to obtain reasonably accurate structural and dynamical properties. Here, we report on an ab initio molecular dynamics study of water in the isothermal-isobaric ensemble using a converged discrete variable representation basis set and an empirical dispersion correction due to Grimme [J. Comp. Chem. 27, 1787 (2006)], 10.1002/jcc.20495. At 300 K and an applied pressure of 1 bar, the density obtained without dispersion corrections is approximately 0.92 g/cm3 while that obtained with dispersion corrections is 1.07 g/cm3, indicating that the empirical dispersion correction overestimates the density by almost as much as it is underestimated without the correction for this converged basis. Radial distribution functions exhibit a loss of structure in the second solvation shell. Comparison of our results with other studies using the same empirical correction suggests the cause of the discrepancy: the Grimme dispersion correction is parameterized for use with a particular basis set; this parameterization is sensitive to this choice and, therefore, is not transferable to other basis sets.

  3. Voltage gating by molecular subunits of Na+ and K+ ion channels: higher-dimensional cubic kinetics, rate constants, and temperature.

    PubMed

    Fohlmeister, Jürgen F

    2015-06-01

    The structural similarity between the primary molecules of voltage-gated Na and K channels (alpha subunits) and activation gating in the Hodgkin-Huxley model is brought into full agreement by increasing the model's sodium kinetics to fourth order (m(3) → m(4)). Both structures then virtually imply activation gating by four independent subprocesses acting in parallel. The kinetics coalesce in four-dimensional (4D) cubic diagrams (16 states, 32 reversible transitions) that show the structure to be highly failure resistant against significant partial loss of gating function. Rate constants, as fitted in phase plot data of retinal ganglion cell excitation, reflect the molecular nature of the gating transitions. Additional dimensions (6D cubic diagrams) accommodate kinetically coupled sodium inactivation and gating processes associated with beta subunits. The gating transitions of coupled sodium inactivation appear to be thermodynamically irreversible; response to dielectric surface charges (capacitive displacement) provides a potential energy source for those transitions and yields highly energy-efficient excitation. A comparison of temperature responses of the squid giant axon (apparently Arrhenius) and mammalian channel gating yields kinetic Q10 = 2.2 for alpha unit gating, whose transitions are rate-limiting at mammalian temperatures; beta unit kinetic Q10 = 14 reproduces the observed non-Arrhenius deviation of mammalian gating at low temperatures; the Q10 of sodium inactivation gating matches the rate-limiting component of activation gating at all temperatures. The model kinetics reproduce the physiologically large frequency range for repetitive firing in ganglion cells and the physiologically observed strong temperature dependence of recovery from inactivation. PMID:25867741

  4. Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations.

    PubMed

    Velazquez, Hector A; Hamelberg, Donald

    2015-02-21

    Cis-trans isomerization of peptidyl-prolyl bonds of the protein backbone plays an important role in numerous biological processes. Cis-trans isomerization can be the rate-limiting step due its extremely slow dynamics, compared to the millisecond time scale of many processes, and is catalyzed by a widely studied family of peptidyl-prolyl cis-trans isomerase enzymes. Also, mechanical forces along the peptide chain can speed up the rate of isomerization, resulting in "mechanical catalysis," and have been used to study peptidyl-prolyl cis-trans isomerization and other mechanical properties of proteins. Here, we use constant force molecular dynamics simulations to study the dynamical effects of phosphorylation on serine/threonine-proline protein motifs that are involved in the function of many proteins and have been implicated in many aberrant biological processes. We show that the rate of cis-trans isomerization is slowed down by phosphorylation, in excellent agreement with experiments. We use a well-grounded theory to describe the force dependent rate of isomerization. The calculated rates at zero force are also in excellent agreement with experimentally measured rates, providing additional validation of the models and force field parameters. Our results suggest that the slowdown in the rate upon phosphorylation is mainly due to an increase in the friction along the peptidyl-prolyl bond angle during isomerization. Our results provide a microscopic description of the dynamical effects of post-translational phosphorylation on cis-trans isomerization and insights into the properties of proteins under tension.

  5. Voltage gating by molecular subunits of Na+ and K+ ion channels: higher-dimensional cubic kinetics, rate constants, and temperature.

    PubMed

    Fohlmeister, Jürgen F

    2015-06-01

    The structural similarity between the primary molecules of voltage-gated Na and K channels (alpha subunits) and activation gating in the Hodgkin-Huxley model is brought into full agreement by increasing the model's sodium kinetics to fourth order (m(3) → m(4)). Both structures then virtually imply activation gating by four independent subprocesses acting in parallel. The kinetics coalesce in four-dimensional (4D) cubic diagrams (16 states, 32 reversible transitions) that show the structure to be highly failure resistant against significant partial loss of gating function. Rate constants, as fitted in phase plot data of retinal ganglion cell excitation, reflect the molecular nature of the gating transitions. Additional dimensions (6D cubic diagrams) accommodate kinetically coupled sodium inactivation and gating processes associated with beta subunits. The gating transitions of coupled sodium inactivation appear to be thermodynamically irreversible; response to dielectric surface charges (capacitive displacement) provides a potential energy source for those transitions and yields highly energy-efficient excitation. A comparison of temperature responses of the squid giant axon (apparently Arrhenius) and mammalian channel gating yields kinetic Q10 = 2.2 for alpha unit gating, whose transitions are rate-limiting at mammalian temperatures; beta unit kinetic Q10 = 14 reproduces the observed non-Arrhenius deviation of mammalian gating at low temperatures; the Q10 of sodium inactivation gating matches the rate-limiting component of activation gating at all temperatures. The model kinetics reproduce the physiologically large frequency range for repetitive firing in ganglion cells and the physiologically observed strong temperature dependence of recovery from inactivation.

  6. Constant energy DFT molecular dynamics simulations of solvated carbohydrates at the B3LYP/6-31+G* level of theory

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The disaccharide, alpha/beta-maltose, has been studied using constant energy ab initio molecular dynamics at the B3LYP/6-31+G* COSMO (solvent) level of theory. Maltose is of particular interest as the variation in glycosidic dihedral angles is dependent upon the starting hydroxyl conformation. Tha...

  7. Communication: Rate coefficients of the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    SciTech Connect

    Meng, Qingyong Chen, Jun Zhang, Dong H.

    2015-09-14

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.

  8. The cosmological constant problem

    SciTech Connect

    Dolgov, A.D.

    1989-05-01

    A review of the cosmological term problem is presented. Baby universe model and the compensating field model are discussed. The importance of more accurate data on the Hubble constant and the Universe age is stressed. 18 refs.

  9. Dependence of the distribution constant in liquid-liquid partition equilibria on the van der Waals molecular surface area.

    PubMed

    Moldoveanu, Serban C; David, Victor

    2013-09-01

    The direct calculation of free energy of interactions between a solute j and two immiscible liquids shows a linear dependence between the (logarithm of) the distribution constant in liquid-liquid partition equilibrium log K(j) and the van der Waals surface area of the solute. The study provides a thermodynamic proof for the formula log K(BA,j) = c1 log K(BC,j) + c2 that describes the linear dependence between (the logarithm of) the distribution constant for a solute j in a solvent system (B/A) and (the logarithm of) the distribution constant for the same solute in a different solvent system (B/C). This relation has been well proven by various experimental studies and it is frequently used in liquid chromatographic separations as well as in liquid-liquid extractions, but was not explained previously based on thermodynamic results. The theory was verified using the prediction of octanol/water distribution constants log K(ow) for a wide range of molecules, including hydrocarbons and compounds with a variety of functional groups. The results have also been verified for the distribution constants in other solvent systems. The expression for the distribution constant obtained in this study also gives a theoretical base for the additive fragment methodology used for the prediction of log K(ow).

  10. Toward Accurate Reaction Energetics for Molecular Line Growth at Surface: Quantum Monte Carlo and Density Functional Theory Calculations

    SciTech Connect

    Kanai, Y; Takeuchi, N

    2009-10-14

    We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.

  11. Accurate and Scalable O(N) Algorithm for First-Principles Molecular-Dynamics Computations on Large Parallel Computers

    SciTech Connect

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-01-01

    We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10-4 Ha/Bohr.

  12. The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties.

    PubMed

    Riahi, Saleh; Rowley, Christopher N

    2014-10-30

    The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.

  13. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.

    PubMed

    Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng

    2014-01-15

    Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application.

  14. The route to MBxNyCz molecular wheels: II. Results using accurate functionals and basis sets

    NASA Astrophysics Data System (ADS)

    Güthler, A.; Mukhopadhyay, S.; Pandey, R.; Boustani, I.

    2014-04-01

    Applying ab initio quantum chemical methods, molecular wheels composed of metal and light atoms were investigated. High quality basis sets 6-31G*, TZPV, and cc-pVTZ as well as exchange and non-local correlation functionals B3LYP, BP86 and B3P86 were used. The ground-state energy and structures of cyclic planar and pyramidal clusters TiBn (for n = 3-10) were computed. In addition, the relative stability and electronic structures of molecular wheels TiBxNyCz (for x, y, z = 0-10) and MBnC10-n (for n = 2 to 5 and M = Sc to Zn) were determined. This paper sustains a follow-up study to the previous one of Boustani and Pandey [Solid State Sci. 14 (2012) 1591], in which the calculations were carried out at the HF-SCF/STO3G/6-31G level of theory to determine the initial stability and properties. The results show that there is a competition between the 2D planar and the 3D pyramidal TiBn clusters (for n = 3-8). Different isomers of TiB10 clusters were also studied and a structural transition of 3D-isomer into 2D-wheel is presented. Substitution boron in TiB10 by carbon or/and nitrogen atoms enhances the stability and leads toward the most stable wheel TiB3C7. Furthermore, the computations show that Sc, Ti and V at the center of the molecular wheels are energetically favored over other transition metal atoms of the first row.

  15. An accurate and scalable O(N) algorithm for First-Principles Molecular Dynamics computations on petascale computers and beyond

    NASA Astrophysics Data System (ADS)

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-03-01

    We present a truly scalable First-Principles Molecular Dynamics algorithm with O(N) complexity and fully controllable accuracy, capable of simulating systems of sizes that were previously impossible with this degree of accuracy. By avoiding global communication, we have extended W. Kohn's condensed matter ``nearsightedness'' principle to a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wavefunctions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 100,000 atoms on 100,000 processors, with a wall-clock time of the order of one minute per molecular dynamics time step. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  16. Constant molecular rotation at the smectic-A to smectic-C* transition in ferroelectric liquid crystals

    NASA Astrophysics Data System (ADS)

    Kremer, F.; Vallerien, S. U.; Kapitza, H.; Zentel, R.; Fischer, E. W.

    1990-09-01

    We present dielectric measurements extended over the frequency range from 106 to 109 Hz on a pure ferroelectric liquid crystal. In clear contrast to the generally attributed origin of the ferroelectricity in liquid crystals arising from a slowing down of the molecular rotation around the long molecular axis, we find by direct observation the corresponding dielectric relaxation unchanged at the smectic-A to smectic-C* transition. This result requires a new interpretation of a recently published degenerate four-wave-mixing experiment by Lalanne et al. [Phys. Rev. Lett. 62, 3046 (1989)].

  17. Relationship between reaction rate constants of organic pollutants and their molecular descriptors during Fenton oxidation and in situ formed ferric-oxyhydroxides.

    PubMed

    Jia, Lijuan; Shen, Zhemin; Su, Pingru

    2016-05-01

    Fenton oxidation is a promising water treatment method to degrade organic pollutants. In this study, 30 different organic compounds were selected and their reaction rate constants (k) were determined for the Fenton oxidation process. Gaussian09 and Material Studio software sets were used to carry out calculations and obtain values of 10 different molecular descriptors for each studied compound. Ferric-oxyhydroxide coagulation experiments were conducted to determine the coagulation percentage. Based upon the adsorption capacity, all of the investigated organic compounds were divided into two groups (Group A and Group B). The percentage adsorption of organic compounds in Group A was less than 15% (wt./wt.) and that in the Group B was higher than 15% (wt./wt.). For Group A, removal of the compounds by oxidation was the dominant process while for Group B, removal by both oxidation and coagulation (as a synergistic process) took place. Results showed that the relationship between the rate constants (k values) and the molecular descriptors of Group A was more pronounced than for Group B compounds. For the oxidation-dominated process, EHOMO and Fukui indices (f(0)x, f(-)x, f(+)x) were the most significant factors. The influence of bond order was more significant for the synergistic process of oxidation and coagulation than for the oxidation-dominated process. The influences of all other molecular descriptors on the synergistic process were weaker than on the oxidation-dominated process.

  18. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    NASA Astrophysics Data System (ADS)

    Zarycz, M. Natalia C.; Sauer, Stephan P. A.; Provasi, Patricio F.

    2014-10-01

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the 1J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the 1J(N-H) coupling constant in NH3. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  19. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    SciTech Connect

    Zarycz, M. Natalia C. Provasi, Patricio F.; Sauer, Stephan P. A.

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the {sup 1}J(C–H) coupling constant of CH{sub 4} using a decomposition into contributions from localized molecular orbitals and compare with the {sup 1}J(N–H) coupling constant in NH{sub 3}. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  20. Relationship between reaction rate constants of organic pollutants and their molecular descriptors during Fenton oxidation and in situ formed ferric-oxyhydroxides.

    PubMed

    Jia, Lijuan; Shen, Zhemin; Su, Pingru

    2016-05-01

    Fenton oxidation is a promising water treatment method to degrade organic pollutants. In this study, 30 different organic compounds were selected and their reaction rate constants (k) were determined for the Fenton oxidation process. Gaussian09 and Material Studio software sets were used to carry out calculations and obtain values of 10 different molecular descriptors for each studied compound. Ferric-oxyhydroxide coagulation experiments were conducted to determine the coagulation percentage. Based upon the adsorption capacity, all of the investigated organic compounds were divided into two groups (Group A and Group B). The percentage adsorption of organic compounds in Group A was less than 15% (wt./wt.) and that in the Group B was higher than 15% (wt./wt.). For Group A, removal of the compounds by oxidation was the dominant process while for Group B, removal by both oxidation and coagulation (as a synergistic process) took place. Results showed that the relationship between the rate constants (k values) and the molecular descriptors of Group A was more pronounced than for Group B compounds. For the oxidation-dominated process, EHOMO and Fukui indices (f(0)x, f(-)x, f(+)x) were the most significant factors. The influence of bond order was more significant for the synergistic process of oxidation and coagulation than for the oxidation-dominated process. The influences of all other molecular descriptors on the synergistic process were weaker than on the oxidation-dominated process. PMID:27155432

  1. Direct measurement of the association constant of HER2/neu antisense oligonucleotide to its target RNA sequence using a molecular beacon.

    PubMed

    Vijayanathan, Veena; Thomas, Thresia; Sigal, Leonard H; Thomas, T J

    2002-08-01

    A molecular beacon approach was developed to directly determine the association constant of RNA-DNA hybrid formation. The molecular beacon was composed of a 15-nt loop structure containing the antisense sequence that can hybridize with the AUG translational start site of the HER2/neu gene, which is overexpressed in a significant proportion of breast, ovarian, and lung tumors. The equilibrium association constant (Ka) of DNA binding to the RNA oligonucleotide was 6.4 +/- 0.14 x 10(7) M(-1) in the presence of 150 mM NaCl at 22 degrees C. The free energy change (AG) associated with RNA-DNA hybrid formation was -10.7 kcal/mole. The melting temperature (Tm) of RNA-DNA hybrid was 64.4 degrees C +/- 1 degree C in the presence of 150 mM NaCl. The RNA-DNA hybrid was more stable than the corresponding DNA-DNA duplex in 150 mM NaCl, as judged by both Ka and Tm data. We also determined the Ka, deltaG, and Tm values of RNA-DNA and DNA-DNA duplex formation in the presence of three monovalent cations, Li+, K+, and Cs+. The feasibility of this method was also investigated using a phosphorothioate molecular beacon. The information generated through this new approach for thermodynamic measurements might be useful for the design of oligonucleotides for antisense therapeutics.

  2. Dielectric constants of binary mixtures of propylene carbonate with dimethyl carbonate and ethylene carbonate from molecular dynamics simulation: comparison between non-polarizable and polarizable force fields

    NASA Astrophysics Data System (ADS)

    Lee, Sanghun; Park, Sung Soo

    2013-01-01

    Using non-polarizable and polarizable molecular dynamics simulations, binary mixtures of propylene carbonate + dimethyl carbonate and propylene carbonate + ethylene carbonate with various compositions were investigated. The polarizable model produces more reasonable estimation of dielectric constants than the non-polarizable model; however, combining the electronic continuum model with the non-polarizable MD improves the comparison between the two models. Fair agreement was found between the results from these simulations and available experimental data. In addition, for a better understanding of the mixing behaviour, the excess dielectric constants over the entire composition were calculated. By comparison of the two mixtures in various mole fractions, distinctive mixing behaviours of propylene carbonate + dimethyl carbonate (poorly symmetric mixture) and propylene carbonate + ethylene carbonate (highly symmetric mixture) were observed.

  3. Effect of solvent on the rate constant for the radiative deactivation of singlet molecular oxygen (/sup 1/. delta. /sub g/O/sub 2/)

    SciTech Connect

    Scurlock, R.D.; Ogilby, P.R.

    1987-08-13

    Relative rate constants for the radiative deactivation (k/sub r/) of singlet molecular oxygen (/sup 3/Sigma/sub g//sup -/O/sub 2/ reverse arrow /sup 1/..delta../sub g/O/sub 2/) have been determined in 15 solvents. A substantial solvent effect is observed. Changes in the value of k/sub r/ can exceed a factor of 20. A reasonably good correlation exists between the solvent polarizability, defined as a function of the solvent refractive index, and the radiative rate constant. We suggest that our data support a model in which /sup 1/..delta../sub g/O/sub 2/ is perturbed through the formation of a discrete oxygen-solvent collision complex.

  4. Measurement of the solar constant

    NASA Technical Reports Server (NTRS)

    Crommelynck, D.

    1981-01-01

    The absolute value of the solar constant and the long term variations that exist in the absolute value of the solar constant were measured. The solar constant is the total irradiance of the Sun at a distance of one astronomical unit. An absolute radiometer removed from the effects of the atmosphere with its calibration tested in situ was used to measure the solar constant. The importance of an accurate knowledge of the solar constant is emphasized.

  5. A molecular copper catalyst for electrochemical water reduction with a large hydrogen-generation rate constant in aqueous solution.

    PubMed

    Zhang, Peili; Wang, Mei; Yang, Yong; Yao, Tianyi; Sun, Licheng

    2014-12-01

    The copper complex [(bztpen)Cu](BF4)2 (bztpen=N-benzyl-N,N',N'-tris(pyridin-2-ylmethyl)ethylenediamine) displays high catalytic activity for electrochemical proton reduction in acidic aqueous solutions, with a calculated hydrogen-generation rate constant (k(obs)) of over 10000 s(-1). A turnover frequency (TOF) of 7000 h(-1) cm(-2) and a Faradaic efficiency of 96% were obtained from a controlled potential electrolysis (CPE) experiment with [(bztpen)Cu](2+) in pH 2.5 buffer solution at -0.90 V versus the standard hydrogen electrode (SHE) over two hours using a glassy carbon electrode. A mechanism involving two proton-coupled reduction steps was proposed for the dihydrogen generation reaction catalyzed by [(bztpen)Cu](2+). PMID:25314646

  6. SFG analysis of the molecular structures at the surfaces and buried interfaces of PECVD ultralow-dielectric constant pSiCOH

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoxian; Myers, John N.; Huang, Huai; Shobha, Hosadurga; Chen, Zhan; Grill, Alfred

    2016-02-01

    PECVD deposited porous SiCOH with ultralow dielectric constant has been successfully integrated as the insulator in advanced interconnects to decrease the RC delay. The effects of NH3 plasma treatment and the effectiveness of the dielectric repair on molecular structures at the surface and buried interface of a pSiCOH film deposited on top of a SiCNH film on a Si wafer were fully characterized using sum frequency generation vibrational spectroscopy (SFG), supplemented by X-ray photoelectron spectroscopy. After exposure to NH3 plasma for 18 s, about 40% of the methyl groups were removed from the pSiCOH surface, and the average orientation of surface methyl groups tilted more towards the surface. The repair method used here effectively repaired the molecular structures at the pSiCOH surface but did not totally recover the entire plasma-damaged layer. Additionally, simulated SFG spectra with various average orientations of methyl groups at the SiCNH/pSiCOH buried interface were compared with the experimental SFG spectra collected using three different laser input angles to determine the molecular structural information at the SiCNH/pSiCOH buried interface after NH3 plasma treatment and repair. The molecular structures including the coverage and the average orientation of methyl groups at the buried interface were found to be unchanged by NH3 plasma treatment and repair.

  7. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

    NASA Astrophysics Data System (ADS)

    Wallace, Jason A.; Shen, Jana K.

    2012-11-01

    Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pKa values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

  8. The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations.

    PubMed

    Fang, Changming; Li, Wun-Fan; Koster, Rik S; Klimeš, Jiří; van Blaaderen, Alfons; van Huis, Marijn A

    2015-01-01

    Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initio approaches can be applied only to small numbers of atoms, while large numbers of atoms are required for having configurations that are representative of a liquid. Here we show that a high-accuracy value for the electronic band gap of water can be obtained by combining beyond-DFT methods and statistical time-averaging. Liquid water is simulated at 300 K using a plane-wave density functional theory molecular dynamics (PW-DFT-MD) simulation and a van der Waals density functional (optB88-vdW). After applying a self-consistent GW correction the band gap of liquid water at 300 K is calculated as 7.3 eV, in good agreement with recent experimental observations in the literature (6.9 eV). For simulations of phase transformations and chemical reactions in water or aqueous solutions whereby an accurate description of the electronic structure is required, we suggest to use these advanced GW corrections in combination with the statistical analysis of quantum mechanical MD simulations.

  9. Energy-based scheme for reconstruction of piecewise constant signals observed in the movement of molecular machines

    NASA Astrophysics Data System (ADS)

    Rosskopf, Joachim; Paul-Yuan, Korbinian; Plenio, Martin B.; Michaelis, Jens

    2016-08-01

    Analyzing the physical and chemical properties of single DNA-based molecular machines such as polymerases and helicases requires to track stepping motion on the length scale of base pairs. Although high-resolution instruments have been developed that are capable of reaching that limit, individual steps are oftentimes hidden by experimental noise which complicates data processing. Here we present an effective two-step algorithm which detects steps in a high-bandwidth signal by minimizing an energy-based model (energy-based step finder, EBS). First, an efficient convex denoising scheme is applied which allows compression to tuples of amplitudes and plateau lengths. Second, a combinatorial clustering algorithm formulated on a graph is used to assign steps to the tuple data while accounting for prior information. Performance of the algorithm was tested on Poissonian stepping data simulated based on published kinetics data of RNA polymerase II (pol II). Comparison to existing step-finding methods shows that EBS is superior in speed while providing competitive step-detection results, especially in challenging situations. Moreover, the capability to detect backtracked intervals in experimental data of pol II as well as to detect stepping behavior of the Phi29 DNA packaging motor is demonstrated.

  10. Energy-based scheme for reconstruction of piecewise constant signals observed in the movement of molecular machines.

    PubMed

    Rosskopf, Joachim; Paul-Yuan, Korbinian; Plenio, Martin B; Michaelis, Jens

    2016-08-01

    Analyzing the physical and chemical properties of single DNA-based molecular machines such as polymerases and helicases requires to track stepping motion on the length scale of base pairs. Although high-resolution instruments have been developed that are capable of reaching that limit, individual steps are oftentimes hidden by experimental noise which complicates data processing. Here we present an effective two-step algorithm which detects steps in a high-bandwidth signal by minimizing an energy-based model (energy-based step finder, EBS). First, an efficient convex denoising scheme is applied which allows compression to tuples of amplitudes and plateau lengths. Second, a combinatorial clustering algorithm formulated on a graph is used to assign steps to the tuple data while accounting for prior information. Performance of the algorithm was tested on Poissonian stepping data simulated based on published kinetics data of RNA polymerase II (pol II). Comparison to existing step-finding methods shows that EBS is superior in speed while providing competitive step-detection results, especially in challenging situations. Moreover, the capability to detect backtracked intervals in experimental data of pol II as well as to detect stepping behavior of the Phi29 DNA packaging motor is demonstrated.

  11. Energy-based scheme for reconstruction of piecewise constant signals observed in the movement of molecular machines.

    PubMed

    Rosskopf, Joachim; Paul-Yuan, Korbinian; Plenio, Martin B; Michaelis, Jens

    2016-08-01

    Analyzing the physical and chemical properties of single DNA-based molecular machines such as polymerases and helicases requires to track stepping motion on the length scale of base pairs. Although high-resolution instruments have been developed that are capable of reaching that limit, individual steps are oftentimes hidden by experimental noise which complicates data processing. Here we present an effective two-step algorithm which detects steps in a high-bandwidth signal by minimizing an energy-based model (energy-based step finder, EBS). First, an efficient convex denoising scheme is applied which allows compression to tuples of amplitudes and plateau lengths. Second, a combinatorial clustering algorithm formulated on a graph is used to assign steps to the tuple data while accounting for prior information. Performance of the algorithm was tested on Poissonian stepping data simulated based on published kinetics data of RNA polymerase II (pol II). Comparison to existing step-finding methods shows that EBS is superior in speed while providing competitive step-detection results, especially in challenging situations. Moreover, the capability to detect backtracked intervals in experimental data of pol II as well as to detect stepping behavior of the Phi29 DNA packaging motor is demonstrated. PMID:27627346

  12. Vicinal coupling constants and protein dynamics.

    PubMed

    Hoch, J C; Dobson, C M; Karplus, M

    1985-07-16

    The effects of motional averaging on the analysis of vicinal spin-spin coupling constants derived from proton NMR studies of proteins have been examined. Trajectories obtained from molecular dynamics simulations of bovine pancreatic trypsin inhibitor and of hen egg white lysozyme were used in conjunction with an expression for the dependence of the coupling constant on the intervening dihedral angle to calculate the time-dependent behavior of the coupling constants. Despite large fluctuations, the time-average values of the coupling constants are not far from those computed for the average structure in the cases where fluctuations occur about a single potential well. The calculated differences show a high correlation with the variation in the magnitude of the fluctuations of individual dihedral angles. For the cases where fluctuations involve multiple sites, large differences are found between the time-average values and the average structure values for the coupling constants. Comparison of the simulation results with the experimental trends suggests that side chains with more than one position are more common in proteins than is inferred from X-ray results. It is concluded that for the main chain, motional effects do not introduce significant errors where vicinal coupling constants are used in structure determinations; however, for side chains, the motional average can alter deductions about the structure. Accurately measured coupling constants are shown to provide information concerning the magnitude of dihedral angle fluctuations.

  13. Are Fundamental Constants Really Constant?

    ERIC Educational Resources Information Center

    Swetman, T. P.

    1972-01-01

    Dirac's classical conclusions, that the values of e2, M and m are constants and the quantity of G decreases with time. Evoked considerable interest among researchers and traces historical development by which further experimental evidence points out that both e and G are constant values. (PS)

  14. The /A 1 Sigma +/ - /X 1 Sigma +/ system of the isotopic lithium hydrides - The molecular constants, potential energy curves, and their adiabatic corrections

    NASA Technical Reports Server (NTRS)

    Vidal, C. R.; Stwalley, W. C.

    1982-01-01

    The molecular constants and their adiabatic corrections have been determined for the (A 1 Sigma +) - (X 1 Sigma +) system of the isotopic lithium hydrides: (Li-6)H, (Li-7)H, (Li-6)D, and (Li-7)D. Using a fully quantum mechanical variational method, the potential energy curves (IPA potentials) are determined. Extending the variational method, we have obtained for the first time adiabatic corrections of potential energy curves from isotopic spectroscopic data. A significant difference between the potential energy curves of the lithium hydrides and the lithium deuterides has been observed. When Li-6 was replaced by Li-7, a significant difference was only observed for the (A 1 Sigma +) state, but not for the (X 1 Sigma +) state.

  15. Effect of a buried ion pair in the hydrophobic core of a protein: An insight from constant pH molecular dynamics study.

    PubMed

    Pathak, Arup K

    2015-03-01

    Constant pH molecular dynamics (CpHMD) is a commonly used sampling method, which incorporates the coupling of conformational flexibility and protonation state of a protein during the simulation by using pH as an external parameter. The effects on the structure and stability of a hyperstable variant of staphylococcal nuclease (Δ+PHS) protein of an artificial charge pair buried in its hydrophobic core are investigated by applying both CpHMD and accelerated molecular dynamics coupled with constant pH (CpHaMD) methods. Generalized Born electrostatics is used to model the solvent water. Two sets of starting coordinates of V23E/L36K variant of Δ+PHS, namely, Maestro generated coordinates from Δ+PHS and crystal structure coordinates of the same are considered for detail investigations. On the basis of root mean square displacement (RMSD) and root mean square fluctuations (RMSF) calculations, it is observed that this variant is stable over a wide range of pH. The calculated pKa values for aspartate and glutamate residues based on both CpHMD and CpHaMD simulations are consistent with the reported experimental values (within ± 0.5 to ± 1.5 pH unit), which clearly indicates that the local chemical environment of the carboxylic acids in V23E/L36K variant are comparable to the parent form. The strong salt bridge interaction between the mutated pair, E23/K36 and additional hydrogen bonds formed in the V23E/L36K variant, may help to compensate for the unfavorable self-energy experienced by the burial of these residues in the hydrophobic core. However, from RMSD, RMSF, and pKa analysis, no significant change in the global conformation of V23E/L36K variant with respect to the parent form, Δ+PHS is noticed. PMID:25363335

  16. Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction

    PubMed Central

    Willow, Soohaeng Yoo; Salim, Michael A.; Kim, Kwang S.; Hirata, So

    2015-01-01

    A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation. PMID:26400690

  17. Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction.

    PubMed

    Willow, Soohaeng Yoo; Salim, Michael A; Kim, Kwang S; Hirata, So

    2015-01-01

    A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation.

  18. Ring polymer molecular dynamics fast computation of rate coefficients on accurate potential energy surfaces in local configuration space: Application to the abstraction of hydrogen from methane

    NASA Astrophysics Data System (ADS)

    Meng, Qingyong; Chen, Jun; Zhang, Dong H.

    2016-04-01

    To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3 reactions, we propose a segmented strategy for fitting suitable potential energy surface (PES), on which ring-polymer molecular dynamics (RPMD) simulations are performed. On the basis of recently developed permutation invariant polynomial neural-network approach [J. Li et al., J. Chem. Phys. 142, 204302 (2015)], PESs in local configuration spaces are constructed. In this strategy, global PES is divided into three parts, including asymptotic, intermediate, and interaction parts, along the reaction coordinate. Since less fitting parameters are involved in the local PESs, the computational efficiency for operating the PES routine is largely enhanced by a factor of ˜20, comparing with that for global PES. On interaction part, the RPMD computational time for the transmission coefficient can be further efficiently reduced by cutting off the redundant part of the child trajectories. For H + CH4, good agreements among the present RPMD rates and those from previous simulations as well as experimental results are found. For D + CH4, on the other hand, qualitative agreement between present RPMD and experimental results is predicted.

  19. How Iron-Containing Proteins Control Dioxygen Chemistry: A Detailed Atomic Level Description Via Accurate Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics Calculations.

    SciTech Connect

    Friesner, Richard A.; Baik, Mu-Hyun; Gherman, Benjamin F.; Guallar, Victor; Wirstam, Maria E.; Murphy, Robert B.; Lippard, Stephen J.

    2003-03-01

    Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C-H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.

  20. MRCI study on the spectroscopic parameters and molecular constants of the X 1Σ +, a3Σ +, A 1Π and C 1Σ - electronic states of the SiO molecule

    NASA Astrophysics Data System (ADS)

    Shi, Deheng; Li, Wentao; Sun, Jinfeng; Zhu, Zunlue

    2012-02-01

    The potential energy curves (PECs) of the X 1Σ +, a3Σ +, A 1Π and C 1Σ - electronic states of the SiO molecule are studied using an ab initio quantum chemical method. The calculations have been made employing the complete active space self-consistent field (CASSCF) method, which is followed by the valence internally contracted multireference configuration interaction (MRCI) approach in combination with several correlation-consistent basis sets. The effect on the PECs by the core-valence correlation and relativistic corrections is included. The way to consider the relativistic correction is to use the third-order Douglas-Kroll Hamiltonian approximation. The core-valence correlation correction is carried out with the cc-pCVQZ basis set, and the relativistic correction is performed at the level of the cc-pVQZ basis set. To obtain more reliable results, the PECs determined by the MRCI calculations are also corrected for size-extensivity errors by means of the Davidson modification (MRCI + Q). The PECs of these electronic states are extrapolated to the complete basis set limit by the total-energy extrapolation scheme. Employing these PECs, the spectroscopic parameters are calculated and compared with those reported in the literature. With these PECs determined by the MRCI + Q/CV + DK + 56 calculations, by solving the radial Schrödinger equation of nuclear motion, 110 vibrational states for the X 1Σ +, 69 for the a3Σ +, 54 for the A 1Π and 67 for the C 1Σ - electronic state are predicted when the rotational quantum number J equals zero. The vibrational manifolds of the first 20 vibrational states are reported and compared with the available RKR data for each electronic state. On the whole, as expected, the most accurate spectroscopic parameters and molecular constants of the SiO molecule are obtained by the MRCI + Q/CV + DK + 56 calculations. And the present molecular constants of the a3Σ +, C 1Σ - and A 1Π electronic states determined by the MRCI + Q/CV + DK

  1. Development and validation of a ReaxFF reactive force field for Fe/Al/Ni alloys: molecular dynamics study of elastic constants, diffusion, and segregation.

    PubMed

    Shin, Yun Kyung; Kwak, Hyunwook; Zou, Chenyu; Vasenkov, Alex V; van Duin, Adri C T

    2012-12-13

    We have developed a ReaxFF force field for Fe/Al/Ni binary alloys based on quantum mechanical (QM) calculations. In addition to the various bulk phases of the binary alloys, the (100), (110) and (111) surface energies and adatom binding energies were included in the training set for the force field parametrization of the Fe/Al/Ni binary alloys. To validate these optimized force fields, we studied (i) elastic constants of the binary alloys at finite temperatures, (ii) diffusivity of alloy components in Al/Ni alloy, and (iii) segregation on the binary alloy surfaces. First, we calculated linear elastic constants of FeAl, FeNi(3), and Ni(3)Al in the temperature range 300 to 1100 K. The temperature dependences of the elastic constants of these three alloys, showing a decrease in C(11), C(12), and C(44) as temperature increases, were in good agreement with the experimental results. We also performed ReaxFF molecular dynamics (MD) simulations for Al or Ni diffusion in the system modeled as Al/Ni mixed layers with the linear composition gradients. At 1000 K, Al diffusivity at the pure Al end was 2 orders of magnitude larger than that in the Al trace layers, probably explaining the nature of different diffusion behavior between molten metals and alloys. However, the diffusivity of Ni at the pure Ni end was only slightly larger than that in the Ni trace layers at the system temperature much lower than the melting temperature of Ni. Third, we investigated the surface segregation in L1(2)-Fe(3)Al, Fe(3)Ni, and Ni(3)Al clusters at high temperature (2500 K). From the analysis of composition distribution of the alloy components from the bulk to the surface layer, it was found that the degree of segregation depended on the chemical composition of the alloy. Al surface segregation occurred most strongly in Fe(3)Al, whereas it occurred most weakly in Ni(3)Al. These results may support the segregation mechanism that surface segregation results from the interplay between the

  2. Dissociation constants of weak acids from ab initio molecular dynamics using metadynamics: influence of the inductive effect and hydrogen bonding on pKa values.

    PubMed

    Tummanapelli, Anil Kumar; Vasudevan, Sukumaran

    2014-11-26

    The theoretical estimation of the dissociation constant, or pKa, of weak acids continues to be a challenging field. Here, we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pKa value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pKa. We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pKa values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pKa values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pKa values.

  3. Variation of Fundamental Constants

    NASA Astrophysics Data System (ADS)

    Flambaum, V. V.

    2006-11-01

    Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. The spatial variation can explain a fine tuning of the fundamental constants which allows humans (and any life) to appear. We appeared in the area of the Universe where the values of the fundamental constants are consistent with our existence. We present a review of recent works devoted to the variation of the fine structure constant α, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra. Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feshbach resonance.

  4. A novel asymmetric-loop molecular beacon-based two-phase hybridization assay for accurate and high-throughput detection of multiple drug resistance-conferring point mutations in Mycobacterium tuberculosis.

    PubMed

    Chen, Qinghai; Wu, Nan; Xie, Meng; Zhang, Bo; Chen, Ming; Li, Jianjun; Zhuo, Lisha; Kuang, Hong; Fu, Weiling

    2012-04-01

    The accurate and high-throughput detection of drug resistance-related multiple point mutations remains a challenge. Although the combination of molecular beacons with bio-immobilization technology, such as microarray, is promising, its application is difficult due to the ineffective immobilization of molecular beacons on the chip surface. Here, we propose a novel asymmetric-loop molecular beacon in which the loop consists of 2 parts. One is complementary to a target, while the other is complementary to an oligonucleotide probe immobilized on the chip surface. With this novel probe, a two-phase hybridization assay can be used for simultaneously detecting multiple point mutations. This assay will have advantages, such as easy probe availability, multiplex detection, low background, and high-efficiency hybridization, and may provide a new avenue for the immobilization of molecular beacons and high-throughput detection of point mutations.

  5. On the importance of having accurate data for astrophysical modelling

    NASA Astrophysics Data System (ADS)

    Lique, Francois

    2016-06-01

    The Herschel telescope and the ALMA and NOEMA interferometers have opened new windows of observation for wavelengths ranging from far infrared to sub-millimeter with spatial and spectral resolutions previously unmatched. To make the most of these observations, an accurate knowledge of the physical and chemical processes occurring in the interstellar and circumstellar media is essential.In this presentation, I will discuss what are the current needs of astrophysics in terms of molecular data and I will show that accurate molecular data are crucial for the proper determination of the physical conditions in molecular clouds.First, I will focus on collisional excitation studies that are needed for molecular lines modelling beyond the Local Thermodynamic Equilibrium (LTE) approach. In particular, I will show how new collisional data for the HCN and HNC isomers, two tracers of star forming conditions, have allowed solving the problem of their respective abundance in cold molecular clouds. I will also present the last collisional data that have been computed in order to analyse new highly resolved observations provided by the ALMA interferometer.Then, I will present the calculation of accurate rate constants for the F+H2 → HF+H and Cl+H2 ↔ HCl+H reactions, which have allowed a more accurate determination of the physical conditions in diffuse molecular clouds. I will also present the recent work on the ortho-para-H2 conversion due to hydrogen exchange that allow more accurate determination of the ortho-to-para-H2 ratio in the universe and that imply a significant revision of the cooling mechanism in astrophysical media.

  6. Accurate calculation of chemical shifts in highly dynamic H2@C60 through an integrated quantum mechanics/molecular dynamics scheme.

    PubMed

    Jiménez-Osés, Gonzalo; García, José I; Corzana, Francisco; Elguero, José

    2011-05-20

    A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values have never been reproduced. The dependence of the final values on the theoretical method and their implications to avoid over interpretation of the obtained results are carefully described.

  7. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  8. Ten Thousand Solar Constants Radiometer

    NASA Technical Reports Server (NTRS)

    Kendall, J. M., Sr.

    1985-01-01

    "Radiometer for Accurate (+ or - 1%) Measurement of Solar Irradiances Equal to 10,000 Solar Constants," gives additional information on radiometer described elsewhere. Self-calibrating, water-cooled, thermopile radiometer measures irradiance produced in solar image formed by parabolic reflector or by multiple-mirror solar installation.

  9. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods.

    PubMed

    Kapil, V; VandeVondele, J; Ceriotti, M

    2016-02-01

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  10. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

    NASA Astrophysics Data System (ADS)

    Kapil, V.; VandeVondele, J.; Ceriotti, M.

    2016-02-01

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  11. Thermodynamic and microscopic equilibrium constants of molecular species formed from pyridoxal 5'-phosphate and 2-amino-3-phosphonopropionic acid in aqueous and D/sub 2/O solution

    SciTech Connect

    Szpoganicz, B.; Martell, A.E.

    1984-09-19

    Schiff base formation between pyridoxal 5'-phosphate (PLP) and 2-amino-3-phosphonopropionic acid (APP) has been investigated by measurement of the corresponding NMR and electronic absorption spectra. A value of 0.26 was found for the formation constant of the completely deprotonated Schiff base species, and is much smaller than the values reported for pyridoxal-..beta..-chloroalanine and pyridoxal-O-phosphoserine. The protonation constants for the aldehyde and hydrate forms of PLP were determined in D/sub 2/O by measurement of the variation of chemical shifts with pD (pH in D/sub 2/O). The hydration constants of PLP were determined in a pD range 2-12, and species distributions were calculated. The protonation constants of the APP-PLP Schiff base determined by NMR in D/sub 2/O were found to have the log values 12.54, 8.10, 6.70, and 5.95, and the species distributions were calculated for a range of pD values. Evidence is reported for hydrogen bonding involving the phosphate and phosphonate groups of the diprotonated Schiff base. The cis and trans forms of the Schiff bases were distinguished with the aid of the nuclear Overhauser effect. 43 references, 9 figures, 3 tables.

  12. Trimodal color-fluorescence-polarization endoscopy aided by a tumor selective molecular probe accurately detects flat lesions in colitis-associated cancer

    PubMed Central

    Charanya, Tauseef; York, Timothy; Bloch, Sharon; Sudlow, Gail; Liang, Kexian; Garcia, Missael; Akers, Walter J.; Rubin, Deborah; Gruev, Viktor; Achilefu, Samuel

    2014-01-01

    Abstract. Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real-time detection of these lesions. Using azoxymethane-dextran sodium sulfate (AOM-DSS) treated mice, which recapitulates human CAC and dysplasia, we show that an octapeptide labeled with a near-infrared (NIR) fluorescent dye selectively identified all precancerous and cancerous lesions. A new thermoresponsive sol-gel formulation allowed topical application of the molecular probe during endoscopy. This method yielded high contrast-to-noise ratios (CNR) between adenomatous tumors (20.6±1.65) and flat lesions (12.1±1.03) and surrounding uninvolved colon tissue versus CNR of inflamed tissues (1.62±0.41). Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy shows a high depolarization contrast in both adenomatous tumors and flat lesions in CAC, reflecting compromised structural integrity of these tissues. Together, the real-time polarization imaging provides real-time validation of suspicious colon tissue highlighted by molecular fluorescence endoscopy. PMID:25473883

  13. Trimodal color-fluorescence-polarization endoscopy aided by a tumor selective molecular probe accurately detects flat lesions in colitis-associated cancer

    NASA Astrophysics Data System (ADS)

    Charanya, Tauseef; York, Timothy; Bloch, Sharon; Sudlow, Gail; Liang, Kexian; Garcia, Missael; Akers, Walter J.; Rubin, Deborah; Gruev, Viktor; Achilefu, Samuel

    2014-12-01

    Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real-time detection of these lesions. Using azoxymethane-dextran sodium sulfate (AOM-DSS) treated mice, which recapitulates human CAC and dysplasia, we show that an octapeptide labeled with a near-infrared (NIR) fluorescent dye selectively identified all precancerous and cancerous lesions. A new thermoresponsive sol-gel formulation allowed topical application of the molecular probe during endoscopy. This method yielded high contrast-to-noise ratios (CNR) between adenomatous tumors (20.6±1.65) and flat lesions (12.1±1.03) and surrounding uninvolved colon tissue versus CNR of inflamed tissues (1.62±0.41). Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy shows a high depolarization contrast in both adenomatous tumors and flat lesions in CAC, reflecting compromised structural integrity of these tissues. Together, the real-time polarization imaging provides real-time validation of suspicious colon tissue highlighted by molecular fluorescence endoscopy.

  14. The Hubble constant.

    PubMed

    Tully, R B

    1993-06-01

    Five methods of estimating distances have demonstrated internal reproducibility at the level of 5-20% rms accuracy. The best of these are the cepheid (and RR Lyrae), planetary nebulae, and surface-brightness fluctuation techniques. Luminosity-line width and Dn-sigma methods are less accurate for an individual case but can be applied to large numbers of galaxies. The agreement is excellent between these five procedures. It is determined that Hubble constant H0 = 90 +/- 10 km.s-1.Mpc-1 [1 parsec (pc) = 3.09 x 10(16) m]. It is difficult to reconcile this value with the preferred world model even in the low-density case. The standard model with Omega = 1 may be excluded unless there is something totally misunderstood about the foundation of the distance scale or the ages of stars. PMID:11607391

  15. The Hubble constant.

    PubMed Central

    Tully, R B

    1993-01-01

    Five methods of estimating distances have demonstrated internal reproducibility at the level of 5-20% rms accuracy. The best of these are the cepheid (and RR Lyrae), planetary nebulae, and surface-brightness fluctuation techniques. Luminosity-line width and Dn-sigma methods are less accurate for an individual case but can be applied to large numbers of galaxies. The agreement is excellent between these five procedures. It is determined that Hubble constant H0 = 90 +/- 10 km.s-1.Mpc-1 [1 parsec (pc) = 3.09 x 10(16) m]. It is difficult to reconcile this value with the preferred world model even in the low-density case. The standard model with Omega = 1 may be excluded unless there is something totally misunderstood about the foundation of the distance scale or the ages of stars. PMID:11607391

  16. Review of Rate Constants and Exploration of Correlations of the Halogen Transfer Reaction of Tri-substituted Carbon-centered Radicals with Molecular Halogens

    SciTech Connect

    Poutsma, Marvin L

    2012-01-01

    Rate constants for the reaction (R 3C + X2 R 3CX + X ; X = F, Cl, Br, and I) are reviewed. Because of curved Arrhenius plots and negative EX values, empirical structure-reactivity correlations are sought for log kX,298 rather than EX. The well-known poor correlation with measures of reaction enthalpy is demonstrated. The best quantitative predictor for R 3C is p, the sum of the Hammett p constants for the three substituents, R . Electronegative substituents with lone pairs, such as halogen or oxygen, thus appear to destabilize the formation of a polarized pre-reaction complex and/or TS ( +R---X---X -) by -inductive/field electron withdrawal while simultaneously stabilizing them by -resonance electron donation. The best quantitative predictor of the reactivity order of the halogens, I2 > Br2 >> Cl2 F2, is the polarizability of the halogen, (X-X). For the data set of 60 rate constants which span 6.5 orders of magnitude, a modestly successful correlation of log kX,298 is achieved with only two parameters, p and (X-X), with a mean unsigned deviation of 0.59 log units. How much of this residual variance is the result of inaccuracies in the data compared with over-simplification of the correlation approach remains to be seen.

  17. Molecular dynamics investigations of ozone on an ab initio potential energy surface with the utilization of pattern-recognition neural network for accurate determination of product formation.

    PubMed

    Le, Hung M; Dinh, Thach S; Le, Hieu V

    2011-10-13

    The singlet-triplet transformation and molecular dissociation of ozone (O(3)) gas is investigated by performing quasi-classical molecular dynamics (MD) simulations on an ab initio potential energy surface (PES) with visible and near-infrared excitations. MP4(SDQ) level of theory with the 6-311g(2d,2p) basis set is executed for three different electronic spin states (singlet, triplet, and quintet). In order to simplify the potential energy function, an approximation is adopted by ignoring the spin-orbit coupling and allowing the molecule to switch favorably and instantaneously to the spin state that is more energetically stable (lowest in energy among the three spin states). This assumption has previously been utilized to study the SiO(2) system as reported by Agrawal et al. (J. Chem. Phys. 2006, 124 (13), 134306). The use of such assumption in this study probably makes the upper limits of computed rate coefficients the true rate coefficients. The global PES for ozone is constructed by fitting 5906 ab initio data points using a 60-neuron two-layer feed-forward neural network. The mean-absolute error and root-mean-squared error of this fit are 0.0446 eV (1.03 kcal/mol) and 0.0756 eV (1.74 kcal/mol), respectively, which reveal very good fitting accuracy. The parameter coefficients of the global PES are reported in this paper. In order to identify the spin state with high confidence, we propose the use of a pattern-recognition neural network, which is trained to predict the spin state of a given configuration (with a prediction accuracy being 95.6% on a set of testing data points). To enhance the prediction effectiveness, a buffer series of five points are validated to confirm the spin state during the MD process to gain better confidence. Quasi-classical MD simulations from 1.2 to 2.4 eV of total internal energy (including zero-point energy) result in rate coefficients of singlet-triplet transformation in the range of 0.027 ps(-1) to 1.21 ps(-1). Also, we find very

  18. Review of rate constants and exploration of correlations of the halogen transfer reaction of trisubstituted carbon-centered radicals with molecular halogens.

    PubMed

    Poutsma, Marvin L

    2012-03-16

    Rate constants for the reaction (R'(3)C(•) + X(2) → R'(3)CX + X(•); X = F, Cl, Br, I) are reviewed. Because of curved Arrhenius plots and negative E(X) values, empirical structure-reactivity correlations are sought for log k(X,298) rather than E(X). The well-known poor correlation with measures of reaction enthalpy is demonstrated. The best quantitative predictor for R'(3)C(•) is Σσ(p), the sum of the Hammett σ(p) constants for the three substituents, R'. Electronegative substituents with lone pairs, such as halogen and oxygen, thus appear to destabilize the formation of a polarized prereaction complex and/or TS ((δ+)R- - -X- - -X(δ-)) by σ inductive/field electron withdrawal while simultaneously stabilizing them by π resonance electron donation. The best quantitative predictor of the reactivity order of the halogens, I(2) > Br(2) ≫ Cl(2) ≈ F(2), is the polarizability of the halogen, α(X(2)). For the data set of 60 rate constants which span 6.5 orders of magnitude, a modestly successful correlation of log k(X,298) is achieved with only two parameters, Σσ(p) and α(X(2)), with a mean unsigned deviation of 0.59 log unit. How much of this residual variance is the result of inaccuracies in the data in comparison with oversimplification of the correlation approach remains to be seen.

  19. Calculated rate constants for the reaction ClO + O yields Cl + O2 between 220 and 1000 deg K. [molecular trajectories and stratospheric ozone

    NASA Technical Reports Server (NTRS)

    Jaffee, R. L.

    1978-01-01

    Classical trajectory calculations are presented for the reaction ClO + O yields Cl + O2, a reaction which is an important step in the chlorine-catalyzed destruction of ozone which is thought to occur in the 220 and 1000 K. The calculated rate constant is 4.36 x 10 to the minus 11th power exp (-191/T)cu cm molecule (-1)s(-1) and its value at 300 K is 2.3 plus or minus 10 to the 11th power cu cm molecule (-1)s(-1), about a factor of 2 lower than recent experimental data. The empirical potential energy surface used in the calculations was constructed to fit experimental data for ClO, O2 and ClOO molecules. Other important features of this potential surface, such as the barrier to reaction, were varied systematically and calculations were performed for a range of conditions to determine the best theoretical rate constants. Results demonstrate the utility of classical trajectory methods for determining activation energies and other kinetic data for important atmospheric reactions.

  20. Novel, Precise, Accurate Ion-Pairing Method to Determine the Related Substances of the Fondaparinux Sodium Drug Substance: Low-Molecular-Weight Heparin

    PubMed Central

    Deshpande, Amol A.; Madhavan, P.; Deshpande, Girish R.; Chandel, Ravi Kumar; Yarbagi, Kaviraj M.; Joshi, Alok R.; Moses Babu, J.; Murali Krishna, R.; Rao, I. M.

    2016-01-01

    Fondaparinux sodium is a synthetic low-molecular-weight heparin (LMWH). This medication is an anticoagulant or a blood thinner, prescribed for the treatment of pulmonary embolism and prevention and treatment of deep vein thrombosis. Its determination in the presence of related impurities was studied and validated by a novel ion-pair HPLC method. The separation of the drug and its degradation products was achieved with the polymer-based PLRPs column (250 mm × 4.6 mm; 5 μm) in gradient elution mode. The mixture of 100 mM n-hexylamine and 100 mM acetic acid in water was used as buffer solution. Mobile phase A and mobile phase B were prepared by mixing the buffer and acetonitrile in the ratio of 90:10 (v/v) and 20:80 (v/v), respectively. Mobile phases were delivered in isocratic mode (2% B for 0–5 min) followed by gradient mode (2–85% B in 5–60 min). An Evaporative Light Scattering Detector (ELSD) was connected to the LC system to detect the responses of chromatographic separation. Further, the drug was subjected to stress studies for acidic, basic, oxidative, photolytic, and thermal degradations as per ICH guidelines and the drug was found to be labile in acid, base hydrolysis, and oxidation, while stable in neutral, thermal, and photolytic degradation conditions. The method provided linear responses over the concentration range of the LOQ to 0.30% for each impurity with respect to the analyte concentration of 12.5 mg/mL, and regression analysis showed a correlation coefficient value (r2) of more than 0.99 for all the impurities. The LOD and LOQ were found to be 1.4 µg/mL and 4.1 µg/mL, respectively, for fondaparinux. The developed ion-pair method was validated as per ICH guidelines with respect to accuracy, selectivity, precision, linearity, and robustness. PMID:27110496

  1. Novel, Precise, Accurate Ion-Pairing Method to Determine the Related Substances of the Fondaparinux Sodium Drug Substance: Low-Molecular-Weight Heparin.

    PubMed

    Deshpande, Amol A; Madhavan, P; Deshpande, Girish R; Chandel, Ravi Kumar; Yarbagi, Kaviraj M; Joshi, Alok R; Moses Babu, J; Murali Krishna, R; Rao, I M

    2016-01-01

    Fondaparinux sodium is a synthetic low-molecular-weight heparin (LMWH). This medication is an anticoagulant or a blood thinner, prescribed for the treatment of pulmonary embolism and prevention and treatment of deep vein thrombosis. Its determination in the presence of related impurities was studied and validated by a novel ion-pair HPLC method. The separation of the drug and its degradation products was achieved with the polymer-based PLRPs column (250 mm × 4.6 mm; 5 μm) in gradient elution mode. The mixture of 100 mM n-hexylamine and 100 mM acetic acid in water was used as buffer solution. Mobile phase A and mobile phase B were prepared by mixing the buffer and acetonitrile in the ratio of 90:10 (v/v) and 20:80 (v/v), respectively. Mobile phases were delivered in isocratic mode (2% B for 0-5 min) followed by gradient mode (2-85% B in 5-60 min). An Evaporative Light Scattering Detector (ELSD) was connected to the LC system to detect the responses of chromatographic separation. Further, the drug was subjected to stress studies for acidic, basic, oxidative, photolytic, and thermal degradations as per ICH guidelines and the drug was found to be labile in acid, base hydrolysis, and oxidation, while stable in neutral, thermal, and photolytic degradation conditions. The method provided linear responses over the concentration range of the LOQ to 0.30% for each impurity with respect to the analyte concentration of 12.5 mg/mL, and regression analysis showed a correlation coefficient value (r(2)) of more than 0.99 for all the impurities. The LOD and LOQ were found to be 1.4 µg/mL and 4.1 µg/mL, respectively, for fondaparinux. The developed ion-pair method was validated as per ICH guidelines with respect to accuracy, selectivity, precision, linearity, and robustness. PMID:27110496

  2. Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-01

    Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min.

  3. Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-01

    Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min. PMID:25158224

  4. Massive sequencing of Ulmus minor’s transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

    PubMed Central

    Perdiguero, Pedro; Venturas, Martin; Cervera, María Teresa; Gil, Luis; Collada, Carmen

    2015-01-01

    Elms, especially Ulmus minor and U. americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i) obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii) perform a functional annotation of the assembled transcriptome, (iii) identify genes potentially involved in the molecular response to environmental stress, and (iv) develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the genome from the most common plant model species. Well-known family proteins and transcription factors involved in abiotic, biotic or both stresses were identified after functional annotation. A total of 30,693 polymorphisms were identified in 7,125 isotigs, a large number of them corresponding to single nucleotide polymorphisms (SNPs; 27,359). In a subset randomly selected for validation, 87% of the SNPs were confirmed. The material generated may be valuable for future Ulmus gene expression, population genomics and association genetics studies, especially taking into account the scarce molecular information available for this genus and the great impact that DED has on elm populations. PMID:26257751

  5. Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease.

    PubMed

    Perdiguero, Pedro; Venturas, Martin; Cervera, María Teresa; Gil, Luis; Collada, Carmen

    2015-01-01

    Elms, especially Ulmus minor and U. americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i) obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii) perform a functional annotation of the assembled transcriptome, (iii) identify genes potentially involved in the molecular response to environmental stress, and (iv) develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the genome from the most common plant model species. Well-known family proteins and transcription factors involved in abiotic, biotic or both stresses were identified after functional annotation. A total of 30,693 polymorphisms were identified in 7,125 isotigs, a large number of them corresponding to single nucleotide polymorphisms (SNPs; 27,359). In a subset randomly selected for validation, 87% of the SNPs were confirmed. The material generated may be valuable for future Ulmus gene expression, population genomics and association genetics studies, especially taking into account the scarce molecular information available for this genus and the great impact that DED has on elm populations. PMID:26257751

  6. Predicting hydration Gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data.

    PubMed

    Garrido, Nuno M; Jorge, Miguel; Queimada, António J; Gomes, José R B; Economou, Ioannis G; Macedo, Eugénia A

    2011-10-14

    The Gibbs energy of hydration is an important quantity to understand the molecular behavior in aqueous systems at constant temperature and pressure. In this work we review the performance of some popular force fields, namely TraPPE, OPLS-AA and Gromos, in reproducing the experimental Gibbs energies of hydration of several alkyl-aromatic compounds--benzene, mono-, di- and tri-substituted alkylbenzenes--using molecular simulation techniques. In the second part of the paper, we report a new model that is able to improve such hydration energy predictions, based on Lennard Jones parameters from the recent TraPPE-EH force field and atomic partial charges obtained from natural population analysis of density functional theory calculations. We apply a scaling factor determined by fitting the experimental hydration energy of only two solutes, and then present a simple rule to generate atomic partial charges for different substituted alkyl-aromatics. This rule has the added advantages of eliminating the unnecessary assumption of fixed charge on every substituted carbon atom and providing a simple guideline for extrapolating the charge assignment to any multi-substituted alkyl-aromatic molecule. The point charges derived here yield excellent predictions of experimental Gibbs energies of hydration, with an overall absolute average deviation of less than 0.6 kJ mol(-1). This new parameter set can also give good predictive performance for other thermodynamic properties and liquid structural information.

  7. Accurate Molecular Dimensions from Stearic Acid Monolayers.

    ERIC Educational Resources Information Center

    Lane, Charles A.; And Others

    1984-01-01

    Discusses modifications in the fatty acid monolayer experiment to reduce the inaccurate moleculary data students usually obtain. Copies of the experimental procedure used and a Pascal computer program to work up the data are available from the authors. (JN)

  8. Theoretical studies of vibrational energies and force constants of diatomic electronic states using algebraic approach and variational method

    NASA Astrophysics Data System (ADS)

    Sun, Weiguo; Hou, Shilin

    2002-05-01

    An algebraic method (AM) is proposed to study the accurate vibrational constants and energies based on an accurate limited experimental/theoretical input data set, and a potential variational method (PVM) is suggested to generate reliable force constants, rotational spectrum constants and rovibrational energies for a diatomic molecular electronic state based on the second order perturbation theory. The vibrational force constants fn's used to evaluate the rotational spectrum constants are determined variationally. The AM generates accurate vibrational constants and energies using standard algebraic approach without any mathematical and/or physical approximations. The accuracy of the AM vibrational constants and energies is uniquely dependent on the quality of the input experimental/theoretical data. Both the AM and the PVM have been applied to study 10 diatomic electronic states of H2, N2, O2, and Br2 molecules. These example studies show that: 1.) the AM not only reproduce the input energies, but also generate the Ev's of high vibrational excited states which may be difficult to obtain experimentally or theoretically; 2.) the PVM vibrational force constants fn's may be used to measure the relative chemical bond strengths of different diatomic electronic states for a molecule quantitatively.

  9. Quantum instanton approximation for thermal rate constants of chemical reactions

    NASA Astrophysics Data System (ADS)

    Miller, William H.; Zhao, Yi; Ceotto, Michele; Yang, Sandy

    2003-07-01

    A quantum mechanical theory for chemical reaction rates is presented which is modeled after the [semiclassical (SC)] instanton approximation. It incorporates the desirable aspects of the instanton picture, which involves only properties of the (SC approximation to the) Boltzmann operator, but corrects its quantitative deficiencies by replacing the SC approximation for the Boltzmann operator by the quantum Boltzmann operator, exp(-βĤ). Since a calculation of the quantum Boltzmann operator is feasible for quite complex molecular systems (by Monte Carlo path integral methods), having an accurate rate theory that involves only the Boltzmann operator could be quite useful. The application of this quantum instanton approximation to several one- and two-dimensional model problems illustrates its potential; e.g., it is able to describe thermal rate constants accurately (˜10-20% error) from high to low temperatures deep in the tunneling regime, and applies equally well to asymmetric and symmetric potentials.

  10. Investigation of the resonance-assisted hydrogen bond in model β-diketones through localized molecular orbital analysis of the spin-spin coupling constants related to the O-H···O hydrogen bond.

    PubMed

    Zarycz, M Natalia C; Provasi, Patricio F

    2015-02-01

    The resonance-assisted hydrogen bond (HB) phenomenon has been studied theoretically by a localized molecular orbital (LMO) decomposition of the spin-spin coupling constants between atoms either involved or close to the O-H···O system of some β-diketones and their saturated counterparts. The analysis, carried out at the level of the second-order polarization propagator approximation, shows that the contributions in terms of LMO to the paramagnetic spin orbital and the spin dipolar Ramsey terms proof the importance of the delocalized π-electron structure supporting the idea of the existence of the resonance-assisted HB phenomenon phenomenon. The LMO contributions to the Fermi contact term indicate mainly the presence of the HB that may or not be linked to the π-electrons.

  11. On the Khinchin Constant

    NASA Technical Reports Server (NTRS)

    Bailey, David H.; Borwein, Jonathan M.; Crandall, Richard E.; Craw, James M. (Technical Monitor)

    1995-01-01

    We prove known identities for the Khinchin constant and develop new identities for the more general Hoelder mean limits of continued fractions. Any of these constants can be developed as a rapidly converging series involving values of the Riemann zeta function and rational coefficients. Such identities allow for efficient numerical evaluation of the relevant constants. We present free-parameter, optimizable versions of the identities, and report numerical results.

  12. The hubble constant.

    PubMed

    Huchra, J P

    1992-04-17

    The Hubble constant is the constant of proportionality between recession velocity and distance in the expanding universe. It is a fundamental property of cosmology that sets both the scale and the expansion age of the universe. It is determined by measurement of galaxy The Hubble constant is the constant of proportionality between recession velocity and development of new techniques for the measurements of galaxy distances, both calibration uncertainties and debates over systematic errors remain. Current determinations still range over nearly a factor of 2; the higher values favored by most local measurements are not consistent with many theories of the origin of large-scale structure and stellar evolution. PMID:17743107

  13. The cosmological constant

    NASA Technical Reports Server (NTRS)

    Carroll, Sean M.; Press, William H.; Turner, Edwin L.

    1992-01-01

    The cosmological constant problem is examined in the context of both astronomy and physics. Effects of a nonzero cosmological constant are discussed with reference to expansion dynamics, the age of the universe, distance measures, comoving density of objects, growth of linear perturbations, and gravitational lens probabilities. The observational status of the cosmological constant is reviewed, with attention given to the existence of high-redshift objects, age derivation from globular clusters and cosmic nuclear data, dynamical tests of Omega sub Lambda, quasar absorption line statistics, gravitational lensing, and astrophysics of distant objects. Finally, possible solutions to the physicist's cosmological constant problem are examined.

  14. Beyond the Hubble Constant

    NASA Astrophysics Data System (ADS)

    1995-08-01

    about the distances to galaxies and thereby about the expansion rate of the Universe. A simple way to determine the distance to a remote galaxy is by measuring its redshift, calculate its velocity from the redshift and divide this by the Hubble constant, H0. For instance, the measured redshift of the parent galaxy of SN 1995K (0.478) yields a velocity of 116,000 km/sec, somewhat more than one-third of the speed of light (300,000 km/sec). From the universal expansion rate, described by the Hubble constant (H0 = 20 km/sec per million lightyears as found by some studies), this velocity would indicate a distance to the supernova and its parent galaxy of about 5,800 million lightyears. The explosion of the supernova would thus have taken place 5,800 million years ago, i.e. about 1,000 million years before the solar system was formed. However, such a simple calculation works only for relatively ``nearby'' objects, perhaps out to some hundred million lightyears. When we look much further into space, we also look far back in time and it is not excluded that the universal expansion rate, i.e. the Hubble constant, may have been different at earlier epochs. This means that unless we know the change of the Hubble constant with time, we cannot determine reliable distances of distant galaxies from their measured redshifts and velocities. At the same time, knowledge about such change or lack of the same will provide unique information about the time elapsed since the Universe began to expand (the ``Big Bang''), that is, the age of the Universe and also its ultimate fate. The Deceleration Parameter q0 Cosmologists are therefore eager to determine not only the current expansion rate (i.e., the Hubble constant, H0) but also its possible change with time (known as the deceleration parameter, q0). Although a highly accurate value of H0 has still not become available, increasing attention is now given to the observational determination of the second parameter, cf. also the Appendix at the

  15. Fundamental Physical Constants

    National Institute of Standards and Technology Data Gateway

    SRD 121 CODATA Fundamental Physical Constants (Web, free access)   This site, developed in the Physics Laboratory at NIST, addresses three topics: fundamental physical constants, the International System of Units (SI), which is the modern metric system, and expressing the uncertainty of measurement results.

  16. Calculation of magnetostriction constants

    NASA Astrophysics Data System (ADS)

    Tatebayashi, T.; Ohtsuka, S.; Ukai, T.; Mori, N.

    1986-02-01

    The magnetostriction constants h1 and h2 for Ni and Fe metals and the anisotropy constants K1 and K2 for Fe metal are calculated on the basis of the approximate d bands obtained by Deegan's prescription, by using Gilat-Raubenheimer's method. The obtained results are compared with the experimental ones.

  17. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  18. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  19. SPLASH: Accurate OH maser positions

    NASA Astrophysics Data System (ADS)

    Walsh, Andrew; Gomez, Jose F.; Jones, Paul; Cunningham, Maria; Green, James; Dawson, Joanne; Ellingsen, Simon; Breen, Shari; Imai, Hiroshi; Lowe, Vicki; Jones, Courtney

    2013-10-01

    The hydroxyl (OH) 18 cm lines are powerful and versatile probes of diffuse molecular gas, that may trace a largely unstudied component of the Galactic ISM. SPLASH (the Southern Parkes Large Area Survey in Hydroxyl) is a large, unbiased and fully-sampled survey of OH emission, absorption and masers in the Galactic Plane that will achieve sensitivities an order of magnitude better than previous work. In this proposal, we request ATCA time to follow up OH maser candidates. This will give us accurate (~10") positions of the masers, which can be compared to other maser positions from HOPS, MMB and MALT-45 and will provide full polarisation measurements towards a sample of OH masers that have not been observed in MAGMO.

  20. Space Shuttle astrodynamical constants

    NASA Technical Reports Server (NTRS)

    Cockrell, B. F.; Williamson, B.

    1978-01-01

    Basic space shuttle astrodynamic constants are reported for use in mission planning and construction of ground and onboard software input loads. The data included here are provided to facilitate the use of consistent numerical values throughout the project.

  1. The Possible Interstellar Anion CH2CN-: Spectroscopic Constants, Vibrational Frequencies, and Other Considerations

    NASA Technical Reports Server (NTRS)

    Fortenberry, Ryan C.; Crawford, T. Daniel; Lee, Timothy J.

    2012-01-01

    The A 1B1 <-1A0 excitation into the dipole-bound state of the cyanomethyl anion (CH2CN??) has been hypothesized as the carrier for one di use interstellar band. However, this particular molecular system has not been detected in the interstellar medium even though the related cyanomethyl radical and the isoelectronic ketenimine molecule have been found. In this study we are employing the use of proven quartic force elds and second-order vibrational perturbation theory to compute accurate spectroscopic constants and fundamental vibrational frequencies for X 1A0 CH2CN?? in order to assist in laboratory studies and astronomical observations. Keywords: Astrochemistry, ISM: molecular anions, Quartic force elds, Rotational constants, Vibrational frequencies

  2. Constant potential pulse polarography

    USGS Publications Warehouse

    Christie, J.H.; Jackson, L.L.; Osteryoung, R.A.

    1976-01-01

    The new technique of constant potential pulse polarography, In which all pulses are to be the same potential, is presented theoretically and evaluated experimentally. The response obtained is in the form of a faradaic current wave superimposed on a constant capacitative component. Results obtained with a computer-controlled system exhibit a capillary response current similar to that observed In normal pulse polarography. Calibration curves for Pb obtained using a modified commercial pulse polarographic instrument are in good accord with theoretical predictions.

  3. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface

    SciTech Connect

    Buryak, Ilya; Vigasin, Andrey A.

    2015-12-21

    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  4. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface

    NASA Astrophysics Data System (ADS)

    Buryak, Ilya; Vigasin, Andrey A.

    2015-12-01

    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  5. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface.

    PubMed

    Buryak, Ilya; Vigasin, Andrey A

    2015-12-21

    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  6. Absolute radiometry and the solar constant

    NASA Technical Reports Server (NTRS)

    Willson, R. C.

    1974-01-01

    A series of active cavity radiometers (ACRs) are described which have been developed as standard detectors for the accurate measurement of irradiance in absolute units. It is noted that the ACR is an electrical substitution calorimeter, is designed for automatic remote operation in any environment, and can make irradiance measurements in the range from low-level IR fluxes up to 30 solar constants with small absolute uncertainty. The instrument operates in a differential mode by chopping the radiant flux to be measured at a slow rate, and irradiance is determined from two electrical power measurements together with the instrumental constant. Results are reported for measurements of the solar constant with two types of ACRs. The more accurate measurement yielded a value of 136.6 plus or minus 0.7 mW/sq cm (1.958 plus or minus 0.010 cal/sq cm per min).

  7. Elastic constants of calcite

    USGS Publications Warehouse

    Peselnick, L.; Robie, R.A.

    1962-01-01

    The recent measurements of the elastic constants of calcite by Reddy and Subrahmanyam (1960) disagree with the values obtained independently by Voigt (1910) and Bhimasenachar (1945). The present authors, using an ultrasonic pulse technique at 3 Mc and 25??C, determined the elastic constants of calcite using the exact equations governing the wave velocities in the single crystal. The results are C11=13.7, C33=8.11, C44=3.50, C12=4.82, C13=5.68, and C14=-2.00, in units of 1011 dyncm2. Independent checks of several of the elastic constants were made employing other directions and polarizations of the wave velocities. With the exception of C13, these values substantially agree with the data of Voigt and Bhimasenachar. ?? 1962 The American Institute of Physics.

  8. Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.

    PubMed

    Puzzarini, Cristina

    2015-11-25

    The structures, relative stabilities, and rotational and vibrational parameters of the Z-C-, E-C-, and N-cyanomethanimine isomers have been evaluated using state-of-the-art quantum-chemical approaches. Equilibrium geometries have been calculated by means of a composite scheme based on coupled-cluster calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The latter approach is proved to provide molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled-cluster theory, including up to single, double, triple, and quadruple excitations, and corrected for core-electron correlation and anharmonic zero-point vibrational energy, have been used to accurately determine relative energies and the Z-E isomerization barrier with an accuracy of about 1 kJ/mol. Vibrational and rotational spectroscopic parameters have been investigated by means of hybrid schemes that allow us to obtain rotational constants accurate to about a few megahertz and vibrational frequencies with a mean absolute error of ∼1%. Where available, for all properties considered, a very good agreement with experimental data has been observed.

  9. The Hubble constant

    NASA Technical Reports Server (NTRS)

    Huchra, John P.

    1992-01-01

    The Hubble constant is the constant of proportionality between recession velocity and distance in the expanding universe. It is a fundamental property of cosmology that sets both the scale and the expansion age of the universe. It is determined by measurement of galaxy radial velocities and distances. Although there has been considerable progress in the development of new techniques for the measurements of galaxy distances, both calibration uncertainties and debates over systematic errors remain. Current determinations still range over nearly a factor of 2; the higher values favored by most local measurements are not consistent with many theories of the origin of large-scale structure and stellar evolution.

  10. Compassion is a constant.

    PubMed

    Scott, Tricia

    2015-11-01

    Compassion is a powerful word that describes an intense feeling of commiseration and a desire to help those struck by misfortune. Most people know intuitively how and when to offer compassion to relieve another person's suffering. In health care, compassion is a constant; it cannot be rationed because emergency nurses have limited time or resources to manage increasing demands.

  11. XrayOpticsConstants

    2005-06-20

    This application (XrayOpticsConstants) is a tool for displaying X-ray and Optical properties for a given material, x-ray photon energy, and in the case of a gas, pressure. The display includes fields such as the photo-electric absorption attenuation length, density, material composition, index of refraction, and emission properties (for scintillator materials).

  12. Compassion is a constant.

    PubMed

    Scott, Tricia

    2015-11-01

    Compassion is a powerful word that describes an intense feeling of commiseration and a desire to help those struck by misfortune. Most people know intuitively how and when to offer compassion to relieve another person's suffering. In health care, compassion is a constant; it cannot be rationed because emergency nurses have limited time or resources to manage increasing demands. PMID:26542898

  13. Accurate Optical Reference Catalogs

    NASA Astrophysics Data System (ADS)

    Zacharias, N.

    2006-08-01

    Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

  14. Wall of fundamental constants

    SciTech Connect

    Olive, Keith A.; Peloso, Marco; Uzan, Jean-Philippe

    2011-02-15

    We consider the signatures of a domain wall produced in the spontaneous symmetry breaking involving a dilatonlike scalar field coupled to electromagnetism. Domains on either side of the wall exhibit slight differences in their respective values of the fine-structure constant, {alpha}. If such a wall is present within our Hubble volume, absorption spectra at large redshifts may or may not provide a variation in {alpha} relative to the terrestrial value, depending on our relative position with respect to the wall. This wall could resolve the contradiction between claims of a variation of {alpha} based on Keck/Hires data and of the constancy of {alpha} based on Very Large Telescope data. We derive the properties of the wall and the parameters of the underlying microscopic model required to reproduce the possible spatial variation of {alpha}. We discuss the constraints on the existence of the low-energy domain wall and describe its observational implications concerning the variation of the fundamental constants.

  15. JCZS: An Intermolecular Potential Database for Performing Accurate Detonation and Expansion Calculations

    SciTech Connect

    Baer, M.R.; Hobbs, M.L.; McGee, B.C.

    1998-11-03

    Exponential-13,6 (EXP-13,6) potential pammeters for 750 gases composed of 48 elements were determined and assembled in a database, referred to as the JCZS database, for use with the Jacobs Cowperthwaite Zwisler equation of state (JCZ3-EOS)~l) The EXP- 13,6 force constants were obtained by using literature values of Lennard-Jones (LJ) potential functions, by using corresponding states (CS) theory, by matching pure liquid shock Hugoniot data, and by using molecular volume to determine the approach radii with the well depth estimated from high-pressure isen- tropes. The JCZS database was used to accurately predict detonation velocity, pressure, and temperature for 50 dif- 3 Accurate predictions were also ferent explosives with initial densities ranging from 0.25 glcm3 to 1.97 g/cm . obtained for pure liquid shock Hugoniots, static properties of nitrogen, and gas detonations at high initial pressures.

  16. Varying constants quantum cosmology

    SciTech Connect

    Leszczyńska, Katarzyna; Balcerzak, Adam; Dabrowski, Mariusz P. E-mail: abalcerz@wmf.univ.szczecin.pl

    2015-02-01

    We discuss minisuperspace models within the framework of varying physical constants theories including Λ-term. In particular, we consider the varying speed of light (VSL) theory and varying gravitational constant theory (VG) using the specific ansätze for the variability of constants: c(a) = c{sub 0} a{sup n} and G(a)=G{sub 0} a{sup q}. We find that most of the varying c and G minisuperspace potentials are of the tunneling type which allows to use WKB approximation of quantum mechanics. Using this method we show that the probability of tunneling of the universe ''from nothing'' (a=0) to a Friedmann geometry with the scale factor a{sub t} is large for growing c models and is strongly suppressed for diminishing c models. As for G varying, the probability of tunneling is large for G diminishing, while it is small for G increasing. In general, both varying c and G change the probability of tunneling in comparison to the standard matter content (cosmological term, dust, radiation) universe models.

  17. Dielectric constant of water in the interface.

    PubMed

    Dinpajooh, Mohammadhasan; Matyushov, Dmitry V

    2016-07-01

    We define the dielectric constant (susceptibility) that should enter the Maxwell boundary value problem when applied to microscopic dielectric interfaces polarized by external fields. The dielectric constant (susceptibility) of the interface is defined by exact linear-response equations involving correlations of statistically fluctuating interface polarization and the Coulomb interaction energy of external charges with the dielectric. The theory is applied to the interface between water and spherical solutes of altering size studied by molecular dynamics (MD) simulations. The effective dielectric constant of interfacial water is found to be significantly lower than its bulk value, and it also depends on the solute size. For TIP3P water used in MD simulations, the interface dielectric constant changes from 9 to 4 when the solute radius is increased from ∼5 to 18 Å.

  18. Simple liquid models with corrected dielectric constants.

    PubMed

    Fennell, Christopher J; Li, Libo; Dill, Ken A

    2012-06-14

    Molecular simulations often use explicit-solvent models. Sometimes explicit-solvent models can give inaccurate values for basic liquid properties, such as the density, heat capacity, and permittivity, as well as inaccurate values for molecular transfer free energies. Such errors have motivated the development of more complex solvents, such as polarizable models. We describe an alternative here. We give new fixed-charge models of solvents for molecular simulations--water, carbon tetrachloride, chloroform, and dichloromethane. Normally, such solvent models are parametrized to agree with experimental values of the neat liquid density and enthalpy of vaporization. Here, in addition to those properties, our parameters are chosen to give the correct dielectric constant. We find that these new parametrizations also happen to give better values for other properties, such as the self-diffusion coefficient. We believe that parametrizing fixed-charge solvent models to fit experimental dielectric constants may provide better and more efficient ways to treat solvents in computer simulations.

  19. Effect of pressure on the proton-proton vicinal coupling constants in 1,1,2-tricholoethane and 1,1,2,2-tetrachloroethane-1- sup 13 C. A new approach to hig-pressure study of molecular conformations

    SciTech Connect

    Yamada, H.; Kazuoka, T.; Sera, A. )

    1988-10-26

    The first observation of a pressure-induced change in the proton-proton vicinal coupling constants, J{sub vic}, are reported here. It is also demonstrated that the experiment possibly provides a new, straightforward approach to conformation studies at high pressure. The pressure effects on coupling constants of 1,1,2-trichloroethane + 10 mol % of cyclopentane, 1,1,2-trichloroethane, and 1,1,2-trichloroethane 1-{sup 13}C are reported. 17 refs., 3 figs.

  20. Elastic constants and dynamics in nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Humpert, Anja; Allen, Michael P.

    2015-09-01

    In this paper, we present molecular dynamics calculations of the Frank elastic constants, and associated time correlation functions, in nematic liquid crystals. We study two variants of the Gay-Berne potential, and use system sizes of half a million molecules, significantly larger than in previous studies of elastic behaviour. Equilibrium orientational fluctuations in reciprocal (k-) space were calculated, to determine the elastic constants by fitting at low |k|; our results indicate that small system size may be a source of inaccuracy in previous work. Furthermore, the dynamics of the Gay-Berne nematic were studied by calculating time correlation functions of components of the order tensor, together with associated components of the velocity field, for a set of wave vectors k. Confirming our earlier work, we found exponential decay for splay and twist correlations, and oscillatory exponential decay for the bend correlation. In this work, we confirm similar behaviour for the corresponding velocity components. In all cases, the decay rates, and oscillation frequencies, were found to be accurately proportional to k2 for small k, as predicted by the equations of nematodynamics. However, the observation of oscillatory bend fluctuations, and corresponding oscillatory shear flow decay, is in contradiction to the usual assumptions appearing in the literature, and in standard texts. We discuss the advantages and drawbacks of using large systems in these calculations.

  1. RNA structure and scalar coupling constants

    SciTech Connect

    Tinoco, I. Jr.; Cai, Z.; Hines, J.V.; Landry, S.M.; SantaLucia, J. Jr.; Shen, L.X.; Varani, G.

    1994-12-01

    Signs and magnitudes of scalar coupling constants-spin-spin splittings-comprise a very large amount of data that can be used to establish the conformations of RNA molecules. Proton-proton and proton-phosphorus splittings have been used the most, but the availability of {sup 13}C-and {sup 15}N-labeled molecules allow many more coupling constants to be used for determining conformation. We will systematically consider the torsion angles that characterize a nucleotide unit and the coupling constants that depend on the values of these torsion angles. Karplus-type equations have been established relating many three-bond coupling constants to torsion angles. However, one- and two-bond coupling constants can also depend on conformation. Serianni and coworkers measured carbon-proton coupling constants in ribonucleosides and have calculated their values as a function of conformation. The signs of two-bond coupling can be very useful because it is easier to measure a sign than an accurate magnitude.

  2. New Quasar Studies Keep Fundamental Physical Constant Constant

    NASA Astrophysics Data System (ADS)

    2004-03-01

    from the Oklo natural reactor. Nevertheless, further progress in this field is expected with the new very-high-accuracy radial velocity spectrometer HARPS on ESO's 3.6-m telescope at the La Silla Observatory (Chile). This spectrograph works at the limit of modern technology and is mostly used to detect new planets around stars other than the Sun - it may provide an order of magnitude improvement on the determination of the variation of alpha. Other fundamental constants can be probed using quasars. In particular, by studying the wavelengths of molecular hydrogen in the remote Universe, one can probe the variations of the ratio between the masses of the proton and the electron. The same team is now engaged in such a large survey with the Very Large Telescope that should lead to unprecedented constraints on this ratio. More Information The research presented in this Press Release is based on papers published in Physical Review Letters ("Limits on the time variation of the electromagnetic fine-structure constant in the low energy limit from absorption lines in the spectra of distant quasars" by Raghunathan Srianand, Hum Chand, Patrick Petitjean, and Bastien Aracil) and in the leading European astronomy journal Astronomy & Astrophysics ("Probing the cosmological variation of the fine-structure constant: Results based on VLT-UVES sample" by Hum Chand, Raghunathan Srianand, Patrick Petitjean, and Bastien Aracil).

  3. Change is a Constant.

    PubMed

    Lubowitz, James H; Provencher, Matthew T; Brand, Jefferson C; Rossi, Michael J; Poehling, Gary G

    2015-06-01

    In 2015, Henry P. Hackett, Managing Editor, Arthroscopy, retires, and Edward A. Goss, Executive Director, Arthroscopy Association of North America (AANA), retires. Association is a positive constant, in a time of change. With change comes a need for continuing education, research, and sharing of ideas. While the quality of education at AANA and ISAKOS is superior and most relevant, the unique reason to travel and meet is the opportunity to interact with innovative colleagues. Personal interaction best stimulates new ideas to improve patient care, research, and teaching. Through our network, we best create innovation.

  4. Cosmology with varying constants.

    PubMed

    Martins, Carlos J A P

    2002-12-15

    The idea of possible time or space variations of the 'fundamental' constants of nature, although not new, is only now beginning to be actively considered by large numbers of researchers in the particle physics, cosmology and astrophysics communities. This revival is mostly due to the claims of possible detection of such variations, in various different contexts and by several groups. I present the current theoretical motivations and expectations for such variations, review the current observational status and discuss the impact of a possible confirmation of these results in our views of cosmology and physics as a whole.

  5. Temperature dependent effective potential method for accurate free energy calculations of solids

    NASA Astrophysics Data System (ADS)

    Hellman, Olle; Steneteg, Peter; Abrikosov, I. A.; Simak, S. I.

    2013-03-01

    We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on ab initio molecular dynamics followed by a mapping onto a model Hamiltonian that describes the lattice dynamics. The formalism and the numerical aspects of the technique are described in detail. A number of practical examples are given, and results are presented, which confirm the usefulness of TDEP within ab initio and classical molecular dynamics frameworks. In particular, we examine from first principles the behavior of force constants upon the dynamical stabilization of the body centered phase of Zr, and show that they become more localized. We also calculate the phase diagram for 4He modeled with the Aziz potential and obtain results which are in favorable agreement both with respect to experiment and established techniques.

  6. Modeling Nonlinear Adsorption with a Single Chemical Parameter: Predicting Chemical Median Langmuir Binding Constants.

    PubMed

    Davis, Craig Warren; Di Toro, Dominic M

    2015-07-01

    Procedures for accurately predicting linear partition coefficients onto various sorbents (e.g., organic carbon, soils, clay) are reliable and well established. However, similar procedures for the prediction of sorption parameters of nonlinear isotherm models are not. The purpose of this paper is to present a procedure for predicting nonlinear isotherm parameters, specifically the median Langmuir binding constants, K̃L, obtained utilizing the single-chemical parameter log-normal Langmuir isotherm developed in the accompanying work. A reduced poly parameter linear free energy relationship (pp-LFER) is able to predict median Langmuir binding constants for graphite, charcoal, and Darco granular activated carbon (GAC) adsorption data. For the larger F400 GAC data set, a single pp-LFER model was insufficient, as a plateau is observed for the median Langmuir binding constants of larger molecular volume sorbates. This volumetric cutoff occurs in proximity to the median pore diameter for F400 GAC. A log-linear relationship exists between the aqueous solubility of these large compounds and their median Langmuir binding constants. Using this relationship for the chemicals above the volumetric cutoff and the pp-LFER below the cutoff, the median Langmuir binding constants can be predicted with a root-mean square error for graphite (n = 13), charcoal (n = 11), Darco GAC (n = 14), and F400 GAC (n = 44) of 0.129, 0.307, 0.407, and 0.424, respectively. PMID:26035017

  7. Modeling Nonlinear Adsorption with a Single Chemical Parameter: Predicting Chemical Median Langmuir Binding Constants.

    PubMed

    Davis, Craig Warren; Di Toro, Dominic M

    2015-07-01

    Procedures for accurately predicting linear partition coefficients onto various sorbents (e.g., organic carbon, soils, clay) are reliable and well established. However, similar procedures for the prediction of sorption parameters of nonlinear isotherm models are not. The purpose of this paper is to present a procedure for predicting nonlinear isotherm parameters, specifically the median Langmuir binding constants, K̃L, obtained utilizing the single-chemical parameter log-normal Langmuir isotherm developed in the accompanying work. A reduced poly parameter linear free energy relationship (pp-LFER) is able to predict median Langmuir binding constants for graphite, charcoal, and Darco granular activated carbon (GAC) adsorption data. For the larger F400 GAC data set, a single pp-LFER model was insufficient, as a plateau is observed for the median Langmuir binding constants of larger molecular volume sorbates. This volumetric cutoff occurs in proximity to the median pore diameter for F400 GAC. A log-linear relationship exists between the aqueous solubility of these large compounds and their median Langmuir binding constants. Using this relationship for the chemicals above the volumetric cutoff and the pp-LFER below the cutoff, the median Langmuir binding constants can be predicted with a root-mean square error for graphite (n = 13), charcoal (n = 11), Darco GAC (n = 14), and F400 GAC (n = 44) of 0.129, 0.307, 0.407, and 0.424, respectively.

  8. About variable constants

    NASA Astrophysics Data System (ADS)

    Blichert-Toft, J.; Albarede, F.

    2011-12-01

    When only modern isotope compositions are concerned, the choice of normalization values is inconsequential provided that their values are universally accepted. No harm is done as long as large amounts of standard reference material with known isotopic differences with respect to the reference value ('anchor point') can be maintained under controlled conditions. For over five decades, the scientific community has been referring to an essentially unavailable SMOW for stable O and H isotopes and to a long-gone belemnite sample for carbon. For radiogenic isotopes, the isotope composition of the daughter element, the parent-daughter ratio, and a particular value of the decay constant are all part of the reference. For the Lu-Hf system, for which the physical measurements of the decay constant have been particularly defective, the reference includes the isotope composition of Hf and the Lu/Hf ratio of an unfortunately heterogeneous chondrite mix that has been successively refined by Patchett and Tatsumoto (1981), Blichert-Toft and Albarede (1997, BTA), and Bouvier et al. (2008, BVP). The \\varepsilonHf(T) difference created by using BTA and BVP is nearly within error (+0.45 epsilon units today and -0.36 at 3 Ga) and therefore of little or no consequence. A more serious issue arises when the chondritic reference is taken to represent the Hf isotope evolution of the Bulk Silicate Earth (BSE): the initial isotope composition of the Solar System, as determined by the indistinguishable intercepts of the external eucrite isochron (Blichert-Toft et al., 2002) and the internal angrite SAH99555 isochron (Thrane et al., 2010), differs from the chondrite value of BTA and BVP extrapolated to 4.56 Ga by ~5 epsilon units. This difference and the overestimated value of the 176Lu decay constant derived from the slopes of these isochrons, have been interpreted as reflecting irradiation of the solar nebula by either gamma (Albarede et al., 2006) or cosmic rays (Thrane et al., 2010) during

  9. When constants are important

    SciTech Connect

    Beiu, V.

    1997-04-01

    In this paper the authors discuss several complexity aspects pertaining to neural networks, commonly known as the curse of dimensionality. The focus will be on: (1) size complexity and depth-size tradeoffs; (2) complexity of learning; and (3) precision and limited interconnectivity. Results have been obtained for each of these problems when dealt with separately, but few things are known as to the links among them. They start by presenting known results and try to establish connections between them. These show that they are facing very difficult problems--exponential growth in either space (i.e. precision and size) and/or time (i.e., learning and depth)--when resorting to neural networks for solving general problems. The paper will present a solution for lowering some constants, by playing on the depth-size tradeoff.

  10. Unitaxial constant velocity microactuator

    DOEpatents

    McIntyre, Timothy J.

    1994-01-01

    A uniaxial drive system or microactuator capable of operating in an ultra-high vacuum environment. The mechanism includes a flexible coupling having a bore therethrough, and two clamp/pusher assemblies mounted in axial ends of the coupling. The clamp/pusher assemblies are energized by voltage-operated piezoelectrics therewithin to operatively engage the shaft and coupling causing the shaft to move along its rotational axis through the bore. The microactuator is capable of repeatably positioning to sub-manometer accuracy while affording a scan range in excess of 5 centimeters. Moreover, the microactuator generates smooth, constant velocity motion profiles while producing a drive thrust of greater than 10 pounds. The system is remotely controlled and piezoelectrically driven, hence minimal thermal loading, vibrational excitation, or outgassing is introduced to the operating environment.

  11. Unitaxial constant velocity microactuator

    DOEpatents

    McIntyre, T.J.

    1994-06-07

    A uniaxial drive system or microactuator capable of operating in an ultra-high vacuum environment is disclosed. The mechanism includes a flexible coupling having a bore therethrough, and two clamp/pusher assemblies mounted in axial ends of the coupling. The clamp/pusher assemblies are energized by voltage-operated piezoelectrics therewithin to operatively engage the shaft and coupling causing the shaft to move along its rotational axis through the bore. The microactuator is capable of repeatably positioning to sub-nanometer accuracy while affording a scan range in excess of 5 centimeters. Moreover, the microactuator generates smooth, constant velocity motion profiles while producing a drive thrust of greater than 10 pounds. The system is remotely controlled and piezoelectrically driven, hence minimal thermal loading, vibrational excitation, or outgassing is introduced to the operating environment. 10 figs.

  12. Constant attitude orbit transfer

    NASA Astrophysics Data System (ADS)

    Cress, Peter; Evans, Michael

    A two-impulse orbital transfer technique is described in which the spacecraft attitude remains constant for both burns, eliminating the need for attitude maneuvers between the burns. This can lead to significant savings in vehicle weight, cost and complexity. Analysis is provided for a restricted class of applications of this transfer between circular orbits. For those transfers with a plane change less than 30 deg, the total velocity cost of the maneuver is less than twelve percent greater than that of an optimum plane split Hohmann transfer. While this maneuver does not minimize velocity requirement, it does provide a means of achieving necessary transfer while substantially reducing the cost and complexity of the spacecraft.

  13. A Constant Pressure Bomb

    NASA Technical Reports Server (NTRS)

    Stevens, F W

    1924-01-01

    This report describes a new optical method of unusual simplicity and of good accuracy suitable to study the kinetics of gaseous reactions. The device is the complement of the spherical bomb of constant volume, and extends the applicability of the relationship, pv=rt for gaseous equilibrium conditions, to the use of both factors p and v. The method substitutes for the mechanical complications of a manometer placed at some distance from the seat of reaction the possibility of allowing the radiant effects of reaction to record themselves directly upon a sensitive film. It is possible the device may be of use in the study of the photoelectric effects of radiation. The method makes possible a greater precision in the measurement of normal flame velocities than was previously possible. An approximate analysis shows that the increase of pressure and density ahead of the flame is negligible until the velocity of the flame approaches that of sound.

  14. Effective and accurate approach for modeling of commensurate-incommensurate transition in krypton monolayer on graphite.

    PubMed

    Ustinov, E A

    2014-10-01

    Commensurate-incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs-Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton-graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton-carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas-solid and solid-solid system.

  15. Effective and accurate approach for modeling of commensurate–incommensurate transition in krypton monolayer on graphite

    SciTech Connect

    Ustinov, E. A.

    2014-10-07

    Commensurate–incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs–Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton–graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton–carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas–solid and solid–solid system.

  16. Effective and accurate approach for modeling of commensurate-incommensurate transition in krypton monolayer on graphite.

    PubMed

    Ustinov, E A

    2014-10-01

    Commensurate-incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs-Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton-graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton-carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas-solid and solid-solid system. PMID:25296827

  17. An accurate and simple quantum model for liquid water.

    PubMed

    Paesani, Francesco; Zhang, Wei; Case, David A; Cheatham, Thomas E; Voth, Gregory A

    2006-11-14

    The path-integral molecular dynamics and centroid molecular dynamics methods have been applied to investigate the behavior of liquid water at ambient conditions starting from a recently developed simple point charge/flexible (SPC/Fw) model. Several quantum structural, thermodynamic, and dynamical properties have been computed and compared to the corresponding classical values, as well as to the available experimental data. The path-integral molecular dynamics simulations show that the inclusion of quantum effects results in a less structured liquid with a reduced amount of hydrogen bonding in comparison to its classical analog. The nuclear quantization also leads to a smaller dielectric constant and a larger diffusion coefficient relative to the corresponding classical values. Collective and single molecule time correlation functions show a faster decay than their classical counterparts. Good agreement with the experimental measurements in the low-frequency region is obtained for the quantum infrared spectrum, which also shows a higher intensity and a redshift relative to its classical analog. A modification of the original parametrization of the SPC/Fw model is suggested and tested in order to construct an accurate quantum model, called q-SPC/Fw, for liquid water. The quantum results for several thermodynamic and dynamical properties computed with the new model are shown to be in a significantly better agreement with the experimental data. Finally, a force-matching approach was applied to the q-SPC/Fw model to derive an effective quantum force field for liquid water in which the effects due to the nuclear quantization are explicitly distinguished from those due to the underlying molecular interactions. Thermodynamic and dynamical properties computed using standard classical simulations with this effective quantum potential are found in excellent agreement with those obtained from significantly more computationally demanding full centroid molecular dynamics

  18. Accurate phase-shift velocimetry in rock.

    PubMed

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models. PMID:27111139

  19. Accurate phase-shift velocimetry in rock

    NASA Astrophysics Data System (ADS)

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  20. Accurate phase-shift velocimetry in rock.

    PubMed

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  1. A new force field of formamide and the effect of the dielectric constant on miscibility.

    PubMed

    de la Luz, Alexander Pérez; Méndez-Maldonado, G Arlette; Núñez-Rojas, Edgar; Bresme, Fernando; Alejandre, José

    2015-06-01

    Current force fields underestimate significantly the dielectric constant of formamide at standard conditions. We present a derivation of an accurate potential for formamide, with a functional form based on the OPLS/AA force field. Our procedure follows the approach introduced by Salas et al. ( J. Chem. Theory Comput. 2015 , 11 , 683 - 693 ) that relies on ab initio calculations and molecular dynamics simulations. We consider several strategies to derive the atomic charges of formamide. We find that the inclusion of polarization effects in the quantum mechanical computations is essential to obtain reliable force fields. By varying the atomic charges and the Lennard-Jones parameters describing the dispersion interactions in the OPLS/AA force field, we derive an optimum set of parameters that provides accurate results for the dielectric constant, surface tension, and bulk density of liquid formamide in a wide range of thermodynamic states. We test the transferability of our parameters to investigate liquid/liquid mixtures. We have chosen as case study an equimolar mixture of formamide and hexan-2-one. This mixture involves two fluids with very different polar characteristics, namely, large differences in their dielectric constants and their performance as solvents. The new potential predicts a liquid/liquid phase separation, in good agreement with experimental data, and highlights the importance of the correct parametrization of the pure liquid phases to investigate liquid mixtures. Finally, we examine the microscopic origin of the observed inmiscibility between formamide and hexa-2-one.

  2. ESTIMATION OF CARBOXYLIC ACID ESTER HYDROLYSIS RATE CONSTANTS

    EPA Science Inventory

    SPARC chemical reactivity models were extended to calculate hydrolysis rate constants for carboxylic acid esters from molecular structure. The energy differences between the initial state and the transition state for a molecule of interest are factored into internal and external...

  3. Determination of the rate constants of molecular processes regulating the level of induced absorption in a laser based on an aqueous-micellar solution of rhodamine 6G with lamp pumping

    SciTech Connect

    Levin, M.B.; Snegov, M.I.; Cherkasov, A.S.

    1987-03-01

    A method of determining the average lifetime tau of the products responsible for inverse induced absorption in aqueous--micellar solutions of rhodamine 6G (R6G) on lamp pumping based on a comparison of threshold intensities of excitation (W/sub th/) in the resonators of a laser with a different Q is proposed. Using the value of tau found (0.2 ..mu..sec) and experimental data on the change in W/sub th/ with the concentration of cyclooctatetraene (COT) added to the solution the rate constant of quenching of the absorbing products by COT molecules (K/sub q/ = 2.6 x 10/sup 7/ M/sup -1/sec/sup -1/) was determined. In the assumption that the absorbing products are triplet dye molecules, the value of the rate constant of interconversion (K/sub 32/) of R6G into an aqueous--micellar solution (K/sub 32/ = 1.3 x 10/sup 7/ sec/sup -1/) was determined. A comparison was made of the values of the constants found with the corresponding values known from the literature.

  4. Assessment of the constant non-unity Lewis number assumption in chemically-reacting flows

    NASA Astrophysics Data System (ADS)

    Burali, Nicholas; Lapointe, Simon; Bobbitt, Brock; Blanquart, Guillaume; Xuan, Yuan

    2016-07-01

    Accurate computation of molecular diffusion coefficients in chemically reacting flows can be an expensive procedure, and the use of constant non-unity Lewis numbers has been adopted often as a cheaper alternative. The goal of the current work is to explore the validity and the limitations of the constant non-unity Lewis number approach in the description of molecular mixing in laminar and turbulent flames. To carry out this analysis, three test cases have been selected, including a lean, highly unstable, premixed hydrogen/air flame, a lean turbulent premixed n-heptane/air flame, and a laminar ethylene/air coflow diffusion flame. For the hydrogen flame, both a laminar and a turbulent configuration have been considered. The three flames are characterised by Lewis numbers which are less than unity, greater than unity, and close to unity, respectively. For each flame, mixture-averaged transport simulations are carried out and used as reference data. The current analysis suggests that, for numerous combustion configurations, the constant non-unity Lewis number approximation leads to small errors when the set of Lewis numbers is chosen properly. For the selected test cases and our numerical framework, the reduction of computational cost is found to be minimal.

  5. Accurate description of calcium solvation in concentrated aqueous solutions.

    PubMed

    Kohagen, Miriam; Mason, Philip E; Jungwirth, Pavel

    2014-07-17

    Calcium is one of the biologically most important ions; however, its accurate description by classical molecular dynamics simulations is complicated by strong electrostatic and polarization interactions with surroundings due to its divalent nature. Here, we explore the recently suggested approach for effectively accounting for polarization effects via ionic charge rescaling and develop a new and accurate parametrization of the calcium dication. Comparison to neutron scattering and viscosity measurements demonstrates that our model allows for an accurate description of concentrated aqueous calcium chloride solutions. The present model should find broad use in efficient and accurate modeling of calcium in aqueous environments, such as those encountered in biological and technological applications.

  6. Dielectric properties of liquid phase molecular clusters using the external field method: molecular dynamics study.

    PubMed

    Abeyrathne, Chathurika D; Halgamuge, Malka N; Farrell, Peter M; Skafidas, Efstratios

    2014-07-21

    We analyzed the dielectric properties of molecular liquids using the external field method with reaction field approximations. The applicability of this method to determine the dielectric properties of molecules with zero (1,4-dioxane) and non-zero (water and bio-molecular aqueous solutions) permanent dipole moment was studied. The relative static dielectric constant obtained using the external field method for polar and non-polar molecular liquids, including molecules with zero permanent dipole moment, agreed well with the experimental values presented in the literature. Our results indicate that the Debye relaxation time constants estimated from the non-equilibrium simulations using the external field method were accurate for molecules whose permanent dipole moments were less than 12 D.

  7. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  8. Accurate determination of optical bandgap and lattice parameters of Zn{sub 1-x}Mg{sub x}O epitaxial films (0{<=}x{<=}0.3) grown by plasma-assisted molecular beam epitaxy on a-plane sapphire

    SciTech Connect

    Laumer, Bernhard; Schuster, Fabian; Stutzmann, Martin; Bergmaier, Andreas; Dollinger, Guenther; Eickhoff, Martin

    2013-06-21

    Zn{sub 1-x}Mg{sub x}O epitaxial films with Mg concentrations 0{<=}x{<=}0.3 were grown by plasma-assisted molecular beam epitaxy on a-plane sapphire substrates. Precise determination of the Mg concentration x was performed by elastic recoil detection analysis. The bandgap energy was extracted from absorption measurements with high accuracy taking electron-hole interaction and exciton-phonon complexes into account. From these results a linear relationship between bandgap energy and Mg concentration is established for x{<=}0.3. Due to alloy disorder, the increase of the photoluminescence emission energy with Mg concentration is less pronounced. An analysis of the lattice parameters reveals that the epitaxial films grow biaxially strained on a-plane sapphire.

  9. A fast and accurate method for the determination of total and soluble fluorine in toothpaste using high-resolution graphite furnace molecular absorption spectrometry and its comparison with established techniques.

    PubMed

    Gleisner, Heike; Einax, Jürgen W; Morés, Silvane; Welz, Bernhard; Carasek, Eduardo

    2011-04-01

    A fast and reliable method has been developed for the determination of total and soluble fluorine in toothpaste, important quality control parameters in dentifrices. The method is based on the molecular absorption of gallium mono-fluoride, GaF, using a commercially available high-resolution continuum source atomic absorption spectrometer. Transversely heated platform tubes with zirconium as permanent chemical modifier were used throughout. Before each sample injection, a palladium and zirconium modifier solution and a gallium reagent were deposited onto the graphite platform and thermally pretreated to transform them into their active forms. The samples were only diluted and introduced directly into the graphite tube together with additional gallium reagent. Under these conditions the fluoride was stable up to a pyrolysis temperature of 550 °C, and the optimum vaporization (molecule formation) temperature was 1550 °C. The GaF molecular absorption was measured at 211.248 nm, and the limits of detection and quantification were 5.2 pg and 17 pg, respectively, corresponding to a limit of quantification of about 30 μg g(-1) (ppm) F in the original toothpaste. The proposed method was used for the determination of total and soluble fluorine content in toothpaste samples from different manufactures. The samples contained different ionic fluoride species and sodium monofluorophosphate (MFP) with covalently bonded fluorine. The results for total fluorine were compared with those obtained with a modified conventional headspace gas chromatographic procedure. Accuracy and precision of the two procedures were comparable, but the proposed procedure was much less labor-intensive, and about five times faster than the latter one.

  10. A fast and accurate method for the determination of total and soluble fluorine in toothpaste using high-resolution graphite furnace molecular absorption spectrometry and its comparison with established techniques.

    PubMed

    Gleisner, Heike; Einax, Jürgen W; Morés, Silvane; Welz, Bernhard; Carasek, Eduardo

    2011-04-01

    A fast and reliable method has been developed for the determination of total and soluble fluorine in toothpaste, important quality control parameters in dentifrices. The method is based on the molecular absorption of gallium mono-fluoride, GaF, using a commercially available high-resolution continuum source atomic absorption spectrometer. Transversely heated platform tubes with zirconium as permanent chemical modifier were used throughout. Before each sample injection, a palladium and zirconium modifier solution and a gallium reagent were deposited onto the graphite platform and thermally pretreated to transform them into their active forms. The samples were only diluted and introduced directly into the graphite tube together with additional gallium reagent. Under these conditions the fluoride was stable up to a pyrolysis temperature of 550 °C, and the optimum vaporization (molecule formation) temperature was 1550 °C. The GaF molecular absorption was measured at 211.248 nm, and the limits of detection and quantification were 5.2 pg and 17 pg, respectively, corresponding to a limit of quantification of about 30 μg g(-1) (ppm) F in the original toothpaste. The proposed method was used for the determination of total and soluble fluorine content in toothpaste samples from different manufactures. The samples contained different ionic fluoride species and sodium monofluorophosphate (MFP) with covalently bonded fluorine. The results for total fluorine were compared with those obtained with a modified conventional headspace gas chromatographic procedure. Accuracy and precision of the two procedures were comparable, but the proposed procedure was much less labor-intensive, and about five times faster than the latter one. PMID:21215545

  11. Damping constant estimation in magnetoresistive readers

    SciTech Connect

    Stankiewicz, Andrzej Hernandez, Stephanie

    2015-05-07

    The damping constant is a key design parameter in magnetic reader design. Its value can be derived from bulk or sheet film ferromagnetic resonance (FMR) line width. However, dynamics of nanodevices is usually defined by presence of non-uniform modes. It triggers new damping mechanisms and produces stronger damping than expected from traditional FMR. This work proposes a device-level technique for damping evaluation, based on time-domain analysis of thermally excited stochastic oscillations. The signal is collected using a high bandwidth oscilloscope, by direct probing of a biased reader. Recorded waveforms may contain different noise signals, but free layer FMR is usually a dominating one. The autocorrelation function is a reflection of the damped oscillation curve, averaging out stochastic contributions. The damped oscillator formula is fitted to autocorrelation data, producing resonance frequency and damping constant values. Restricting lag range allows for mitigation of the impact of other phenomena (e.g., reader instability) on the damping constant. For a micromagnetically modeled reader, the technique proves to be much more accurate than the stochastic FMR line width approach. Application to actual reader waveforms yields a damping constant of ∼0.03.

  12. Toward more accurate loss tangent measurements in reentrant cavities

    SciTech Connect

    Moyer, R. D.

    1980-05-01

    Karpova has described an absolute method for measurement of dielectric properties of a solid in a coaxial reentrant cavity. His cavity resonance equation yields very accurate results for dielectric constants. However, he presented only approximate expressions for the loss tangent. This report presents more exact expressions for that quantity and summarizes some experimental results.

  13. Accurate Mass Measurements in Proteomics

    SciTech Connect

    Liu, Tao; Belov, Mikhail E.; Jaitly, Navdeep; Qian, Weijun; Smith, Richard D.

    2007-08-01

    To understand different aspects of life at the molecular level, one would think that ideally all components of specific processes should be individually isolated and studied in details. Reductionist approaches, i.e., studying one biological event at a one-gene or one-protein-at-a-time basis, indeed have made significant contributions to our understanding of many basic facts of biology. However, these individual “building blocks” can not be visualized as a comprehensive “model” of the life of cells, tissues, and organisms, without using more integrative approaches.1,2 For example, the emerging field of “systems biology” aims to quantify all of the components of a biological system to assess their interactions and to integrate diverse types of information obtainable from this system into models that could explain and predict behaviors.3-6 Recent breakthroughs in genomics, proteomics, and bioinformatics are making this daunting task a reality.7-14 Proteomics, the systematic study of the entire complement of proteins expressed by an organism, tissue, or cell under a specific set of conditions at a specific time (i.e., the proteome), has become an essential enabling component of systems biology. While the genome of an organism may be considered static over short timescales, the expression of that genome as the actual gene products (i.e., mRNAs and proteins) is a dynamic event that is constantly changing due to the influence of environmental and physiological conditions. Exclusive monitoring of the transcriptomes can be carried out using high-throughput cDNA microarray analysis,15-17 however the measured mRNA levels do not necessarily correlate strongly with the corresponding abundances of proteins,18-20 The actual amount of functional proteins can be altered significantly and become independent of mRNA levels as a result of post-translational modifications (PTMs),21 alternative splicing,22,23 and protein turnover.24,25 Moreover, the functions of expressed

  14. Accurate spring constant calibration for very stiff atomic force microscopy cantilevers.

    PubMed

    Grutzik, Scott J; Gates, Richard S; Gerbig, Yvonne B; Smith, Douglas T; Cook, Robert F; Zehnder, Alan T

    2013-11-01

    There are many atomic force microscopy (AFM) applications that rely on quantifying the force between the AFM cantilever tip and the sample. The AFM does not explicitly measure force, however, so in such cases knowledge of the cantilever stiffness is required. In most cases, the forces of interest are very small, thus compliant cantilevers are used. A number of methods have been developed that are well suited to measuring low stiffness values. However, in some cases a cantilever with much greater stiffness is required. Thus, a direct, traceable method for calibrating very stiff (approximately 200 N/m) cantilevers is presented here. The method uses an instrumented and calibrated nanoindenter to determine the stiffness of a reference cantilever. This reference cantilever is then used to measure the stiffness of a number of AFM test cantilevers. This method is shown to have much smaller uncertainty than previously proposed methods. An example application to fracture testing of nanoscale silicon beam specimens is included.

  15. Accurate spring constant calibration for very stiff atomic force microscopy cantilevers

    SciTech Connect

    Grutzik, Scott J.; Zehnder, Alan T.; Gates, Richard S.; Gerbig, Yvonne B.; Smith, Douglas T.; Cook, Robert F.

    2013-11-15

    There are many atomic force microscopy (AFM) applications that rely on quantifying the force between the AFM cantilever tip and the sample. The AFM does not explicitly measure force, however, so in such cases knowledge of the cantilever stiffness is required. In most cases, the forces of interest are very small, thus compliant cantilevers are used. A number of methods have been developed that are well suited to measuring low stiffness values. However, in some cases a cantilever with much greater stiffness is required. Thus, a direct, traceable method for calibrating very stiff (approximately 200 N/m) cantilevers is presented here. The method uses an instrumented and calibrated nanoindenter to determine the stiffness of a reference cantilever. This reference cantilever is then used to measure the stiffness of a number of AFM test cantilevers. This method is shown to have much smaller uncertainty than previously proposed methods. An example application to fracture testing of nanoscale silicon beam specimens is included.

  16. Accurate, conformation-dependent predictions of solvent effects on protein ionization constants

    PubMed Central

    Barth, P.; Alber, T.; Harbury, P. B.

    2007-01-01

    Predicting how aqueous solvent modulates the conformational transitions and influences the pKa values that regulate the biological functions of biomolecules remains an unsolved challenge. To address this problem, we developed FDPB_MF, a rotamer repacking method that exhaustively samples side chain conformational space and rigorously calculates multibody protein–solvent interactions. FDPB_MF predicts the effects on pKa values of various solvent exposures, large ionic strength variations, strong energetic couplings, structural reorganizations and sequence mutations. The method achieves high accuracy, with root mean square deviations within 0.3 pH unit of the experimental values measured for turkey ovomucoid third domain, hen lysozyme, Bacillus circulans xylanase, and human and Escherichia coli thioredoxins. FDPB_MF provides a faithful, quantitative assessment of electrostatic interactions in biological macromolecules. PMID:17360348

  17. New Quasar Studies Keep Fundamental Physical Constant Constant

    NASA Astrophysics Data System (ADS)

    2004-03-01

    Very Large Telescope sets stringent limit on possible variation of the fine-structure constant over cosmological time Summary Detecting or constraining the possible time variations of fundamental physical constants is an important step toward a complete understanding of basic physics and hence the world in which we live. A step in which astrophysics proves most useful. Previous astronomical measurements of the fine structure constant - the dimensionless number that determines the strength of interactions between charged particles and electromagnetic fields - suggested that this particular constant is increasing very slightly with time. If confirmed, this would have very profound implications for our understanding of fundamental physics. New studies, conducted using the UVES spectrograph on Kueyen, one of the 8.2-m telescopes of ESO's Very Large Telescope array at Paranal (Chile), secured new data with unprecedented quality. These data, combined with a very careful analysis, have provided the strongest astronomical constraints to date on the possible variation of the fine structure constant. They show that, contrary to previous claims, no evidence exist for assuming a time variation of this fundamental constant. PR Photo 07/04: Relative Changes with Redshift of the Fine Structure Constant (VLT/UVES) A fine constant To explain the Universe and to represent it mathematically, scientists rely on so-called fundamental constants or fixed numbers. The fundamental laws of physics, as we presently understand them, depend on about 25 such constants. Well-known examples are the gravitational constant, which defines the strength of the force acting between two bodies, such as the Earth and the Moon, and the speed of light. One of these constants is the so-called "fine structure constant", alpha = 1/137.03599958, a combination of electrical charge of the electron, the Planck constant and the speed of light. The fine structure constant describes how electromagnetic forces hold

  18. Multiscale reactive molecular dynamics

    PubMed Central

    Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.

    2012-01-01

    Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062

  19. Analytical treatment of two-center overlap integral with respect to same screening constants over Slater type orbitals

    NASA Astrophysics Data System (ADS)

    Ćopuroǧlu, Ebru; Mamedov, Bahtiyar A.

    2016-08-01

    By the use of Löwdin- α radial function, an alternative method is introduced for two-center overlap integral over Slater type orbitals (STOs) at same screening constants (SSC). Notice that the overlap integrals with SSC have an important role in accurate evaluation of multicenter multielectron molecular integrals arising in combined Hartree-Fock-Roothaan (CHFR) theory. This approximation provides us simple and efficient expression for the two-center overlap integrals. To show the effectiveness of established formula we have compared our results with available literature data. The method ensures high performance with a very short CPU time.

  20. Components of Dielectric Constants of Ionic Liquids

    NASA Astrophysics Data System (ADS)

    Izgorodina, Ekaterina I.

    2010-03-01

    In this study ab initio-based methods were used to calculate electronic polarizability and dipole moment of ions comprising ionic liquids [1]. The test set consisted of a number of anions and cations routinely used in the ionic liquid field. As expected, in the first approximation electronic polarizability volume turned out to be proportional to the ion volume, also calculated by means of ab initio theory. For ionic liquid ions this means that their electronic polarizabilities are at least an order of magnitude larger than those of traditional molecular solvents like water and DMSO. On this basis it may seem surprising that most of ionic liquids actually possess modest dielectric constants, falling the narrow range between 10 and 15. The lower than first expected dielectric constants of ionic liquids has been explored in this work via explicit calculations of the electronic and orientation polarization contributions to the dielectric constant using the Clausius-Mossotti equation and the Onsager theory for polar dielectric materials. We determined that the electronic polarization contribution to the dielectric constant was rather small (between 1.9 and 2.2) and comparable to that of traditional molecular solvents. These findings were explained by the interplay between two quantities, increasing electronic polarizability of ions and decreasing number of ions present in the unit volume; although electronic polarizability is usually relatively large for ionic liquid ions, due to their size there are fewer ions present per unit volume (by a factor of 10 compared to traditional molecular solvents). For ionic liquids consisting of ions with zero (e.g. BF4) or negligible (e.g. NTf2) dipole moments the calculated orientation polarization does not contribute enough to account for the whole of the measured values of the dielectric constants. We suggest that in ionic liquids an additional type of polarization, ``ionic polarization'', originating from small movements of the

  1. Accurate Potential Energy Curves for the Ground Electronic States of NeH^{+} and ArH^{+}

    NASA Astrophysics Data System (ADS)

    Coxon, John A.; Hajigeorgiou, Photos G.

    2013-06-01

    All available microwave and infrared spectroscopic line positions for the ground electronic states of the molecular cations NeH^{+} and ArH^{+} were employed in a direct potential fitting procedure to determine compact analytical potential curves and radial functions describing breakdown of the Born-Oppenheimer approximation. For NeH^{+}, 17 adjustable parameters were required to represent a total of 183 line positions for 4 isotopologues, whereas for ArH^{+}, 23 adjustable parameters were required to represent 440 line positions for 6 isotopologues. The MLR3 potential energy functional form was employed, taking full account of the proper 1/r{^4} limiting long-range dependence of the ion-atom dispersion energy interactions. Accurate vibrational energies, rotational constants and centrifugal distortion constants have been calculated for both diatomic cations.

  2. Constant-Pressure Hydraulic Pump

    NASA Technical Reports Server (NTRS)

    Galloway, C. W.

    1982-01-01

    Constant output pressure in gas-driven hydraulic pump would be assured in new design for gas-to-hydraulic power converter. With a force-multiplying ring attached to gas piston, expanding gas would apply constant force on hydraulic piston even though gas pressure drops. As a result, pressure of hydraulic fluid remains steady, and power output of the pump does not vary.

  3. Molecular Diagnostics

    PubMed Central

    Choe, Hyonmin; Deirmengian, Carl A.; Hickok, Noreen J.; Morrison, Tiffany N.; Tuan, Rocky S.

    2015-01-01

    Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid, polymerase chain reaction–based detection of bacterial genes, and metabolomic determination of responses to orthopaedic infection. PMID:25808967

  4. A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.

    PubMed

    Yamagishi, Junya; Okimoto, Noriaki; Morimoto, Gentaro; Taiji, Makoto

    2014-11-01

    The Poisson-Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N- and C-terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules.

  5. Profitable capitation requires accurate costing.

    PubMed

    West, D A; Hicks, L L; Balas, E A; West, T D

    1996-01-01

    In the name of costing accuracy, nurses are asked to track inventory use on per treatment basis when more significant costs, such as general overhead and nursing salaries, are usually allocated to patients or treatments on an average cost basis. Accurate treatment costing and financial viability require analysis of all resources actually consumed in treatment delivery, including nursing services and inventory. More precise costing information enables more profitable decisions as is demonstrated by comparing the ratio-of-cost-to-treatment method (aggregate costing) with alternative activity-based costing methods (ABC). Nurses must participate in this costing process to assure that capitation bids are based upon accurate costs rather than simple averages. PMID:8788799

  6. Constant-force approach to discontinuous potentials.

    PubMed

    Orea, Pedro; Odriozola, Gerardo

    2013-06-01

    Aiming to approach the thermodynamical properties of hard-core systems by standard molecular dynamics simulation, we propose setting a repulsive constant-force for overlapping particles. That is, the discontinuity of the pair potential is replaced by a linear function with a large negative slope. Hence, the core-core repulsion, usually modeled with a power function of distance, yields a large force as soon as the cores slightly overlap. This leads to a quasi-hardcore behavior. The idea is tested for a triangle potential of short range. The results obtained by replica exchange molecular dynamics for several repulsive forces are contrasted with the ones obtained for the discontinuous potential and by means of replica exchange Monte Carlo. We found remarkable agreements for the vapor-liquid coexistence densities as well as for the surface tension.

  7. Ab initio molecular orbital/Rice-Ramsperger-Kassel-Marcus theory study of multichannel rate constants for the unimolecular decomposition of benzene and the H+C6H5 reaction over the ground electronic state

    NASA Astrophysics Data System (ADS)

    Mebel, A. M.; Lin, M. C.; Chakraborty, D.; Park, J.; Lin, S. H.; Lee, Y. T.

    2001-05-01

    The potential energy surface for the unimolecular decomposition of benzene and H+C6H5 recombination has been studied by the ab initio G2M(cc, MP2) method. The results show that besides direct emission of a hydrogen atom occurring without an exit channel barrier, the benzene molecule can undergo sequential 1,2-hydrogen shifts to o-, m-, and p-C6H6 and then lose a H atom with exit barriers of about 6 kcal/mol. o-C6H6 can eliminate a hydrogen molecule with a barrier of 121.4 kcal/mol relative to benzene. o- and m-C6H6 can also isomerize to acyclic isomers, ac-C6H6, with barriers of 110.7 and 100.6 kcal/mol, respectively, but in order to form m-C6H6 from benzene the system has to overcome a barrier of 108.6 kcal/mol for the 1,2-H migration from o-C6H6 to m-C6H6. The bimolecular H+C6H5 reaction is shown to be more complicated than the unimolecular fragmentation reaction due to the presence of various metathetical processes, such as H-atom disproportionation or addition to different sites of the ring. The addition to the radical site is barrierless, the additions to the o-, m-, and p-positions have entrance barriers of about 6 kcal/mol and the disproportionation channel leading to o-benzyne+H2 has a barrier of 7.6 kcal/mol. The Rice-Ramsperger-Kassel-Marcus and transition-state theory methods were used to compute the total and individual rate constants for various channels of the two title reactions under different temperature/pressure conditions. A fit of the calculated total rates for unimolecular benzene decomposition gives the expression 2.26×1014exp(-53 300/T)s-1 for T=1000-3000 K and atmospheric pressure. This finding is significantly different from the recommended rate constant, 9.0×1015exp(-54 060/T) s-1, obtained by kinetic modeling assuming only the H+C6H5 product channel. At T=1000 K, the branching ratios for the formation of H+C6H5 and ac-C6H6 are 29% and 71%, respectively. H+C6H5 becomes the major channel at T⩾1200 K. The total rate for the bimolecular H

  8. Computational study on Kerr constants of neutral and ionized gases

    NASA Astrophysics Data System (ADS)

    Sato, M.; Kumada, A.; Hidaka, K.

    2015-08-01

    In order to quantitatively examine the measurement capability of Poisson's field using electro-optic Kerr-effect (EOKE), Kerr constants of neutral molecules and ions are examined by means of first principle calculations. We have systematically computed Kerr constants of neutral molecules and ions of several molecular symmetry groups, with consistent theory level and basis sets. Computed Kerr constants of neutral molecules (N2, CO2, SF6, and CF3I) ranging across two orders of magnitudes are within 50% error of the experimental values, which are comparable to the scattering between experimental values itself. The results show that SF6 has smaller Kerr constant due to its high molecular symmetry compared to those of N2 and CO2. In contrast, CF3I has large Kerr constant due to its permanent dipole. Computed Kerr constants for anions are larger by two orders of magnitude than those of neutral molecules, probably due to the shielding effect. For cations, the opposite holds true; however, due to anisotropic polarizability, computed Kerr constants for some cations are comparable to neutral molecules, while others show smaller values. The ratio of Kerr constants of ions to those of neutral molecules are at most 102; EOKE is valid for measuring electric field in weakly ionized gas whose ionization degree is smaller than 10-3.

  9. Constants and Variables of Nature

    SciTech Connect

    Sean Carroll

    2009-04-03

    It is conventional to imagine that the various parameters which characterize our physical theories, such as the fine structure constant or Newton’s gravitational constant, are truly “constant”, in the sense that they do not change from place to place or time to time. Recent developments in both theory and observation have led us to re-examine this assumption, and to take seriously the possibility that our supposed constants are actually gradually changing. I will discuss why we might expect these parameters to vary, and what observation and experiment have to say about the issue.

  10. Computing the dielectric constant of liquid water at constant dielectric displacement

    NASA Astrophysics Data System (ADS)

    Zhang, Chao; Sprik, Michiel

    2016-04-01

    The static dielectric constant of liquid water is computed using classical force field based molecular dynamics simulation at fixed electric displacement D . The method to constrain the electric displacement is the finite-temperature classical variant of the constant D method developed by Stengel, Spaldin, and Vanderbilt [Nat. Phys. 5, 304 (2009), 10.1038/nphys1185]. There is also a modification of this scheme imposing fixed values of the macroscopic field E . The method is applied to the popular SPC/E model of liquid water. We compare four different estimates of the dielectric constant, two obtained from fluctuations of the polarization at D =0 and E =0 and two from the variation of polarization with finite D and E . It is found that all four estimates agree when properly converged. The computational effort to achieve convergence varies, however, with constant D calculations being substantially more efficient. We attribute this difference to the much shorter relaxation time of longitudinal polarization compared to transverse polarization accelerating constant D calculations.

  11. QSPR prediction of the hydroxyl radical rate constant of water contaminants.

    PubMed

    Borhani, Tohid Nejad Ghaffar; Saniedanesh, Mohammadhossein; Bagheri, Mehdi; Lim, Jeng Shiun

    2016-07-01

    In advanced oxidation processes (AOPs), the aqueous hydroxyl radical (HO) acts as a strong oxidant to react with organic contaminants. The hydroxyl radical rate constant (kHO) is important for evaluating and modelling of the AOPs. In this study, quantitative structure-property relationship (QSPR) method is applied to model the hydroxyl radical rate constant for a diverse dataset of 457 water contaminants from 27 various chemical classes. The constricted binary particle swarm optimization and multiple-linear regression (BPSO-MLR) are used to obtain the best model with eight theoretical descriptors. An optimized feed forward neural network (FFNN) is developed to investigate the complex performance of the selected molecular parameters with kHO. Although the FFNN prediction results are more accurate than those obtained using BPSO-MLR, the application of the latter is much more convenient. Various internal and external validation techniques indicate that the obtained models could predict the logarithmic hydroxyl radical rate constants of a large number of water contaminants with less than 4% absolute relative error. Finally, the above-mentioned proposed models are compared to those reported earlier and the structural factors contributing to the AOP degradation efficiency are discussed. PMID:27124124

  12. Accurate upwind-monotone (nonoscillatory) methods for conservation laws

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1992-01-01

    The well known MUSCL scheme of Van Leer is constructed using a piecewise linear approximation. The MUSCL scheme is second order accurate at the smooth part of the solution except at extrema where the accuracy degenerates to first order due to the monotonicity constraint. To construct accurate schemes which are free from oscillations, the author introduces the concept of upwind monotonicity. Several classes of schemes, which are upwind monotone and of uniform second or third order accuracy are then presented. Results for advection with constant speed are shown. It is also shown that the new scheme compares favorably with state of the art methods.

  13. Varying Constants, Gravitation and Cosmology

    NASA Astrophysics Data System (ADS)

    Uzan, Jean-Philippe

    2011-12-01

    Fundamental constants are a cornerstone of our physical laws. Any constant varying in space and/or time would reflect the existence of an almost massless field that couples to matter. This will induce a violation of the universality of free fall. Thus, it is of utmost importance for our understanding of gravity and of the domain of validity of general relativity to test for their constancy. We detail the relations between the constants, the tests of the local position invariance and of the universality of free fall. We then review the main experimental and observational constraints that have been obtained from atomic clocks, the Oklo phenomenon, solar system observations, meteorite dating, quasar absorption spectra, stellar physics, pulsar timing, the cosmic microwave background and big bang nucleosynthesis. At each step we describe the basics of each system, its dependence with respect to the constants, the known systematic effects and the most recent constraints that have been obtained. We then describe the main theoretical frameworks in which the low-energy constants may actually be varying and we focus on the unification mechanisms and the relations between the variation of different constants. To finish, we discuss the more speculative possibility of understanding their numerical values and the apparent fine-tuning that they confront us with.

  14. Accurate documentation and wound measurement.

    PubMed

    Hampton, Sylvie

    This article, part 4 in a series on wound management, addresses the sometimes routine yet crucial task of documentation. Clear and accurate records of a wound enable its progress to be determined so the appropriate treatment can be applied. Thorough records mean any practitioner picking up a patient's notes will know when the wound was last checked, how it looked and what dressing and/or treatment was applied, ensuring continuity of care. Documenting every assessment also has legal implications, demonstrating due consideration and care of the patient and the rationale for any treatment carried out. Part 5 in the series discusses wound dressing characteristics and selection.

  15. Protein apparent dielectric constant and its temperature dependence from remote chemical shift effects.

    PubMed

    An, Liaoyuan; Wang, Yefei; Zhang, Ning; Yan, Shihai; Bax, Ad; Yao, Lishan

    2014-09-17

    A NMR protocol is introduced that permits accurate measurement of minute, remote chemical shift perturbations (CSPs), caused by a mutation-induced change in the electric field. Using protein GB3 as a model system, (1)H(N) CSPs in K19A and K19E mutants can be fitted to small changes in the electric field at distal sites in the protein using the Buckingham equation, yielding an apparent dielectric constant εa of 8.6 ± 0.8 at 298 K. These CSPs, and their derived εa value, scale strongly with temperature. For example, CSPs at 313 K are about ∼30% smaller than those at 278 K, corresponding to an effective εa value of about 7.3 at 278 K and 10.5 at 313 K. Molecular dynamics simulations in explicit solvent indicate that solvent water makes a significant contribution to εa.

  16. Constant fields and constant gradients in open ionic channels.

    PubMed

    Chen, D P; Barcilon, V; Eisenberg, R S

    1992-05-01

    Ions enter cells through pores in proteins that are holes in dielectrics. The energy of interaction between ion and charge induced on the dielectric is many kT, and so the dielectric properties of channel and pore are important. We describe ionic movement by (three-dimensional) Nemst-Planck equations (including flux and net charge). Potential is described by Poisson's equation in the pore and Laplace's equation in the channel wall, allowing induced but not permanent charge. Asymptotic expansions are constructed exploiting the long narrow shape of the pore and the relatively high dielectric constant of the pore's contents. The resulting one-dimensional equations can be integrated numerically; they can be analyzed when channels are short or long (compared with the Debye length). Traditional constant field equations are derived if the induced charge is small, e.g., if the channel is short or if the total concentration gradient is zero. A constant gradient of concentration is derived if the channel is long. Plots directly comparable to experiments are given of current vs voltage, reversal potential vs. concentration, and slope conductance vs. concentration. This dielectric theory can easily be tested: its parameters can be determined by traditional constant field measurements. The dielectric theory then predicts current-voltage relations quite different from constant field, usually more linear, when gradients of total concentration are imposed. Numerical analysis shows that the interaction of ion and channel can be described by a mean potential if, but only if, the induced charge is negligible, that is to say, the electric field is spatially constant.

  17. Constant fields and constant gradients in open ionic channels.

    PubMed Central

    Chen, D P; Barcilon, V; Eisenberg, R S

    1992-01-01

    Ions enter cells through pores in proteins that are holes in dielectrics. The energy of interaction between ion and charge induced on the dielectric is many kT, and so the dielectric properties of channel and pore are important. We describe ionic movement by (three-dimensional) Nemst-Planck equations (including flux and net charge). Potential is described by Poisson's equation in the pore and Laplace's equation in the channel wall, allowing induced but not permanent charge. Asymptotic expansions are constructed exploiting the long narrow shape of the pore and the relatively high dielectric constant of the pore's contents. The resulting one-dimensional equations can be integrated numerically; they can be analyzed when channels are short or long (compared with the Debye length). Traditional constant field equations are derived if the induced charge is small, e.g., if the channel is short or if the total concentration gradient is zero. A constant gradient of concentration is derived if the channel is long. Plots directly comparable to experiments are given of current vs voltage, reversal potential vs. concentration, and slope conductance vs. concentration. This dielectric theory can easily be tested: its parameters can be determined by traditional constant field measurements. The dielectric theory then predicts current-voltage relations quite different from constant field, usually more linear, when gradients of total concentration are imposed. Numerical analysis shows that the interaction of ion and channel can be described by a mean potential if, but only if, the induced charge is negligible, that is to say, the electric field is spatially constant. Images FIGURE 1 PMID:1376159

  18. Computational calculation of equilibrium constants: addition to carbonyl compounds.

    PubMed

    Gómez-Bombarelli, Rafael; González-Pérez, Marina; Pérez-Prior, María Teresa; Calle, Emilio; Casado, Julio

    2009-10-22

    Hydration reactions are relevant for understanding many organic mechanisms. Since the experimental determination of hydration and hemiacetalization equilibrium constants is fairly complex, computational calculations now offer a useful alternative to experimental measurements. In this work, carbonyl hydration and hemiacetalization constants were calculated from the free energy differences between compounds in solution, using absolute and relative approaches. The following conclusions can be drawn: (i) The use of a relative approach in the calculation of hydration and hemiacetalization constants allows compensation of systematic errors in the solvation energies. (ii) On average, the methodology proposed here can predict hydration constants within +/- 0.5 log K(hyd) units for aldehydes. (iii) Hydration constants can be calculated for ketones and carboxylic acid derivatives within less than +/- 1.0 log K(hyd), on average, at the CBS-Q level of theory. (iv) The proposed methodology can predict hemiacetal formation constants accurately at the MP2 6-31++G(d,p) level using a common reference. If group references are used, the results obtained using the much cheaper DFT-B3LYP 6-31++G(d,p) level are almost as accurate. (v) In general, the best results are obtained if a common reference for all compounds is used. The use of group references improves the results at the lower levels of theory, but at higher levels, this becomes unnecessary. PMID:19761202

  19. Computational Calculation of Equilibrium Constants: Addition to Carbonyl Compounds

    NASA Astrophysics Data System (ADS)

    Gómez-Bombarelli, Rafael; González-Pérez, Marina; Pérez-Prior, María Teresa; Calle, Emilio; Casado, Julio

    2009-09-01

    Hydration reactions are relevant for understanding many organic mechanisms. Since the experimental determination of hydration and hemiacetalization equilibrium constants is fairly complex, computational calculations now offer a useful alternative to experimental measurements. In this work, carbonyl hydration and hemiacetalization constants were calculated from the free energy differences between compounds in solution, using absolute and relative approaches. The following conclusions can be drawn: (i) The use of a relative approach in the calculation of hydration and hemiacetalization constants allows compensation of systematic errors in the solvation energies. (ii) On average, the methodology proposed here can predict hydration constants within ± 0.5 log Khyd units for aldehydes. (iii) Hydration constants can be calculated for ketones and carboxylic acid derivatives within less than ± 1.0 log Khyd, on average, at the CBS-Q level of theory. (iv) The proposed methodology can predict hemiacetal formation constants accurately at the MP2 6-31++G(d,p) level using a common reference. If group references are used, the results obtained using the much cheaper DFT-B3LYP 6-31++G(d,p) level are almost as accurate. (v) In general, the best results are obtained if a common reference for all compounds is used. The use of group references improves the results at the lower levels of theory, but at higher levels, this becomes unnecessary.

  20. Effective cosmological constant induced by stochastic fluctuations of Newton's constant

    NASA Astrophysics Data System (ADS)

    de Cesare, Marco; Lizzi, Fedele; Sakellariadou, Mairi

    2016-09-01

    We consider implications of the microscopic dynamics of spacetime for the evolution of cosmological models. We argue that quantum geometry effects may lead to stochastic fluctuations of the gravitational constant, which is thus considered as a macroscopic effective dynamical quantity. Consistency with Riemannian geometry entails the presence of a time-dependent dark energy term in the modified field equations, which can be expressed in terms of the dynamical gravitational constant. We suggest that the late-time accelerated expansion of the Universe may be ascribed to quantum fluctuations in the geometry of spacetime rather than the vacuum energy from the matter sector.

  1. Extension of the AMBER force field for nitroxide radicals and combined QM/MM/PCM approach to the accurate determination of EPR parameters of DMPOH in solution

    PubMed Central

    Hermosilla, Laura; Prampolini, Giacomo; Calle, Paloma; García de la Vega, José Manuel; Brancato, Giuseppe; Barone, Vincenzo

    2015-01-01

    A computational strategy that combines both time-dependent and time-independent approaches is exploited to accurately model molecular dynamics and solvent effects on the isotropic hyperfine coupling constants of the DMPO-H nitroxide. Our recent general force field for nitroxides derived from AMBER ff99SB is further extended to systems involving hydrogen atoms in β-positions with respect to NO. The resulting force-field has been employed in a series of classical molecular dynamics simulations, comparing the computed EPR parameters from selected molecular configurations to the corresponding experimental data in different solvents. The effect of vibrational averaging on the spectroscopic parameters is also taken into account, by second order vibrational perturbation theory involving semi-diagonal third energy derivatives together first and second property derivatives. PMID:26584116

  2. Maximum terminal velocity turns at constant altitude

    NASA Astrophysics Data System (ADS)

    Eisler, G. Richard; Hull, David G.

    An optimal control problem is formulated for a maneuvering reentry vehicle to execute a maximum terminal velocity turn at constant altitude to a fixed final position. A control solution technique is devised which uses a Newton scheme to repetitively solve a nonlinear algebraic system for two parameters to provide the on-line guidance. The turn control takes advantage of the high dynamic pressure at the beginning of the flight path; the lift solution acts to null deviations from the prescribed altitude. Control solutions are compared for a continuously updated, approximate physical model, for a simulation of the approximate optimal guidance in a true physical model, and for a parameter optimization solution for the true model. End constraint satisfaction is excellent. Overall trajectory agreement is good, if the assumed atmospheric model is reasonably accurate.

  3. Maximum terminal velocity turns at constant altitude

    SciTech Connect

    Eisler, G.R.; Hull, D.G.

    1987-01-01

    An optimal control problem is formulated for a maneuvering reentry vehicle to execute a maximum terminal velocity turn at constant altitude to a fixed final position. A control solution technique is devised which uses a Newton scheme to repetitively solve a nonlinear algebraic system for two parameters to provide the on-line guidance. The turn control takes advantage of the high dynamic pressure at the beginning of the flight path; the lift solution acts to null deviations from the prescribed altitude. Control solutions are compared for a continuously updated, approximate physical model, for a simulation of the approximate optimal guidance in a true physical model, and for a parameter optimization solution for the true model. End constraint satisfaction is excellent. Overall trajectory agreement is good, if the assumed atmospheric model is reasonably accurate.

  4. Optical constants of solid methane

    NASA Technical Reports Server (NTRS)

    Khare, Bishun N.; Thompson, W. R.; Sagan, C.; Arakawa, E. T.; Bruel, C.; Judish, J. P.; Khanna, R. K.; Pollack, J. B.

    1989-01-01

    Methane is the most abundant simple organic molecule in the outer solar system bodies. In addition to being a gaseous constituent of the atmospheres of the Jovian planets and Titan, it is present in the solid form as a constituent of icy surfaces such as those of Triton and Pluto, and as cloud condensate in the atmospheres of Titan, Uranus, and Neptune. It is expected in the liquid form as a constituent of the ocean of Titan. Cometary ices also contain solid methane. The optical constants for both solid and liquid phases of CH4 for a wide temperature range are needed for radiative transfer calculations, for studies of reflection from surfaces, and for modeling of emission in the far infrared and microwave regions. The astronomically important visual to near infrared measurements of solid methane optical constants are conspicuously absent from the literature. Preliminary results are presented of the optical constants of solid methane for the 0.4 to 2.6 micron region. K is reported for both the amorphous and the crystalline (annealed) states. Using the previously measured values of the real part of the refractive index, n, of liquid methane at 110 K n is computed for solid methane using the Lorentz-Lorentz relationship. Work is in progress to extend the measurements of optical constants n and k for liquid and solid to both shorter and longer wavelengths, eventually providing a complete optical constants database for condensed CH4.

  5. Optical constants of solid methane

    NASA Technical Reports Server (NTRS)

    Khare, Bishun N.; Thompson, W. R.; Sagan, C.; Arakawa, E. T.; Bruel, C.; Judish, J. P.; Khanna, R. K.; Pollack, J. B.

    1990-01-01

    Methane is the most abundant simple organic molecule in the outer solar system bodies. In addition to being a gaseous constituent of the atmospheres of the Jovian planets and Titan, it is present in the solid form as a constituent of icy surfaces such as those of Triton and Pluto, and as cloud condensate in the atmospheres of Titan, Uranus, and Neptune. It is expected in the liquid form as a constituent of the ocean of Titan. Cometary ices also contain solid methane. The optical constants for both solid and liquid phases of CH4 for a wide temperature range are needed for radiative transfer calculations, for studies of reflection from surfaces, and for modeling of emission in the far infrared and microwave regions. The astronomically important visual to near infrared measurements of solid methane optical constants are conspicuously absent from the literature. Preliminary results are presented on the optical constants of solid methane for the 0.4 to 2.6 micrometer region. Deposition onto a substrate at 10 K produces glassy (semi-amorphous) material. Annealing this material at approximately 33 K for approximately 1 hour results in a crystalline material as seen by sharper, more structured bands and negligible background extinction due to scattering. The constant k is reported for both the amorphous and the crystalline (annealed) states. Typical values (at absorption maxima) are in the .001 to .0001 range. Below lambda = 1.1 micrometers the bands are too weak to be detected by transmission through the films less than or equal to 215 micrometers in thickness, employed in the studies to date. Using previously measured values of the real part of the refractive index, n, of liquid methane at 110 K, n is computed for solid methane using the Lorentz-Lorenz relationship. Work is in progress to extend the measurements of optical constants n and k for liquid and solid to both shorter and longer wavelengths, eventually providing a complete optical constants database for

  6. Accurate thickness measurement of graphene

    NASA Astrophysics Data System (ADS)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  7. Accurate thickness measurement of graphene.

    PubMed

    Shearer, Cameron J; Slattery, Ashley D; Stapleton, Andrew J; Shapter, Joseph G; Gibson, Christopher T

    2016-03-29

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  8. Cosmologies with variable gravitational constant

    SciTech Connect

    Narkikar, J.V.

    1983-03-01

    In 1937 Dirac presented an argument, based on the socalled large dimensionless numbers, which led him to the conclusion that the Newtonian gravitational constant G changes with epoch. Towards the end of the last century Ernst Mach had given plausible arguments to link the property of inertia of matter to the large scale structure of the universe. Mach's principle also leads to cosmological models with a variable gravitational constant. Three cosmologies which predict a variable G are discussed in this paper both from theoretical and observational points of view.

  9. Elastic constants for 8-OCB

    NASA Astrophysics Data System (ADS)

    Czechowski, Grzegorz; Zywucki, B.; Jadzyn, Jan

    1993-10-01

    The Frederiks transitions for the n-octyloxycyanobiphenyl (8-OCB) placed in the external magnetic and electric field as a function of the temperature have been studied. On the basis of threshold values Bc and Uc, the elastic constants for splay, bend and twist modes are determined. The magnetic anisotropy of 8-OCB as a function of temperature has been determined. The K11 and K33 elastic constants show the pretransitional nematic- smectic A effect. The values of critical exponents obtained from the temperature dependence of K11 and K33 in the vicinity of N-SA phase transition are discussed.

  10. Boltzmann's constant: A laboratory experiment

    NASA Astrophysics Data System (ADS)

    Kruglak, Haym

    1989-03-01

    The mean-square displacement of a latex microsphere is determined from its projection on a TV monitor. The distribution of displacement is shown to be Gaussian. Boltzmann's constant, calculated from the pooled data of several observers, is in excellent agreement with the accepted value. The experiment is designed for one laboratory period in the advanced undergraduate laboratory.

  11. The 1% concordance Hubble constant

    SciTech Connect

    Bennett, C. L.; Larson, D.; Weiland, J. L.; Hinshaw, G.

    2014-10-20

    The determination of the Hubble constant has been a central goal in observational astrophysics for nearly a hundred years. Extraordinary progress has occurred in recent years on two fronts: the cosmic distance ladder measurements at low redshift and cosmic microwave background (CMB) measurements at high redshift. The CMB is used to predict the current expansion rate through a best-fit cosmological model. Complementary progress has been made with baryon acoustic oscillation (BAO) measurements at relatively low redshifts. While BAO data do not independently determine a Hubble constant, they are important for constraints on possible solutions and checks on cosmic consistency. A precise determination of the Hubble constant is of great value, but it is more important to compare the high and low redshift measurements to test our cosmological model. Significant tension would suggest either uncertainties not accounted for in the experimental estimates or the discovery of new physics beyond the standard model of cosmology. In this paper we examine in detail the tension between the CMB, BAO, and cosmic distance ladder data sets. We find that these measurements are consistent within reasonable statistical expectations and we combine them to determine a best-fit Hubble constant of 69.6 ± 0.7 km s{sup –1} Mpc{sup –1}. This value is based upon WMAP9+SPT+ACT+6dFGS+BOSS/DR11+H {sub 0}/Riess; we explore alternate data combinations in the text. The combined data constrain the Hubble constant to 1%, with no compelling evidence for new physics.

  12. Variation of fundamental constants: theory

    NASA Astrophysics Data System (ADS)

    Flambaum, Victor

    2008-05-01

    Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. There are some hints for the variation of different fundamental constants in quasar absorption spectra and Big Bang nucleosynthesis data. A large number of publications (including atomic clocks) report limits on the variations. We want to study the variation of the main dimensionless parameters of the Standard Model: 1. Fine structure constant alpha (combination of speed of light, electron charge and Plank constant). 2. Ratio of the strong interaction scale (LambdaQCD) to a fundamental mass like electron mass or quark mass which are proportional to Higgs vacuum expectation value. The proton mass is propotional to LambdaQCD, therefore, the proton-to-electron mass ratio comes into this second category. We performed necessary atomic, nuclear and QCD calculations needed to study variation of the fundamental constants using the Big Bang Nucleosynthsis, quasar spectra, Oklo natural nuclear reactor and atomic clock data. The relative effects of the variation may be enhanced in transitions between narrow close levels in atoms, molecules and nuclei. If one will study an enhanced effect, the relative value of systematic effects (which are not enhanced) may be much smaller. Note also that the absolute magnitude of the variation effects in nuclei (e.g. in very narrow 7 eV transition in 229Th) may be 5 orders of magnitude larger than in atoms. A different possibility of enhancement comes from the inversion transitions in molecules where splitting between the levels is due to the quantum tunneling amplitude which has strong, exponential dependence on the electron to proton mass ratio. Our study of NH3 quasar spectra has already given the best limit on the variation of electron to proton mass ratio.

  13. Varying Fine-Structure Constant and the Cosmological Constant Problem

    NASA Astrophysics Data System (ADS)

    Fujii, Yasunori

    We start with a brief account of the latest analysis of the Oklo phenomenon providing the still most stringent constraint on time variability of the fine-structure constant α. Comparing this with the recent result from the measurement of distant QSO's appears to indicate a non-uniform time-dependence, which we argue to be related to another recent finding of the accelerating universe. This view is implemented in terms of the scalar-tensor theory, applied specifically to the small but nonzero cosmological constant. Our detailed calculation shows that these two phenomena can be understood in terms of a common origin, a particular behavior of the scalar field, dilaton. We also sketch how this theoretical approach makes it appropriate to revisit non-Newtonian gravity featuring small violation of Weak Equivalence Principle at medium distances.

  14. Probing the flexibility of internal rotation in silylated phenols with the NMR scalar spin-spin coupling constants.

    PubMed

    Sychrovský, Vladimír; Benda, Ladislav; Prokop, Alexandr; Blechta, Vratislav; Schraml, Jan; Spirko, Vladimír

    2008-06-12

    The rotation of a trimethylsiloxy (TMSO) group in three silylated phenols (with three different ortho substituents -H, -CH3, and -C(CH3)3) was studied with the NMR (n)J(Si,C), n = 2, 3, 4, 5, scalar spin-spin coupling between the (29)Si nucleus of the TMSO group and the (13)C nuclei of the phenyl ring. The internal rotation potential calculated with the B3LYP and MP2 calculation methods including the effect of a solvent environment (gas phase, chloroform, and water) was used for the calculation of the dynamical averages of the scalar coupling constants in the framework of the rigid-bender formalism. Solvent effects, the quality of the rotational potential, and the applicability of the classical molecular dynamic to the problem is discussed. Quantum effects have a sizable impact on scalar couplings, particularly for the internal rotational states well localized within the wells of the potential surfaces for the TMSO group. The overall difference between the experimental and theoretical scalar couplings calculated for the global energy-minima structures (static model) decreases substantially for both model potentials (B3LYP, MP2) when the molecular motion of the TMSO group is taken into account. The calculated data indicate that the inclusion of molecular motion is necessary for the accurate calculation of the scalar coupling constants and their reliable structural interpretation for any system which possesses a large-amplitude motion. PMID:18491850

  15. Remote Sensing of Salinity: The Dielectric Constant of Sea Water

    NASA Technical Reports Server (NTRS)

    LeVine, David M.; Lang, R.; Utku, C.; Tarkocin, Y.

    2011-01-01

    Global monitoring of sea surface salinity from space requires an accurate model for the dielectric constant of sea water as a function of salinity and temperature to characterize the emissivity of the surface. Measurements are being made at 1.413 GHz, the center frequency of the Aquarius radiometers, using a resonant cavity and the perturbation method. The cavity is operated in a transmission mode and immersed in a liquid bath to control temperature. Multiple measurements are made at each temperature and salinity. Error budgets indicate a relative accuracy for both real and imaginary parts of the dielectric constant of about 1%.

  16. Three pion nucleon coupling constants

    NASA Astrophysics Data System (ADS)

    Ruiz Arriola, E.; Amaro, J. E.; Navarro Pérez, R.

    2016-08-01

    There exist four pion nucleon coupling constants, fπ0pp, - fπ0nn, fπ+pn/2 and fπ-np/2 which coincide when up and down quark masses are identical and the electron charge is zero. While there is no reason why the pion-nucleon-nucleon coupling constants should be identical in the real world, one expects that the small differences might be pinned down from a sufficiently large number of independent and mutually consistent data. Our discussion provides a rationale for our recent determination fp2 = 0.0759(4),f 02 = 0.079(1),f c2 = 0.0763(6), based on a partial wave analysis of the 3σ self-consistent nucleon-nucleon Granada-2013 database comprising 6713 published data in the period 1950-2013.

  17. Quaternions as astrometric plate constants

    NASA Technical Reports Server (NTRS)

    Jefferys, William H.

    1987-01-01

    A new method for solving problems in relative astrometry is proposed. In it, the relationship between the measured quantities and the components of the position vector of a star is modeled using quaternions, in effect replacing the plate constants of a standard four-plate-constant solution with the four components of a quaternion. The method allows a direct solution for the position vectors of the stars, and hence for the equatorial coordinates. Distortions, magnitude, and color effects are readily incorporated into the formalism, and the method is directly applicable to overlapping-plate problems. The advantages of the method include the simplicity of the resulting equations, their freedom from singularities, and the fact that trigonometric functions and tangential point transformations are not needed to model the plate material. A global solution over the entire sky is possible.

  18. Three pion nucleon coupling constants

    NASA Astrophysics Data System (ADS)

    Ruiz Arriola, E.; Amaro, J. E.; Navarro Pérez, R.

    2016-08-01

    There exist four pion nucleon coupling constants, fπ0pp, ‑ fπ0nn, fπ+pn/2 and fπ‑np/2 which coincide when up and down quark masses are identical and the electron charge is zero. While there is no reason why the pion-nucleon-nucleon coupling constants should be identical in the real world, one expects that the small differences might be pinned down from a sufficiently large number of independent and mutually consistent data. Our discussion provides a rationale for our recent determination fp2 = 0.0759(4),f 02 = 0.079(1),f c2 = 0.0763(6), based on a partial wave analysis of the 3σ self-consistent nucleon-nucleon Granada-2013 database comprising 6713 published data in the period 1950-2013.

  19. Time-Varying Fundamental Constants

    NASA Astrophysics Data System (ADS)

    Olive, Keith

    2003-04-01

    Recent data from quasar absorption systems can be interpreted as arising from a time variation in the fine-structure constant. However, there are numerous cosmological, astro-physical, and terrestrial bounds on any such variation. These includes bounds from Big Bang Nucleosynthesis (from the ^4He abundance), the Oklo reactor (from the resonant neutron capture cross-section of Sm), and from meteoretic lifetimes of heavy radioactive isotopes. The bounds on the variation of the fine-structure constant are significantly strengthened in models where all gauge and Yukawa couplings vary in a dependent manner, as would be expected in unified theories. Models which are consistent with all data are severly challenged when Equivalence Principle constraints are imposed.

  20. Simulating Supercapacitors: Can We Model Electrodes As Constant Charge Surfaces?

    PubMed

    Merlet, Céline; Péan, Clarisse; Rotenberg, Benjamin; Madden, Paul A; Simon, Patrice; Salanne, Mathieu

    2013-01-17

    Supercapacitors based on an ionic liquid electrolyte and graphite or nanoporous carbon electrodes are simulated using molecular dynamics. We compare a simplified electrode model in which a constant, uniform charge is assigned to each carbon atom with a realistic model in which a constant potential is applied between the electrodes (the carbon charges are allowed to fluctuate). We show that the simulations performed with the simplified model do not provide a correct description of the properties of the system. First, the structure of the adsorbed electrolyte is partly modified. Second, dramatic differences are observed for the dynamics of the system during transient regimes. In particular, upon application of a constant applied potential difference, the increase in the temperature, due to the Joule effect, associated with the creation of an electric current across the cell follows Ohm's law, while unphysically high temperatures are rapidly observed when constant charges are assigned to each carbon atom. PMID:26283432

  1. Simulating Supercapacitors: Can We Model Electrodes As Constant Charge Surfaces?

    PubMed

    Merlet, Céline; Péan, Clarisse; Rotenberg, Benjamin; Madden, Paul A; Simon, Patrice; Salanne, Mathieu

    2013-01-17

    Supercapacitors based on an ionic liquid electrolyte and graphite or nanoporous carbon electrodes are simulated using molecular dynamics. We compare a simplified electrode model in which a constant, uniform charge is assigned to each carbon atom with a realistic model in which a constant potential is applied between the electrodes (the carbon charges are allowed to fluctuate). We show that the simulations performed with the simplified model do not provide a correct description of the properties of the system. First, the structure of the adsorbed electrolyte is partly modified. Second, dramatic differences are observed for the dynamics of the system during transient regimes. In particular, upon application of a constant applied potential difference, the increase in the temperature, due to the Joule effect, associated with the creation of an electric current across the cell follows Ohm's law, while unphysically high temperatures are rapidly observed when constant charges are assigned to each carbon atom.

  2. Accurate free energy calculation along optimized paths.

    PubMed

    Chen, Changjun; Xiao, Yi

    2010-05-01

    The path-based methods of free energy calculation, such as thermodynamic integration and free energy perturbation, are simple in theory, but difficult in practice because in most cases smooth paths do not exist, especially for large molecules. In this article, we present a novel method to build the transition path of a peptide. We use harmonic potentials to restrain its nonhydrogen atom dihedrals in the initial state and set the equilibrium angles of the potentials as those in the final state. Through a series of steps of geometrical optimization, we can construct a smooth and short path from the initial state to the final state. This path can be used to calculate free energy difference. To validate this method, we apply it to a small 10-ALA peptide and find that the calculated free energy changes in helix-helix and helix-hairpin transitions are both self-convergent and cross-convergent. We also calculate the free energy differences between different stable states of beta-hairpin trpzip2, and the results show that this method is more efficient than the conventional molecular dynamics method in accurate free energy calculation.

  3. Molecular Data from Solar Spectroscopy

    NASA Astrophysics Data System (ADS)

    Grevesse, N.; Sauval, A. J.

    1992-03-01

    We show through a few examples how the analysis of molecular transitions present in the solar visible and infrared spectrum can be used to refine our knowledge of the molecular constants and to test the accuracy of available molecular data like transition probabilities and dissociation energies for a few diatomic molecules. Key words: ATOMIC PROCESSES - MOLECULAR PROCESSES - SUN: ATMOSPHERE - SUN: SPECTRA

  4. Elasticity of crystalline molecular explosives

    SciTech Connect

    Hooks, Daniel E.; Ramos, Kyle J.; Bolme, C. A.; Cawkwell, Marc J.

    2015-04-14

    Crystalline molecular explosives are key components of engineered explosive formulations. In precision applications a high degree of consistency and predictability is desired under a range of conditions to a variety of stimuli. Prediction of behaviors from mechanical response and failure to detonation initiation and detonation performance of the material is linked to accurate knowledge of the material structure and first stage of deformation: elasticity. The elastic response of pentaerythritol tetranitrate (PETN), cyclotrimethylene trinitramine (RDX), and cyclotetramethylene tetranitramine (HMX), including aspects of material and measurement variability, and computational methods are described in detail. Experimental determinations of elastic tensors are compared, and an evaluation of sources of error is presented. Furthermore, computed elastic constants are also compared for these materials and for triaminotrinitrobenzene (TATB), for which there are no measurements.

  5. Elasticity of crystalline molecular explosives

    DOE PAGES

    Hooks, Daniel E.; Ramos, Kyle J.; Bolme, C. A.; Cawkwell, Marc J.

    2015-04-14

    Crystalline molecular explosives are key components of engineered explosive formulations. In precision applications a high degree of consistency and predictability is desired under a range of conditions to a variety of stimuli. Prediction of behaviors from mechanical response and failure to detonation initiation and detonation performance of the material is linked to accurate knowledge of the material structure and first stage of deformation: elasticity. The elastic response of pentaerythritol tetranitrate (PETN), cyclotrimethylene trinitramine (RDX), and cyclotetramethylene tetranitramine (HMX), including aspects of material and measurement variability, and computational methods are described in detail. Experimental determinations of elastic tensors are compared, andmore » an evaluation of sources of error is presented. Furthermore, computed elastic constants are also compared for these materials and for triaminotrinitrobenzene (TATB), for which there are no measurements.« less

  6. Star polymers rupture induced by constant forces

    NASA Astrophysics Data System (ADS)

    García, N. A.; Febbo, M.; Vega, D. A.; Milchev, A.

    2014-10-01

    In this work, we study the breakage process of an unknotted three-arm star-shaped polymer when it is pulled from its free ends by a constant force. The star polymer configuration is described through an array of monomers coupled by anharmonic bonds, while the rupture process is tracked in three-dimensional space by means of Langevin Molecular Dynamics simulations. The interaction between monomers is described by a Morse potential, while a Weeks-Chandler-Anderson energetic contribution accounts for the excluded volume interaction. We explore the effect of the molecular architecture on the distributions of rupture times over a broad interval of pulling forces and star configurations. It was found that the rupture time distribution of the individual star arms is strongly affected by the star configuration imposed by the pulling forces and the length of the arms. We also observed that for large pulling forces the rupture time distributions resemble the dominant features observed for linear polymer chains. The model introduced here provides the basic ingredients to describe the effects of tensile forces on stress-induced degradation of branched macromolecules and polymer networks.

  7. Star polymers rupture induced by constant forces.

    PubMed

    García, N A; Febbo, M; Vega, D A; Milchev, A

    2014-10-28

    In this work, we study the breakage process of an unknotted three-arm star-shaped polymer when it is pulled from its free ends by a constant force. The star polymer configuration is described through an array of monomers coupled by anharmonic bonds, while the rupture process is tracked in three-dimensional space by means of Langevin Molecular Dynamics simulations. The interaction between monomers is described by a Morse potential, while a Weeks-Chandler-Anderson energetic contribution accounts for the excluded volume interaction. We explore the effect of the molecular architecture on the distributions of rupture times over a broad interval of pulling forces and star configurations. It was found that the rupture time distribution of the individual star arms is strongly affected by the star configuration imposed by the pulling forces and the length of the arms. We also observed that for large pulling forces the rupture time distributions resemble the dominant features observed for linear polymer chains. The model introduced here provides the basic ingredients to describe the effects of tensile forces on stress-induced degradation of branched macromolecules and polymer networks. PMID:25362341

  8. Molecular thermometry.

    PubMed

    McCabe, Kevin M; Hernandez, Mark

    2010-05-01

    Conventional temperature measurements rely on material responses to heat, which can be detected visually. When Galileo developed an air expansion based device to detect temperature changes, Santorio, a contemporary physician, added a scale to create the first thermometer. With this instrument, patients' temperatures could be measured, recorded, and related to changing health conditions. Today, advances in materials science and bioengineering provide new ways to report temperature at the molecular level in real time. In this review, the scientific foundations and history of thermometry underpin a discussion of the discoveries emerging from the field of molecular thermometry. Intracellular nanogels and heat sensing biomolecules have been shown to accurately report temperature changes at the nanoscale. Various systems will soon provide the ability to accurately measure temperature changes at the tissue, cellular, and even subcellular level, allowing for detection and monitoring of very small changes in local temperature. In the clinic, this will lead to enhanced detection of tumors and localized infection, and accurate and precise monitoring of hyperthermia-based therapies. Some nanomaterial systems have even demonstrated a theranostic capacity for heat-sensitive, local delivery of chemotherapeutics. Just as early thermometry rapidly moved into the clinic, so too will these molecular thermometers.

  9. Molecular Thermometry

    PubMed Central

    McCabe, Kevin M.; Hernandez, Mark

    2010-01-01

    Conventional temperature measurements rely on material responses to heat, which can be detected visually. When Galileo developed an air expansion based device to detect temperature changes, Santorio, a contemporary physician, added a scale to create the first thermometer. With this instrument, patients’ temperatures could be measured, recorded and related to changing health conditions. Today, advances in materials science and bioengineering provide new ways to report temperature at the molecular level in real time. In this review the scientific foundations and history of thermometry underpin a discussion of the discoveries emerging from the field of molecular thermometry. Intracellular nanogels and heat sensing biomolecules have been shown to accurately report temperature changes at the nano-scale. Various systems will soon provide the ability to accurately measure temperature changes at the tissue, cellular, and even sub-cellular level, allowing for detection and monitoring of very small changes in local temperature. In the clinic this will lead to enhanced detection of tumors and localized infection, and accurate and precise monitoring of hyperthermia based therapies. Some nanomaterial systems have even demonstrated a theranostic capacity for heat-sensitive, local delivery of chemotherapeutics. Just as early thermometry moved into the clinic, so too will these molecular thermometers. PMID:20139796

  10. Strong resetting of the mammalian clock by constant light followed by constant darkness

    PubMed Central

    Chen, Rongmin; Seo, Dong-oh; Bell, Elijah; von Gall, Charlotte; Lee, Choogon

    2008-01-01

    The mammalian molecular circadian clock in the suprachiasmatic nuclei (SCN) regulates locomotor activity rhythms as well as clocks in peripheral tissues (Reppert and Weaver, 2002; Ko and Takahashi, 2006). Constant light (LL) can induce behavioral and physiological arrhythmicity, by desynchronizing clock cells in the SCN (Ohta et al., 2005). We examined how the disordered clock cells resynchronize by probing the molecular clock and measuring behavior in mice transferred from LL to constant darkness (DD). The circadian locomotor activity rhythms disrupted in LL become robustly rhythmic again from the beginning of DD, and the starting phase of the rhythm in DD is specific, not random, suggesting that the desynchronized clock cells are quickly reset in an unconventional manner by the L:D transition. By measuring mPERIOD protein rhythms, we showed that the SCN and peripheral tissue clocks quickly become rhythmic again in phase with the behavioral rhythms. We propose that this resetting mechanism may be different from conventional phase shifting, which involves light-induction of Period genes (Albrecht et al., 1997; Shearman et al., 1997; Shigeyoshi et al., 1997). Using our functional insights, we could shift the circadian phase of locomotor activity rhythms by 12 hours using a 15-hour LL treatment: essentially producing phase reversal by a single light pulse, a feat that has not been reported previously in wild-type mice and that has potential clinical utility. PMID:19005049

  11. Millikan's measurement of Planck's constant

    NASA Astrophysics Data System (ADS)

    Franklin, Allan

    2013-12-01

    Robert Millikan is famous for measuring the charge of the electron. His result was better than any previous measurement and his method established that there was a fundamental unit of charge, or charge quantization. He is less well-known for his measurement of Planck's constant, although, as discussed below, he is often mistakenly given credit for providing significant evidence in support of Einstein's photon theory of light.1 His Nobel Prize citation was "for his work on the elementary electric charge of electricity and the photoelectric effect," an indication of the significance of his work on the photoelectric effect.

  12. Chandra Independently Determines Hubble Constant

    NASA Astrophysics Data System (ADS)

    2006-08-01

    A critically important number that specifies the expansion rate of the Universe, the so-called Hubble constant, has been independently determined using NASA's Chandra X-ray Observatory. This new value matches recent measurements using other methods and extends their validity to greater distances, thus allowing astronomers to probe earlier epochs in the evolution of the Universe. "The reason this result is so significant is that we need the Hubble constant to tell us the size of the Universe, its age, and how much matter it contains," said Max Bonamente from the University of Alabama in Huntsville and NASA's Marshall Space Flight Center (MSFC) in Huntsville, Ala., lead author on the paper describing the results. "Astronomers absolutely need to trust this number because we use it for countless calculations." Illustration of Sunyaev-Zeldovich Effect Illustration of Sunyaev-Zeldovich Effect The Hubble constant is calculated by measuring the speed at which objects are moving away from us and dividing by their distance. Most of the previous attempts to determine the Hubble constant have involved using a multi-step, or distance ladder, approach in which the distance to nearby galaxies is used as the basis for determining greater distances. The most common approach has been to use a well-studied type of pulsating star known as a Cepheid variable, in conjunction with more distant supernovae to trace distances across the Universe. Scientists using this method and observations from the Hubble Space Telescope were able to measure the Hubble constant to within 10%. However, only independent checks would give them the confidence they desired, considering that much of our understanding of the Universe hangs in the balance. Chandra X-ray Image of MACS J1149.5+223 Chandra X-ray Image of MACS J1149.5+223 By combining X-ray data from Chandra with radio observations of galaxy clusters, the team determined the distances to 38 galaxy clusters ranging from 1.4 billion to 9.3 billion

  13. Henry's law constants of polyols

    NASA Astrophysics Data System (ADS)

    Compernolle, S.; Müller, J.-F.

    2014-05-01

    Henry's law constants (HLC) are derived for several polyols bearing between 2 and 6 hydroxyl groups, based on literature data for water activity, vapour pressure and/or solubility. Depending on the case, infinite dilution activity coefficients (IDACs), solid state pressures or activity coefficient ratios are obtained as intermediary results. For most compounds, these are the first values reported, while others compare favourably with literature data in most cases. Using these values and those from a previous work (Compernolle and Müller, 2014), an assessment is made on the partitioning of polyols, diacids and hydroxy acids to droplet and aqueous aerosol.

  14. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  15. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2013-07-01 2013-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  16. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2011-07-01 2011-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  17. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  18. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2012-07-01 2012-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  19. Correction for instrument time constant in determination of reaction kinetics.

    SciTech Connect

    Chilton, Marie; Clark, Jared; Thomas, Nathan; Nicholson, Allen; Hansen, Lee D.; Hansen, Clifford W.; Hansen, Jaron

    2010-02-01

    Rates of reactions can be expressed as dn/dt = kcf(n) where n is moles of reaction, k is a rate constant, c is a proportionality constant, and f(n) is a function of the properties of the sample. When the instrument time constant, ?, and k are sufficiently comparable that measured rates are significantly affected by instrument response, correction for instrument response must be done to obtain accurate reaction kinetics. Correction for instrument response has previously been done by truncating early data or by use of the Tian equation. Both methods can lead to significant errors. We describe a method for simultaneous determination of ?, k, and c by fitting equations describing the combined instrument response and rate law to rates observed as a function of time. The method was tested with data on the heat rate from acid-catalyzed hydrolysis of sucrose.

  20. Atomic force microscopy spring constant determination in viscous liquids.

    PubMed

    Pirzer, Tobias; Hugel, Thorsten

    2009-03-01

    The spring constant of cantilever in atomic force microscopy (AFM) is often calibrated from thermal noise spectra. Essential for accurate implementation of this "thermal noise method" is an appropriate fitting function and procedure. Here, we survey the commonly used fitting functions and examine their applicability in a range of environments. We find that viscous liquid environments are extremely problematic due to the frequency dependent nature of the damping coefficient. The deviations from the true spring constant were sometimes more than 100% when utilizing the fit routines built into the three investigated commercial AFM instruments; similar problems can arise with homebuilt AFMs. We discuss the reasons for this problem, especially the limits of the fitting process. Finally, we present a thermal noise based procedure and an improved fit function to determine the spring constant with AFMs in fluids of various viscosities. PMID:19334955

  1. Atomic force microscopy spring constant determination in viscous liquids

    SciTech Connect

    Pirzer, Tobias; Hugel, Thorsten

    2009-03-15

    The spring constant of cantilever in atomic force microscopy (AFM) is often calibrated from thermal noise spectra. Essential for accurate implementation of this 'thermal noise method' is an appropriate fitting function and procedure. Here, we survey the commonly used fitting functions and examine their applicability in a range of environments. We find that viscous liquid environments are extremely problematic due to the frequency dependent nature of the damping coefficient. The deviations from the true spring constant were sometimes more than 100% when utilizing the fit routines built into the three investigated commercial AFM instruments; similar problems can arise with homebuilt AFMs. We discuss the reasons for this problem, especially the limits of the fitting process. Finally, we present a thermal noise based procedure and an improved fit function to determine the spring constant with AFMs in fluids of various viscosities.

  2. Transferability of anharmonic force fields in simulations of molecular vibrations.

    PubMed

    Parchanský, Václav; Bour, Petr

    2010-07-28

    Accurate simulations of vibrational molecular spectra require precise molecular force fields, at least with cubic and quartic anharmonic corrections beyond the harmonic limits. Generation of such force field terms becomes computationally prohibitive for larger molecules. In this work, an alternate possibility is explored, where approximate anharmonic force field components are obtained from molecular fragments. Transferability properties of the cubic and incomplete quartic fields are discussed and tested on model oligoproline molecules. Automatic transfer schemes including cubic, two and three atomic quartic force constants are developed and implemented. The results indicate that the main vibrational interactions in molecules are local and the anharmonic constants are mostly well amendable to the transfer. Exact anharmonic normal mode force fields of larger molecules compared very well to those obtained from smaller molecular parts. The most important changes in vibrational spectra caused by the anharmonic interactions could be reproduced with two and three atomic force field terms. The transfer scheme thus provides molecular anharmonic force fields without a significant loss of accuracy and brings significant savings of computer time and memory needed to generate molecular vibrational energies and spectra.

  3. Stability constant estimator user`s guide

    SciTech Connect

    Hay, B.P.; Castleton, K.J.; Rustad, J.R.

    1996-12-01

    The purpose of the Stability Constant Estimator (SCE) program is to estimate aqueous stability constants for 1:1 complexes of metal ions with ligands by using trends in existing stability constant data. Such estimates are useful to fill gaps in existing thermodynamic databases and to corroborate the accuracy of reported stability constant values.

  4. Note: Spring constant calibration of nanosurface-engineered atomic force microscopy cantilevers

    SciTech Connect

    Ergincan, O. Palasantzas, G.; Kooi, B. J.

    2014-02-15

    The determination of the dynamic spring constant (k{sub d}) of atomic force microscopy cantilevers is of crucial importance for converting cantilever deflection to accurate force data. Indeed, the non-destructive, fast, and accurate measurement method of the cantilever dynamic spring constant by Sader et al. [Rev. Sci. Instrum. 83, 103705 (2012)] is confirmed here for plane geometry but surface modified cantilevers. It is found that the measured spring constants (k{sub eff}, the dynamic one k{sub d}), and the calculated (k{sub d,1}) are in good agreement within less than 10% error.

  5. Note: spring constant calibration of nanosurface-engineered atomic force microscopy cantilevers.

    PubMed

    Ergincan, O; Palasantzas, G; Kooi, B J

    2014-02-01

    The determination of the dynamic spring constant (kd) of atomic force microscopy cantilevers is of crucial importance for converting cantilever deflection to accurate force data. Indeed, the non-destructive, fast, and accurate measurement method of the cantilever dynamic spring constant by Sader et al. [Rev. Sci. Instrum. 83, 103705 (2012)] is confirmed here for plane geometry but surface modified cantilevers. It is found that the measured spring constants (keff, the dynamic one kd), and the calculated (kd,1) are in good agreement within less than 10% error.

  6. Accurate pressure gradient calculations in hydrostatic atmospheric models

    NASA Technical Reports Server (NTRS)

    Carroll, John J.; Mendez-Nunez, Luis R.; Tanrikulu, Saffet

    1987-01-01

    A method for the accurate calculation of the horizontal pressure gradient acceleration in hydrostatic atmospheric models is presented which is especially useful in situations where the isothermal surfaces are not parallel to the vertical coordinate surfaces. The present method is shown to be exact if the potential temperature lapse rate is constant between the vertical pressure integration limits. The technique is applied to both the integration of the hydrostatic equation and the computation of the slope correction term in the horizontal pressure gradient. A fixed vertical grid and a dynamic grid defined by the significant levels in the vertical temperature distribution are employed.

  7. Accurate fluorescence quantum yield determination by fluorescence correlation spectroscopy.

    PubMed

    Kempe, Daryan; Schöne, Antonie; Fitter, Jörg; Gabba, Matteo

    2015-04-01

    Here, we present a comparative method for the accurate determination of fluorescence quantum yields (QYs) by fluorescence correlation spectroscopy. By exploiting the high sensitivity of single-molecule spectroscopy, we obtain the QYs of samples in the microliter range and at (sub)nanomolar concentrations. Additionally, in combination with fluorescence lifetime measurements, our method allows the quantification of both static and collisional quenching constants. Thus, besides being simple and fast, our method opens up the possibility to photophysically characterize labeled biomolecules under application-relevant conditions and with low sample consumption, which is often important in single-molecule studies.

  8. Asympotics with positive cosmological constant

    NASA Astrophysics Data System (ADS)

    Bonga, Beatrice; Ashtekar, Abhay; Kesavan, Aruna

    2014-03-01

    Since observations to date imply that our universe has a positive cosmological constant, one needs an extension of the theory of isolated systems and gravitational radiation in full general relativity from the asymptotically flat to asymptotically de Sitter space-times. In current definitions, one mimics the boundary conditions used in asymptotically AdS context to conclude that the asymptotic symmetry group is the de Sitter group. However, these conditions severely restricts radiation and in fact rules out non-zero flux of energy, momentum and angular momentum carried by gravitational waves. Therefore, these formulations of asymptotically de Sitter space-times are uninteresting beyond non-radiative spacetimes. The situation is compared and contrasted with conserved charges and fluxes at null infinity in asymptotically flat space-times.

  9. Henry's law constants of polyols

    NASA Astrophysics Data System (ADS)

    Compernolle, S.; Müller, J.-F.

    2014-12-01

    Henry's law constants (HLC) are derived for several polyols bearing between 2 and 6 hydroxyl groups, based on literature data for water activity, vapour pressure and/or solubility. While deriving HLC and depending on the case, also infinite dilution activity coefficients (IDACs), solid state vapour pressures or activity coefficient ratios are obtained as intermediate results. An error analysis on the intermediate quantities and the obtained HLC is included. For most compounds, these are the first values reported, while others compare favourably with literature data in most cases. Using these values and those from a previous work (Compernolle and Müller, 2014), an assessment is made on the partitioning of polyols, diacids and hydroxy acids to droplet and aqueous aerosol.

  10. Philicities, Fugalities, and Equilibrium Constants.

    PubMed

    Mayr, Herbert; Ofial, Armin R

    2016-05-17

    The mechanistic model of Organic Chemistry is based on relationships between rate and equilibrium constants. Thus, strong bases are generally considered to be good nucleophiles and poor nucleofuges. Exceptions to this rule have long been known, and the ability of iodide ions to catalyze nucleophilic substitutions, because they are good nucleophiles as well as good nucleofuges, is just a prominent example for exceptions from the general rule. In a reaction series, the Leffler-Hammond parameter α = δΔG(⧧)/δΔG° describes the fraction of the change in the Gibbs energy of reaction, which is reflected in the change of the Gibbs energy of activation. It has long been considered as a measure for the position of the transition state; thus, an α value close to 0 was associated with an early transition state, while an α value close to 1 was considered to be indicative of a late transition state. Bordwell's observation in 1969 that substituent variation in phenylnitromethanes has a larger effect on the rates of deprotonation than on the corresponding equilibrium constants (nitroalkane anomaly) triggered the breakdown of this interpretation. In the past, most systematic investigations of the relationships between rates and equilibria of organic reactions have dealt with proton transfer reactions, because only for few other reaction series complementary kinetic and thermodynamic data have been available. In this Account we report on a more general investigation of the relationships between Lewis basicities, nucleophilicities, and nucleofugalities as well as between Lewis acidities, electrophilicities, and electrofugalities. Definitions of these terms are summarized, and it is suggested to replace the hybrid terms "kinetic basicity" and "kinetic acidity" by "protophilicity" and "protofugality", respectively; in this way, the terms "acidity" and "basicity" are exclusively assigned to thermodynamic properties, while "philicity" and "fugality" refer to kinetics

  11. Accurate Thermal Conductivities from First Principles

    NASA Astrophysics Data System (ADS)

    Carbogno, Christian

    2015-03-01

    In spite of significant research efforts, a first-principles determination of the thermal conductivity at high temperatures has remained elusive. On the one hand, Boltzmann transport techniques that include anharmonic effects in the nuclear dynamics only perturbatively become inaccurate or inapplicable under such conditions. On the other hand, non-equilibrium molecular dynamics (MD) methods suffer from enormous finite-size artifacts in the computationally feasible supercells, which prevent an accurate extrapolation to the bulk limit of the thermal conductivity. In this work, we overcome this limitation by performing ab initio MD simulations in thermodynamic equilibrium that account for all orders of anharmonicity. The thermal conductivity is then assessed from the auto-correlation function of the heat flux using the Green-Kubo formalism. Foremost, we discuss the fundamental theory underlying a first-principles definition of the heat flux using the virial theorem. We validate our approach and in particular the techniques developed to overcome finite time and size effects, e.g., by inspecting silicon, the thermal conductivity of which is particularly challenging to converge. Furthermore, we use this framework to investigate the thermal conductivity of ZrO2, which is known for its high degree of anharmonicity. Our calculations shed light on the heat resistance mechanism active in this material, which eventually allows us to discuss how the thermal conductivity can be controlled by doping and co-doping. This work has been performed in collaboration with R. Ramprasad (University of Connecticut), C. G. Levi and C. G. Van de Walle (University of California Santa Barbara).

  12. Determination of the Hubble constant.

    PubMed

    Freedman, W L; Feng, L L

    1999-09-28

    Establishing accurate extragalactic distances has provided an immense challenge to astronomers since the 1920s. The situation has improved dramatically as better detectors have become available, and as several new, promising techniques have been developed. For the first time in the history of this difficult field, relative distances to galaxies are being compared on a case-by-case basis, and their quantitative agreement is being established. New instrumentation, the development of new techniques for measuring distances, and recent measurements with the Hubble Space telescope all have resulted in new distances to galaxies with precision at the +/-5-20% level. The current statistical uncertainty in some methods for measuring H(0) is now only a few percent; with systematic errors, the total uncertainty is approaching +/-10%. Hence, the historical factor-of-two uncertainty in the value of the H(0) is now behind us.

  13. Determination of the Hubble constant

    PubMed Central

    Freedman, Wendy L.; Feng, Long Long

    1999-01-01

    Establishing accurate extragalactic distances has provided an immense challenge to astronomers since the 1920s. The situation has improved dramatically as better detectors have become available, and as several new, promising techniques have been developed. For the first time in the history of this difficult field, relative distances to galaxies are being compared on a case-by-case basis, and their quantitative agreement is being established. New instrumentation, the development of new techniques for measuring distances, and recent measurements with the Hubble Space telescope all have resulted in new distances to galaxies with precision at the ±5–20% level. The current statistical uncertainty in some methods for measuring H0 is now only a few percent; with systematic errors, the total uncertainty is approaching ±10%. Hence, the historical factor-of-two uncertainty in the value of the H0 is now behind us. PMID:10500124

  14. Determination of the Hubble constant.

    PubMed

    Freedman, W L; Feng, L L

    1999-09-28

    Establishing accurate extragalactic distances has provided an immense challenge to astronomers since the 1920s. The situation has improved dramatically as better detectors have become available, and as several new, promising techniques have been developed. For the first time in the history of this difficult field, relative distances to galaxies are being compared on a case-by-case basis, and their quantitative agreement is being established. New instrumentation, the development of new techniques for measuring distances, and recent measurements with the Hubble Space telescope all have resulted in new distances to galaxies with precision at the +/-5-20% level. The current statistical uncertainty in some methods for measuring H(0) is now only a few percent; with systematic errors, the total uncertainty is approaching +/-10%. Hence, the historical factor-of-two uncertainty in the value of the H(0) is now behind us. PMID:10500124

  15. Spin-rotation and NMR shielding constants in HCl

    SciTech Connect

    Jaszuński, Michał; Repisky, Michal; Demissie, Taye B.; Komorovsky, Stanislav; Malkin, Elena; Ruud, Kenneth; Garbacz, Piotr; Jackowski, Karol; Makulski, Włodzimierz

    2013-12-21

    The spin-rotation and nuclear magnetic shielding constants are analysed for both nuclei in the HCl molecule. Nonrelativistic ab initio calculations at the CCSD(T) level of approximation show that it is essential to include relativistic effects to obtain spin-rotation constants consistent with accurate experimental data. Our best estimates for the spin-rotation constants of {sup 1}H{sup 35}Cl are C{sub Cl}  = −53.914 kHz and C{sub H}  = 42.672 kHz (for the lowest rovibrational level). For the chlorine shielding constant, the ab initio value computed including the relativistic corrections, σ(Cl) = 976.202 ppm, provides a new absolute shielding scale; for hydrogen we find σ(H) = 31.403 ppm (both at 300 K). Combining the theoretical results with our new gas-phase NMR experimental data allows us to improve the accuracy of the magnetic dipole moments of both chlorine isotopes. For the hydrogen shielding constant, including relativistic effects yields better agreement between experimental and computed values.

  16. Is There a Cosmological Constant?

    NASA Technical Reports Server (NTRS)

    Kochanek, Christopher; Oliversen, Ronald J. (Technical Monitor)

    2002-01-01

    The grant contributed to the publication of 18 refereed papers and 5 conference proceedings. The primary uses of the funding have been for page charges, travel for invited talks related to the grant research, and the support of a graduate student, Charles Keeton. The refereed papers address four of the primary goals of the proposal: (1) the statistics of radio lenses as a probe of the cosmological model (#1), (2) the role of spiral galaxies as lenses (#3), (3) the effects of dust on statistics of lenses (#7, #8), and (4) the role of groups and clusters as lenses (#2, #6, #10, #13, #15, #16). Four papers (#4, #5, #11, #12) address general issues of lens models, calibrations, and the relationship between lens galaxies and nearby galaxies. One considered cosmological effects in lensing X-ray sources (#9), and two addressed issues related to the overall power spectrum and theories of gravity (#17, #18). Our theoretical studies combined with the explosion in the number of lenses and the quality of the data obtained for them is greatly increasing our ability to characterize and understand the lens population. We can now firmly conclude both from our study of the statistics of radio lenses and our survey of extinctions in individual lenses that the statistics of optically selected quasars were significantly affected by extinction. However, the limits on the cosmological constant remain at lambda < 0.65 at a 2-sigma confidence level, which is in mild conflict with the results of the Type la supernova surveys. We continue to find that neither spiral galaxies nor groups and clusters contribute significantly to the production of gravitational lenses. The lack of group and cluster lenses is strong evidence for the role of baryonic cooling in increasing the efficiency of galaxies as lenses compared to groups and clusters of higher mass but lower central density. Unfortunately for the ultimate objective of the proposal, improved constraints on the cosmological constant, the next

  17. Violation of fundamental symmetries and variation of fundamental constants in atomic phenomena

    SciTech Connect

    Flambaum, V. V.

    2007-06-13

    We present a review of recent works on variation of fundamental constants and violation of parity in atoms and nuclei.Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental 'constants' in expanding Universe. The spatial variation can explain fine tuning of the fundamental constants which allows humans (and any life) to appear. We appeared in the area of the Universe where the values of the fundamental constants are consistent with our existence.We describe recent works devoted to the variation of the fine structure constant {alpha}, strong interaction and fundamental masses (Higgs vacuum). There are some hints for the variation in quasar absorption spectra, Big Bang nucleosynthesis, and Oklo natural nuclear reactor data.A very promising method to search for the variation consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transitions between very close atomic and molecular energy levels. A new idea is to build a 'nuclear' clock based on UV transition in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude. Measurements of violation of fundamental symmetries, parity (P) and time reversal (T), in atoms allows one to test unification theories in atomic experiments. We have developed an accurate method of many-body calculations - all-orders summation of dominating diagrams in residual e-e interaction. To calculate QED radiative corrections to energy levels and electromagnetic amplitudes in many-electron atoms and molecules we derived the ''radiative potential'' and the low-energy theorem. This method is simple and can be easily incorporated into any many-body theory approach. Using the radiative correction and many-body calculations we obtained the PNC amplitude EPNC = -0.898(1 {+-} 0.5%) x 10-11ieaB(-QW/N). From the measurements of the PNC amplitude we extracted the Cs weak charge QW = -72.66(29)exp(36)theor. The

  18. Violation of fundamental symmetries and variation of fundamental constants in atomic phenomena

    NASA Astrophysics Data System (ADS)

    Flambaum, V. V.

    2007-06-01

    We present a review of recent works on variation of fundamental constants and violation of parity in atoms and nuclei. Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. The spatial variation can explain fine tuning of the fundamental constants which allows humans (and any life) to appear. We appeared in the area of the Universe where the values of the fundamental constants are consistent with our existence. We describe recent works devoted to the variation of the fine structure constant α, strong interaction and fundamental masses (Higgs vacuum). There are some hints for the variation in quasar absorption spectra, Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transitions between very close atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on UV transition in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Measurements of violation of fundamental symmetries, parity (P) and time reversal (T), in atoms allows one to test unification theories in atomic experiments. We have developed an accurate method of many-body calculations - all-orders summation of dominating diagrams in residual e-e interaction. To calculate QED radiative corrections to energy levels and electromagnetic amplitudes in many-electron atoms and molecules we derived the ``radiative potential'' and the low-energy theorem. This method is simple and can be easily incorporated into any many-body theory approach. Using the radiative correction and many-body calculations we obtained the PNC amplitude EPNC = -0.898(1 +/- 0.5%) × 10-11ieaB(-QW/N). From the measurements of the PNC amplitude we extracted the Cs weak charge QW = -72.66(29)exp(36)theor. The

  19. Spectroscopic Constants of the Known Electronic States of Lead Monofluoride

    SciTech Connect

    McRaven, C.P.; Sivakumar, P.; Shafer-Ray, N.E.; Hall, G.E.; Sears, T.J.

    2010-08-01

    Based on measurements made by mass-resolved 1 + 1{prime} + 1{double_prime} resonance-enhanced multiphoton ionization spectroscopy, we have determined new molecular constants describing the rotational and fine structure levels of the B, D, E, and F states of the most abundant isotopic variant {sup 208}Pb{sup 19}F, and we summarize the spectroscopic constants for all the know electronic states of the radical. Many spectroscopic constants for the isotopologues {sup 206}Pb{sup 19}F and {sup 207}Pb{sup 19}F have also been determined. The symmetry of the D-state is found to be {sup 2}{pi}{sub 1/2}, and the F-state is found to be an {Omega} = 3/2 state.

  20. FOREWORD: International determination of the Avogadro constant International determination of the Avogadro constant

    NASA Astrophysics Data System (ADS)

    Massa, Enrico; Nicolaus, Arnold

    2011-04-01

    This issue of Metrologia collects papers about the results of an international research project aimed at the determination of the Avogadro constant, NA, by counting the atoms in a silicon crystal highly enriched with the isotope 28Si. Fifty years ago, Egidi [1] thought about realizing an atomic mass standard. In 1965, Bonse and Hart [2] operated the first x-ray interferometer, thus paving the way to the achievement of Egidi's dream, and soon Deslattes et al [3] completed the first counting of the atoms in a natural silicon crystal. The present project, outlined by Zosi [4] in 1983, began in 2004 by combining the experiences and capabilities of the BIPM, INRIM, IRMM, NIST, NPL, NMIA, NMIJ and PTB. The start signal, ratified by a memorandum of understanding, was a contract for the production of a silicon crystal highly enriched with 28Si. The enrichment process was undertaken by the Central Design Bureau of Machine Building in St Petersburg. Subsequently, a polycrystal was grown in the Institute of Chemistry of High-Purity Substances of the Russian Academy of Sciences in Nizhny Novgorod and a 28Si boule was grown and purified by the Leibniz-Institut für Kristallzüchtung in Berlin. Isotope enrichment made it possible to apply isotope dilution mass spectroscopy, to determine the Avogadro constant with unprecedented accuracy, and to fulfil Egidi's dream. To convey Egidi's 'fantasy' into practice, two 28Si kilogram prototypes shaped as quasi-perfect spheres were manufactured by the Australian Centre for Precision Optics; their isotopic composition, molar mass, mass, volume, density and lattice parameter were accurately determined and their surfaces were chemically and physically characterized at the atomic scale. The paper by Andreas et al reviews the work carried out; it collates all the findings and illustrates how Avogadro's constant was obtained. Impurity concentration and gradients in the enriched crystal were measured by infrared spectroscopy and taken into

  1. More-Accurate Model of Flows in Rocket Injectors

    NASA Technical Reports Server (NTRS)

    Hosangadi, Ashvin; Chenoweth, James; Brinckman, Kevin; Dash, Sanford

    2011-01-01

    An improved computational model for simulating flows in liquid-propellant injectors in rocket engines has been developed. Models like this one are needed for predicting fluxes of heat in, and performances of, the engines. An important part of predicting performance is predicting fluctuations of temperature, fluctuations of concentrations of chemical species, and effects of turbulence on diffusion of heat and chemical species. Customarily, diffusion effects are represented by parameters known in the art as the Prandtl and Schmidt numbers. Prior formulations include ad hoc assumptions of constant values of these parameters, but these assumptions and, hence, the formulations, are inaccurate for complex flows. In the improved model, these parameters are neither constant nor specified in advance: instead, they are variables obtained as part of the solution. Consequently, this model represents the effects of turbulence on diffusion of heat and chemical species more accurately than prior formulations do, and may enable more-accurate prediction of mixing and flows of heat in rocket-engine combustion chambers. The model has been implemented within CRUNCH CFD, a proprietary computational fluid dynamics (CFD) computer program, and has been tested within that program. The model could also be implemented within other CFD programs.

  2. An Accurate and Dynamic Computer Graphics Muscle Model

    NASA Technical Reports Server (NTRS)

    Levine, David Asher

    1997-01-01

    A computer based musculo-skeletal model was developed at the University in the departments of Mechanical and Biomedical Engineering. This model accurately represents human shoulder kinematics. The result of this model is the graphical display of bones moving through an appropriate range of motion based on inputs of EMGs and external forces. The need existed to incorporate a geometric muscle model in the larger musculo-skeletal model. Previous muscle models did not accurately represent muscle geometries, nor did they account for the kinematics of tendons. This thesis covers the creation of a new muscle model for use in the above musculo-skeletal model. This muscle model was based on anatomical data from the Visible Human Project (VHP) cadaver study. Two-dimensional digital images from the VHP were analyzed and reconstructed to recreate the three-dimensional muscle geometries. The recreated geometries were smoothed, reduced, and sliced to form data files defining the surfaces of each muscle. The muscle modeling function opened these files during run-time and recreated the muscle surface. The modeling function applied constant volume limitations to the muscle and constant geometry limitations to the tendons.

  3. An Alcohol Test for Drifting Constants

    NASA Astrophysics Data System (ADS)

    Jansen, P.; Bagdonaite, J.; Ubachs, W.; Bethlem, H. L.; Kleiner, I.; Xu, L.-H.

    2013-06-01

    The Standard Model of physics is built on the fundamental constants of nature, however without providing an explanation for their values, nor requiring their constancy over space and time. Molecular spectroscopy can address this issue. Recently, we found that microwave transitions in methanol are extremely sensitive to a variation of the proton-to-electron mass ratio μ, due to a fortuitous interplay between classically forbidden internal rotation and rotation of the molecule as a whole. In this talk, we will explain the origin of this effect and how the sensitivity coefficients in methanol are calculated. In addition, we set a limit on a possible cosmological variation of μ by comparing transitions in methanol observed in the early Universe with those measured in the laboratory. Based on radio-astronomical observations of PKS1830-211, we deduce a constraint of Δμ/μ=(0.0± 1.0)× 10^{-7} at redshift z = 0.89, corresponding to a look-back time of 7 billion years. While this limit is more constraining and systematically more robust than previous ones, the methanol method opens a new search territory for probing μ-variation on cosmological timescales. P. Jansen, L.-H. Xu, I. Kleiner, W. Ubachs, and H.L. Bethlem Phys. Rev. Lett. {106}(100801) 2011. J. Bagdonaite, P. Jansen, C. Henkel, H.L. Bethlem, K.M. Menten, and W. Ubachs Science {339}(46) 2013.

  4. Capacitive Cells for Dielectric Constant Measurement

    ERIC Educational Resources Information Center

    Aguilar, Horacio Munguía; Maldonado, Rigoberto Franco

    2015-01-01

    A simple capacitive cell for dielectric constant measurement in liquids is presented. As an illustrative application, the cell is used for measuring the degradation of overheated edible oil through the evaluation of their dielectric constant.

  5. High voltage compliance constant current ballast

    NASA Technical Reports Server (NTRS)

    Rosenthal, L. A.

    1976-01-01

    A ballast circuit employing a constant current diode and a vacuum tube that can provide a constant current over a voltage range of 1000 volts. The simple circuit can prove useful in studying voltage breakdown characteristics.

  6. Temporal variation of coupling constants and nucleosynthesis

    NASA Astrophysics Data System (ADS)

    Oberhummer, H.; Csótó, A.; Fairbairn, M.; Schlattl, H.; Sharma, M. M.

    2003-05-01

    We investigate the triple-alpha process and the Oklo phenomenon to obtain constraints on possible cosmological time variations of fundamental constants. Specifically we study cosmological temporal constraints for the fine structure constant and nucleon and meson masses.

  7. Accurate theoretical chemistry with coupled pair models.

    PubMed

    Neese, Frank; Hansen, Andreas; Wennmohs, Frank; Grimme, Stefan

    2009-05-19

    Quantum chemistry has found its way into the everyday work of many experimental chemists. Calculations can predict the outcome of chemical reactions, afford insight into reaction mechanisms, and be used to interpret structure and bonding in molecules. Thus, contemporary theory offers tremendous opportunities in experimental chemical research. However, even with present-day computers and algorithms, we cannot solve the many particle Schrodinger equation exactly; inevitably some error is introduced in approximating the solutions of this equation. Thus, the accuracy of quantum chemical calculations is of critical importance. The affordable accuracy depends on molecular size and particularly on the total number of atoms: for orientation, ethanol has 9 atoms, aspirin 21 atoms, morphine 40 atoms, sildenafil 63 atoms, paclitaxel 113 atoms, insulin nearly 800 atoms, and quaternary hemoglobin almost 12,000 atoms. Currently, molecules with up to approximately 10 atoms can be very accurately studied by coupled cluster (CC) theory, approximately 100 atoms with second-order Møller-Plesset perturbation theory (MP2), approximately 1000 atoms with density functional theory (DFT), and beyond that number with semiempirical quantum chemistry and force-field methods. The overwhelming majority of present-day calculations in the 100-atom range use DFT. Although these methods have been very successful in quantum chemistry, they do not offer a well-defined hierarchy of calculations that allows one to systematically converge to the correct answer. Recently a number of rather spectacular failures of DFT methods have been found-even for seemingly simple systems such as hydrocarbons, fueling renewed interest in wave function-based methods that incorporate the relevant physics of electron correlation in a more systematic way. Thus, it would be highly desirable to fill the gap between 10 and 100 atoms with highly correlated ab initio methods. We have found that one of the earliest (and now

  8. Fundamental Constants and Tests with Simple Atoms

    NASA Astrophysics Data System (ADS)

    Tan, Joseph

    2015-05-01

    Precise measurements with simple atoms provide stringent tests of physical laws, improving the accuracy of fundamental constants--a set of which will be selected to fully define the proposed New International System of Units. This talk focuses on the atomic constants (namely, the Rydberg constant, the fine-structure constant, and the proton charge radius), discussing the impact of the proton radius obtained from the Lamb-shift measurements in muonic hydrogen. Significant discrepancies persist despite years of careful examination: the slightly smaller proton radius obtained from muonic hydrogen requires the Rydberg constant and the fine-structure constant to have values that disagree significantly with the CODATA recommendations. After giving a general overview, I will discuss our effort to produce one-electron ions in Rydberg states, to enable a different test of theory and measurement of the Rydberg constant.

  9. Mud handling improved with a constant-volume riser

    SciTech Connect

    Baker, R.J. )

    1990-09-24

    Marine risers currently deployed by floating drilling units incorporate a telescopic joint to accommodate vessel movement, primarily heave. This vertical telescopic movement changes the internal volume of the riser and causes fluctuations in the return-mud flow rate. Flow fluctuations make accurate measurement of the return mud difficult. The significance is that these measurements are vital for the early detection of well bore influx or downhole mud losses. Erratic mud flow also adversely affects the efficiency of the solids-removal equipment and potentially increases the risk of discharging whole mud to the environment. To overcome these adverse effects, a design for a telescopic joint is proposed (constant volume riser or CVR) in which the internal riser volume remains constant, irrespective of movement, thus permitting a uniform flow rate of mud returns.

  10. Mill profiler machines soft materials accurately

    NASA Technical Reports Server (NTRS)

    Rauschl, J. A.

    1966-01-01

    Mill profiler machines bevels, slots, and grooves in soft materials, such as styrofoam phenolic-filled cores, to any desired thickness. A single operator can accurately control cutting depths in contour or straight line work.

  11. Leveraging Two Kinect Sensors for Accurate Full-Body Motion Capture.

    PubMed

    Gao, Zhiquan; Yu, Yao; Zhou, Yu; Du, Sidan

    2015-09-22

    Accurate motion capture plays an important role in sports analysis, the medical field and virtual reality. Current methods for motion capture often suffer from occlusions, which limits the accuracy of their pose estimation. In this paper, we propose a complete system to measure the pose parameters of the human body accurately. Different from previous monocular depth camera systems, we leverage two Kinect sensors to acquire more information about human movements, which ensures that we can still get an accurate estimation even when significant occlusion occurs. Because human motion is temporally constant, we adopt a learning analysis to mine the temporal information across the posture variations. Using this information, we estimate human pose parameters accurately, regardless of rapid movement. Our experimental results show that our system can perform an accurate pose estimation of the human body with the constraint of information from the temporal domain.

  12. Leveraging Two Kinect Sensors for Accurate Full-Body Motion Capture

    PubMed Central

    Gao, Zhiquan; Yu, Yao; Zhou, Yu; Du, Sidan

    2015-01-01

    Accurate motion capture plays an important role in sports analysis, the medical field and virtual reality. Current methods for motion capture often suffer from occlusions, which limits the accuracy of their pose estimation. In this paper, we propose a complete system to measure the pose parameters of the human body accurately. Different from previous monocular depth camera systems, we leverage two Kinect sensors to acquire more information about human movements, which ensures that we can still get an accurate estimation even when significant occlusion occurs. Because human motion is temporally constant, we adopt a learning analysis to mine the temporal information across the posture variations. Using this information, we estimate human pose parameters accurately, regardless of rapid movement. Our experimental results show that our system can perform an accurate pose estimation of the human body with the constraint of information from the temporal domain. PMID:26402681

  13. Using multistate dynamical corrections to compute classically exact diffusion constants at arbitrary temperature

    SciTech Connect

    Voter, A.F.; Doll, J.D.; Cohen, J.M.

    1989-02-01

    A method is presented for computing the classically exact, surface or bulk diffusion constant of a point defect at arbitrary temperature. The thermal diffusion constant is expressed using the squared jump length averaged over all possible final states to which the atom can jump. The rate constants that weight this sum are computed using transition state theory and molecular dynamics within a recently developed many-state dynamical corrections formalism. While these rate constants are valid only in the rare-event regime (i.e., at low temperature), it is shown that for a periodic lattice of equivalent binding sites, the resulting diffusion contants is valid at any temperature for which the lattice sites remain well defined. It is thus possible to compute classically exact surface or bulk diffusion constant for an arbitrary interatomic potential, without the time scale limitations of direct molecular dynamics.

  14. An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

    1995-01-01

    A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

  15. Emergent cosmological constant from colliding electromagnetic waves

    SciTech Connect

    Halilsoy, M.; Mazharimousavi, S. Habib; Gurtug, O. E-mail: habib.mazhari@emu.edu.tr

    2014-11-01

    In this study we advocate the view that the cosmological constant is of electromagnetic (em) origin, which can be generated from the collision of em shock waves coupled with gravitational shock waves. The wave profiles that participate in the collision have different amplitudes. It is shown that, circular polarization with equal amplitude waves does not generate cosmological constant. We also prove that the generation of the cosmological constant is related to the linear polarization. The addition of cross polarization generates no cosmological constant. Depending on the value of the wave amplitudes, the generated cosmological constant can be positive or negative. We show additionally that, the collision of nonlinear em waves in a particular class of Born-Infeld theory also yields a cosmological constant.

  16. Effective elastic constants of polycrystalline aggregates

    NASA Astrophysics Data System (ADS)

    Bonilla, Luis L.

    A METHOD is presented for the determination of the effective elastic constants of a transversely isotropic aggregate of weakly anisotropic crystallites with cubic symmetry. The results obtained generalize those given in the literature for the second and third order elastic constants. In addition, the second moments and the binary angular correlations of the second order stiffnesses are obtained. It is also explained how these moments can be used to find the two-point correlations of the elastic constants.

  17. Constant voltage electro-slag remelting control

    DOEpatents

    Schlienger, Max E.

    1996-01-01

    A system for controlling electrode gap in an electro-slag remelt furnace has a constant regulated voltage and an eletrode which is fed into the slag pool at a constant rate. The impedance of the circuit through the slag pool is directly proportional to the gap distance. Because of the constant voltage, the system current changes are inversely proportional to changes in gap. This negative feedback causes the gap to remain stable.

  18. Constant voltage electro-slag remelting control

    DOEpatents

    Schlienger, M.E.

    1996-10-22

    A system for controlling electrode gap in an electro-slag remelt furnace has a constant regulated voltage and an electrode which is fed into the slag pool at a constant rate. The impedance of the circuit through the slag pool is directly proportional to the gap distance. Because of the constant voltage, the system current changes are inversely proportional to changes in gap. This negative feedback causes the gap to remain stable. 1 fig.

  19. Modification of the characteristic gravitational constants

    NASA Astrophysics Data System (ADS)

    Vujičić, V. A.

    2006-08-01

    In the educational and scientific literature the numerical values of gravitational constants are seen as only approximately correct. The numerical values are different in work by various researchers, as also are the formulae and definitions of constants employed. In this paper, on the basis of Newton’s laws and Kepler’s laws we prove that it is necessary to modify the characteristic gravitational constants and their definitions. The formula for the geocentric gravitational constant of the satellites Kosmos N and the Moon are calculated.

  20. Formation of molecular ions by radiative association of cold trapped atoms and ions

    NASA Astrophysics Data System (ADS)

    Dulieu, Olivier; da Silva, Humberto, Jr.; Aymar, Mireille; Raoult, Maurice

    2015-05-01

    Radiative emission during cold collisions between trapped laser-cooled Rb atoms and alkaline-earth ions (Ca+ , Sr+ , Ba+) and Yb+ are studied theoretically, using accurate effective-core-potential based quantum chemistry calculations of potential energy curves and transition dipole moments of the related molecular ions. Radiative association of molecular ions is predicted to occur for all systems with a cross section two to ten times larger than the radiative charge transfer one. Partial and total rate constants are also calculated and compared to available experiments. Narrow shape resonances are expected, which could be detectable at low temperature with an experimental resolution at the limit of the present standards. Vibrational distributions show that the final molecular ions are not created in their ground state level. Supported by the Marie-Curie ITN ``COMIQ: Cold Molecular Ions at the Quantum limit'' of the EU (#607491).

  1. Heavy-meson decay constants from QCD sum rules

    SciTech Connect

    Lucha, Wolfgang; Melikhov, Dmitri; Simula, Silvano

    2010-12-22

    We sketch a recent sum-rule extraction of the decay constants of the heavy pseudoscalar mesons D, D{sub s}, B, and B{sub s} from the two-point correlator of heavy-light pseudoscalar currents. Our main emphasis lies on the control over all the uncertainties in the decay constants, related both to the input QCD parameters and to the limited accuracy of the method of sum rules. Gaining this control has become possible by application of our new procedure of extracting hadron observables based on a dual threshold depending on the Borel parameter. For the charmed-meson decay constants, we find fD = (206.2{+-}7.3{sub (OPE)}{+-}5.1{sub (syst)}) MeV, fD{sub s} = (245.3{+-}15.7{sub (OPE)}{+-}4.5{sub (syst)}) MeV. For the beauty mesons, the decay constants turn out to be extremely sensitive to the precise value of the {ovr MS} mass of the b-quark, {bar m}{sub b}({bar m}{sub b}). By requiring our sum-rule estimate to match the average of the lattice determinations of f{sub B}, we extract the rather accurate value {bar m}{sub b}({bar m}{sub b}) = (4.245{+-}0.025) GeV. Feeding this parameter value into our sum-rule formalism leads to the beauty-meson decay constants fB = (193.4{+-}12.3{sub (OPE)}{+-}4.3{sub (syst)}) MeV, fB{sub s} = (232.5{+-}18.6{sub (OPE)}{+-}2.4{sub (syst)}) MeV.

  2. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    SciTech Connect

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempirical OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.

  3. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    DOE PAGES

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  4. Accurate Anharmonic IR Spectra from Integrated Cc/dft Approach

    NASA Astrophysics Data System (ADS)

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Carnimeo, Ivan; Puzzarini, Cristina

    2014-06-01

    The recent implementation of the computation of infrared (IR) intensities beyond the double harmonic approximation [1] paved the route to routine calculations of infrared spectra for a wide set of molecular systems. Contrary to common beliefs, second-order perturbation theory is able to deliver results of high accuracy provided that anharmonic resonances are properly managed [1,2]. It has been already shown for several small closed- and open shell molecular systems that the differences between coupled cluster (CC) and DFT anharmonic wavenumbers are mainly due to the harmonic terms, paving the route to introduce effective yet accurate hybrid CC/DFT schemes [2]. In this work we present that hybrid CC/DFT models can be applied also to the IR intensities leading to the simulation of highly accurate fully anharmonic IR spectra for medium-size molecules, including ones of atmospheric interest, showing in all cases good agreement with experiment even in the spectral ranges where non-fundamental transitions are predominant[3]. [1] J. Bloino and V. Barone, J. Chem. Phys. 136, 124108 (2012) [2] V. Barone, M. Biczysko, J. Bloino, Phys. Chem. Chem. Phys., 16, 1759-1787 (2014) [3] I. Carnimeo, C. Puzzarini, N. Tasinato, P. Stoppa, A. P. Charmet, M. Biczysko, C. Cappelli and V. Barone, J. Chem. Phys., 139, 074310 (2013)

  5. Accurate measure by weight of liquids in industry

    SciTech Connect

    Muller, M.R.

    1992-12-12

    This research's focus was to build a prototype of a computerized liquid dispensing system. This liquid metering system is based on the concept of altering the representative volume to account for temperature changes in the liquid to be dispensed. This is actualized by using a measuring tank and a temperature compensating displacement plunger. By constantly monitoring the temperature of the liquid, the plunger can be used to increase or decrease the specified volume to more accurately dispense liquid with a specified mass. In order to put the device being developed into proper engineering perspective, an extensive literature review was undertaken on all areas of industrial metering of liquids with an emphasis on gravimetric methods.

  6. Accurate measure by weight of liquids in industry. Final report

    SciTech Connect

    Muller, M.R.

    1992-12-12

    This research`s focus was to build a prototype of a computerized liquid dispensing system. This liquid metering system is based on the concept of altering the representative volume to account for temperature changes in the liquid to be dispensed. This is actualized by using a measuring tank and a temperature compensating displacement plunger. By constantly monitoring the temperature of the liquid, the plunger can be used to increase or decrease the specified volume to more accurately dispense liquid with a specified mass. In order to put the device being developed into proper engineering perspective, an extensive literature review was undertaken on all areas of industrial metering of liquids with an emphasis on gravimetric methods.

  7. [Molecular genetics and determination of time since death - short communication].

    PubMed

    Šaňková, Markéta; Račanská, Michaela

    2016-01-01

    Estimation of time since death, i.e. the post-mortem interval (PMI), is one of the most problematic issues in forensic practice. Accurate determination of the PMI still remains very complicated task even for an experienced forensic pathologist.Physical changes including algor, livor and rigor mortis can be observed already during the first hours after death of an individual. Unfortunately, the estimation of PMI on the basis of these changes is often burdened with a certain degree of inaccuracy, which is caused by the temperature of surrounding environment, constitution of the body, cause of the death, location of the body, drug abuse etc.Accurate PMI estimation requires assessment of such parameters, which change constantly from the moment of death, but independently on ambient factors. According to current research in the field of molecular biology, it appears that a post-mortem degradation of nucleic acids (both DNA and RNA) will correspond to this definition. PMID:27526264

  8. Fractionating Polymer Microspheres as Highly Accurate Density Standards.

    PubMed

    Bloxham, William H; Hennek, Jonathan W; Kumar, Ashok A; Whitesides, George M

    2015-07-21

    This paper describes a method of isolating small, highly accurate density-standard beads and characterizing their densities using accurate and experimentally traceable techniques. Density standards have a variety of applications, including the characterization of density gradients, which are used to separate objects in a variety of fields. Glass density-standard beads can be very accurate (±0.0001 g cm(-3)) but are too large (3-7 mm in diameter) for many applications. When smaller density standards are needed, commercial polymer microspheres are often used. These microspheres have standard deviations in density ranging from 0.006 to 0.021 g cm(-3); these distributions in density make these microspheres impractical for applications demanding small steps in density. In this paper, commercial microspheres are fractionated using aqueous multiphase systems (AMPS), aqueous mixture of polymers and salts that spontaneously separate into phases having molecularly sharp steps in density, to isolate microspheres having much narrower distributions in density (standard deviations from 0.0003 to 0.0008 g cm(-3)) than the original microspheres. By reducing the heterogeneity in densities, this method reduces the uncertainty in the density of any specific bead and, therefore, improves the accuracy within the limits of the calibration standards used to characterize the distributions in density.

  9. Classically exact surface diffusion constants at arbitrary temperature

    SciTech Connect

    Voter, A.F.; Cohen, J.M.

    1989-05-01

    An expression is presented for computing the classical diffusion constant of a point defect (e.g., an adatom) in an infinite lattice of binding sites at arbitrary temperature. The transition state theory diffusion constant is simply multiplied by a dynamical correction factor that is computed from short-time classical trajectories initiated at the site boundaries. The time scale limitations of direct molecular dynamics are thus avoided in the low- and middle-temperature regimes. The expression results from taking the time derivative of the particle mean-square displacement in the lattice-discretized coordinate system. Applications are presented for surface diffusion on fcc(100) and fcc(111) Lennard-Jones crystal faces.

  10. Classically exact surface diffusion constants at arbitrary temperature

    SciTech Connect

    Voter, A.F.; Cohen, J.M.

    1988-01-01

    An expression is presented for computing the classical diffusion constant of a point defect (e.g., adatom) in an infinite lattice of binding sites at arbitrary temperature. The transition state theory diffusion constant is simply multiplied by a dynamical correction factor that is computed from short-time classical trajectories initiated at the site boundaries. The time scale limitations of direct molecular dynamics are thus avoided in the low and middle temperature regimes. The expression resulted from taking the time derivative of the particle mean square displacement in the lattice-discretized coordinate system. Applications are presented for surface diffusion on fcc(100) and fcc(111) Lennard-Jones crystal faces. 14 refs., 3 figs.

  11. Modified chemiluminescent NO analyzer accurately measures NOX

    NASA Technical Reports Server (NTRS)

    Summers, R. L.

    1978-01-01

    Installation of molybdenum nitric oxide (NO)-to-higher oxides of nitrogen (NOx) converter in chemiluminescent gas analyzer and use of air purge allow accurate measurements of NOx in exhaust gases containing as much as thirty percent carbon monoxide (CO). Measurements using conventional analyzer are highly inaccurate for NOx if as little as five percent CO is present. In modified analyzer, molybdenum has high tolerance to CO, and air purge substantially quenches NOx destruction. In test, modified chemiluminescent analyzer accurately measured NO and NOx concentrations for over 4 months with no denegration in performance.

  12. Varying constant cosmologies and cosmic singularities

    NASA Astrophysics Data System (ADS)

    Dabrowski, Mariusz P.; Marosek, Konrad

    2013-02-01

    We review standard and non-standard cosmological singularities paying special attention onto those which are of a weak type and do not necessarily exhibit geodesic incompletness. Then, we discuss how these singularities can be weakened, strengthened, or avoided due to the time-variation of the physical constants such as the speed of light c and the gravitational constant G.

  13. On the Utility of the Molecular Oxygen Dayglow Emissions as Proxies for Middle Atmospheric Ozone

    NASA Technical Reports Server (NTRS)

    Mlynczak, Martin G.; Olander, Daphne S.

    1995-01-01

    Molecular oxygen dayglow emissions arise in part from processes related to the Hartley band photolysis of ozone. It is therefore possible to derive daytime ozone concentrations from measurements of the volume emission rate of either dayglow. The accuracy to which the ozone concentration can be inferred depends on the accuracy to which numerous kinetic and spectroscopic rate constants are known, including rates which describe the excitation of molecular oxygen by processes that are not related to the ozone concentration. We find that several key rate constants must be known to better than 7 percent accuracy in order to achieve an inferred ozone concentration accurate to 15 percent from measurements of either dayglow. Currently, accuracies for various parameters typically range from 5 to 100 percent.

  14. String theory, cosmology and varying constants

    NASA Astrophysics Data System (ADS)

    Damour, Thibault

    In string theory the coupling `constants' appearing in the low-energy effective Lagrangian are determined by the vacuum expectation values of some (a priori) massless scalar fields (dilaton, moduli). This naturally leads one to expect a correlated variation of all the coupling constants, and an associated violation of the equivalence principle. We review some string-inspired theoretical models which incorporate such a spacetime variation of coupling constants while remaining naturally compatible both with phenomenological constraints coming from geochemical data (Oklo; Rhenium decay) and with present equivalence principle tests. Barring a very unnatural fine-tuning of parameters, a variation of the fine-structure constant as large as that recently `observed' by Webb et al. in quasar absorption spectra appears to be incompatible with these phenomenological constraints. Independently of any model, it is emphasized that the best experimental probe of varying constants are high-precision tests of the universality of free fall, such as MICROSCOPE and STEP.

  15. Determination of the Hubble Space Telescope effective conic-constant error from direct image measurements.

    PubMed

    Meinel, A B; Meinel, M P; Schulte, D H

    1993-04-01

    Direct measurement of discernible features in the Hubble Space Telescope (HST) imagery has enabled a self-consistent determination to be made of the effective conic constant of HST images taken with planetary camera 6 (PC-6) of the wide field and planetary camera. Before being corrected for the contribution from PC-6, the conic constant is - 1.01429 +/- 0.0002. The correction for PC-6 is less accurately determined but probably lies between -0.0002 and 0.0004. As a result the HST optics are characterized best by a conic constant of - 1.0140 +/- 0.0003 as obtained from direct image measurements.

  16. 4-Component correlated all-electron study on Eka-actinium Fluoride (E121F) including Gaunt interaction: Accurate analytical form, bonding and influence on rovibrational spectra

    NASA Astrophysics Data System (ADS)

    Amador, Davi H. T.; de Oliveira, Heibbe C. B.; Sambrano, Julio R.; Gargano, Ricardo; de Macedo, Luiz Guilherme M.

    2016-10-01

    A prolapse-free basis set for Eka-Actinium (E121, Z = 121), numerical atomic calculations on E121, spectroscopic constants and accurate analytical form for the potential energy curve of diatomic E121F obtained at 4-component all-electron CCSD(T) level including Gaunt interaction are presented. The results show a strong and polarized bond (≈181 kcal/mol in strength) between E121 and F, the outermost frontier molecular orbitals from E121F should be fairly similar to the ones from AcF and there is no evidence of break of periodic trends. Moreover, the Gaunt interaction, although small, is expected to influence considerably the overall rovibrational spectra.

  17. Technique for measuring the dielectric constant of thin materials

    NASA Technical Reports Server (NTRS)

    Sarabandi, K.; Ulaby, F. T.

    1988-01-01

    A practical technique for measuring the dielectric constant of vegetation leaves and similarly thin materials is presented. A rectangular section of the leaf is placed in the tranverse plane in a rectangular waveguide and the magnitude and phase of the reflection coefficient are measured over the desired frequency band using a vector network analyzer. By treating the leaf as an infinitesimally thin resistive sheet, an explicit expression for its dielectric constant is obtained in terms of the reflection coefficient. Because of the thin-sheet approximation, however, this approach is valid only at frequencies below 1.5 GHz. To extend the technique to higher frequencies, higher order approximations are derived and their accuracies are compared to the exact dielectric-slab solution. For a material whose thickness is 0.5 mm or less, the proposed technique was found to provide accurate values of its dielectric constant up to frequencies of 12 GHz or higher. The technique was used to measure the 8 to 12 GHz dielectric spectrum for vegetation leaves, teflon and rock samples.

  18. Parameter identification of material constants in a composite shell structure

    SciTech Connect

    Martinez, D.R.; Carne, T.G.

    1988-01-01

    One of the basic requirements in engineering analysis is the development of a mathematical model describing the system. Frequently, comparisons with test data are used as a measurement of the adequacy of the model. An attempt is typically made to update or improve the model to provide a test-verified analysis tool. System identification provides a systematic procedure for accomplishing this task. The terms system identification, parameter estimation, and model correlation all refer to techniques that use test information to update or verify mathematical models. The goal of system identification is to improve the correlation of model predictions with measured test data, and produce accurate, predictive models. For nonmetallic structures the modeling task is often difficult due to uncertainties in the elastic constants. In this work a parameter identification procedure was used to determine the elastic constants of a cylindrical, graphite epoxy composite shell. A finite element model of the shell was created, which included uncertain orthotropic elastic constants. A modal survey test was then performed on the shell. The resulting modal data, along with the finite element model of the shell, were used in a Bayes estimation algorithm. This permitted the use of covariance matrices to weight the confidence in the initial parameter values as well as confidence in the measured test data. The estimation procedure also employed the concept of successive linearization to obtain an approximate solution to the original nonlinear estimation problem. 17 refs., 7 figs.

  19. Improved in situ spring constant calibration for colloidal probe atomic force microscopy.

    PubMed

    McBride, Sean P; Law, Bruce M

    2010-11-01

    In colloidal probe atomic force microscopy (AFM) surface forces cannot be measured without an accurate determination of the cantilever spring constant. The effective spring constant k depends upon the cantilever geometry and therefore should be measured in situ; additionally, k may be coupled to other measurement parameters. For example, colloidal probe AFM is frequently used to measure the slip length b at solid/liquid boundaries by comparing the measured hydrodynamic force with Vinogradova slip theory (V-theory). However, in this measurement k and b are coupled, hence, b cannot be accurately determined without knowing k to high precision. In this paper, a new in situ spring constant calibration method based upon the residuals, namely, the difference between experimental force-distance data and V-theory is presented and contrasted with two other popular spring constant determination methods. In this residuals calibration method, V-theory is fitted to the experimental force-distance data for a range of systematically varied spring constants where the only adjustable parameter in V-theory is the slip length b. The optimal spring constant k is that value where the residuals are symmetrically displaced about zero for all colloidal probe separations. This residual spring constant calibration method is demonstrated by studying three different liquids (n-decanol, n-hexadecane, and n-octane) and two different silane coated colloidal probe-silicon wafer systems (n-hexadecyltrichlorosilane and n-dodecyltrichlorosilane).

  20. Improved in situ spring constant calibration for colloidal probe atomic force microscopy

    SciTech Connect

    McBride, Sean P.; Law, Bruce M.

    2010-11-15

    In colloidal probe atomic force microscopy (AFM) surface forces cannot be measured without an accurate determination of the cantilever spring constant. The effective spring constant k depends upon the cantilever geometry and therefore should be measured in situ; additionally, k may be coupled to other measurement parameters. For example, colloidal probe AFM is frequently used to measure the slip length b at solid/liquid boundaries by comparing the measured hydrodynamic force with Vinogradova slip theory (V-theory). However, in this measurement k and b are coupled, hence, b cannot be accurately determined without knowing k to high precision. In this paper, a new in situ spring constant calibration method based upon the residuals, namely, the difference between experimental force-distance data and V-theory is presented and contrasted with two other popular spring constant determination methods. In this residuals calibration method, V-theory is fitted to the experimental force-distance data for a range of systematically varied spring constants where the only adjustable parameter in V-theory is the slip length b. The optimal spring constant k is that value where the residuals are symmetrically displaced about zero for all colloidal probe separations. This residual spring constant calibration method is demonstrated by studying three different liquids (n-decanol, n-hexadecane, and n-octane) and two different silane coated colloidal probe-silicon wafer systems (n-hexadecyltrichlorosilane and n-dodecyltrichlorosilane).

  1. Can Appraisers Rate Work Performance Accurately?

    ERIC Educational Resources Information Center

    Hedge, Jerry W.; Laue, Frances J.

    The ability of individuals to make accurate judgments about others is examined and literature on this subject is reviewed. A wide variety of situational factors affects the appraisal of performance. It is generally accepted that the purpose of the appraisal influences the accuracy of the appraiser. The instrumentation, or tools, available to the…

  2. Accurate pointing of tungsten welding electrodes

    NASA Technical Reports Server (NTRS)

    Ziegelmeier, P.

    1971-01-01

    Thoriated-tungsten is pointed accurately and quickly by using sodium nitrite. Point produced is smooth and no effort is necessary to hold the tungsten rod concentric. The chemically produced point can be used several times longer than ground points. This method reduces time and cost of preparing tungsten electrodes.

  3. Computing classically exact diffusion constants using short-time trajectories

    SciTech Connect

    Voter, A. F.

    1989-07-10

    The classical diffusion constant of a point defect in an infinite lattice of binding sites is shown to be expressible as transition-state-theory rates multiplied by dynamical correction factors computed from short-time classical trajectories initiated at the site boundaries. The expression, which results from time differentiating the lattice-discretized mean-square displacement, is valid at any temperature for which the site lattice is well defined. It thus avoids both the time-scale limitations of direct molecular dynamics and the rare-event requirements of standard dynamical-correction methods.

  4. Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging.

    PubMed

    Dracínský, Martin; Kaminský, Jakub; Bour, Petr

    2009-03-01

    Relative importance of anharmonic corrections to molecular vibrational energies, nuclear magnetic resonance (NMR) chemical shifts, and J-coupling constants was assessed for a model set of methane derivatives, differently charged alanine forms, and sugar models. Molecular quartic force fields and NMR parameter derivatives were obtained quantum mechanically by a numerical differentiation. In most cases the harmonic vibrational function combined with the property second derivatives provided the largest correction of the equilibrium values, while anharmonic corrections (third and fourth energy derivatives) were found less important. The most computationally expensive off-diagonal quartic energy derivatives involving four different coordinates provided a negligible contribution. The vibrational corrections of NMR shifts were small and yielded a convincing improvement only for very accurate wave function calculations. For the indirect spin-spin coupling constants the averaging significantly improved already the equilibrium values obtained at the density functional theory level. Both first and complete second shielding derivatives were found important for the shift corrections, while for the J-coupling constants the vibrational parts were dominated by the diagonal second derivatives. The vibrational corrections were also applied to some isotopic effects, where the corrected values reasonably well reproduced the experiment, but only if a full second-order expansion of the NMR parameters was included. Contributions of individual vibrational modes for the averaging are discussed. Similar behavior was found for the methane derivatives, and for the larger and polar molecules. The vibrational averaging thus facilitates interpretation of previous experimental results and suggests that it can make future molecular structural studies more reliable. Because of the lengthy numerical differentiation required to compute the NMR parameter derivatives their analytical implementation in

  5. On geometrically unified fields and universal constants

    NASA Astrophysics Data System (ADS)

    Fabbri, Luca

    2013-07-01

    We consider the Cartan extension of Riemann geometry as the basis upon which to build the Sciama-Kibble completion of Einstein gravity, developing the most general theory in which torsion and metric have two independent coupling constants: the main problem of the ESK theory was that torsion, having the Newton constant, was negligible beyond the Planck scale, but in this {ESK}2 theory torsion, with its own coupling constant, may be relevant much further Planck scales; further consequences of these torsionally-induced interactions will eventually be discussed.

  6. The Determination of the Strong Coupling Constant

    NASA Astrophysics Data System (ADS)

    Dissertori, Günther

    2016-10-01

    The strong coupling constant is one of the fundamental parameters of the Standard Theory of particle physics. In this review I will briefly summarise the theoretical framework, within which the strong coupling constant is defined and how it is connected to measurable observables. Then I will give an historical overview of its experimental determinations and discuss the current status and world average value. Among the many different techniques used to determine this coupling constant in the context of quantum chromodynamics, I will focus in particular on a number of measurements carried out at the Large Electron-Positron Collider (LEP) and the Large Hadron Collider (LHC) at CERN.

  7. Laser Propulsion and the Constant Momentum Mission

    NASA Astrophysics Data System (ADS)

    Larson, C. William; Mead, Franklin B.; Knecht, Sean D.

    2004-03-01

    We show that perfect propulsion requires a constant momentum mission, as a consequence of Newton's second law. Perfect propulsion occurs when the velocity of the propelled mass in the inertial frame of reference matches the velocity of the propellant jet in the rocket frame of reference. We compare constant momentum to constant specific impulse propulsion, which, for a given specification of the mission delta V, has an optimum specific impulse that maximizes the propelled mass per unit jet kinetic energy investment. We also describe findings of more than 50 % efficiency for conversion of laser energy into jet kinetic energy by ablation of solids.

  8. Laser Propulsion and the Constant Momentum Mission

    SciTech Connect

    Larson, C. William; Mead, Franklin B. Jr.; Knecht, Sean D.

    2004-03-30

    We show that perfect propulsion requires a constant momentum mission, as a consequence of Newton's second law. Perfect propulsion occurs when the velocity of the propelled mass in the inertial frame of reference matches the velocity of the propellant jet in the rocket frame of reference. We compare constant momentum to constant specific impulse propulsion, which, for a given specification of the mission delta V, has an optimum specific impulse that maximizes the propelled mass per unit jet kinetic energy investment. We also describe findings of more than 50 % efficiency for conversion of laser energy into jet kinetic energy by ablation of solids.

  9. Constants and Pseudo-Constants of Coupled Beam Motion in the PEP-II Rings

    SciTech Connect

    Decker, F.J.; Colocho, W.S.; Wang, M.H.; Yan, Y.T.; Yocky, G.; /SLAC

    2011-11-01

    Constants of beam motion help as cross checks to analyze beam diagnostics and the modeling procedure. Pseudo-constants, like the betatron mismatch parameter or the coupling parameter det C, are constant till certain elements in the beam line change them. This can be used to visually find the non-desired changes, pinpointing errors compared with the model.

  10. Feedback about More Accurate versus Less Accurate Trials: Differential Effects on Self-Confidence and Activation

    ERIC Educational Resources Information Center

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-01-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected by feedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On Day 1, participants performed a golf putting task under one of…

  11. A spectrofluorimetric method for determining the association constants of pyrene with cyclodextrins based on polarity variation

    NASA Astrophysics Data System (ADS)

    Kusumoto, Yoshihumi

    1987-05-01

    The association constants of pyrene inclusion complexes with β-cyclodextrin and methylated β-cyclodextrins were determined using equations which provide an accurate description of the variation in the vibronic-band-intensity ratio of pyrene monomer fluorescence in the presence of cyclodextrins.

  12. The effect of receptor clustering on diffusion-limited forward rate constants.

    PubMed Central

    Goldstein, B; Wiegel, F W

    1983-01-01

    The effect of receptor clustering on the diffusion-limited forward rate constant (k+) is studied theoretically by modeling cell surface receptors by hemispheres distributed on a plane. We give both exact results and bounds. The exact results are obtained using an electrostatic analogue and applying the method of the images. Accurate upper bounds on k+ are found from a variational principle. PMID:6309261

  13. Feedback about more accurate versus less accurate trials: differential effects on self-confidence and activation.

    PubMed

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-06-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected byfeedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On day 1, participants performed a golf putting task under one of two conditions: one group received feedback on the most accurate trials, whereas another group received feedback on the least accurate trials. On day 2, participants completed an anxiety questionnaire and performed a retention test. Shin conductance level, as a measure of arousal, was determined. The results indicated that feedback about more accurate trials resulted in more effective learning as well as increased self-confidence. Also, activation was a predictor of performance. PMID:22808705

  14. Accurate global potential energy surface for the H + OH+ collision

    NASA Astrophysics Data System (ADS)

    Gannouni, M. A.; Jaidane, N. E.; Halvick, P.; Stoecklin, T.; Hochlaf, M.

    2014-05-01

    We mapped the global three-dimensional potential energy surface (3D-PES) of the water cation at the MRCI/aug-cc-pV5Z including the basis set superposition (BSSE) correction. This PES covers the molecular region and the long ranges close to the H + OH+(X3Σ-), the O + H2+(X2Σg+), and the hydrogen exchange channels. The quality of the PES is checked after comparison to previous experimental and theoretical results of the spectroscopic constants of H2O+(tilde X2B1) and of the diatomic fragments, the vibronic spectrum, the dissociation energy, and the barrier to linearity for H2O+(tilde X2B1). Our data nicely approach those measured and computed previously. The long range parts reproduce quite well the diatomic potentials. In whole, a good agreement is found, which validates our 3D-PES.

  15. How the cosmological constant affects gravastar formation

    SciTech Connect

    Chan, R.; Silva, M.F.A. da; Rocha, P. E-mail: mfasnic@gmail.com

    2009-12-01

    Here we generalized a previous model of gravastar consisted of an internal de Sitter spacetime, a dynamical infinitely thin shell with an equation of state, but now we consider an external de Sitter-Schwarzschild spacetime. We have shown explicitly that the final output can be a black hole, a ''bounded excursion'' stable gravastar, a stable gravastar, or a de Sitter spacetime, depending on the total mass of the system, the cosmological constants, the equation of state of the thin shell and the initial position of the dynamical shell. We have found that the exterior cosmological constant imposes a limit to the gravastar formation, i.e., the exterior cosmological constant must be smaller than the interior cosmological constant. Besides, we have also shown that, in the particular case where the Schwarzschild mass vanishes, no stable gravastar can be formed, but we still have formation of black hole.

  16. The Solar Constant: A Take Home Lab

    ERIC Educational Resources Information Center

    Eaton, B. G.; And Others

    1977-01-01

    Describes a method that uses energy from the sun, absorbed by aluminum discs, to melt ice, and allows the determination of the solar constant. The take-home equipment includes Styrofoam cups, a plastic syringe, and aluminum discs. (MLH)

  17. The Rate Constant for Fluorescence Quenching

    ERIC Educational Resources Information Center

    Legenza, Michael W.; Marzzacco, Charles J.

    1977-01-01

    Describes an experiment that utilizes fluorescence intensity measurements from a Spectronic 20 to determine the rate constant for the fluorescence quenching of various aromatic hydrocarbons by carbon tetrachloride in an ethanol solvent. (MLH)

  18. Two highly accurate methods for pitch calibration

    NASA Astrophysics Data System (ADS)

    Kniel, K.; Härtig, F.; Osawa, S.; Sato, O.

    2009-11-01

    Among profiles, helix and tooth thickness pitch is one of the most important parameters of an involute gear measurement evaluation. In principle, coordinate measuring machines (CMM) and CNC-controlled gear measuring machines as a variant of a CMM are suited for these kinds of gear measurements. Now the Japan National Institute of Advanced Industrial Science and Technology (NMIJ/AIST) and the German national metrology institute the Physikalisch-Technische Bundesanstalt (PTB) have each developed independently highly accurate pitch calibration methods applicable to CMM or gear measuring machines. Both calibration methods are based on the so-called closure technique which allows the separation of the systematic errors of the measurement device and the errors of the gear. For the verification of both calibration methods, NMIJ/AIST and PTB performed measurements on a specially designed pitch artifact. The comparison of the results shows that both methods can be used for highly accurate calibrations of pitch standards.

  19. Accurate guitar tuning by cochlear implant musicians.

    PubMed

    Lu, Thomas; Huang, Juan; Zeng, Fan-Gang

    2014-01-01

    Modern cochlear implant (CI) users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼ 30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task. PMID:24651081

  20. Accurate Guitar Tuning by Cochlear Implant Musicians

    PubMed Central

    Lu, Thomas; Huang, Juan; Zeng, Fan-Gang

    2014-01-01

    Modern cochlear implant (CI) users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task. PMID:24651081

  1. Preparation and accurate measurement of pure ozone.

    PubMed

    Janssen, Christof; Simone, Daniela; Guinet, Mickaël

    2011-03-01

    Preparation of high purity ozone as well as precise and accurate measurement of its pressure are metrological requirements that are difficult to meet due to ozone decomposition occurring in pressure sensors. The most stable and precise transducer heads are heated and, therefore, prone to accelerated ozone decomposition, limiting measurement accuracy and compromising purity. Here, we describe a vacuum system and a method for ozone production, suitable to accurately determine the pressure of pure ozone by avoiding the problem of decomposition. We use an inert gas in a particularly designed buffer volume and can thus achieve high measurement accuracy and negligible degradation of ozone with purities of 99.8% or better. The high degree of purity is ensured by comprehensive compositional analyses of ozone samples. The method may also be applied to other reactive gases. PMID:21456766

  2. Accurate guitar tuning by cochlear implant musicians.

    PubMed

    Lu, Thomas; Huang, Juan; Zeng, Fan-Gang

    2014-01-01

    Modern cochlear implant (CI) users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼ 30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task.

  3. Accurate modeling of parallel scientific computations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Townsend, James C.

    1988-01-01

    Scientific codes are usually parallelized by partitioning a grid among processors. To achieve top performance it is necessary to partition the grid so as to balance workload and minimize communication/synchronization costs. This problem is particularly acute when the grid is irregular, changes over the course of the computation, and is not known until load time. Critical mapping and remapping decisions rest on the ability to accurately predict performance, given a description of a grid and its partition. This paper discusses one approach to this problem, and illustrates its use on a one-dimensional fluids code. The models constructed are shown to be accurate, and are used to find optimal remapping schedules.

  4. Line gas sampling system ensures accurate analysis

    SciTech Connect

    Not Available

    1992-06-01

    Tremendous changes in the natural gas business have resulted in new approaches to the way natural gas is measured. Electronic flow measurement has altered the business forever, with developments in instrumentation and a new sensitivity to the importance of proper natural gas sampling techniques. This paper reports that YZ Industries Inc., Snyder, Texas, combined its 40 years of sampling experience with the latest in microprocessor-based technology to develop the KynaPak 2000 series, the first on-line natural gas sampling system that is both compact and extremely accurate. This means the composition of the sampled gas must be representative of the whole and related to flow. If so, relative measurement and sampling techniques are married, gas volumes are accurately accounted for and adjustments to composition can be made.

  5. Accurate mask model for advanced nodes

    NASA Astrophysics Data System (ADS)

    Zine El Abidine, Nacer; Sundermann, Frank; Yesilada, Emek; Ndiaye, El Hadji Omar; Mishra, Kushlendra; Paninjath, Sankaranarayanan; Bork, Ingo; Buck, Peter; Toublan, Olivier; Schanen, Isabelle

    2014-07-01

    Standard OPC models consist of a physical optical model and an empirical resist model. The resist model compensates the optical model imprecision on top of modeling resist development. The optical model imprecision may result from mask topography effects and real mask information including mask ebeam writing and mask process contributions. For advanced technology nodes, significant progress has been made to model mask topography to improve optical model accuracy. However, mask information is difficult to decorrelate from standard OPC model. Our goal is to establish an accurate mask model through a dedicated calibration exercise. In this paper, we present a flow to calibrate an accurate mask enabling its implementation. The study covers the different effects that should be embedded in the mask model as well as the experiment required to model them.

  6. Minimalist Relativistic Force Field: Prediction of Proton-Proton Coupling Constants in (1)H NMR Spectra Is Perfected with NBO Hybridization Parameters.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2015-05-15

    We previously developed a reliable method for multiparametric scaling of Fermi contacts to achieve fast and accurate prediction of proton-proton spin-spin coupling constants (SSCC) in (1)H NMR. We now report that utilization of NBO hybridization coefficients for carbon atoms in the involved C-H bonds allows for a significant simplification of this parametric scheme, requiring only four general types of SSCCs: geminal, vicinal, 1,3-, and long-range constants. The method is optimized for inexpensive B3LYP/6-31G(d) molecular geometries. A new DU8 basis set, based on a training set of 475 experimental spin-spin coupling constants, is developed for hydrogen and common non-hydrogen atoms (Li, B, C, N, O, F, Si, P, S, Cl, Se, Br, I) to calculate Fermi contacts. On a test set of 919 SSCCs from a diverse collection of natural products and complex synthetic molecules the method gave excellent accuracy of 0.29 Hz (rmsd) with the maximum unsigned error not exceeding 1 Hz.

  7. Minimalist Relativistic Force Field: Prediction of Proton-Proton Coupling Constants in (1)H NMR Spectra Is Perfected with NBO Hybridization Parameters.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2015-05-15

    We previously developed a reliable method for multiparametric scaling of Fermi contacts to achieve fast and accurate prediction of proton-proton spin-spin coupling constants (SSCC) in (1)H NMR. We now report that utilization of NBO hybridization coefficients for carbon atoms in the involved C-H bonds allows for a significant simplification of this parametric scheme, requiring only four general types of SSCCs: geminal, vicinal, 1,3-, and long-range constants. The method is optimized for inexpensive B3LYP/6-31G(d) molecular geometries. A new DU8 basis set, based on a training set of 475 experimental spin-spin coupling constants, is developed for hydrogen and common non-hydrogen atoms (Li, B, C, N, O, F, Si, P, S, Cl, Se, Br, I) to calculate Fermi contacts. On a test set of 919 SSCCs from a diverse collection of natural products and complex synthetic molecules the method gave excellent accuracy of 0.29 Hz (rmsd) with the maximum unsigned error not exceeding 1 Hz. PMID:25885091

  8. Computing the Kirkwood g-Factor by Combining Constant Maxwell Electric Field and Electric Displacement Simulations: Application to the Dielectric Constant of Liquid Water.

    PubMed

    Zhang, Chao; Hutter, Jürg; Sprik, Michiel

    2016-07-21

    In his classic 1939 paper, Kirkwood linked the macroscopic dielectric constant of polar liquids to the local orientational order as measured by the g-factor (later named after him) and suggested that the corresponding dielectric constant at short-range is effectively equal to the macroscopic value just after "a distance of molecular magnitude" [ Kirkwood, J. Chem. Phys., 1939, 7, 911 ]. Here, we show a simple approach to extract the short-ranged Kirkwood g-factor from molecular dynamics (MD) simulation by superposing the outcomes of constant electric field E and constant electric displacement D simulations [ Zhang and Sprik, Phys. Rev. B: Condens. Matter Mater. Phys., 2016, 93, 144201 ]. Rather than from the notoriously slow fluctuations of the dipole moment of the full MD cell, the dielectric constant can now be estimated from dipole fluctuations at short-range, accelerating the convergence. Exploiting this feature, we computed the bulk dielectric constant of liquid water modeled in the generalized gradient approximation (PBE) to density functional theory and found it to be at least 40% larger than the experimental value.

  9. Accurate maser positions for MALT-45

    NASA Astrophysics Data System (ADS)

    Jordan, Christopher; Bains, Indra; Voronkov, Maxim; Lo, Nadia; Jones, Paul; Muller, Erik; Cunningham, Maria; Burton, Michael; Brooks, Kate; Green, James; Fuller, Gary; Barnes, Peter; Ellingsen, Simon; Urquhart, James; Morgan, Larry; Rowell, Gavin; Walsh, Andrew; Loenen, Edo; Baan, Willem; Hill, Tracey; Purcell, Cormac; Breen, Shari; Peretto, Nicolas; Jackson, James; Lowe, Vicki; Longmore, Steven

    2013-10-01

    MALT-45 is an untargeted survey, mapping the Galactic plane in CS (1-0), Class I methanol masers, SiO masers and thermal emission, and high frequency continuum emission. After obtaining images from the survey, a number of masers were detected, but without accurate positions. This project seeks to resolve each maser and its environment, with the ultimate goal of placing the Class I methanol maser into a timeline of high mass star formation.

  10. Accurate maser positions for MALT-45

    NASA Astrophysics Data System (ADS)

    Jordan, Christopher; Bains, Indra; Voronkov, Maxim; Lo, Nadia; Jones, Paul; Muller, Erik; Cunningham, Maria; Burton, Michael; Brooks, Kate; Green, James; Fuller, Gary; Barnes, Peter; Ellingsen, Simon; Urquhart, James; Morgan, Larry; Rowell, Gavin; Walsh, Andrew; Loenen, Edo; Baan, Willem; Hill, Tracey; Purcell, Cormac; Breen, Shari; Peretto, Nicolas; Jackson, James; Lowe, Vicki; Longmore, Steven

    2013-04-01

    MALT-45 is an untargeted survey, mapping the Galactic plane in CS (1-0), Class I methanol masers, SiO masers and thermal emission, and high frequency continuum emission. After obtaining images from the survey, a number of masers were detected, but without accurate positions. This project seeks to resolve each maser and its environment, with the ultimate goal of placing the Class I methanol maser into a timeline of high mass star formation.

  11. A priori predictions of the rotational constants for HC13N, HC15N, C5O

    NASA Technical Reports Server (NTRS)

    DeFrees, D. J.; McLean, A. D.

    1989-01-01

    Ab initio molecular orbital theory is used to estimate the rotational constant for several carbon-chain molecules that are candidates for discovery in interstellar space. These estimated rotational constants can be used in laboratory or astronomical searches for the molecules. The rotational constant for HC13N is estimated to be 0.1073 +/- 0.0002 GHz and its dipole moment 5.4 D. The rotational constant for HC15N is estimated to be 0.0724 GHz, with a somewhat larger uncertainty. The rotational constant of C5O is estimated to be 1.360 +/- 2% GHz and its dipole moment 4.4. D.

  12. Accelerated molecular dynamics methods

    SciTech Connect

    Perez, Danny

    2011-01-04

    The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.

  13. Inflation with a constant rate of roll

    NASA Astrophysics Data System (ADS)

    Motohashi, Hayato; Starobinsky, Alexei A.; Yokoyama, Jun'ichi

    2015-09-01

    We consider an inflationary scenario where the rate of inflaton roll defined by ̈phi/H dot phi remains constant. The rate of roll is small for slow-roll inflation, while a generic rate of roll leads to the interesting case of 'constant-roll' inflation. We find a general exact solution for the inflaton potential required for such inflaton behaviour. In this model, due to non-slow evolution of background, the would-be decaying mode of linear scalar (curvature) perturbations may not be neglected. It can even grow for some values of the model parameter, while the other mode always remains constant. However, this always occurs for unstable solutions which are not attractors for the given potential. The most interesting particular cases of constant-roll inflation remaining viable with the most recent observational data are quadratic hilltop inflation (with cutoff) and natural inflation (with an additional negative cosmological constant). In these cases even-order slow-roll parameters approach non-negligible constants while the odd ones are asymptotically vanishing in the quasi-de Sitter regime.

  14. Binding constants of membrane-anchored receptors and ligands depend strongly on the nanoscale roughness of membranes.

    PubMed

    Hu, Jinglei; Lipowsky, Reinhard; Weikl, Thomas R

    2013-09-17

    Cell adhesion and the adhesion of vesicles to the membranes of cells or organelles are pivotal for immune responses, tissue formation, and cell signaling. The adhesion processes depend sensitively on the binding constant of the membrane-anchored receptor and ligand proteins that mediate adhesion, but this constant is difficult to measure in experiments. We have investigated the binding of membrane-anchored receptor and ligand proteins with molecular dynamics simulations. We find that the binding constant of the anchored proteins strongly decreases with the membrane roughness caused by thermally excited membrane shape fluctuations on nanoscales. We present a theory that explains the roughness dependence of the binding constant for the anchored proteins from membrane confinement and that relates this constant to the binding constant of soluble proteins without membrane anchors. Because the binding constant of soluble proteins is readily accessible in experiments, our results provide a useful route to compute the binding constant of membrane-anchored receptor and ligand proteins.

  15. Molecular spintronics.

    PubMed

    Sanvito, Stefano

    2011-06-01

    The electron spin made its debut in the device world only two decades ago but today our ability of detecting the spin state of a moving electron underpins the entire magnetic data storage industry. This technological revolution has been driven by a constant improvement in our understanding on how spins can be injected, manipulated and detected in the solid state, a field which is collectively named Spintronics. Recently a number of pioneering experiments and theoretical works suggest that organic materials can offer similar and perhaps superior performances in making spin-devices than the more conventional inorganic metals and semiconductors. Furthermore they can pave the way for radically new device concepts. This is Molecular Spintronics, a blossoming research area aimed at exploring how the unique properties of the organic world can marry the requirements of spin-devices. Importantly, after a first phase, where most of the research was focussed on exporting the concepts of inorganic spintronics to organic materials, the field has moved to a more mature age, where the exploitation of the unique properties of molecules has begun to emerge. Molecular spintronics now collects a diverse and interdisciplinary community ranging from device physicists to synthetic chemists to surface scientists. In this critical review, I will survey this fascinating, rapidly evolving, field with a particular eye on new directions and opportunities. The main differences and challenges with respect to standard spintronics will be discussed and so will be the potential cross-fertilization with other fields (177 references).

  16. High Frequency QRS ECG Accurately Detects Cardiomyopathy

    NASA Technical Reports Server (NTRS)

    Schlegel, Todd T.; Arenare, Brian; Poulin, Gregory; Moser, Daniel R.; Delgado, Reynolds

    2005-01-01

    High frequency (HF, 150-250 Hz) analysis over the entire QRS interval of the ECG is more sensitive than conventional ECG for detecting myocardial ischemia. However, the accuracy of HF QRS ECG for detecting cardiomyopathy is unknown. We obtained simultaneous resting conventional and HF QRS 12-lead ECGs in 66 patients with cardiomyopathy (EF = 23.2 plus or minus 6.l%, mean plus or minus SD) and in 66 age- and gender-matched healthy controls using PC-based ECG software recently developed at NASA. The single most accurate ECG parameter for detecting cardiomyopathy was an HF QRS morphological score that takes into consideration the total number and severity of reduced amplitude zones (RAZs) present plus the clustering of RAZs together in contiguous leads. This RAZ score had an area under the receiver operator curve (ROC) of 0.91, and was 88% sensitive, 82% specific and 85% accurate for identifying cardiomyopathy at optimum score cut-off of 140 points. Although conventional ECG parameters such as the QRS and QTc intervals were also significantly longer in patients than controls (P less than 0.001, BBBs excluded), these conventional parameters were less accurate (area under the ROC = 0.77 and 0.77, respectively) than HF QRS morphological parameters for identifying underlying cardiomyopathy. The total amplitude of the HF QRS complexes, as measured by summed root mean square voltages (RMSVs), also differed between patients and controls (33.8 plus or minus 11.5 vs. 41.5 plus or minus 13.6 mV, respectively, P less than 0.003), but this parameter was even less accurate in distinguishing the two groups (area under ROC = 0.67) than the HF QRS morphologic and conventional ECG parameters. Diagnostic accuracy was optimal (86%) when the RAZ score from the HF QRS ECG and the QTc interval from the conventional ECG were used simultaneously with cut-offs of greater than or equal to 40 points and greater than or equal to 445 ms, respectively. In conclusion 12-lead HF QRS ECG employing

  17. Pause Point Spectra in DNA Constant-Force Unzipping

    PubMed Central

    Weeks, J. D.; Lucks, J. B.; Kafri, Y.; Danilowicz, C.; Nelson, D. R.; Prentiss, M.

    2005-01-01

    Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the locations of pause points can be extracted in the form of a pause point spectrum. A simple theoretical model of DNA constant-force unzipping is presented, which generates theoretical pause point spectra through Monte Carlo simulation of the unzipping process. The locations of peaks in the experimental and theoretical pause point spectra are found to be nearly coincident below 6000 basepairs for unzipping the bacteriophage λ-genome. The model only requires the sequence, temperature, and a set of empirical basepair binding and stacking energy parameters, and the good agreement with experiment suggests that pause point locations are primarily determined by the DNA sequence. The model is also used to predict pause point spectra for the bacteriophage φX174 genome. The algorithm for extracting the pause point spectrum might also be useful for studying related systems which exhibit pausing behavior such as molecular motors. PMID:15695634

  18. Doubly hybrid density functional for accurate descriptions of nonbond interactions, thermochemistry, and thermochemical kinetics

    PubMed Central

    Zhang, Ying; Xu, Xin; Goddard, William A.

    2009-01-01

    We develop and validate a density functional, XYG3, based on the adiabatic connection formalism and the Görling–Levy coupling-constant perturbation expansion to the second order (PT2). XYG3 is a doubly hybrid functional, containing 3 mixing parameters. It has a nonlocal orbital-dependent component in the exchange term (exact exchange) plus information about the unoccupied Kohn–Sham orbitals in the correlation part (PT2 double excitation). XYG3 is remarkably accurate for thermochemistry, reaction barrier heights, and nonbond interactions of main group molecules. In addition, the accuracy remains nearly constant with system size. PMID:19276116

  19. FAST TRACK COMMUNICATION Accurate estimate of α variation and isotope shift parameters in Na and Mg+

    NASA Astrophysics Data System (ADS)

    Sahoo, B. K.

    2010-12-01

    We present accurate calculations of fine-structure constant variation coefficients and isotope shifts in Na and Mg+ using the relativistic coupled-cluster method. In our approach, we are able to discover the roles of various correlation effects explicitly to all orders in these calculations. Most of the results, especially for the excited states, are reported for the first time. It is possible to ascertain suitable anchor and probe lines for the studies of possible variation in the fine-structure constant by using the above results in the considered systems.

  20. Accurate diagnosis of Helicobacter pylori. Other tests.

    PubMed

    Bravos, E D; Gilman, R H

    2000-12-01

    The application of polymerase chain reaction (PCR) with respect to Helicobacter pylori is useful for molecular epidemiologic aspects and detection purposes. The authors address the current detection methods by PCR aimed at detecting H. pylori in clinical samples collected by less invasive methods, such as gastric juice, saliva, dental plaque, and feces. Enzyme immunoassay also is discussed.

  1. Direct computation of parameters for accurate polarizable force fields

    SciTech Connect

    Verstraelen, Toon Vandenbrande, Steven; Ayers, Paul W.

    2014-11-21

    We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.

  2. Accurate Determination of Conformational Transitions in Oligomeric Membrane Proteins

    PubMed Central

    Sanz-Hernández, Máximo; Vostrikov, Vitaly V.; Veglia, Gianluigi; De Simone, Alfonso

    2016-01-01

    The structural dynamics governing collective motions in oligomeric membrane proteins play key roles in vital biomolecular processes at cellular membranes. In this study, we present a structural refinement approach that combines solid-state NMR experiments and molecular simulations to accurately describe concerted conformational transitions identifying the overall structural, dynamical, and topological states of oligomeric membrane proteins. The accuracy of the structural ensembles generated with this method is shown to reach the statistical error limit, and is further demonstrated by correctly reproducing orthogonal NMR data. We demonstrate the accuracy of this approach by characterising the pentameric state of phospholamban, a key player in the regulation of calcium uptake in the sarcoplasmic reticulum, and by probing its dynamical activation upon phosphorylation. Our results underline the importance of using an ensemble approach to characterise the conformational transitions that are often responsible for the biological function of oligomeric membrane protein states. PMID:26975211

  3. High-Accuracy Quartic Force Field Calculations for the Spectroscopic Constants and Vibrational Frequencies of 1(exp 1)A' l-C3H(-): A Possible Link to Lines Observed in the Horsehead Nebula PDR

    NASA Technical Reports Server (NTRS)

    Fortenberry, Ryan C.; Huang, Xinchuan; Crawford, T. Daniel; Lee, Timothy J.

    2013-01-01

    It has been shown that rotational lines observed in the Horsehead nebula photon-dominated-region (PDR) are probably not caused by l-C3H+, as was originally suggested. In the search for viable alternative candidate carriers, quartic force fields are employed here to provide highly accurate rotational constants, as well as fundamental vibrational frequencies, for another candidate carrier: 1 (sup 1)A' C3H(-). The ab initio computed spectroscopic constants provided in this work are, compared to those necessary to define the observed lines, as accurate as the computed spectroscopic constants for many of the known interstellar anions. Additionally, the computed D-eff for C3H(-) is three times closer to the D deduced from the observed Horsehead nebula lines relative to l-C3H(+). As a result, 1 (sup 1)A' C3H(-). is a more viable candidate for these observed rotational transitions and would be the seventh confirmed interstellar anion detected within the past decade and the first C(sub n)H(-) molecular anion with an odd n.

  4. Molecular Models in Biology

    ERIC Educational Resources Information Center

    Goodman, Richard E.

    1970-01-01

    Describes types of molecular models (ball-and-stick, framework, and space-filling) and evaluates commercially available kits. Gives instructions for constructive models from polystyrene balls and pipe-cleaners. Models are useful for class demonstrations although not sufficiently accurate for research use. Illustrations show biologically important…

  5. A simple, sensitive, and accurate alcohol electrode

    SciTech Connect

    Verduyn, C.; Scheffers, W.A.; Van Dijken, J.P.

    1983-04-01

    The construction and performance of an enzyme electrode is described which specifically detects lower primary aliphatic alcohols in aqueous solutions. The electrode consists of a commercial Clark-type oxygen electrode on which alcohol oxidase (E.C. 1.1.3.13) and catalase were immobilized. The decrease in electrode current is linearly proportional to ethanol concentrations betwee 1 and 25 ppm. The response of the electrode remains constant during 400 assays over a period of two weeks. The response time is between 1 and 2 min. Assembly of the electrode takes less than 1 h.

  6. Accurately Mapping M31's Microlensing Population

    NASA Astrophysics Data System (ADS)

    Crotts, Arlin

    2004-07-01

    We propose to augment an existing microlensing survey of M31 with source identifications provided by a modest amount of ACS {and WFPC2 parallel} observations to yield an accurate measurement of the masses responsible for microlensing in M31, and presumably much of its dark matter. The main benefit of these data is the determination of the physical {or "einstein"} timescale of each microlensing event, rather than an effective {"FWHM"} timescale, allowing masses to be determined more than twice as accurately as without HST data. The einstein timescale is the ratio of the lensing cross-sectional radius and relative velocities. Velocities are known from kinematics, and the cross-section is directly proportional to the {unknown} lensing mass. We cannot easily measure these quantities without knowing the amplification, hence the baseline magnitude, which requires the resolution of HST to find the source star. This makes a crucial difference because M31 lens m ass determinations can be more accurate than those towards the Magellanic Clouds through our Galaxy's halo {for the same number of microlensing events} due to the better constrained geometry in the M31 microlensing situation. Furthermore, our larger survey, just completed, should yield at least 100 M31 microlensing events, more than any Magellanic survey. A small amount of ACS+WFPC2 imaging will deliver the potential of this large database {about 350 nights}. For the whole survey {and a delta-function mass distribution} the mass error should approach only about 15%, or about 6% error in slope for a power-law distribution. These results will better allow us to pinpoint the lens halo fraction, and the shape of the halo lens spatial distribution, and allow generalization/comparison of the nature of halo dark matter in spiral galaxies. In addition, we will be able to establish the baseline magnitude for about 50, 000 variable stars, as well as measure an unprecedentedly deta iled color-magnitude diagram and luminosity

  7. Accurate upwind methods for the Euler equations

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1993-01-01

    A new class of piecewise linear methods for the numerical solution of the one-dimensional Euler equations of gas dynamics is presented. These methods are uniformly second-order accurate, and can be considered as extensions of Godunov's scheme. With an appropriate definition of monotonicity preservation for the case of linear convection, it can be shown that they preserve monotonicity. Similar to Van Leer's MUSCL scheme, they consist of two key steps: a reconstruction step followed by an upwind step. For the reconstruction step, a monotonicity constraint that preserves uniform second-order accuracy is introduced. Computational efficiency is enhanced by devising a criterion that detects the 'smooth' part of the data where the constraint is redundant. The concept and coding of the constraint are simplified by the use of the median function. A slope steepening technique, which has no effect at smooth regions and can resolve a contact discontinuity in four cells, is described. As for the upwind step, existing and new methods are applied in a manner slightly different from those in the literature. These methods are derived by approximating the Euler equations via linearization and diagonalization. At a 'smooth' interface, Harten, Lax, and Van Leer's one intermediate state model is employed. A modification for this model that can resolve contact discontinuities is presented. Near a discontinuity, either this modified model or a more accurate one, namely, Roe's flux-difference splitting. is used. The current presentation of Roe's method, via the conceptually simple flux-vector splitting, not only establishes a connection between the two splittings, but also leads to an admissibility correction with no conditional statement, and an efficient approximation to Osher's approximate Riemann solver. These reconstruction and upwind steps result in schemes that are uniformly second-order accurate and economical at smooth regions, and yield high resolution at discontinuities.

  8. Accurate measurement of unsteady state fluid temperature

    NASA Astrophysics Data System (ADS)

    Jaremkiewicz, Magdalena

    2016-07-01

    In this paper, two accurate methods for determining the transient fluid temperature were presented. Measurements were conducted for boiling water since its temperature is known. At the beginning the thermometers are at the ambient temperature and next they are immediately immersed into saturated water. The measurements were carried out with two thermometers of different construction but with the same housing outer diameter equal to 15 mm. One of them is a K-type industrial thermometer widely available commercially. The temperature indicated by the thermometer was corrected considering the thermometers as the first or second order inertia devices. The new design of a thermometer was proposed and also used to measure the temperature of boiling water. Its characteristic feature is a cylinder-shaped housing with the sheath thermocouple located in its center. The temperature of the fluid was determined based on measurements taken in the axis of the solid cylindrical element (housing) using the inverse space marching method. Measurements of the transient temperature of the air flowing through the wind tunnel using the same thermometers were also carried out. The proposed measurement technique provides more accurate results compared with measurements using industrial thermometers in conjunction with simple temperature correction using the inertial thermometer model of the first or second order. By comparing the results, it was demonstrated that the new thermometer allows obtaining the fluid temperature much faster and with higher accuracy in comparison to the industrial thermometer. Accurate measurements of the fast changing fluid temperature are possible due to the low inertia thermometer and fast space marching method applied for solving the inverse heat conduction problem.

  9. Extracting kinetic rate constants from surface plasmon resonance array systems.

    PubMed

    Rich, Rebecca L; Cannon, Michelle J; Jenkins, Jerry; Pandian, Prabhakar; Sundaram, Shankar; Magyar, Rachelle; Brockman, Jennifer; Lambert, Jeremy; Myszka, David G

    2008-02-01

    Surface plasmon resonance imaging systems, such as Flexchip from Biacore, are capable of monitoring hundreds of reaction spots simultaneously within a single flow cell. Interpreting the binding kinetics in a large-format flow cell presents a number of potential challenges, including accounting for mass transport effects and spot-to-spot sample depletion. We employed a combination of computer simulations and experimentation to characterize these effects across the spotted array and established that a simple two-compartment model may be used to accurately extract intrinsic rate constants from the array under mass transport-limited conditions. Using antibody systems, we demonstrate that the spot-to-spot variability in the binding kinetics was <9%. We also illustrate the advantage of globally fitting binding data from multiple spots within an array for a system that is mass transport limited.

  10. The GMO Sumrule and the πNN Coupling Constant

    NASA Astrophysics Data System (ADS)

    Ericson, T. E. O.; Loiseau, B.; Thomas, A. W.

    The isovector GMO sumrule for forward πN scattering is critically evaluated using the precise π-p and π-d scattering lengths obtained recently from pionic atom measurements. The charged πNN coupling constant is then deduced with careful analysis of systematic and statistical sources of uncertainties. This determination gives directly from data gc2(GMO)/4π = 14.17±0.09 (statistic) ±0.17 (systematic) or fc2/ 4π=0.078(11). This value is half-way between that of indirect methods (phase-shift analyses) and the direct evaluation from from backward np differential scattering cross sections (extrapolation to pion pole). From the π-p and π-d scattering lengths our analysis leads also to accurate values for (1/2)(aπ-p+aπ-n) and (1/2) (aπ-p-aπ-n).

  11. The first accurate description of an aurora

    NASA Astrophysics Data System (ADS)

    Schröder, Wilfried

    2006-12-01

    As technology has advanced, the scientific study of auroral phenomena has increased by leaps and bounds. A look back at the earliest descriptions of aurorae offers an interesting look into how medieval scholars viewed the subjects that we study.Although there are earlier fragmentary references in the literature, the first accurate description of the aurora borealis appears to be that published by the German Catholic scholar Konrad von Megenberg (1309-1374) in his book Das Buch der Natur (The Book of Nature). The book was written between 1349 and 1350.

  12. New law requires 'medically accurate' lesson plans.

    PubMed

    1999-09-17

    The California Legislature has passed a bill requiring all textbooks and materials used to teach about AIDS be medically accurate and objective. Statements made within the curriculum must be supported by research conducted in compliance with scientific methods, and published in peer-reviewed journals. Some of the current lesson plans were found to contain scientifically unsupported and biased information. In addition, the bill requires material to be "free of racial, ethnic, or gender biases." The legislation is supported by a wide range of interests, but opposed by the California Right to Life Education Fund, because they believe it discredits abstinence-only material.

  13. Accurate density functional thermochemistry for larger molecules.

    SciTech Connect

    Raghavachari, K.; Stefanov, B. B.; Curtiss, L. A.; Lucent Tech.

    1997-06-20

    Density functional methods are combined with isodesmic bond separation reaction energies to yield accurate thermochemistry for larger molecules. Seven different density functionals are assessed for the evaluation of heats of formation, Delta H 0 (298 K), for a test set of 40 molecules composed of H, C, O and N. The use of bond separation energies results in a dramatic improvement in the accuracy of all the density functionals. The B3-LYP functional has the smallest mean absolute deviation from experiment (1.5 kcal mol/f).

  14. New law requires 'medically accurate' lesson plans.

    PubMed

    1999-09-17

    The California Legislature has passed a bill requiring all textbooks and materials used to teach about AIDS be medically accurate and objective. Statements made within the curriculum must be supported by research conducted in compliance with scientific methods, and published in peer-reviewed journals. Some of the current lesson plans were found to contain scientifically unsupported and biased information. In addition, the bill requires material to be "free of racial, ethnic, or gender biases." The legislation is supported by a wide range of interests, but opposed by the California Right to Life Education Fund, because they believe it discredits abstinence-only material. PMID:11366835

  15. Universality: Accurate Checks in Dyson's Hierarchical Model

    NASA Astrophysics Data System (ADS)

    Godina, J. J.; Meurice, Y.; Oktay, M. B.

    2003-06-01

    In this talk we present high-accuracy calculations of the susceptibility near βc for Dyson's hierarchical model in D = 3. Using linear fitting, we estimate the leading (γ) and subleading (Δ) exponents. Independent estimates are obtained by calculating the first two eigenvalues of the linearized renormalization group transformation. We found γ = 1.29914073 ± 10 -8 and, Δ = 0.4259469 ± 10-7 independently of the choice of local integration measure (Ising or Landau-Ginzburg). After a suitable rescaling, the approximate fixed points for a large class of local measure coincide accurately with a fixed point constructed by Koch and Wittwer.

  16. Accurate, noninvasive detection of Helicobacter pylori DNA from stool samples: potential usefulness for monitoring treatment.

    PubMed

    Shuber, Anthony P; Ascaño, Jennifer J; Boynton, Kevin A; Mitchell, Anastasia; Frierson, Henry F; El-Rifai, Wa'el; Powell, Steven M

    2002-01-01

    A novel DNA assay demonstrating sensitive and accurate detection of Helicobacter pylori from stool samples is reported. Moreover, in three individuals tested for therapeutic response, the assay showed the disappearance of H. pylori DNA during treatment. Thus, this noninvasive molecular biology-based assay has the potential to be a powerful diagnostic tool given its ability to specifically identify H. pylori DNA.

  17. Dielectric-dependent Density Functionals for Accurate Electronic Structure Calculations of Molecules and Solids

    NASA Astrophysics Data System (ADS)

    Skone, Jonathan; Govoni, Marco; Galli, Giulia

    Dielectric-dependent hybrid [DDH] functionals have recently been shown to yield highly accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than standard GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. In the present talk we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using material dependent, non-empirical parameters. Comparing with state of the art GW calculations and experiment, we show that such RS hybrids yield accurate electronic properties of both molecules and solids, including energy gaps, photoelectron spectra and absolute ionization potentials. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and DOE-BES.

  18. Accurate shear measurement with faint sources

    SciTech Connect

    Zhang, Jun; Foucaud, Sebastien; Luo, Wentao E-mail: walt@shao.ac.cn

    2015-01-01

    For cosmic shear to become an accurate cosmological probe, systematic errors in the shear measurement method must be unambiguously identified and corrected for. Previous work of this series has demonstrated that cosmic shears can be measured accurately in Fourier space in the presence of background noise and finite pixel size, without assumptions on the morphologies of galaxy and PSF. The remaining major source of error is source Poisson noise, due to the finiteness of source photon number. This problem is particularly important for faint galaxies in space-based weak lensing measurements, and for ground-based images of short exposure times. In this work, we propose a simple and rigorous way of removing the shear bias from the source Poisson noise. Our noise treatment can be generalized for images made of multiple exposures through MultiDrizzle. This is demonstrated with the SDSS and COSMOS/ACS data. With a large ensemble of mock galaxy images of unrestricted morphologies, we show that our shear measurement method can achieve sub-percent level accuracy even for images of signal-to-noise ratio less than 5 in general, making it the most promising technique for cosmic shear measurement in the ongoing and upcoming large scale galaxy surveys.

  19. Accurate basis set truncation for wavefunction embedding

    NASA Astrophysics Data System (ADS)

    Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.

    2013-07-01

    Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.

  20. Accurate determination of characteristic relative permeability curves

    NASA Astrophysics Data System (ADS)

    Krause, Michael H.; Benson, Sally M.

    2015-09-01

    A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.

  1. How Accurately can we Calculate Thermal Systems?

    SciTech Connect

    Cullen, D; Blomquist, R N; Dean, C; Heinrichs, D; Kalugin, M A; Lee, M; Lee, Y; MacFarlan, R; Nagaya, Y; Trkov, A

    2004-04-20

    I would like to determine how accurately a variety of neutron transport code packages (code and cross section libraries) can calculate simple integral parameters, such as K{sub eff}, for systems that are sensitive to thermal neutron scattering. Since we will only consider theoretical systems, we cannot really determine absolute accuracy compared to any real system. Therefore rather than accuracy, it would be more precise to say that I would like to determine the spread in answers that we obtain from a variety of code packages. This spread should serve as an excellent indicator of how accurately we can really model and calculate such systems today. Hopefully, eventually this will lead to improvements in both our codes and the thermal scattering models that they use in the future. In order to accomplish this I propose a number of extremely simple systems that involve thermal neutron scattering that can be easily modeled and calculated by a variety of neutron transport codes. These are theoretical systems designed to emphasize the effects of thermal scattering, since that is what we are interested in studying. I have attempted to keep these systems very simple, and yet at the same time they include most, if not all, of the important thermal scattering effects encountered in a large, water-moderated, uranium fueled thermal system, i.e., our typical thermal reactors.

  2. Accurate Stellar Parameters for Exoplanet Host Stars

    NASA Astrophysics Data System (ADS)

    Brewer, John Michael; Fischer, Debra; Basu, Sarbani; Valenti, Jeff A.

    2015-01-01

    A large impedement to our understanding of planet formation is obtaining a clear picture of planet radii and densities. Although determining precise ratios between planet and stellar host are relatively easy, determining accurate stellar parameters is still a difficult and costly undertaking. High resolution spectral analysis has traditionally yielded precise values for some stellar parameters but stars in common between catalogs from different authors or analyzed using different techniques often show offsets far in excess of their uncertainties. Most analyses now use some external constraint, when available, to break observed degeneracies between surface gravity, effective temperature, and metallicity which can otherwise lead to correlated errors in results. However, these external constraints are impossible to obtain for all stars and can require more costly observations than the initial high resolution spectra. We demonstrate that these discrepencies can be mitigated by use of a larger line list that has carefully tuned atomic line data. We use an iterative modeling technique that does not require external constraints. We compare the surface gravity obtained with our spectral synthesis modeling to asteroseismically determined values for 42 Kepler stars. Our analysis agrees well with only a 0.048 dex offset and an rms scatter of 0.05 dex. Such accurate stellar gravities can reduce the primary source of uncertainty in radii by almost an order of magnitude over unconstrained spectral analysis.

  3. Optimizing constant wavelength neutron powder diffractometers

    NASA Astrophysics Data System (ADS)

    Cussen, Leo D.

    2016-06-01

    This article describes an analytic method to optimize constant wavelength neutron powder diffractometers. It recasts the accepted mathematical description of resolution and intensity in terms of new variables and includes terms for vertical divergence, wavelength and some sample scattering effects. An undetermined multiplier method is applied to the revised equations to minimize the RMS value of resolution width at constant intensity and fixed wavelength. A new understanding of primary spectrometer transmission (presented elsewhere) can then be applied to choose beam elements to deliver an optimum instrument. Numerical methods can then be applied to choose the best wavelength.

  4. Dielectric constants of soils at microwave frequencies

    NASA Technical Reports Server (NTRS)

    Geiger, F. E.; Williams, D.

    1972-01-01

    A knowledge of the complex dielectric constant of soils is essential in the interpretation of microwave airborne radiometer data of the earth's surface. Measurements were made at 37 GHz on various soils from the Phoenix, Ariz., area. Extensive data have been obtained for dry soil and soil with water content in the range from 0.6 to 35 percent by dry weight. Measurements were made in a two arm microwave bridge and results were corrected for reflections at the sample interfaces by solution of the parallel dielectric plate problem. The maximum dielectric constants are about a factor of 3 lower than those reported for similar soils at X-band frequencies.

  5. Microfabricated microengine with constant rotation rate

    SciTech Connect

    Romero, L.A.; Dickey, F.M.

    1999-09-21

    A microengine uses two synchronized linear actuators as a power source and converts oscillatory motion from the actuators into constant rotational motion via direct linkage connection to an output gear or wheel. The microengine provides output in the form of a continuously rotating output gear that is capable of delivering drive torque at a constant rotation to a micromechanism. The output gear can have gear teeth on its outer perimeter for directly contacting a micromechanism requiring mechanical power. The gear is retained by a retaining means which allows said gear to rotate freely. The microengine is microfabricated of polysilicon on one wafer using surface micromachining batch fabrication.

  6. Atomic Weights No Longer Constants of Nature

    SciTech Connect

    Coplen, T.B.; Holden, N.

    2011-03-01

    Many of us grew up being taught that the standard atomic weights we found in the back of our chemistry textbooks or on the Periodic Table of the Chemical Elements hanging on the wall of our chemistry classroom are constants of nature. This was common knowledge for more than a century and a half, but not anymore. The following text explains how advances in chemical instrumentation and isotopic analysis has changed the way we view atomic weights and why they are no longer constants of nature.

  7. Atomic weights: no longer constants of nature

    USGS Publications Warehouse

    Coplen, Tyler B.; Holden, Norman E.

    2011-01-01

    Many of us were taught that the standard atomic weights we found in the back of our chemistry textbooks or on the Periodic Table of the Chemical Elements hanging on the wall of our chemistry classroom are constants of nature. This was common knowledge for more than a century and a half, but not anymore. The following text explains how advances in chemical instrumentation and isotopic analysis have changed the way we view atomic weights and why they are no longer constants of nature

  8. TOPICAL REVIEW The cosmological constant puzzle

    NASA Astrophysics Data System (ADS)

    Bass, Steven D.

    2011-04-01

    The accelerating expansion of the Universe points to a small positive vacuum energy density and negative vacuum pressure. A strong candidate is the cosmological constant in Einstein's equations of general relativity. Possible contributions are zero-point energies and the condensates associated with spontaneous symmetry breaking. The vacuum energy density extracted from astrophysics is 1056 times smaller than the value expected from quantum fields and standard model particle physics. Is the vacuum energy density time dependent? We give an introduction to the cosmological constant puzzle and ideas how to solve it.

  9. Cosmological constant in scale-invariant theories

    SciTech Connect

    Foot, Robert; Kobakhidze, Archil; Volkas, Raymond R.

    2011-10-01

    The incorporation of a small cosmological constant within radiatively broken scale-invariant models is discussed. We show that phenomenologically consistent scale-invariant models can be constructed which allow a small positive cosmological constant, providing certain relation between the particle masses is satisfied. As a result, the mass of the dilaton is generated at two-loop level. Another interesting consequence is that the electroweak symmetry-breaking vacuum in such models is necessarily a metastable ''false'' vacuum which, fortunately, is not expected to decay on cosmological time scales.

  10. Environmental dependence of masses and coupling constants

    SciTech Connect

    Olive, Keith A.; Pospelov, Maxim

    2008-02-15

    We construct a class of scalar field models coupled to matter that lead to the dependence of masses and coupling constants on the ambient matter density. Such models predict a deviation of couplings measured on the Earth from values determined in low-density astrophysical environments, but do not necessarily require the evolution of coupling constants with the redshift in the recent cosmological past. Additional laboratory and astrophysical tests of {delta}{alpha} and {delta}(m{sub p}/m{sub e}) as functions of the ambient matter density are warranted.

  11. Our Universe from the cosmological constant

    SciTech Connect

    Barrau, Aurélien; Linsefors, Linda E-mail: linda.linsefors@lpsc.in2p3.fr

    2014-12-01

    The issue of the origin of the Universe and of its contents is addressed in the framework of bouncing cosmologies, as described for example by loop quantum gravity. If the current acceleration is due to a true cosmological constant, this constant is naturally conserved through the bounce and the Universe should also be in a (contracting) de Sitter phase in the remote past. We investigate here the possibility that the de Sitter temperature in the contracting branch fills the Universe with radiation that causes the bounce and the subsequent inflation and reheating. We also consider the possibility that this gives rise to a cyclic model of the Universe and suggest some possible tests.

  12. Microfabricated microengine with constant rotation rate

    DOEpatents

    Romero, Louis A.; Dickey, Fred M.

    1999-01-01

    A microengine uses two synchronized linear actuators as a power source and converts oscillatory motion from the actuators into constant rotational motion via direct linkage connection to an output gear or wheel. The microengine provides output in the form of a continuously rotating output gear that is capable of delivering drive torque at a constant rotation to a micromechanism. The output gear can have gear teeth on its outer perimeter for directly contacting a micromechanism requiring mechanical power. The gear is retained by a retaining means which allows said gear to rotate freely. The microengine is microfabricated of polysilicon on one wafer using surface micromachining batch fabrication.

  13. Constant-pressure simulations with dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Trofimov, S. Y.; Nies, E. L. F.; Michels, M. A. J.

    2005-10-01

    Dissipative particle dynamics (DPD) is a mesoscopic simulation method for studying hydrodynamic behavior of complex fluids. Ideally, a mesoscopic model should correctly represent the thermodynamic and hydrodynamic properties of a real system beyond certain length and time scales. Traditionally defined DPD quite successfully mimics hydrodynamics but is not flexible enough to accurately describe the thermodynamics of a real system. The so-called multibody DPD (MDPD) is a pragmatic extension of the classical DPD that allows one to prescribe the thermodynamic behavior of a system with only a small performance impact. In an earlier paper [S. Y. Trofimov, E. L. F. Nies, and M. A. J. Michels, J. Chem. Phys. 117, 9383 (2002)] we much improved the accuracy of the MDPD model for strongly nonideal systems, which are of most practical interest. The ability to correctly reproduce the equation of state of realistic systems in turn makes simulations at constant pressure sensible and useful. This situation of constant-pressure conditions is very common in experimental studies of (soft) condensed matter but has so far remained unexplored with the traditional DPD. Here, as a proof of concept, we integrate a modified version of the Andersen barostat into our improved MDPD model and make an evaluation of the performance of the new model on a set of single- and multicomponent systems. The modification of the barostat suppresses the "unphysical" volume oscillations after a sudden pressure change and simplifies the equilibration of the system.

  14. Constant-pressure simulations with dissipative particle dynamics.

    PubMed

    Trofimov, S Y; Nies, E L F; Michels, M A J

    2005-10-01

    Dissipative particle dynamics (DPD) is a mesoscopic simulation method for studying hydrodynamic behavior of complex fluids. Ideally, a mesoscopic model should correctly represent the thermodynamic and hydrodynamic properties of a real system beyond certain length and time scales. Traditionally defined DPD quite successfully mimics hydrodynamics but is not flexible enough to accurately describe the thermodynamics of a real system. The so-called multibody DPD (MDPD) is a pragmatic extension of the classical DPD that allows one to prescribe the thermodynamic behavior of a system with only a small performance impact. In an earlier paper [S. Y. Trofimov, E. L. F. Nies, and M. A. J. Michels, J. Chem. Phys. 117, 9383 (2002)] we much improved the accuracy of the MDPD model for strongly nonideal systems, which are of most practical interest. The ability to correctly reproduce the equation of state of realistic systems in turn makes simulations at constant pressure sensible and useful. This situation of constant-pressure conditions is very common in experimental studies of (soft) condensed matter but has so far remained unexplored with the traditional DPD. Here, as a proof of concept, we integrate a modified version of the Andersen barostat into our improved MDPD model and make an evaluation of the performance of the new model on a set of single- and multicomponent systems. The modification of the barostat suppresses the "unphysical" volume oscillations after a sudden pressure change and simplifies the equilibration of the system.

  15. Parameter identification of material constants in a composite shell structure

    NASA Technical Reports Server (NTRS)

    Martinez, David R.; Carne, Thomas G.

    1988-01-01

    One of the basic requirements in engineering analysis is the development of a mathematical model describing the system. Frequently comparisons with test data are used as a measurement of the adequacy of the model. An attempt is typically made to update or improve the model to provide a test verified analysis tool. System identification provides a systematic procedure for accomplishing this task. The terms system identification, parameter estimation, and model correlation all refer to techniques that use test information to update or verify mathematical models. The goal of system identification is to improve the correlation of model predictions with measured test data, and produce accurate, predictive models. For nonmetallic structures the modeling task is often difficult due to uncertainties in the elastic constants. A finite element model of the shell was created, which included uncertain orthotropic elastic constants. A modal survey test was then performed on the shell. The resulting modal data, along with the finite element model of the shell, were used in a Bayes estimation algorithm. This permitted the use of covariance matrices to weight the confidence in the initial parameter values as well as confidence in the measured test data. The estimation procedure also employed the concept of successive linearization to obtain an approximate solution to the original nonlinear estimation problem.

  16. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    DOE PAGES

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0more » to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.« less

  17. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    SciTech Connect

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.

  18. Evaluation of constant-Weber-number scaling for icing tests

    NASA Technical Reports Server (NTRS)

    Anderson, David N.

    1996-01-01

    Previous studies showed that for conditions simulating an aircraft encountering super-cooled water droplets the droplets may splash before freezing. Other surface effects dependent on the water surface tension may also influence the ice accretion process. Consequently, the Weber number appears to be important in accurately scaling ice accretion. A scaling method which uses a constant-Weber-number approach has been described previously; this study provides an evaluation of this scaling method. Tests are reported on cylinders of 2.5 to 15-cm diameter and NACA 0012 airfoils with chords of 18 to 53 cm in the NASA Lewis Icing Research Tunnel (IRT). The larger models were used to establish reference ice shapes, the scaling method was applied to determine appropriate scaled test conditions using the smaller models, and the ice shapes were compared. Icing conditions included warm glaze, horn glaze and mixed. The smallest size scaling attempted was 1/3, and scale and reference ice shapes for both cylinders and airfoils indicated that the constant-Weber-number scaling method was effective for the conditions tested.

  19. Infrared Spectra and Optical Constants of Elusive Amorphous Methane

    NASA Technical Reports Server (NTRS)

    Gerakines, Perry A.; Hudson, Reggie L.

    2015-01-01

    New and accurate laboratory results are reported for amorphous methane (CH4) ice near 10 K for the study of the interstellar medium (ISM) and the outer Solar System. Near- and mid-infrared (IR) data, including spectra, band strengths, absorption coefficients, and optical constants, are presented for the first time for this seldom-studied amorphous solid. The apparent IR band strength near 1300 cm(exp -1) (7.69 micrometer) for amorphous CH4 is found to be about 33% higher than the value long used by IR astronomers to convert spectral observations of interstellar CH4 into CH4 abundances. Although CH4 is most likely to be found in an amorphous phase in the ISM, a comparison of results from various laboratory groups shows that the earlier CH4 band strength at 1300 cm(exp -1) (7.69 micrometer) was derived from IR spectra of ices that were either partially or entirely crystalline CH4 Applications of the new amorphous-CH4 results are discussed, and all optical constants are made available in electronic form.

  20. Infrared Spectra and Optical Constants of Acetylene and Ethane Ices

    NASA Astrophysics Data System (ADS)

    Moore, Marla H.; Ferrante, R. F.; Hudson, R. L.; Moore, W. J.

    2012-10-01

    Hydrocarbon-containing ices have characteristic absorption bands in both the mid- and near-infrared spectral regions, yet accurate optical constants are not available for most of these molecules. Ices with a hydrocarbon component have been identified on several TNOs (1) and the presence of volatiles, such as hydrocarbons, is inferred for intermediate or large TNOs based on sublimation models (2, 3). In our laboratory we recently have undertaken low-temperature spectroscopic studies of C2 hydrocarbons. We report IR spectra for acetylene (C2H2) and ethane (C2H6) ice in both the amorphous and crystalline phases at multiple temperatures. We include measurements of the refractive index at 670 nm for both the amorphous and crystalline phases of each ice. The optical constants, the real (n) and imaginary (k) components of the complex index of refraction, were determined from 7000 - 400 cm-1 (1.4 - 25 microns) at multiple temperatures using a Kramers-Kronig analysis. A goal of the present work is to provide a data base of optical constants of C2 molecules similar to that of Hudgins et al. (4) and Moore et al. (5). These values, as well as our calculated individual band strengths, will have great practical importance for the ongoing analysis of TNO spectra. (1) Brown, M.E. et al., Astron J., 133, 284, 2007. (2) Delsanti, A. et al., A&A, 52, A40, 2010. (3) Schaller, E. L. & Brown, M. E., ApJ, 659, L61, 2007. (4) Hudgins, D. M. et al., ApJS, 86, 713, 1993. (5) Moore, M. H. et al., ApJS, 191, 96, 2010. This work is supported by NASA’s Planetary Atmospheres, Outer Planets, and Cassini Data Analysis programs, and The Goddard Center for Astrobiology.