Science.gov

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. An Empirical Approach to Obtaining Accurate Molecular Rotational Constants for Isotopically-Substituted Species from AB Initio Calculations

    NASA Astrophysics Data System (ADS)

    McGuire, Brett A.; Carroll, P. Brandon; Blake, Geoffrey A.

    2013-06-01

    Recent advances in microwave spectroscopy, namely the development of broadband, chirped-pulse Fourier-transform microwave spectrometers, allow the acquisition of rotational spectra of isotopically-substituted species in natural abundance. The characterization and assignment of these spectra is of particular interest as it applies to astrochemical observations of such species in the interstellar medium. Here, we demonstrate an empirical method for determining rotational constants to aid in the initial assignment of such spectra using a combination of laboratory data and ab initio calculations. The result is an increase in the accuracy of these constants by as much as two orders of magnitude versus those resulting from simple structure optimizations. We have applied this method to a variety of species including diatomic molecules (e.g. HCl), large molecules with internal motion (e.g. CH_3COOH), ions (e.g. HCO^+), clusters (e.g. H_2O\\cdotH_2O), and long carbon chain molecules (e.g. HC_7N). We present the results of these analyses and comment on the applicability of this method to other systems.

  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

    NASA Astrophysics Data System (ADS)

    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, NA. 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 108 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 improved

  5. 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

  6. Accurate rotational constants for linear interstellar carbon chains: achieving experimental accuracy

    NASA Astrophysics Data System (ADS)

    Etim, Emmanuel E.; Arunan, Elangannan

    2017-01-01

    Linear carbon chain molecular species remain the dominant theme in interstellar chemistry. Their continuous astronomical observation depends on the availability of accurate spectroscopic parameters. Accurate rotational constants are reported for hundreds of molecular species of astrophysical, spectroscopy and chemical interests from the different linear carbon chains; C_{{n}}H, C_{{n}}H-, C_{{n}}N, C_{{n}}N-, C_{{n}}O, C_{{n}}S, HC_{{n}}S, C_{{n}}Si, CH3(CC)_{{n}}H, HC_{{n}}N, DC_{2{n}+1}N, HC_{2{n}}NC, and CH3(C≡C)_{{n}}CN using three to four moments of inertia calculated from the experimental rotational constants coupled with those obtained from the optimized geometries at the Hartree Fock level. The calculated rotational constants are obtained from the corrected moments of inertia at the Hartfree Fock geometries. The calculated rotational constants show accuracy of few kHz below irrespective of the chain length and terminating groups. The obtained accuracy of few kHz places these rotational constants as excellent tools for both astronomical and laboratory detection of these molecular species of astrophysical interest. From the numerous unidentified lines from different astronomical surveys, transitions corresponding to known and new linear carbon chains could be found using these rotational constants. The astrophysical, spectroscopic and chemical implications of these results are discussed.

  7. A more accurate value for the Avogadro constant

    SciTech Connect

    De Bievre, P.; Valkiers, S.; Becker, P.

    1994-12-31

    Significant improvements in the method to determine the absolute molar mass of Silicon have been achieved and are reported. They enable to reduce the uncertainty contribution of the molar mass to the uncertainty of a previously published Avogadro Constant NA. The new value for NA and its reduced uncertainty is reported.

  8. Accurate measurements of the acoustical physical constants of synthetic alpha-quartz for SAW devices.

    PubMed

    Kushibiki, Juin-ichi; Takanaga, Izumi; Nishiyama, Shouichi

    2002-01-01

    Accurate measurements of the acoustical physical constants (elastic constants, piezoelectric constants, dielectric constants, and density) of commercially available and widely used surface acoustic wave (SAW)-grade synthetic a-quartz are reported. The propagation directions and modes of bulk waves optimal for accurately determining the constants were selected through numerical calculations, and three principal X-, Y-, and Z-cut specimens and several rotated Y-cut specimens were prepared from a single crystal ingot to determine the constants and to confirm their accuracy. All of the constants were determined through highly accurate measurements of the longitudinal velocities, shear velocities, dielectric constants, and density. The velocity values measured for the specimens that were not used to determine the constants agreed well with those calculated from the determined constants, within a difference of +/- 0.20 m/s (+/- 0.004%).

  9. Accurate methods for large molecular systems.

    PubMed

    Gordon, Mark S; Mullin, Jonathan M; Pruitt, Spencer R; Roskop, Luke B; Slipchenko, Lyudmila V; Boatz, Jerry A

    2009-07-23

    Three exciting new methods that address the accurate prediction of processes and properties of large molecular systems are discussed. The systematic fragmentation method (SFM) and the fragment molecular orbital (FMO) method both decompose a large molecular system (e.g., protein, liquid, zeolite) into small subunits (fragments) in very different ways that are designed to both retain the high accuracy of the chosen quantum mechanical level of theory while greatly reducing the demands on computational time and resources. Each of these methods is inherently scalable and is therefore eminently capable of taking advantage of massively parallel computer hardware while retaining the accuracy of the corresponding electronic structure method from which it is derived. The effective fragment potential (EFP) method is a sophisticated approach for the prediction of nonbonded and intermolecular interactions. Therefore, the EFP method provides a way to further reduce the computational effort while retaining accuracy by treating the far-field interactions in place of the full electronic structure method. The performance of the methods is demonstrated using applications to several systems, including benzene dimer, small organic species, pieces of the alpha helix, water, and ionic liquids.

  10. Elucidation of constant current density molecular plating

    NASA Astrophysics Data System (ADS)

    Vascon, A.; Santi, S.; Isse, A. A.; Reich, T.; Drebert, J.; Christ, H.; Düllmann, Ch. E.; Eberhardt, K.

    2012-12-01

    The production of thin layers by means of constant current or constant voltage electrolysis in organic media is commonly known as molecular plating. Despite the fact that this method has been applied for decades and is known to be among the most efficient ones for obtaining quantitative deposition, a full elucidation of the molecular plating is still lacking. In order to get a general understanding of the process and hence set the basis for further improvements of the method, constant current density electrolysis experiments were carried out in a mixture of isopropanol and isobutanol containing millimolar amounts of HNO3 together with [Nd(NO3)3·6H2O] used as a model electrolyte. The process was investigated by considering the influence of different parameters, namely the electrolyte concentrations (i.e., Nd(NO3)3·6H2O: 0.11, 0.22, 0.44 mM, and HNO3: 0.3, 0.4 mM), the applied current (i.e., 2 mA and 6 mA), and the surface roughness of the deposition substrates (i.e., a few tens to several hundreds of nm). The response of the process to changes of these parameters was monitored recording cell potential curves, which showed to be strongly influenced by the investigated conditions. The produced layers were characterized using γ-ray spectroscopy for the evaluation of Nd deposition yields, X-ray photoelectron spectroscopy for chemical analysis of the surfaces, and atomic force microscopy for surface roughness evaluation. X-ray photoelectron spectroscopy results clearly indicate that Nd is present only as Nd3+ on the cathodic surface after molecular plating. The results obtained from this characterization and some basic features inferred from the study of the cell potential curves were used to interpret the different behaviours of the deposition processes as a consequence of the applied variables.

  11. Molecular dynamics at constant Cauchy stress.

    PubMed

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

    2016-05-14

    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.

  12. Accurate quartic and sextic centrifugal distortion constants of CH3CP

    NASA Astrophysics Data System (ADS)

    Bizzocchi, L.; Cludi, L.; Degli Esposti, C.

    2003-03-01

    1-Phosphapropyne has been produced in the gas phase by pyrolysis of a mixture of ethane and phosphorus trichloride. The ground state rotational spectra of the most abundant isotopomer and of the isotopic variants 13CH3CP and CH313CP have been investigated in the millimeter and submillimeter wave regions obtaining very accurate values of the quartic centrifugal distortion constants DJ and DJK and of the sextic distortion constants HJK and HKJ.

  13. Accurate Determination of the Boltzmann Constant by Doppler Spectroscopy Towards a New Definition of the Kelvin

    NASA Astrophysics Data System (ADS)

    Sow, P. L. T.; Merji, S.; Tokunaga, S. K.; Lemarchand, C.; Triki, M.; Borde, C.; Chardonnet, C.; Darquie, B.; Daussy, C.

    2013-06-01

    Accurate molecular spectroscopy in the mid-infrared region allows precision measurements of fundamental constants. For instance, measuring the linewidth of an isolated Doppler-broadened absorption line of ammonia around 10 μm enables a determination of the Boltzmann constant k_{{B}}. We report on our latest measurements. The main systematic effects, including the temperature control, will be discussed and an error budget will be presented in which the global uncertainty on systematic effects is at the level of a few ppm. This is valid provided that data is recorded under the optimized experimental conditions determined by the studies of systematic effects and provided that spectra are fitted to the speed-dependent Voigt profile, identified as the most suitable lineshape for our measurements. A determination of k_{{B}} by Doppler spectroscopy with a combined uncertainty of a few ppm is within reach. This is comparable to the best current uncertainty obtained using acoustic methods and would make a significant contribution to any new value of k_{{B}} determined by the CODATA. Furthermore, having multiple independent measurements at these accuracies opens the possibility of defining the Kelvin by fixing k_{{B}}, an exciting prospect considering the upcoming redefinition of the International System of Units (SI). C. Lemarchand, M. Triki, B. Darquié, C. J. Bordé, C. Chardonnet and C. Daussy, New J. Phys. 13, 073028 (2011). M. Triki, C. Lemarchand, B. Darquié, P. L. T. Sow, V. Roncin, C. Chardonnet, and C. Daussy, Phys. Rev. A 85, 062510 (2012).

  14. 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.

  15. 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.

  16. 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.

  17. 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%.

  18. 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.

  19. Accurate Measurements of Multiple-Bond 13C- 1H Coupling Constants from Phase-Sensitive 2D INEPT Spectra

    NASA Astrophysics Data System (ADS)

    Ding, Keyang

    1999-10-01

    Measurements of multiple-bond 13C-1H coupling constants are of great interest for the assignment of nonprotonated 13C resonances and the elucidation of molecular conformation in solution. Usually, the heteronuclear multiple-bond coupling constants were measured either by the JCH splittings mostly in selective 2D spectra or in 3D spectra, which are time consuming, or by the cross peak intensity analysis in 2D quantitative heteronuclear J correlation spectra (1994, G. Zhu, A. Renwick, and A. Bax, J. Magn. Reson. A 110, 257; 1994, A. Bax, G. W. Vuister, S. Grzesiek, F. Delaglio, A. C. Wang, R. Tschudin, and G. Zhu, Methods Enzymol. 239, 79.), which suffer from the accuracy problem caused by the signal-to-noise ratio and the nonpure absorptive peak patterns. Concerted incrementation of the duration for developing proton antiphase magnetization with respect to carbon-13 and the evolution time for proton chemical shift in different steps in a modified INEPT pulse sequence provides a new method for accurate measurements of heteronuclear multiple-bond coupling constants in a single 2D experiment.

  20. 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.

  1. Accurate mass replacement method for the sediment concentration measurement with a constant volume container

    NASA Astrophysics Data System (ADS)

    Ban, Yunyun; Chen, Tianqin; Yan, Jun; Lei, Tingwu

    2017-04-01

    The measurement of sediment concentration in water is of great importance in soil erosion research and soil and water loss monitoring systems. The traditional weighing method has long been the foundation of all the other measuring methods and instrument calibration. The development of a new method to replace the traditional oven-drying method is of interest in research and practice for the quick and efficient measurement of sediment concentration, especially field measurements. A new method is advanced in this study for accurately measuring the sediment concentration based on the accurate measurement of the mass of the sediment-water mixture in the confined constant volume container (CVC). A sediment-laden water sample is put into the CVC to determine its mass before the CVC is filled with water and weighed again for the total mass of the water and sediments in the container. The known volume of the CVC, the mass of sediment-laden water, and sediment particle density are used to calculate the mass of water, which is replaced by sediments, therefore sediment concentration of the sample is calculated. The influence of water temperature was corrected by measuring water density to determine the temperature of water before measurements were conducted. The CVC was used to eliminate the surface tension effect so as to obtain the accurate volume of water and sediment mixture. Experimental results showed that the method was capable of measuring the sediment concentration from 0.5 up to 1200 kg m‑3. A good liner relationship existed between the designed and measured sediment concentrations with all the coefficients of determination greater than 0.999 and the averaged relative error less than 0.2%. All of these seem to indicate that the new method is capable of measuring a full range of sediment concentration above 0.5 kg m‑3 to replace the traditional oven-drying method as a standard method for evaluating and calibrating other methods.

  2. 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.

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

    PubMed

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

    2016-08-07

    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.

  4. 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.

  5. 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.

  6. Anharmonic force constants extracted from first-principles molecular dynamics: applications to heat transfer simulations.

    PubMed

    Tadano, T; Gohda, Y; Tsuneyuki, S

    2014-06-04

    A systematic method to calculate anharmonic force constants of crystals is presented. The method employs the direct-method approach, where anharmonic force constants are extracted from the trajectory of first-principles molecular dynamics simulations at high temperature. The method is applied to Si where accurate cubic and quartic force constants are obtained. We observe that higher-order correction is crucial to obtain accurate force constants from the trajectory with large atomic displacements. The calculated harmonic and anharmonic force constants are, then, combined with the Boltzmann transport equation (BTE) and non-equilibrium molecular dynamics (NEMD) methods in calculating the thermal conductivity. The BTE approach successfully predicts the lattice thermal conductivity of bulk Si, whereas NEMD shows considerable underestimates. To evaluate the linear extrapolation method employed in NEMD to estimate bulk values, we analyze the size dependence in NEMD based on BTE calculations. We observe strong nonlinearity in the size dependence of NEMD in Si, which can be ascribed to acoustic phonons having long mean-free-paths and carrying considerable heat. Subsequently, we also apply the whole method to a thermoelectric material Mg2Si and demonstrate the reliability of the NEMD method for systems with low thermal conductivities.

  7. 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.

  8. S3 HMBC hetero: Spin-State-Selective HMBC for accurate measurement of long-range heteronuclear coupling constants

    NASA Astrophysics Data System (ADS)

    Hoeck, Casper; Gotfredsen, Charlotte H.; Sørensen, Ole W.

    2017-02-01

    A novel method, Spin-State-Selective (S3) HMBC hetero, for accurate measurement of heteronuclear coupling constants is introduced. The method extends the S3 HMBC technique for measurement of homonuclear coupling constants by appending a pulse sequence element that interchanges the polarization in 13C-1H methine pairs. This amounts to converting the spin-state selectivity from 1H spin states to 13C spin states in the spectra of long-range coupled 1H spins, allowing convenient measurement of heteronuclear coupling constants similar to other S3 or E.COSY-type methods. As usual in this type of techniques, the accuracy of coupling constant measurement is independent of the size of the coupling constant of interest. The merits of the new method are demonstrated by application to vinyl acetate, the alkaloid strychnine, and the carbohydrate methyl β-maltoside.

  9. 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.

  10. 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.

  11. Stresses and elastic constants of crystalline sodium, from molecular dynamics

    SciTech Connect

    Schiferl, S.K.

    1985-02-01

    The stresses and the elastic constants of bcc sodium are calculated by molecular dynamics (MD) for temperatures to T = 340K. The total adiabatic potential of a system of sodium atoms is represented by pseudopotential model. The resulting expression has two terms: a large, strictly volume-dependent potential, plus a sum over ion pairs of a small, volume-dependent two-body potential. The stresses and the elastic constants are given as strain derivatives of the Helmholtz free energy. The resulting expressions involve canonical ensemble averages (and fluctuation averages) of the position and volume derivatives of the potential. An ensemble correction relates the results to MD equilibrium averages. Evaluation of the potential and its derivatives requires the calculation of integrals with infinite upper limits of integration, and integrand singularities. Methods for calculating these integrals and estimating the effects of integration errors are developed. A method is given for choosing initial conditions that relax quickly to a desired equilibrium state. Statistical methods developed earlier for MD data are extended to evaluate uncertainties in fluctuation averages, and to test for symmetry. 45 refs., 10 figs., 4 tabs.

  12. Investigation of the Composition and Formation Constant of Molecular Complexes

    PubMed Central

    Sahai, R.; Loper, G. L.; Lin, S. H.; Eyring, H.

    1974-01-01

    It has been the purpose of the present paper to investigate and explore the conditions under which the linear relation between Δ/CD0 and Δ in the Hanna-Ashbaugh-Foster-Fyfe equation for the evaluation of equilibrium constants holds, (CD0 is initial concentration of a donor and Δ is the observed chemical shift relative to the chemical shift of the acceptor) to obtain the equation representing the exact linear relation between Δ/CD0 and Δ, when the linear relation between Δ/CD0 and Δ holds, and to discuss how to use the Job method in nuclear magnetic resonance measurements to determine the stoichiometry of molecular complexes. We have found that the conventional belief that CD0 should always be chosen to be much greater than CA0 (initial concentration of acceptor) is not necessarily always true and the exact linear relation between Δ/CD0 and Δ is represented by the equation Δ/CD0 = K1Δ0/(1 + K1CA0) - K1Δ/(1 + K1CA0)2, where K1 is the formation constant of the complex. It is shown that in the Job method of nuclear magnetic resonance measurements one has to plot ΔCA0 against the mole fraction, and the mole fraction at the maximum should give us the composition of the complex. Theoretical results have been verified experimentally on the weak interaction between naphthalene and methyl iodide. PMID:16592155

  13. Benchmarking density-functional theory calculations of NMR shielding constants and spin-rotation constants using accurate coupled-cluster calculations.

    PubMed

    Teale, Andrew M; Lutnæs, Ola B; Helgaker, Trygve; Tozer, David J; Gauss, Jürgen

    2013-01-14

    Accurate sets of benchmark nuclear-magnetic-resonance shielding constants and spin-rotation constants are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the calculated coupled-cluster constants is established by a careful comparison with experimental data, taking into account zero-point vibrational corrections. Coupled-cluster basis-set convergence is analyzed and extrapolation techniques are employed to estimate basis-set-limit quantities, thereby establishing an accurate benchmark data set. Together with the set provided for rotational g-tensors and magnetizabilities in our previous work [O. B. Lutnæs, A. M. Teale, T. Helgaker, D. J. Tozer, K. Ruud, and J. Gauss, J. Chem. Phys. 131, 144104 (2009)], it provides a substantial source of consistently calculated high-accuracy data on second-order magnetic response properties. The utility of this benchmark data set is demonstrated by examining a wide variety of Kohn-Sham exchange-correlation functionals for the calculation of these properties. None of the existing approximate functionals provide an accuracy competitive with that provided by CCSD or CCSD(T) theory. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of Kohn-Sham calculations constrained to give the same electronic density. Routes to future improvements are discussed in light of this comparison.

  14. 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.

  15. Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer.

    PubMed

    Donnini, Serena; Ullmann, R Thomas; Groenhof, Gerrit; Grubmüller, Helmut

    2016-03-08

    In constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approach to maintain neutrality of the simulation box in constant pH molecular dynamics simulations, while maintaining an accurate description of all protonation fluctuations. Specifically, we introduce a proton buffer that, like a buffer in experiment, can exchange protons with the biomolecule enabling its charge to fluctuate. To keep the total charge of the system constant, the uptake and release of protons by the buffer are coupled to the titration of the biomolecule with a constraint. We find that, because the fluctuation of the total charge (number of protons) of a typical biomolecule is much smaller than the number of titratable sites of the biomolecule, the number of buffer sites required to maintain overall charge neutrality without compromising the charge fluctuations of the biomolecule, is typically much smaller than the number of titratable sites, implying markedly enhanced simulation and sampling efficiency.

  16. Nuclear magnetic shielding constants of liquid water: Insights from hybrid quantum mechanics/molecular mechanics models

    NASA Astrophysics Data System (ADS)

    Kongsted, Jacob; Nielsen, Christian B.; Mikkelsen, Kurt V.; Christiansen, Ove; Ruud, Kenneth

    2007-01-01

    We present a gauge-origin independent method for the calculation of nuclear magnetic shielding tensors of molecules in a structured and polarizable environment. The method is based on a combination of density functional theory (DFT) or Hartree-Fock wave functions with molecular mechanics. The method is unique in the sense that it includes three important properties that need to be fulfilled in accurate calculations of nuclear magnetic shielding constants: (i) the model includes electron correlation effects, (ii) the model uses gauge-including atomic orbitals to give gauge-origin independent results, and (iii) the effect of the environment is treated self-consistently using a discrete reaction-field methodology. The authors present sample calculations of the isotropic nuclear magnetic shielding constants of liquid water based on a large number of solute-solvent configurations derived from molecular dynamics simulations employing potentials which treat solvent polarization either explicitly or implicitly. For both the O17 and H1 isotropic shielding constants the best predicted results compare fairly well with the experimental data, i.e., they reproduce the experimental solvent shifts to within 4ppm for the O17 shielding and 1ppm for the H1 shielding.

  17. Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pKa Calculations.

    PubMed

    Dobrev, Plamen; Donnini, Serena; Groenhof, Gerrit; Grubmüller, Helmut

    2017-01-10

    Correct protonation of titratable groups in biomolecules is crucial for their accurate description by molecular dynamics simulations. In the context of constant pH simulations, an additional protonation degree of freedom is introduced for each titratable site, allowing the protonation state to change dynamically with changing structure or electrostatics. Here, we extend previous approaches for an accurate description of chemically coupled titrating sites. A second reaction coordinate is used to switch between two tautomeric states of an amino acid with chemically coupled titratable sites, such as aspartate (Asp), glutamate (Glu), and histidine (His). To this aim, we test a scheme involving three protonation states. To facilitate charge neutrality as required for periodic boundary conditions and Particle Mesh Ewald (PME) electrostatics, titration of each respective amino acid is coupled to a "water" molecule that is charged in the opposite direction. Additionally, a force field modification for Amber99sb is introduced and tested for the description of carboxyl group protonation. Our three states model is tested by titration simulations of Asp, Glu, and His, yielding a good agreement, reproducing the correct geometry of the groups in their different protonation forms. We further show that the ion concentration change due to the neutralizing "water" molecules does not significantly affect the protonation free energies of the titratable groups, suggesting that the three states model provides a good description of biomolecular dynamics at constant pH.

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

    PubMed

    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 B0 = 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 B0 value, RR-RCS measurements in a room temperature gas cell give the rotational constants Bv of the five lowest-lying thermally populated vibrationally excited states ν7/8, ν9, ν11/12, ν13, and ν14/15. Their Bv constants differ from B0 by between -1.02 MHz and +2.23 MHz. Combining the B0 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 re(C-C) = 1.3866(3) Å and re(C-F) = 1.3244(4) Å. These agree with the CCSD(T)/wCVQZ re bond lengths calculated by Demaison et al. within ±0.0005 Å. We also calculate the semi-experimental thermally averaged bond lengths rg(C-C)=1.3907(3) Å and rg(C-F)=1.3250(4) Å. These are at least ten times more accurate than two sets of experimental gas-phase electron diffraction rg bond lengths measured in the 1960s.

  19. On the accurate molecular dynamics analysis of biological molecules

    NASA Astrophysics Data System (ADS)

    Yamashita, Takefumi

    2016-12-01

    As the evolution of computational technology has now enabled long molecular dynamics (MD) simulation, the evaluation of many physical properties shows improved convergence. Therefore, we can examine the detailed conditions of MD simulations and perform quantitative MD analyses. In this study, we address the quantitative and accuracy aspects of MD simulations using two example systems. First, it is found that several conditions of the MD simulations influence the area/lipid of the lipid bilayer. Second, we successfully detect the small but important differences in antibody motion between the antigen-bound and unbound states.

  20. Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study

    PubMed Central

    Williams, Sarah L; Blachly, Patrick G; McCammon, J Andrew

    2011-01-01

    A constant pH molecular dynamics method has been used in the blind prediction of pKa values of titratable residues in wild type and mutated structures of the Staphylococcal nuclease (SNase) protein. The predicted values have been subsequently compared to experimental values provided by the laboratory of García-Moreno. CpHMD performs well in predicting the pKa of solvent-exposed residues. For residues in the protein interior, the CpHMD method encounters some difficulties in reaching convergence and predicting the pKa values for residues having strong interactions with neighboring residues. These results show the need to accurately and sufficiently sample conformational space in order to obtain pKa values consistent with experimental results. PMID:22072520

  1. 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)

  2. 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…

  3. 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.

  4. 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.

  5. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

    PubMed

    De Jong, Djurre H; Schäfer, Lars V; De Vries, Alex H; Marrink, Siewert J; Berendsen, Herman J C; Grubmüller, Helmut

    2011-07-15

    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.

  6. 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.

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

    PubMed Central

    Yogurtcu, Osman N.; Johnson, Margaret E.

    2015-01-01

    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

  8. 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.

  9. 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.

  10. Accurate analytical measurements in the atomic force microscope: a microfabricated spring constant standard potentially traceable to the SI

    NASA Astrophysics Data System (ADS)

    Cumpson, Peter J.; Hedley, John

    2003-12-01

    Calibration of atomic force microscope (AFM) cantilevers is necessary for the measurement of nanonewton and piconewton forces, which are critical to analytical applications of AFM in the analysis of polymer surfaces, biological structures and organic molecules at nanoscale lateral resolution. We have developed a compact and easy-to-use reference artefact for this calibration, using a method that allows traceability to the SI (Système International). Traceability is crucial to ensure that force measurements by AFM are comparable to those made by optical tweezers and other methods. The new non-contact calibration method measures the spring constant of these artefacts, by a combination of electrical measurements and Doppler velocimetry. The device was fabricated by silicon surface micromachining. The device allows AFM cantilevers to be calibrated quite easily by the 'cantilever-on-reference' method, with our reference device having a spring constant uncertainty of around ± 5% at one standard deviation. A simple substitution of the analogue velocimeter used in this work with a digital model should reduce this uncertainty to around ± 2%. Both are significant improvements on current practice, and allow traceability to the SI for the first time at these nanonewton levels.

  11. S(3) HMBC: Spin-State-Selective HMBC for accurate measurement of homonuclear coupling constants. Application to strychnine yielding thirteen hitherto unreported J(HH).

    PubMed

    Kjaerulff, Louise; Benie, Andrew J; Hoeck, Casper; Gotfredsen, Charlotte H; Sørensen, Ole W

    2016-02-01

    A novel method, Spin-State-Selective (S(3)) HMBC, for accurate measurement of homonuclear coupling constants is introduced. As characteristic for S(3) techniques, S(3) HMBC yields independent subspectra corresponding to particular passive spin states and thus allows determination of coupling constants between detected spins and homonuclear coupling partners along with relative signs. In the presented S(3) HMBC experiment, spin-state selection occurs via large one-bond coupling constants ensuring high editing accuracy and unequivocal sign determination of the homonuclear long-range relative to the associated one-bond coupling constant. The sensitivity of the new experiment is comparable to that of regular edited HMBC and the accuracy of the J/RDC measurement is as usual for E.COSY and S(3)-type experiments independent of the size of the homonuclear coupling constant of interest. The merits of the method are demonstrated by an application to strychnine where thirteen J(HH) coupling constants not previously reported could be measured.

  12. On the errors in molecular dipole moments derived from accurate diffraction data.

    PubMed

    Coppens; Volkov; Abramov; Koritsanszky

    1999-09-01

    The error in the molecular dipole moment as derived from accurate X-ray diffraction data is shown to be origin dependent in the general case. It is independent of the choice of origin if an electroneutrality constraint is introduced, even when additional constraints are applied to the monopole populations. If a constraint is not applied to individual moieties, as is appropriate for multicomponent crystals or crystals containing molecular ions, the geometric center of the entity considered is a suitable choice of origin for the error treatment.

  13. Molecular dynamics simulation of vapour-liquid nucleation of water with constant energy

    NASA Astrophysics Data System (ADS)

    Duška, Michal; Němec, Tomáš; Hrubý, Jan; Vinš, Václav; Planková, Barbora

    2015-05-01

    The paper describes molecular dynamics study of nucleation of water in NVE ensemble. The numerical simulation was performed with the DL_POLY. The metastable steam consisting of 10976 water molecules with TIP4P/2005 potential was driven on the desired energy level by a simulation at constant temperature, and then the nucleation at constant energy was studied for several tens of nanoseconds, which was sufficient for clusters to evolve at hundred molecules size. The results were compared with the previously published results and the classical nucleation theory predictions.

  14. 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.

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

    DOE PAGES

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

    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

    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.

  17. Direct Molecular Simulation of Gradient-Driven Diffusion of Large Molecules using Constant Pressure

    SciTech Connect

    Heffelfinger, G.S.; Thompson, A.P.

    1998-12-23

    Dual control volume grand canonical molecular dynamics (DCV-GCMD) is a boundary-driven non-equilibrium molecular dynamics technique for simulating gradient driven diffusion in multi-component systems. Two control volumes are established at opposite ends of the simulation box. Constant temperature and chemical potential of diffusing species are imposed in the control volumes. This results in stable chemical potential gradients and steady-state diffusion fluxes in the region between the control volumes. We present results and detailed analysis for a new constant-pressure variant of the DCV-GCMD method in which one of the diffusing species for which a steady-state diffusion flux exists does not have to be inserted or deIeted. Constant temperature, pressure and chemical potential of all diffusing species except one are imposed in the control volumes. The constant-pressure method can be applied to situations in which insertion and deletion of large molecules would be prohibitively difficult. As an exampIe, we used the method to shnulate diffusion in a biruuy mixture of spherical particles with a 2:1 size ratio. Steady-state diffusion fluxes of both diffbsi.ng species were established. The constant-pressure diffision coefficients agreed closely with the results of the standard constant-volume calculations. In addition, we show how the concentration, chemical potential and flux profiles can be used to calculate kwd binary and Maxwell-Stefim diffusion coefficients. In the case of the 2:1 size ratio mixture, we found that the binary dlffision coefficients were asymmetric and composition dependent, whereas the Maxwell-Stefan diffision coefficients changed very little with composition and were symmetric. This last result verified that the Gibbs-Duhem relation was satisfied locally, thus validating the assumption of local equilibrium.

  18. CAST: a new program package for the accurate characterization of large and flexible molecular systems.

    PubMed

    Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

    2014-09-15

    The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request.

  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 phosphoregulation of kinetochore–microtubule affinity requires unconstrained molecular interactions

    PubMed Central

    Zaytsev, Anatoly V.; Sundin, Lynsie J.R.; DeLuca, Keith F.

    2014-01-01

    Accurate chromosome segregation relies on dynamic interactions between microtubules (MTs) and the NDC80 complex, a major kinetochore MT-binding component. Phosphorylation at multiple residues of its Hec1 subunit may tune kinetochore–MT binding affinity for diverse mitotic functions, but molecular details of such phosphoregulation remain elusive. Using quantitative analyses of mitotic progression in mammalian cells, we show that Hec1 phosphorylation provides graded control of kinetochore–MT affinity. In contrast, modeling the kinetochore interface with repetitive MT binding sites predicts a switchlike response. To reconcile these findings, we hypothesize that interactions between NDC80 complexes and MTs are not constrained, i.e., the NDC80 complexes can alternate their binding between adjacent kinetochore MTs. Experiments using cells with phosphomimetic Hec1 mutants corroborate predictions of such a model but not of the repetitive sites model. We propose that accurate regulation of kinetochore–MT affinity is driven by incremental phosphorylation of an NDC80 molecular “lawn,” in which the NDC80–MT bonds reorganize dynamically in response to the number and stability of MT attachments. PMID:24982430

  1. Sub-Doppler millimetre-wave spectroscopy of DBS and HBS: accurate values of nuclear electric and magnetic hyperfine structure constants.

    PubMed

    Bizzocchi, Luca; Esposti, Claudio Degli; Dore, Luca

    2008-02-07

    The unstable thioborine molecule and its deuterated variant have been produced by a high-temperature reaction between hydrogen sulfide and crystalline boron at 1100 degrees C in a flow system. Five rotational transitions from J = 2 <-- 1, to J = 6 <-- 5 have been recorded with sub-Doppler resolution for the vibrational ground state of H10/11BS and D10/11BS using the Lamb-dip technique. The hyperfine structure due to the electric quadrupole interaction of deuterium nucleus has been resolved yielding the first experimental determination of the deuterium quadrupole coupling constant in thioborine, which is 0.1403(75) MHz in D11 BS and 0.1360(38) MHz in D10BS. Fairly accurate values of 10/11B spin-rotation coupling constants and of the hydrogen-boron spin-spin coupling constants have also been determined. Additionally, the hyperfine structure of the rotational lines for the nu2 = 1 excited state has been investigated, thus obtaining information on the asymmetry of the electric field gradient at the B nucleus in the bending state.

  2. 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.

  3. A hierarchical approach to accurate predictions of macroscopic thermodynamic behavior from quantum mechanics and molecular simulations

    NASA Astrophysics Data System (ADS)

    Garrison, Stephen L.

    2005-07-01

    The combination of molecular simulations and potentials obtained from quantum chemistry is shown to be able to provide reasonably accurate thermodynamic property predictions. Gibbs ensemble Monte Carlo simulations are used to understand the effects of small perturbations to various regions of the model Lennard-Jones 12-6 potential. However, when the phase behavior and second virial coefficient are scaled by the critical properties calculated for each potential, the results obey a corresponding states relation suggesting a non-uniqueness problem for interaction potentials fit to experimental phase behavior. Several variations of a procedure collectively referred to as quantum mechanical Hybrid Methods for Interaction Energies (HM-IE) are developed and used to accurately estimate interaction energies from CCSD(T) calculations with a large basis set in a computationally efficient manner for the neon-neon, acetylene-acetylene, and nitrogen-benzene systems. Using these results and methods, an ab initio, pairwise-additive, site-site potential for acetylene is determined and then improved using results from molecular simulations using this initial potential. The initial simulation results also indicate that a limited range of energies important for accurate phase behavior predictions. Second virial coefficients calculated from the improved potential indicate that one set of experimental data in the literature is likely erroneous. This prescription is then applied to methanethiol. Difficulties in modeling the effects of the lone pair electrons suggest that charges on the lone pair sites negatively impact the ability of the intermolecular potential to describe certain orientations, but that the lone pair sites may be necessary to reasonably duplicate the interaction energies for several orientations. Two possible methods for incorporating the effects of three-body interactions into simulations within the pairwise-additivity formulation are also developed. A low density

  4. 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.

  5. Accurate determination of plasmonic fields in molecular junctions by current rectification at optical frequencies.

    PubMed

    Arielly, Rani; Ofarim, Ayelet; Noy, Gilad; Selzer, Yoram

    2011-07-13

    Current rectification, i.e., induction of dc current by oscillating electromagnetic fields, is demonstrated in molecular junctions at an optical frequency. The magnitude of rectification is used to accurately determine the effective oscillating potentials in the junctions induced by the irradiating laser. Since the gap size of the junctions used in this study is precisely determined by the length of the embedded molecules, the oscillating potential can be used to calculate the plasmonic enhancement of the electromagnetic field in the junctions. With a set of junctions based on alkyl thiolated molecules with identical HOMO-LUMO gap and different lengths, an exponential dependence of the plasmonic field enhancement on gap size is observed.

  6. 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.

  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. 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.

  9. 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

  10. 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).

  11. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    PubMed

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  12. Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins.

    PubMed

    O'Brien, Edward P; Brooks, Bernard R; Thirumalai, D

    2009-05-05

    Experiments show that for many two-state folders the free energy of the native state, DeltaG(ND)([C]), changes linearly as the denaturant concentration, [C], is varied. The slope {m = [dDeltaG(ND)([C])]/(d[C])}, is nearly constant. According to the transfer model, the m-value is associated with the difference in the surface area between the native (N) and denatured (D) state, which should be a function of DeltaR(g)(2), the difference in the square of the radius of gyration between the D and N states. Single-molecule experiments show that the R(g) of the structurally heterogeneous denatured state undergoes an equilibrium collapse transition as [C] decreases, which implies m also should be [C]-dependent. We resolve the conundrum between constant m-values and [C]-dependent changes in R(g) using molecular simulations of a coarse-grained representation of protein L, and the molecular transfer model, for which the equilibrium folding can be accurately calculated as a function of denaturant (urea) concentration. In agreement with experiment, we find that over a large range of denaturant concentration (>3 M) the m-value is a constant, whereas under strongly renaturing conditions (<3 M), it depends on [C]. The m-value is a constant above [C] > 3 M because the [C]-dependent changes in the surface area of the backbone groups, which make the largest contribution to m, are relatively narrow in the denatured state. The burial of the backbone and hydrophobic side chains gives rise to substantial surface area changes below [C] < 3 M, leading to collapse in the denatured state of protein L. Dissection of the contribution of various amino acids to the total surface area change with [C] shows that both the sequence context and residual structure are important. There are [C]-dependent variations in the surface area for chemically identical groups such as the backbone or Ala. Consequently, the midpoints of transition of individual residues vary significantly (which we call the Holtzer

  13. 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.

  14. Acidic range titration of HEWL using a constant-pH molecular dynamics method.

    PubMed

    Machuqueiro, Miguel; Baptista, António M

    2008-07-01

    In this work, we present the first application to a protein of the stochastic constant-pH molecular dynamics (MD) method with the inclusion of proton tautomerism. The acidic titration of HEWL was performed under different conditions. Both generalized reaction field (GRF) and particle mesh Ewald (PME) methods were used in the treatment of the long range electrostatics and, even though the PME simulations revealed to be more stable, the better results were obtained using GRF (pK(a) RMSD of 0.82 for GRF and 1.13 for PME). The results using PME at different dielectric constants (2, 4, and 8) also revealed that there was no significant improvement in pK(a)'s prediction upon increasing the dielectric constant. The secondary structure analysis of HEWL revealed a remarkably stable protein in the acidic pH range. The beta-sheet strands (unlike the alpha-helices) seem to be destabilized upon pH decrease, suggesting that the beta-domain is less stable than the alpha-domain. The four principal alpha-helices were also ordered according to their stability in the acidic pH range and the results (4 < 1 < 2 approximately = 3) were consistent with the ones obtained in thermal denaturation studies.

  15. 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.

  16. 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.

  17. 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.

  18. The estimation of tumor cell percentage for molecular testing by pathologists is not accurate.

    PubMed

    Smits, Alexander J J; Kummer, J Alain; de Bruin, Peter C; Bol, Mijke; van den Tweel, Jan G; Seldenrijk, Kees A; Willems, Stefan M; Offerhaus, G Johan A; de Weger, Roel A; van Diest, Paul J; Vink, Aryan

    2014-02-01

    Molecular pathology is becoming more and more important in present day pathology. A major challenge for any molecular test is its ability to reliably detect mutations in samples consisting of mixtures of tumor cells and normal cells, especially when the tumor content is low. The minimum percentage of tumor cells required to detect genetic abnormalities is a major variable. Information on tumor cell percentage is essential for a correct interpretation of the result. In daily practice, the percentage of tumor cells is estimated by pathologists on hematoxylin and eosin (H&E)-stained slides, the reliability of which has been questioned. This study aimed to determine the reliability of estimated tumor cell percentages in tissue samples by pathologists. On 47 H&E-stained slides of lung tumors a tumor area was marked. The percentage of tumor cells within this area was estimated independently by nine pathologists, using categories of 0-5%, 6-10%, 11-20%, 21-30%, and so on, until 91-100%. As gold standard, the percentage of tumor cells was counted manually. On average, the range between the lowest and the highest estimate per sample was 6.3 categories. In 33% of estimates, the deviation from the gold standard was at least three categories. The mean absolute deviation was 2.0 categories (range between observers 1.5-3.1 categories). There was a significant difference between the observers (P<0.001). If 20% of tumor cells were considered the lower limit to detect a mutation, samples with an insufficient tumor cell percentage (<20%) would have been estimated to contain enough tumor cells in 27/72 (38%) observations, possibly causing false negative results. In conclusion, estimates of tumor cell percentages on H&E-stained slides are not accurate, which could result in misinterpretation of test results. Reliability could possibly be improved by using a training set with feedback.

  19. Recent development and application of constant pH molecular dynamics.

    PubMed

    Chen, Wei; Morrow, Brian H; Shi, Chuanyin; Shen, Jana K

    2014-01-01

    Solution pH is a critical environmental factor for chemical and biological processes. Over the last decade, significant efforts have been made in the development of constant pH molecular dynamics (pHMD) techniques for gaining detailed insights into pH-coupled dynamical phenomena. In this article we review the advancement of this field in the past five years, placing a special emphasis on the development of the all-atom continuous pHMD technique. We discuss various applications, including the prediction of pKa shifts for proteins, nucleic acids and surfactant assemblies, elucidation of pH-dependent population shifts, protein-protein and protein-RNA binding, as well as the mechanisms of pH-dependent self-assembly and phase transitions of surfactants and peptides. We also discuss future directions for the further improvement of the pHMD techniques.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. Quantitative structure-property relationships for predicting Henry's law constant from molecular structure.

    PubMed

    Dearden, John C; Schüürmann, Gerrit

    2003-08-01

    Various models are available for the prediction of Henry's law constant (H) or the air-water partition coefficient (Kaw), its dimensionless counterpart. Incremental methods are based on structural features such as atom types, bond types, and local structural environments; other regression models employ physicochemical properties, structural descriptors such as connectivity indices, and descriptors reflecting the electronic structure. There are also methods to calculate H from the ratio of vapor pressure (p(v)) and water solubility (S(w)) that in turn can be estimated from molecular structure, and quantum chemical continuum-solvation models to predict H via the solvation-free energy (deltaG(s)). This review is confined to methods that calculate H from molecular structure without experimental information and covers more than 40 methods published in the last 26 years. For a subset of eight incremental methods and four continuum-solvation models, a comparative analysis of their prediction performance is made using a test set of 700 compounds that includes a significant number of more complex and drug-like chemical structures. The results reveal substantial differences in the application range as well as in the prediction capability, a general decrease in prediction performance with decreasing H, and surprisingly large individual prediction errors, which are particularly striking for some quantum chemical schemes. The overall best-performing method appears to be the bond contribution method as implemented in the HENRYWIN software package, yielding a predictive squared correlation coefficient (q2) of 0.87 and a standard error of 1.03 log units for the test set.

  7. Perspective: tipping the scales: search for drifting constants from molecular spectra.

    PubMed

    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(-14)/yr from a laboratory experiment performed in the present epoch. On a cosmological time scale, the variation is limited to ∣Δμ∕μ∣ < 10(-5) for look-back times of 10-12× 10(9) years and to ∣Δμ∕μ∣ < 10(-7) for look-back times of 7× 10(9) years. The last result, obtained from high-redshift observation of methanol, translates into μ̇/μ=(1.4±1.4)×10(-17)/yr if a linear rate of change is assumed.

  8. Simulating botulinum neurotoxin with constant pH molecular dynamics in Generalized Born implicit solvent

    NASA Astrophysics Data System (ADS)

    Chen, Yongzhi; Chen, Xin; Deng, Yuefan

    2007-07-01

    A new method was proposed by Mongan et al. for constant pH molecular dynamics simulation and was implemented in AMBER 8 package. Protonation states are modeled with different charge sets, and titrating residues are sampled from a Boltzmann distribution of protonation states. The simulation periodically adopts Monte Carlo sampling based on Generalized Born (GB) derived energies. However, when this approach was applied to a bio-toxin, Botulinum Neurotoxin Type A (BoNT/A) at pH 4.4, 4.7, 5.0, 6.8 and 7.2, the pK predictions yielded by the method were inconsistent with the experimental values. The systems being simulated were divergent. Furthermore, the system behaviors in a very weak acidic solution (pH 6.8) and in a very weak basic solution (pH 7.2) were significantly different from the neutral case (pH 7.0). Hence, we speculate this method may require further study for modeling large biomolecule.

  9. 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.

  10. An accurate theoretical description for electronic transport properties of single molecular junctions

    NASA Astrophysics Data System (ADS)

    Luo, Yi

    2002-03-01

    We have developed a new theoretical approach to characterize the electron transport process in molecular devices based on the elastic-scattering Green's function theory in connection with the hybrid density functional theory without using any fitting parameters. Two molecular devices with benzene-1,4-dithiol and octanedithiol molecules embedded between two gold electrodes have been studied. The calculated current-voltage characteristics are in very good agreement with existing experimental results reported by Reed et. al for benzene-1,4-dithiol [Science, 278(1997) 252] and by Cui et al. for octanedithiol [Science, 294(2001) 571]. Our approach is very straightforward and can apply to quite large systems. Most importantly, it provides a reliable way to design and optimize molecular devices theoretically, thereby avoiding extremely difficult, time consuming laboratory tests.

  11. Accurate determination of pyridine-poly(amidoamine) dendrimer absolute binding constants with the OPLS-AA force field and direct integration of radial distribution functions.

    PubMed

    Peng, Yong; Kaminski, George A

    2005-08-11

    OPLS-AA force field and direct integration of intermolecular radial distribution functions (RDF) were employed to calculate absolute binding constants of pyridine molecules to amino group (NH2) and amide group hydrogen atoms in and first generation poly(amidoamine) dendrimers in chloroform. The average errors in the absolute and relative association constants, as predicted with the calculations, are 14.1% and 10.8%, respectively, which translate into ca. 0.08 and 0.06 kcal/mol errors in the absolute and relative binding free energies. We believe that this level of accuracy proves the applicability of the OPLS-AA, force field, in combination with the direct RDF integration, to reproducing and predicting absolute intermolecular association constants of low magnitudes (ca. 0.2-2.0 range).

  12. Accurate Determination of Pyridine -- Poly (Amidoamine) Dendrimer Absolute Binding Constants with the OPLS-AA Force Field and Direct Integration of Radial Distribution Functions

    NASA Astrophysics Data System (ADS)

    Peng, Yong; Kaminski, George

    2006-03-01

    OPLS-AA force field and direct integration of intermolecular radial distribution functions (RDF) were employed to calculate absolute binding constants of pyridine molecules to NH2 and amide group hydrogen atoms in 0th and 1st generation poly (amidoamine) dendrimers in chloroform. The average errors in the absolute and relative association constants, as predicted with the calculations, are 14.1% and 10.8%, respectively, which translate into ca. 0.08 kcal/mol and 0.06 kcal/mol errors in the absolute and relative binding free energies. We believe that this level of accuracy proves the applicability of the OPLS-AA, force field, in combination with the direct RDF integration, to reproducing and predicting absolute intermolecular association constants of low magnitudes (ca. 0.2 -- 2.0 range).

  13. Communication: Constant uncertainty molecular dynamics: A simple and efficient algorithm to incorporate quantum nature into a real-time molecular dynamics simulation.

    PubMed

    Hasegawa, Taisuke

    2016-11-07

    We propose a novel molecular dynamics (MD) algorithm for approximately dealing with a nuclear quantum dynamics in a real-time MD simulation. We have found that real-time dynamics of the ensemble of classical particles acquires quantum nature by introducing a constant quantum mechanical uncertainty constraint on its classical dynamics. The constant uncertainty constraint is handled by the Lagrange multiplier method and implemented into a conventional MD algorithm. The resulting constant uncertainty molecular dynamics (CUMD) is applied to the calculation of quantum position autocorrelation functions on quartic and Morse potentials. The test calculations show that CUMD gives better performance than ring-polymer MD because of the inclusion of the quantum zero-point energy during real-time evolution as well as the quantum imaginary-time statistical effect stored in an initial condition. The CUMD approach will be a possible starting point for new real-time quantum dynamics simulation in condensed phase.

  14. Communication: Constant uncertainty molecular dynamics: A simple and efficient algorithm to incorporate quantum nature into a real-time molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Hasegawa, Taisuke

    2016-11-01

    We propose a novel molecular dynamics (MD) algorithm for approximately dealing with a nuclear quantum dynamics in a real-time MD simulation. We have found that real-time dynamics of the ensemble of classical particles acquires quantum nature by introducing a constant quantum mechanical uncertainty constraint on its classical dynamics. The constant uncertainty constraint is handled by the Lagrange multiplier method and implemented into a conventional MD algorithm. The resulting constant uncertainty molecular dynamics (CUMD) is applied to the calculation of quantum position autocorrelation functions on quartic and Morse potentials. The test calculations show that CUMD gives better performance than ring-polymer MD because of the inclusion of the quantum zero-point energy during real-time evolution as well as the quantum imaginary-time statistical effect stored in an initial condition. The CUMD approach will be a possible starting point for new real-time quantum dynamics simulation in condensed phase.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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 103-105 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.

  16. 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.

  17. 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.

  18. Establishment of an accurate and fast detection method using molecular beacons in loop-mediated isothermal amplification assay

    PubMed Central

    Liu, Wei; Huang, Simo; Liu, Ningwei; Dong, Derong; Yang, Zhan; Tang, Yue; Ma, Wen; He, Xiaoming; Ao, Da; Xu, Yaqing; Zou, Dayang; Huang, Liuyu

    2017-01-01

    This study established a constant-temperature fluorescence quantitative detection method, combining loop-mediated isothermal amplification (LAMP) with molecular beacons. The advantages of LAMP are its convenience and efficiency, as it does not require a thermocycler and results are easily visualized by the naked eye. However, a major disadvantage of current LAMP techniques is the use of indirect evaluation methods (e.g., electrophoresis, SYBR Green I dye, precipitation, hydroxynaphthol blue dye, the turbidimetric method, calcein/Mn2+ dye, and the composite probe method), which cannot distinguish between the desired products and products of nonspecific amplification, thereby leading to false positives. Use of molecular beacons avoids this problem because molecular beacons produce fluorescence signals only when binding to target DNA, thus acting as a direct indicator of amplification products. Our analyses determined the optimal conditions for molecular beacons as an evaluation tool in LAMP: beacon length of 25–45 bp, beacon concentration of 0.6–1 pmol/μL, and reaction temperature of 60–65 °C. In conclusion, we validated a novel molecular beacon loop-mediated isothermal amplification method (MB-LAMP), realizing the direct detection of LAMP product. PMID:28059137

  19. Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

    PubMed Central

    Kind, Tobias; Fiehn, Oliver

    2007-01-01

    Background Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas. Results An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80–99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries. Conclusion The seven rules enable an

  20. 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

    2015-12-05

    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.

  1. Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB).

    PubMed

    Brandenburg, Jan Gerit; Grimme, Stefan

    2014-06-05

    The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.

  2. Energy disposal and thermal rate constants for the OH + HBr and OH + DBr reactions: quasiclassical trajectory calculations on an accurate potential energy surface.

    PubMed

    de Oliveira-Filho, Antonio G S; Ornellas, Fernando R; Bowman, Joel M

    2014-12-26

    We report reaction cross sections, energy disposal, and rate constants for the OH + HBr → Br + H2O and OH + DBr → Br + HDO reactions from quasiclassical trajectory calculations using an ab initio potential energy surface [ de Oliveira-Filho , A. G. S. ; Ornellas , F. R. ; Bowman , J. M. J. Phys. Chem. Lett. 2014 , 5 , 706 - 712 ]. Comparison with available experiments are made and generally show good agreement.

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

    PubMed

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

    2016-07-03

    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.

  4. 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...

  5. 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.

  6. 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.

  7. Towards More Accurate Measurements of the Ionization Energy of Molecular Hydrogen

    NASA Astrophysics Data System (ADS)

    Sprecher, D.; Beyer, M.; Liu, J.; Merkt, F.; Salumbides, E.; Eikema, K. S. E.; Ubachs, W.; Jungen, Ch.

    2013-06-01

    With two electrons and two protons, molecular hydrogen is the simplest molecule displaying all features of a chemical bond. H_2 is therefore a fundamental system for testing molecular quantum mechanics and quantum electrodynamics in molecules. The test can be performed by comparing measured and calculated intervals between different rovibronic states of H_2. Two further quantities that can be used for this test are the dissociation and ionization energies of H_2, and considerable efforts have been invested over more than 80 years to improve the precision and accuracy of experimental and theoretical determination of these two quantities. The current status of the comparison is that the theoretical and experimental values of the ionization and dissociation energies of H_2 agree within the combined uncertainty of 30 MHz (see also). The factors currently limiting the precision of the experimental determination will be discussed and the strategies that are being implemented towards overcoming these limitations will be presented. A long-term goal is to achieve a precision of better than 15 kHz, which is the ultimate limit imposed on the accuracy of the theoretical determination by the current uncertainty of the proton-to-electron mass ratio. E. J. Salumbides, G. D. Dickenson, T. I. Ivanov and W. Ubachs, {Phys. Rev. Lett.} 107 (4), 043005 (2011). K. Piszczatowski, G. Lach, M. Przybytek, J. Komasa, K. Pachuckiand and B. Jeziorski, {J. Chem. Theory Comput.} 5 (11), 3039 (2009). J. Liu, E. J. Salumbides, U. Hollenstein, J. C. J. Koelemeij, K. S. E. Eikema, W. Ubachs and F. Merkt, {J. Chem. Phys.} 130 (17), 174306 (2009). D. Sprecher, Ch. Jungen, W. Ubachs and F. Merkt, {Faraday Discuss.} 150, 51 (2011).

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Effect of Solvent Dielectric Properties on the Spontaneous-Emission Rate Constant of Molecular Singlet Oxygen

    NASA Astrophysics Data System (ADS)

    Jarnikova, E. S.; Parkhats, M. V.; Stasheuski, A. S.; Dzhagarov, B. M.

    2017-01-01

    Quantum yields and luminescence lifetimes of singlet oxygen in 18 different solvents and binary mixtures were measured using laser fluorometry. The results allowed a direct effect of the refractive index on the radiative rate constant kr of the singlet-oxygen a 1 Δ g → X 3 Σ g - transition caused by a change of photon state density in addition to an indirect effect through a local-field factor to be determined. The experimentally observed rise of kr with increasing medium refractive index could not be explained by the influence of only these two factors. The discrepancy was overcome by taking into account changes of the singlet-oxygen transition dipole moment. Consideration of all three factors explained the influence of the medium on rate constant kr

  14. Accurate vibrational spectra via molecular tailoring approach: a case study of water clusters at MP2 level.

    PubMed

    Sahu, Nityananda; Gadre, Shridhar R

    2015-01-07

    In spite of the recent advents in parallel algorithms and computer hardware, high-level calculation of vibrational spectra of large molecules is still an uphill task. To overcome this, significant effort has been devoted to the development of new algorithms based on fragmentation methods. The present work provides the details of an efficient and accurate procedure for computing the vibrational spectra of large clusters employing molecular tailoring approach (MTA). The errors in the Hessian matrix elements and dipole derivatives arising due to the approximation nature of MTA are reduced by grafting the corrections from a smaller basis set. The algorithm has been tested out for obtaining vibrational spectra of neutral and charged water clusters at Møller-Plesset second order level of theory, and benchmarking them against the respective full calculation (FC) and/or experimental results. For (H2O)16 clusters, the estimated vibrational frequencies are found to differ by a maximum of 2 cm(-1) with reference to the corresponding FC values. Unlike the FC, the MTA-based calculations including grafting procedure can be performed on a limited hardware, yet take a fraction of the FC time. The present methodology, thus, opens a possibility of the accurate estimation of the vibrational spectra of large molecular systems, which is otherwise impossible or formidable.

  15. Accurate vibrational spectra via molecular tailoring approach: A case study of water clusters at MP2 level

    NASA Astrophysics Data System (ADS)

    Sahu, Nityananda; Gadre, Shridhar R.

    2015-01-01

    In spite of the recent advents in parallel algorithms and computer hardware, high-level calculation of vibrational spectra of large molecules is still an uphill task. To overcome this, significant effort has been devoted to the development of new algorithms based on fragmentation methods. The present work provides the details of an efficient and accurate procedure for computing the vibrational spectra of large clusters employing molecular tailoring approach (MTA). The errors in the Hessian matrix elements and dipole derivatives arising due to the approximation nature of MTA are reduced by grafting the corrections from a smaller basis set. The algorithm has been tested out for obtaining vibrational spectra of neutral and charged water clusters at Møller-Plesset second order level of theory, and benchmarking them against the respective full calculation (FC) and/or experimental results. For (H2O)16 clusters, the estimated vibrational frequencies are found to differ by a maximum of 2 cm-1 with reference to the corresponding FC values. Unlike the FC, the MTA-based calculations including grafting procedure can be performed on a limited hardware, yet take a fraction of the FC time. The present methodology, thus, opens a possibility of the accurate estimation of the vibrational spectra of large molecular systems, which is otherwise impossible or formidable.

  16. 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.

  17. Accurate schemes for calculation of thermodynamic properties of liquid mixtures from molecular dynamics simulations.

    PubMed

    Caro, Miguel A; Laurila, Tomi; Lopez-Acevedo, Olga

    2016-12-28

    We explore different schemes for improved accuracy of entropy calculations in aqueous liquid mixtures from molecular dynamics (MD) simulations. We build upon the two-phase thermodynamic (2PT) model of Lin et al. [J. Chem. Phys. 119, 11792 (2003)] and explore new ways to obtain the partition between the gas-like and solid-like parts of the density of states, as well as the effect of the chosen ideal "combinatorial" entropy of mixing, both of which have a large impact on the results. We also propose a first-order correction to the issue of kinetic energy transfer between degrees of freedom (DoF). This problem arises when the effective temperatures of translational, rotational, and vibrational DoF are not equal, either due to poor equilibration or reduced system size/time sampling, which are typical problems for ab initio MD. The new scheme enables improved convergence of the results with respect to configurational sampling, by up to one order of magnitude, for short MD runs. To ensure a meaningful assessment, we perform MD simulations of liquid mixtures of water with several other molecules of varying sizes: methanol, acetonitrile, N, N-dimethylformamide, and n-butanol. Our analysis shows that results in excellent agreement with experiment can be obtained with little computational effort for some systems. However, the ability of the 2PT method to succeed in these calculations is strongly influenced by the choice of force field, the fluidicity (hard-sphere) formalism employed to obtain the solid/gas partition, and the assumed combinatorial entropy of mixing. We tested two popular force fields, GAFF and OPLS with SPC/E water. For the mixtures studied, the GAFF force field seems to perform as a slightly better "all-around" force field when compared to OPLS+SPC/E.

  18. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

    PubMed

    Chen, Wei; Shen, Jana K

    2014-10-15

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma.

  19. Constant temperature molecular dynamics of a protein in water by high-order decomposition of the Liouville operator

    NASA Astrophysics Data System (ADS)

    Ishida, Hisashi; Kidera, Akinori

    1998-08-01

    Among algorithms that are used to solve the equations of motion, the symplectic integrator (SI) has the advantage of conserving the phase space volume and ensuring a stable simulation. However, incorporating the explicit formula of the SI in a molecular simulation is feasible only for the systems whose Hamiltonian is described by K(p)+V(q), where the kinetic energy K and the potential energy V depend only on momenta p and coordinates q, respectively. Due to this limitation, explicit SI integrators cannot directly be applied to the Nosé-Hoover equations of motion for the constant temperature molecular dynamics (MD) simulation. In this article, by applying the formula of the decomposition of the exponential Liouville operator to the Nosé-Hoover equations, we have obtained a series of integrators for the constant temperature simulation which have the correct form of the Jacobian of the Nosé-Hoover equations. The systems examined here are liquid water and a protein in water. From the results of the constant temperature simulations, where several variations of the integrators were employed, we show that a combination of the Suzuki's second order formula and the fourth order symplectic integrator of Calvo and Sanz-Serna generates a trajectory of much higher accuracy than the nonsymplectic Gear predictor-corrector method for a given amount of CPU time.

  20. Retrieving the Molecular Composition of Planet-Forming Material: An Accurate Non-LTE Radiative Transfer Code for JWST

    NASA Astrophysics Data System (ADS)

    Pontoppidan, Klaus

    Based on the observed distributions of exoplanets and dynamical models of their evolution, the primary planet-forming regions of protoplanetary disks are thought to span distances of 1-20 AU from typical stars. A key observational challenge of the next decade will be to understand the links between the formation of planets in protoplanetary disks and the chemical composition of exoplanets. Potentially habitable planets in particular are likely formed by solids growing within radii of a few AU, augmented by unknown contributions from volatiles formed at larger radii of 10-50 AU. The basic chemical composition of these inner disk regions is characterized by near- to far-infrared (2-200 micron) emission lines from molecular gas at temperatures of 50-1500 K. A critical step toward measuring the chemical composition of planet-forming regions is therefore to convert observed infrared molecular line fluxes, profiles and images to gas temperatures, densities and molecular abundances. However, current techniques typically employ approximate radiative transfer methods and assumptions of local thermodynamic equilibrium (LTE) to retrieve abundances, leading to uncertainties of orders of magnitude and inconclusive comparisons to chemical models. Ultimately, the scientific impact of the high quality spectroscopic data expected from the James Webb Space Telescope (JWST) will be limited by the availability of radiative transfer tools for infrared molecular lines. We propose to develop a numerically accurate, non-LTE 3D line radiative transfer code, needed to interpret mid-infrared molecular line observations of protoplanetary and debris disks in preparation for the James Webb Space Telescope (JWST). This will be accomplished by adding critical functionality to the existing Monte Carlo code LIME, which was originally developed to support (sub)millimeter interferometric observations. In contrast to existing infrared codes, LIME calculates the exact statistical balance of arbitrary

  1. 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

  2. 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).

  3. 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(+).

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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+.

  5. 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.

  6. Acidity Constant (pKa ) Calculation of Large Solvated Dye Molecules: Evaluation of Two Advanced Molecular Dynamics Methods.

    PubMed

    De Meyer, Thierry; Ensing, Bernd; Rogge, Sven M J; De Clerck, Karen; Meijer, Evert Jan; Van Speybroeck, Veronique

    2016-11-04

    pH-Sensitive dyes are increasingly applied on polymer substrates for the creation of novel sensor materials. Recently, these dye molecules were modified to form a covalent bond with the polymer host. This had a large influence on the pH-sensitive properties, in particular on the acidity constant (pKa ). Obtaining molecular control over the factors that influence the pKa value is mandatory for the future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level at which the pKa values of large solvated dye molecules can be predicted with high accuracy. Two MD methods were used in this work: steered or restrained MD and the insertion/deletion scheme. Both were first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule bromothymol blue. Excellent agreement with experimental values was obtained, which opens perspectives for using these methods for designing dye molecules.

  7. Millimeter-wave rotational spectrum and molecular constants of diatomic gallium iodide

    NASA Astrophysics Data System (ADS)

    Nair, K. P. R.; Schütze-Pahlmann, H.-U.; Hoeft, J.

    1980-03-01

    The gas-phase molecular spectrum of Gal has been detected in the millimeter wavelength region. The molecules are produced by vapourising a mixture of gallium and lead iodide into an evaculated cell. Analysis of the observed rotational transitions yields the following molecular parameters for 69Ga 127I: Y01 = 1706.89645(83) MHz, Y11 = -5.68714(53) MHz, Y21 = 6.329(43) kHz, Y02 = -0.472713(60) kHz, Y12 = 0.472(38) Hz, ω e = 216.38 cm -1, ω exe= 0.471 cm -1, and for 71Ga 127I: y 01 = 1675.72004(71) MHz, Y11 = -5.53277(57) MHz, Y21 = 5.995(34) kHz, Y02 = -0.455700(51) kHz, y12 = 0.522(40) Hz, ω e = 214.37 cm -1, and ω exe = 0.458 cm -1. The equilibrium internuclear distance obtained for Gal is re = 2.574667(12) Å.

  8. 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.

  9. 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.

  10. 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.).

  11. Use of Mo/ller-Plesset perturbation theory in molecular calculations: Spectroscopic constants of first row diatomic molecules

    SciTech Connect

    Dunning, T.H. , Jr.; Peterson, K.A.

    1998-03-01

    The convergence of Mo/ller{endash}Plesset perturbation expansions (MP2{endash}MP4/MP5) for the spectroscopic constants of a selected set of diatomic molecules (BH, CH, HF, N{sub 2}, CO, and F{sub 2}) has been investigated. It was found that the second-order perturbation contributions to the spectroscopic constants are strongly dependent on basis set, more so for HF and CO than for BH. The MP5 contributions for HF were essentially zero for the cc-pVDZ basis set, but increased significantly with basis set illustrating the difficulty of using small basis sets as benchmarks for correlated calculations. The convergence behavior of the {ital exact} Mo/ller{endash}Plesset perturbation expansions were investigated using estimates of the {ital complete basis set limits} obtained using large correlation consistent basis sets. For BH and CH, the perturbation expansions of the spectroscopic constants converge monotonically toward the experimental values, while for HF, N{sub 2}, CO, and F{sub 2}, the expansions oscillate about the experimental values. The perturbation expansions are, in general, only slowly converging and, for HF, N{sub 2}, CO, and F{sub 2}, appear to be far from convergence at MP4. In fact, for HF, N{sub 2}, and CO, the errors in the calculated spectroscopic constants for the MP4 method are {ital larger} than those for the MP2 method (the only exception is D{sub e}). The current study, combined with other recent studies, raises serious doubts about the use of Mo/ller{endash}Plesset perturbation theory to describe electron correlation effects in atomic and molecular calculations. {copyright} {ital 1998 American Institute of Physics.}

  12. Study on spectroscopic parameters and molecular constants of HC1(X1Σ+) molecule by using multireference configuration interaction approach

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-Niu; Shi, De-Heng; Zhang, Jin-Ping; Zhu, Zun-Lüe; Sun, Jin-Feng

    2010-05-01

    Equilibrium internuclear separations, harmonic frequencies and potential energy curves (PECs) of HC1(X1Σ+) molecule are investigated by using the highly accurate valence internally contracted multireference configuration interaction (MRCI) approach in combination with a series of correlation-consistent basis sets in the valence range. The PECs are all fitted to the Murrell-Sorbie function, and they are used to accurately derive the spectroscopic parameters (De, D0, ωeχe, αe and Be). Compared with the available measurements, the PEC obtained at the basis set, aug-cc-pV5Z, is selected to investigate the vibrational manifolds. The constants D0, De, Re, ωe, ωeχe, αe and Be at this basis set are 4.4006 eV, 4.5845 eV, 0.12757 nm, 2993.33 cm-1, 52.6273 cm-1, 0.2981 cm-1 and 10.5841 cm-1, respectively, which almost perfectly conform to the available experimental results. With the potential determined at the MRCI/aug-cc-pV5Z level of theory, by numerically solving the radial Schrödinger equation of nuclear motion in the adiabatic approximation, a total of 21 vibrational levels are predicted. Complete vibrational levels, classical turning points, inertial rotation and centrifugal distortion constants are reproduced, which are in excellent agreement with the available Rydberg-Klein-Rees data. Most of these theoretical vibrational manifolds are reported for the first time to the best of our knowledge.

  13. Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.

    PubMed

    Arcon, Juan Pablo; Defelipe, Lucas A; Modenutti, Carlos P; López, Elias D; Alvarez-Garcia, Daniel; Barril, Xavier; Turjanski, Adrián G; Martí, Marcelo A

    2017-03-31

    One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Because of its low cost relative to its experimental sibling, molecular dynamics (MD) simulations in the presence of different solvent probes mimicking specific types of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots. However, a systematic comparison of different probes and their real predictive power from a quantitative and thermodynamic point of view is still missing. In the present work, we have performed MD simulations of 18 different proteins in pure water as well as water mixtures of ethanol, acetamide, acetonitrile and methylammonium acetate, leading to a total of 5.4 μs simulation time. For each system, we determined the corresponding solvent sites, defined as space regions adjacent to the protein surface where the probability of finding a probe atom is higher than that in the bulk solvent. Finally, we compared the identified solvent sites with 121 different protein-ligand complexes and used them to perform molecular docking and ligand binding free energy estimates. Our results show that combining solely water and ethanol sites allows sampling over 70% of all possible protein-ligand interactions, especially those that coincide with ligand-based pharmacophoric points. Most important, we also show how the solvent sites can be used to significantly improve ligand docking in terms of both accuracy and precision, and that accurate predictions of ligand binding free energies, along with relative ranking of ligand affinity, can be performed.

  14. 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...

  15. 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

  16. Partition coefficient vs. binding constant: How best to assess molecular lipophilicity.

    PubMed

    Cevc, Gregor

    2015-05-01

    Partition coefficient, P, is the preferred descriptor of molecular lipo- or hydrophilicity, and thus of relationships between a solute (S, e.g., a drug), a polar medium (W, e.g., an aqueous buffer), and an essentially apolar, organic, medium or a drug carrier (O). The coefficient is commonly identified with the linear ratio of solute quantities in the two media, P=nSO/nSW, even to characterise solute association with or binding to a surface (e.g., of a HPLC column or a drug carrier). To check the latter practice correctness-and credibility of the prevailing P definition-this paper compares an ideal solute distribution between two separate homogeneous fluid media (i.e., partitioning) to solute association with a uniform surface immersed in one such medium (i.e., binding). This reveals that solute partitioning and binding fundamentally differ and can only exceptionally be described, or analysed, with similar equations. Nonlinearised formulae that describe partitioning (Eq. (9)) and binding (Eq. (11)) can yield similar lipophilicity descriptor values only if solute preparation is relatively dilute; employing a large organic medium fraction is helpful in this respect. Additional prerequisites for partitioning and binding models match are: 1:1 stoichiometry at the association maximum and identical interfacial area of solute and organic medium molecules. If these requirements are not met, binding model yields different, potentially somewhat higher, but more often up to >10 times lower results than partitioning model. The main reason is saturation of organic medium with solute molecules. Partitioning model excludes this phenomenon, which cannot always be prevented by focussing on dilute solute preparations. The current practice of using a linear model and approximate equations to study partitioning or binding can cause large errors (>10(3)×), and is one possible reason for the notoriously high experimental logP values scattering. The latter makes logP predictions more

  17. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

    PubMed

    Huang, Yandong; Chen, Wei; Wallace, Jason A; Shen, Jana

    2016-11-08

    Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pKa's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pKa shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.

  18. 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.

  19. 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.

  20. Efficient and accurate determination of lattice-vacancy diffusion coefficients via non equilibrium ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sangiovanni, D. G.; Hellman, O.; Alling, B.; Abrikosov, I. A.

    2016-03-01

    We revisit the color-diffusion algorithm [Aeberhard et al., Phys. Rev. Lett. 108, 095901 (2012), 10.1103/PhysRevLett.108.095901] in non equilibrium ab initio molecular dynamics (NE-AIMD) and propose a simple efficient approach for the estimation of monovacancy jump rates in crystalline solids at temperatures well below melting. Color-diffusion applied to monovacancy migration entails that one lattice atom (colored atom) is accelerated toward the neighboring defect site by an external constant force F. Considering bcc molybdenum between 1000 and 2800 K as a model system, NE-AIMD results show that the colored-atom jump rate kNE increases exponentially with the force intensity F , up to F values far beyond the linear-fitting regime employed previously. Using a simple model, we derive an analytical expression which reproduces the observed kNE(F ) dependence on F . Equilibrium rates extrapolated by NE-AIMD results are in excellent agreement with those of unconstrained dynamics. The gain in computational efficiency achieved with our approach increases rapidly with decreasing temperatures and reaches a factor of 4 orders of magnitude at the lowest temperature considered in the present study.

  1. 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.

  2. 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

  3. A modified ELISA accurately measures secretion of high molecular weight hyaluronan (HA) by Graves' disease orbital cells.

    PubMed

    Krieger, Christine C; Gershengorn, Marvin C

    2014-02-01

    Excess production of hyaluronan (hyaluronic acid [HA]) in the retro-orbital space is a major component of Graves' ophthalmopathy, and regulation of HA production by orbital cells is a major research area. In most previous studies, HA was measured by ELISAs that used HA-binding proteins for detection and rooster comb HA as standards. We show that the binding efficiency of HA-binding protein in the ELISA is a function of HA polymer size. Using gel electrophoresis, we show that HA secreted from orbital cells is primarily comprised of polymers more than 500 000. We modified a commercially available ELISA by using 1 million molecular weight HA as standard to accurately measure HA of this size. We demonstrated that IL-1β-stimulated HA secretion is at least 2-fold greater than previously reported, and activation of the TSH receptor by an activating antibody M22 from a patient with Graves' disease led to more than 3-fold increase in HA production in both fibroblasts/preadipocytes and adipocytes. These effects were not consistently detected with the commercial ELISA using rooster comb HA as standard and suggest that fibroblasts/preadipocytes may play a more prominent role in HA remodeling in Graves' ophthalmopathy than previously appreciated.

  4. Nuclear Quantum Effects in Liquid Water: A Highly Accurate ab initio Path-Integral Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Distasio, Robert A., Jr.; Santra, Biswajit; Ko, Hsin-Yu; Car, Roberto

    2014-03-01

    In this work, we report highly accurate ab initio path-integral molecular dynamics (AI-PIMD) simulations on liquid water at ambient conditions utilizing the recently developed PBE0+vdW(SC) exchange-correlation functional, which accounts for exact exchange and a self-consistent pairwise treatment of van der Waals (vdW) or dispersion interactions, combined with nuclear quantum effects (via the colored-noise generalized Langevin equation). The importance of each of these effects in the theoretical prediction of the structure of liquid water will be demonstrated by a detailed comparative analysis of the predicted and experimental oxygen-oxygen (O-O), oxygen-hydrogen (O-H), and hydrogen-hydrogen (H-H) radial distribution functions as well as other structural properties. In addition, we will discuss the theoretically obtained proton momentum distribution, computed using the recently developed Feynman path formulation, in light of the experimental deep inelastic neutron scattering (DINS) measurements. DOE: DE-SC0008626, DOE: DE-SC0005180.

  5. Acidity Constant (pK a) Calculation of Large Solvated Dye Molecules: Evaluation of Two Advanced Molecular Dynamics Methods

    PubMed Central

    De Meyer, Thierry; Ensing, Bernd; Rogge, Sven M. J.; De Clerck, Karen

    2016-01-01

    Abstract pH‐Sensitive dyes are increasingly applied on polymer substrates for the creation of novel sensor materials. Recently, these dye molecules were modified to form a covalent bond with the polymer host. This had a large influence on the pH‐sensitive properties, in particular on the acidity constant (pK a). Obtaining molecular control over the factors that influence the pK a value is mandatory for the future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level at which the pK a values of large solvated dye molecules can be predicted with high accuracy. Two MD methods were used in this work: steered or restrained MD and the insertion/deletion scheme. Both were first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule bromothymol blue. Excellent agreement with experimental values was obtained, which opens perspectives for using these methods for designing dye molecules. PMID:27570194

  6. Self-assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics.

    PubMed

    Morrow, Brian H; Koenig, Peter H; Shen, Jana K

    2013-12-03

    Recent interest in the development of surfactant-based nanodelivery systems targeting tumor sites has sparked our curiosity in understanding the detailed mechanism of the self-assembly and phase transitions of pH-sensitive surfactants. Toward this goal, we applied a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with the hybrid-solvent scheme and pH-based replica-exchange protocol, to study the de novo self-assembly of 30 and 40 lauric acids, a simple model titratable surfactant. We observed the formation of a gel-state bilayer at low and intermediate pH and a spherical micelle at high pH, with the phase transition starting at 20-30% ionization and being completed at 50%. The degree of cooperativity for the transition increases from the 30-mer to the 40-mer. The calculated apparent or bulk pKa value is 7.0 for the 30-mer and 7.5 for the 40-mer. Congruent with experiment, these data demonstrate that CpHMD is capable of accurately modeling large conformational transitions of surfactant systems while allowing the simultaneous proton titration of constituent molecules. We suggest that CpHMD simulations may become a useful tool in aiding in the design and development of pH-sensitive nanocarriers for a variety of biomedical and technological applications.

  7. 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.

  8. 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.

  9. 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.

  10. Test of variational transition state theory and multidimensional semiclassical transmission coefficient methods against accurate quantal rate constants for H + H/sub 2//HD, D + H/sub 2/, and O + H/sub 2//D/sub 2//HD, including intra- and intermolecular kinetic isotope effects

    SciTech Connect

    Garrett, B.C.; Truhlar, D.G.; Schatz, G.C.

    1986-05-28

    Rate constants and kinetic isotope effects for the title reactions have been calculated by using accurate quantum dynamical methods and used to test the accuracy of corresponding rate constants from conventional and variational transition state theory. The quantum dynamical rate constants are estimated to be within 35% of the exact rate constants for the potential surfaces chosen for this comparison. For all the reactions considered, the conventional and variational transition state theory rate constants with unit transmission coefficient are found to be very close to each other (better than 7%) but in poor agreement with the accurate quantum results (off by factors of 6-22 at 300 K). This indicates that although variational effects are small, tunnelling makes a very important contribution to the rate constants, and it is found that this tunnelling contribution is described quantitatively for all the reactions considered with use of the least action ground state (LAG) transmission coefficient. The combination of improved canonical variational theory (ICVT) and LAG yields rate constants which have an average error (considering all the reactions and temperatures studied) of 15% compared to the accurate quantum rate constants, and in only one case (D + H/sub 2/ at 200 K) does the ICVT/LAG rate constant differ by more than 35% from the accurate value. The comparison of ICVT/LAG kinetic isotope effects is found to be similarly good, with the worst comparisons occurring for intramolecular (X + HD) isotope ratios.

  11. Test of variational transition-state theory and multidimensional semiclassical transmission coefficient methods against accurate quantal rate constants for H + H/sub 2//HD, D + H/sub 2/, and O + H/sub 2//D/sub 2//HD, including intra- and intermolecular kinetic isotope effects

    SciTech Connect

    Garrett, B.C.; Truhlar, D.G.; Schatz, G.C.

    1986-01-01

    Rate constants and kinetic isotope effects for the title reactions were calculated using accurate quantum-dynamical methods, and used to test the accuracy of corresponding rate constants from conventional and variational transition-state theory. The quantum-dynamical rate constants are estimated to be within 35% of the exact rate constants for the potential energy surfaces chosen for this comparison. For all the reactions considered, the conventional and variational transition-state theory rate constants with unit transmission coefficient are found to be very close to each other (better than 7%), but in poor agreement with the accurate quantum results (off by factors of 6-22 at 300K). This indicates that although variational effects are small, tunneling makes a very important contribution to the rate constants, and it is found that the tunneling contribution is described quantitatively for all the reactions considered using the least-action ground state (LAG) transmission coefficient. The combination of improved canonical variational theory (ICVT) and LAG yields rate constants that have an average error (considering all the reactions and temperatures studied) of only 15% compared to the accurate quantal rate constants, and in only one case (D + H/sub 2/ at 200K) does the ICVT/LAG rate constant differ by more than 35% from the accurate value. The comparison of ICVT/LAG kinetic isotope effects is found to be similarly good, with worst comparisons occurring for intramolecular (X+HD) isotope ratios.

  12. 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.

  13. 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.

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

    PubMed Central

    2015-01-01

    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 (m3 → m4). 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

  15. 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...

  16. 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.

  17. 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.

  18. Accurate and scalable O(N) algorithm for first-principles molecular-dynamics computations on large parallel computers.

    PubMed

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-01-31

    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 7×10(-4)  Ha/Bohr.

  19. 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.

  20. 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.

  1. Detection of the N = 3-2 transition of CCH in Orion and determination of the molecular rotational constants

    NASA Astrophysics Data System (ADS)

    Ziurys, L. M.; Saykally, R. J.; Plambeck, R. L.; Erickson, N. R.

    1982-03-01

    We report the detection of five hyperfine components of the N = 3-2 transition of CCH in Orion A. From an analysis of this data combined with N = 1-0 data from previous observations, the rotational constants (B0 and D0) were determined, and the values of the fine structure (γ) and hyperfine constants (b, c) were improved. We predict the frequencies of additional rotational transitions of CCH up to N = 5-4. A rotational temperature and column density are estimated on the basis of the 3-2 data.

  2. 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.

  3. 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.

  4. Molecular statics calculations of proton binding to goethite surfaces: A new approach to estimation of stability constants for multisite surface complexation models

    NASA Astrophysics Data System (ADS)

    Rustad, James R.; Felmy, Andrew R.; Hay, Benjamin P.

    1996-05-01

    A new approach to estimating stability constants for proton binding in multisite surface complexation models is presented. The method is based on molecular statics computation of energies for the formation of proton vacancies and interstitials in ideal periodic slabs representing the (100), (110), (010), (001), and (021) surfaces of goethite. Gas-phase energies of clusters representing the hydrolysis products of ferric iron are calculated using the same potential energy functions used for the surface. These energies are linearly related to the hydrolysis constants for ferric iron in aqueous solution. Stability constants for proton binding at goethite surfaces are estimated by assuming the same log K- Δ E relationship for goethite surface protonation reactions. These stability constants predict a pH of zero charge of 8.9, in adequate agreement with measurements on CO 2-free goethite. The estimated stability constants differ significantly from previous estimations based on Pauling bond strength. We find that nearly all the surface oxide ions are reactive; nineteen of the twenty-six surface sites investigated have log Kint between 7.7 and 9.4. This implies a site density between fifteen and sixteen reactive sites/nm for crystals dominated by (110) and (021) crystal faces.

  5. Dynamics of the C(1D)+D2 reaction: a comparison of crossed molecular-beam experiments with quasiclassical trajectory and accurate statistical calculations.

    PubMed

    Balucani, Nadia; Capozza, Giovanni; Segoloni, Enrico; Russo, Andrea; Bobbenkamp, Rolf; Casavecchia, Piergiorgio; Gonzalez-Lezana, Tomas; Rackham, Edward J; Bañares, Luis; Aoiz, F Javier

    2005-06-15

    In this paper we report a combined experimental and theoretical study on the dynamics of the insertion reaction C((1)D)+D(2) at 15.5 kJ mol(-1) collision energy. Product angular and velocity distributions have been obtained in crossed beam experiments and quasiclassical trajectory (QCT) and rigorous statistical calculations have been performed on the recent and accurate ab initio potential energy surface of Bussery-Honvault, Honvault, and Launay at the energy of the experiment. The molecular-beam results have been simulated using the theoretical calculations. Good agreement between experiment and both QCT and statistical predictions is found.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

    PubMed

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

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the (1)J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the (1)J(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.

  10. 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

    2014-12-08

    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+).

  11. Upper limit on the rate constant for isotope exchange between molecular oxygen and ozone at 298 K

    NASA Technical Reports Server (NTRS)

    Anderson, S. M.; Morton, J.; Mauersberger, K.

    1987-01-01

    The gas phase bimolecular isotope exchange reaction between molecular oxygen and ozone has been investigated directly for the first time. Its rate coefficient is found to be less than 2 x 10 to the -25th cu cm/sec at 298 K, over six orders of magnitude below recent estimates. Much faster exchange was observed over condensed ozone at 77 K, suggesting isotopic scrambling is catalyzed under these conditions. The low rate coefficient implies that homogeneous exchange between ground state oxygen and ozone molecules cannot play a significant role in heavy ozone chemistry.

  12. 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.

  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. 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.

  15. 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.

  16. 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.

    PubMed

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

    2016-04-21

    To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3reactions, 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.

  17. 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

  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. Accurate tuning of emission of GaInAsP/InP heterostructures in multiwafer gas-source molecular-beam epitaxy

    NASA Astrophysics Data System (ADS)

    Lelarge, F.; Gaborit, F.; Gentner, J. L.

    2005-03-01

    Photoluminescence wavelength emission of Ga xIn 1-xAs yP 1-y/InP heterostructures grown in multiwafer gas-source molecular-beam epitaxy (GSMBE) is studied in detail for both bulk and multiple quantum well (MQWs) heterostructures. Excellent photoluminescence wavelength uniformity is reported in 4×2-in. configuration, demonstrating the compatibility of GSMBE process with large-scale 1.55 μm telecom laser production. A strong dependence of wavelength uniformity on group-V/group-III flux ratio is reported and analyzed quantitatively. An empirical model based on the interplay between group-V elements incorporation and gas distribution is proposed to predict the influence of AsH 3 and PH 3 fluxes on As content in the solid. This understanding opens the way to an accurate tuning of wavelength dispersion of Ga xIn 1-xAs yP 1-y/InP MQWs grown in multiwafer GSMBE system.

  20. First principles molecular dynamics studies of elastic constants, ideal tensile strength, chemistry of crack initiation, and surface and cohesive energies in amorphous silicon

    NASA Astrophysics Data System (ADS)

    Shodja, Hossein M.; Tabatabaei, Maryam; Esfarjani, Keivan

    2014-09-01

    First principles Kohn-Sham density functional theory (DFT)-based molecular dynamics (MD) is employed to investigate some physical and mechanical properties of amorphous Si (a-Si) samples, as-quenched and annealed containing dangling and floating bonds as well as distorted tetrahedral bonds. The total energy and true stress as functions of the engineering strain for a-Si samples subjected to uniaxial tensile stress as well as uniaxial extension are obtained. It is well-known that the electron density of the state of matters can be determined via ab initio DFT-based MD with high accuracy. Using this technique, such inherent properties as the elastic constants, ideal tensile strength, ultimate tensile strength, and surface and cohesive energies will be calculated. Since the employed ab initio MD, in contrast to the empirical potentials simulations, is capable of providing the evolution of the electronic charge distribution, we can afford to study the chemistry of crack initiation and reconstructed surfaces at final rupture. The calculated cohesive and surface energies are compared with the available theoretical and experimental results; Tyson's empirical relation and universal binding energy relations (UBERs) are also examined. The calculated elastic constants using the symmetry-general scheme satisfy well the isotropic relation ?. To date, the ab initio MD samples of a-Si generated from the completely melted scheme were all free of three-fold-coordinated Si. In contrast, as we will show, by implementing special thermal treatments, generation of all inherent structural defects is possible. Based on the electronic charge distribution, dative bonds and trigonal prisms for, respectively, floating and dangling bonds have been observed.

  1. MRCI study on the spectroscopic parameters and molecular constants of the X1Σ+, a3Σ+, A1Π and C1Σ- electronic states of the SiO molecule.

    PubMed

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

    2012-02-15

    The potential energy curves (PECs) of the X(1)Σ(+), a(3)Σ(+), A(1)Π and C(1)Σ(-) 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(1)Σ(+), 69 for the a(3)Σ(+), 54 for the A(1)Π and 67 for the C(1)Σ(-) 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 a(3)Σ(+), C(1)Σ(-) and A(1)Π electronic states determined by the MRCI

  2. Determination of anisotropic optical constants and surface coverage of molecular films using polarized visible ATR spectroscopy. Application to adsorbed cytochrome c films.

    PubMed

    Runge, Anne F; Rasmussen, Nicole C; Saavedra, S Scott; Mendes, Sergio B

    2005-01-13

    This article describes a method to determine the anisotropic optical constants and surface coverage of molecular films using polarized attenuated total reflectance (ATR) absorbance measurements. We have extended the transfer-matrix formalism to describe birefringent and dichroic films in ATR geometries and have combined it with an iterative numerical procedure to determine the anisotropic values of both the real (n) and imaginary (k) parts of the complex refractive index of the film under investigation. Anisotropic values of the imaginary part of the refractive index (k) allow for the determination of the surface coverage and one order parameter of the film. To illustrate this approach, we have used cytochrome c (cyt c) protein films adsorbed to glass and indium tin oxide (ITO) surfaces. Experimental results show that cyt c films on these surfaces, which were formed under identical conditions, have significant differences in their surface coverages (11.2 +/- 0.4 pmol/cm(2) on glass and 21.7 +/- 0.9 pmol/cm(2) on ITO); however, their order parameters are similar (0.30 +/- 0.02 on glass and 0.36 +/- 0.04 on ITO).

  3. Accurate analytical approximation of asteroid deflection with constant tangential thrust

    NASA Astrophysics Data System (ADS)

    Bombardelli, Claudio; Baù, Giulio

    2012-11-01

    We present analytical formulas to estimate the variation of achieved deflection for an Earth-impacting asteroid following a continuous tangential low-thrust deflection strategy. Relatively simple analytical expressions are obtained with the aid of asymptotic theory and the use of Peláez orbital elements set, an approach that is particularly suitable to the asteroid deflection problem and is not limited to small eccentricities. The accuracy of the proposed formulas is evaluated numerically showing negligible error for both early and late deflection campaigns. The results will be of aid in planning future low-thrust asteroid deflection missions.

  4. The Hubble Constant

    NASA Astrophysics Data System (ADS)

    Freedman, Wendy; Madore, Barry; Mager, Violet; Persson, Eric; Rigby, Jane; Sturch, Laura

    2008-12-01

    We present a plan to measure a value of the Hubble constant having a final systematic uncertainty of only 3% by taking advantage of Spitzer's unique mid-infrared capabilities. This involves using IRAC to undertake a fundamental recalibration of the Cepheid distance scale and progressively moving it out to pure Hubble flow by an application of a revised mid-IR Tully-Fisher relation. The calibration and application, in one coherent and self-consistent program, will go continuously from distances of parsecs to several hundred megaparsecs. It will provide a first-ever mid-IR calibration of Cepheids in the Milky Way, LMC and Key Project spiral galaxies and a first-ever measurement and calibration of the TF relation at mid-infrared wavelengths, and finally a calibration of Type Ia SNe. Most importantly this program will be undertaken with a single instrument, on a single telescope, working exclusively at mid-infrared wavelengths that are far removed from the obscuring effects of dust extinction. Using Spitzer in this focused way will effectively eliminate all of the major systematics in the Cepheid and TF distance scales that have been the limiting factors in all previous applications, including the HST Key Project. By executing this program, based exclusively on Spitzer data, we will deliver a value of the Hubble constant, having a statistical precision better than 11%, with all currently known systematics quantified and constrained to a level of less than 3%. A value of Ho determined to this level of systematic accuracy is required for up-coming cosmology experiments, including Planck. A more accurate value of the Hubble constant will directly result in other contingently measured cosmological parameters (e.g., Omega_m, Omega_L, & w) having their covariant uncertainties reduced significantly now. Any further improvements using this route will have to await JWST, for which this study is designed to provide a lasting and solid foundation, and ultimately a value of Ho

  5. 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.

  6. Far-Infrared Rotational and Fine-Structure Transition Frequencies and Molecular Constants of 14NO and 15NO in the X2Pi (v = 0) State.

    PubMed

    Varberg; Stroh; Evenson

    1999-07-01

    We have made highly accurate measurements of the absorption spectrum of the 14NO and 15NO isotopomers of nitric oxide in the far-infrared. Pure rotational transitions up to J" = 3712 within the 2Pi1/2 and 2Pi3/2 spin components and several 2Pi3/2 <-- 2Pi1/2 fine-structure transitions were recorded within the ground vibrational state. A least-squares fit to these data combined with some lambda-doubling and rotational transitions measured by previous workers has resulted in accurate values for the rotational, fine, and hyperfine parameters of these two isotopomers. Most of the far-infrared transitions reported here have an experimental uncertainty of about 20 kHz and will be useful for astronomers and atmospheric scientists studying this important molecule. The more accurate calculated frequencies will also be useful as spectroscopic calibration standards. Copyright 1999 Academic Press.

  7. Determination of the molecular complexation constant between alprostadil and alpha-cyclodextrin by conductometry: implications for a freeze-dried formulation.

    PubMed

    Sheehy, Philip M; Ramstad, Tore

    2005-10-04

    The binding constant between alprostadil (PGE1) and alpha-cyclodextrin (alpha-CD) was determined at four temperatures using conductance measurements. Alpha-cyclodextrin is an excipient material in Caverject dual chamber syringe (DCS) that was added to enhance stability. The binding constant was used to calculate the amount of PGE1 free upon reconstitution and injection, since only the free drug is clinically active. The conductivity measurement is based on a decrease in specific conductance as alprostadil is titrated with alpha-CD. The change in conductivity was plotted versus free ligand concentration (alpha-CD) to generate a binding curve. As the value of the binding constant proved to be dependent on substrate concentration, it is really a pseudo binding constant. A value of 742+/-60 M(-1) was obtained for a 0.5 mM solution of alprostadil at 27 degrees C and a value of 550+/-52 M(-1) at 37 degrees C. These results compare favorably to values previously obtained by NMR and capillary electrophoresis. Calculation of the fraction PGE1 free upon reconstitution and injection show it to approach the desired outcome of one. Hence, the amount of drug delivered by Caverject DCS is nominally equivalent to that delivered by Caverject S. Po., a predecessor product that contains no alpha-cyclodextrin.

  8. 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

  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

    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.

  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

    SciTech Connect

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

    2016-02-07

    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. 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

  12. 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.

  13. Determination by NMR of the binding constant for the molecular complex between alprostadil and alpha-cyclodextrin. Implications for a freeze-dried formulation.

    PubMed

    Ramstad, Tore; Hadden, Chad E; Martin, Gary E; Speaker, Stanley M; Teagarden, Dirk L; Thamann, Thomas J

    2005-05-30

    A binding constant was determined for the complexation reaction between alprostadil (PGE1) and alpha-cyclodextrin (alpha-CD). This constant was used to calculate the fraction PGE1 free upon reconstitution of Caverject dual chamber syringe, indicated for the treatment of erectile dysfunction. The determination was based on the measurement of the chemical shift of the C20 methyl protons of PGE1. The observed chemical shift varies as a linear function of the amount of PGE1 bound. The binding constant was obtained from the binding isotherm, a curve of the observed chemical shift versus free ligand (alpha-CD) concentration, through the application of non-linear regression analysis. A value K11 = 966 M(-1) +/- 130 M(-1) (2s), measured at 27 degrees C, was obtained. This value is in good agreement with those reported in the literature. The percent PGE1 free was subsequently calculated for the reconstituted solution and in the corpora cavernosum after injection. The latter showed PGE1 to be delivered essentially quantitatively to the targeted site.

  14. 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.

  15. 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

  16. 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.

  17. Use of an exchange method to estimate the association and dissociation rate constants of cadmium complexes formed with low-molecular-weight organic acids commonly exuded by plant roots.

    PubMed

    Schneider, André; Nguyen, Christophe

    2011-01-01

    Organic acids released from plant roots can form complexes with cadmium (Cd) in the soil solution and influence metal bioavailability not only due to the nature and concentration of the complexes but also due to their lability. The lability of a complex influences its ability to buffer changes in the concentration of free ions (Cd); it depends on the association (, m mol s) and dissociation (, s) rate constants. A resin exchange method was used to estimate and (m mol s), which is the conditional estimate of depending on the calcium (Ca) concentration in solution. The constants were estimated for oxalate, citrate, and malate, three low-molecular-weight organic acids commonly exuded by plant roots and expected to strongly influence Cd uptake by plants. For all three organic acids, the and estimates were around 2.5 10 m mol s and 1.3 × 10 s, respectively. Based on the literature, these values indicate that the Cd- low-molecular-weight organic acids complexes formed between Cd and low-molecular-weight organic acids may be less labile than complexes formed with soil soluble organic matter but more labile than those formed with aminopolycarboxylic chelates.

  18. Fully relativistic rovibrational energies and spectroscopic constants of the lowest X:(1)0(+)g, A':(1)2( u ), A:(1)1 ( u ), B':(1)0(-)u and B:(1)0(+)u states of molecular chlorine.

    PubMed

    Machado, Daniel F S; Silva, Valter H C; Esteves, Cristiano S; Gargano, Ricardo; Macedo, Luiz G M; Mundim, Kleber C; de Oliveira, Heibbe C B

    2012-09-01

    The main goal of this paper is to present the rovibrational energies and spectroscopic constants of the Cl(2) molecular system in the relativistic states [Formula: see text], A':(1)2( u ), A:(1)1( u ), [Formula: see text] and [Formula: see text]. More precisely, we have evaluated the Cl(2) ω ( e ), ω ( e ) x ( e ), ω ( e ) y ( e ), α ( e ), γ ( e ) and B ( e ) rovibrational spectroscopic constants using two different procedures. The first was obtained by combining the rovibrational energies, calculated through solving Schrödinger's nuclear equation and the diatomic rovibrational energy equation. The second was obtained by using the Dunham method. The calculated properties are in good agreement with available experimental data.

  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. Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling

    NASA Astrophysics Data System (ADS)

    Pérez-Castillo, Yunierkis; Froeyen, Matheus; Cabrera-Pérez, Miguel Ángel; Nowé, Ann

    2011-04-01

    Bacterial β-ketoacyl-acyl carrier protein synthase III (FabH) has become an attractive target for the development of new antibacterial agents which can overcome the increased resistance of these pathogens to antibiotics in clinical use. Despite several efforts have been dedicated to find inhibitors for this enzyme, it is not a straightforward task, mainly due its high flexibility which makes difficult the structure-based design of FabH inhibitors. Here, we present for the first time a Molecular Dynamics (MD) study of the E. colil FabH enzyme to explore its conformational space. We compare the flexibility of this enzyme for the unliganded protein and an enzyme-inhibitor complex and find a correspondence between our modeling results and the experimental evidence previously reported for this enzyme. Furthermore, through a 100 ns MD simulation of the unliganded enzyme we extract useful information related to the concerted motions that take place along the principal components of displacement. We also establish a relation between the presence of water molecules in the oxyanion hole with the conformational stability of structural important loops. Representative conformations of the binding pocket along the whole trajectory of the unliganded protein are selected through cluster analysis and we find that they contain a conformational diversity which is not provided by the X-ray structures of ecFabH. As a proof of this last hypothesis, we use a set of 10 FabH inhibitors and show that they cannot be correctly modeled in any available X-ray structure, while by using our set of conformations extracted from the MD simulations, this task can be accomplish. Finally, we show the ability of short MD simulations for the refinement of the docking binding poses and for MM-PBSA calculations to predict stable protein-inhibitor complexes in this enzyme.

  1. Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate.

    PubMed

    Chen, Liao Y

    2015-04-14

    Computing the free energy of binding a ligand to a protein is a difficult task of essential importance for which purpose various theoretical/computational approaches have been pursued. In this paper, we develop a hybrid steered molecular dynamics (hSMD) method capable of resolving one ligand–protein complex within a few wall-clock days with high enough accuracy to compare with the experimental data. This hSMD approach is based on the relationship between the binding affinity and the potential of mean force (PMF) in the established literature. It involves simultaneously steering n (n = 1, 2, 3, ...) centers of mass of n selected segments of the ligand using n springs of infinite stiffness. Steering the ligand from a single initial state chosen from the bound state ensemble to the corresponding dissociated state, disallowing any fluctuations of the pulling centers along the way, one can determine a 3n-dimensional PMF curve connecting the two states by sampling a small number of forward and reverse pulling paths. This PMF constitutes a large but not the sole contribution to the binding free energy. Two other contributors are (1) the partial partition function containing the equilibrium fluctuations of the ligand at the binding site and the deviation of the initial state from the PMF minimum and (2) the partial partition function containing rotation and fluctuations of the ligand around one of the pulling centers that is fixed at a position far from the protein. We implement this hSMD approach for two ligand–protein complexes whose structures were determined and whose binding affinities were measured experimentally: caprylic acid binding to bovine β-lactoglobulin and glutathione binding to Schistosoma japonicum glutathione S-transferase tyrosine 7 to phenylalanine mutant. Our computed binding affinities agree with the experimental data within a factor of 1.5. The total time of computation for these two all-atom model systems (consisting of 96K and 114K atoms

  2. 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

  3. Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H + C2H6 reaction.

    PubMed

    Chakraborty, Arindam; Zhao, Yan; Lin, Hai; Truhlar, Donald G

    2006-01-28

    This article presents a multifaceted study of the reaction H+C(2)H(6)-->H(2)+C(2)H(5) and three of its deuterium-substituted isotopologs. First we present high-level electronic structure calculations by the W1, G3SX, MCG3-MPWB, CBS-APNO, and MC-QCISD/3 methods that lead to a best estimate of the barrier height of 11.8+/-0.5 kcal/mol. Then we obtain a specific reaction parameter for the MPW density functional in order that it reproduces the best estimate of the barrier height; this yields the MPW54 functional. The MPW54 functional, as well as the MPW60 functional that was previously parametrized for the H+CH(4) reaction, is used with canonical variational theory with small-curvature tunneling to calculate the rate constants for all four ethane reactions from 200 to 2000 K. The final MPW54 calculations are based on curvilinear-coordinate generalized-normal-mode analysis along the reaction path, and they include scaled frequencies and an anharmonic C-C bond torsion. They agree with experiment within 31% for 467-826 K except for a 38% deviation at 748 K; the results for the isotopologs are predictions since these rate constants have never been measured. The kinetic isotope effects (KIEs) are analyzed to reveal the contributions from subsets of vibrational partition functions and from tunneling, which conspire to yield a nonmonotonic temperature dependence for one of the KIEs. The stationary points and reaction-path potential of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy surface that combines a semiempirical valence bond formalism for the reactive part of the molecule with a standard molecular mechanics force field for the rest; this may be considered to be either an extension of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum-mechanical/molecular mechanical (QM/MM) method in which the QM part is semiempirical valence bond theory; that is, the new potential

  4. Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H +C2H6 reaction

    NASA Astrophysics Data System (ADS)

    Chakraborty, Arindam; Zhao, Yan; Lin, Hai; Truhlar, Donald G.

    2006-01-01

    This article presents a multifaceted study of the reaction H +C2H6→H2+C2H5 and three of its deuterium-substituted isotopologs. First we present high-level electronic structure calculations by the W1, G3SX, MCG3-MPWB, CBS-APNO, and MC-QCISD/3 methods that lead to a best estimate of the barrier height of 11.8±0.5kcal/mol. Then we obtain a specific reaction parameter for the MPW density functional in order that it reproduces the best estimate of the barrier height; this yields the MPW54 functional. The MPW54 functional, as well as the MPW60 functional that was previously parametrized for the H +CH4 reaction, is used with canonical variational theory with small-curvature tunneling to calculate the rate constants for all four ethane reactions from 200 to 2000 K. The final MPW54 calculations are based on curvilinear-coordinate generalized-normal-mode analysis along the reaction path, and they include scaled frequencies and an anharmonic C-C bond torsion. They agree with experiment within 31% for 467-826 K except for a 38% deviation at 748 K; the results for the isotopologs are predictions since these rate constants have never been measured. The kinetic isotope effects (KIEs) are analyzed to reveal the contributions from subsets of vibrational partition functions and from tunneling, which conspire to yield a nonmonotonic temperature dependence for one of the KIEs. The stationary points and reaction-path potential of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy surface that combines a semiempirical valence bond formalism for the reactive part of the molecule with a standard molecular mechanics force field for the rest; this may be considered to be either an extension of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum-mechanical/molecular mechanical (QM/MM) method in which the QM part is semiempirical valence bond theory; that is, the new potential

  5. BDflex: A method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from Brownian dynamics simulations

    NASA Astrophysics Data System (ADS)

    Greives, Nicholas; Zhou, Huan-Xiang

    2012-10-01

    A method developed by Northrup et al. [J. Chem. Phys. 80, 1517 (1984)], 10.1063/1.446900 for calculating protein-ligand binding rate constants (ka) from Brownian dynamics (BD) simulations has been widely used for rigid molecules. Application to flexible molecules is limited by the formidable computational cost to treat conformational fluctuations during the long BD simulations necessary for ka calculation. Here, we propose a new method called BDflex for ka calculation that circumvents this problem. The basic idea is to separate the whole space into an outer region and an inner region, and formulate ka as the product of kE and bar η _d, which are obtained by separately solving exterior and interior problems. kE is the diffusion-controlled rate constant for the ligand in the outer region to reach the dividing surface between the outer and inner regions; in this exterior problem conformational fluctuations can be neglected. bar η _d is the probability that the ligand, starting from the dividing surface, will react at the binding site rather than escape to infinity. The crucial step in reducing the determination of bar η _d to a problem confined to the inner region is a radiation boundary condition imposed on the dividing surface; the reactivity on this boundary is proportional to kE. By confining the ligand to the inner region and imposing the radiation boundary condition, we avoid multiple-crossing of the dividing surface before reaction at the binding site and hence dramatically cut down the total simulation time, making the treatment of conformational fluctuations affordable. BDflex is expected to have wide applications in problems where conformational fluctuations of the molecules are crucial for productive ligand binding, such as in cases where transient widening of a bottleneck allows the ligand to access the binding pocket, or the binding site is properly formed only after ligand entrance induces the closure of a lid.

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

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-05

    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.

  7. Determination of individual side-chain conformations, tertiary conformations, and molecular topography of tyrocidine A from scalar coupling constants and chemical shifts.

    PubMed

    Kuo, M C; Gibbons, W A

    1979-12-25

    We report for the decapeptide tyrocidine A: (a) H alpha and H beta chemical shifts and scalar coupling constants for most residues of tyrocidine A in methanol-d4 and dimethyl-d6 sulfoxide (Me2so-d6) and the H alpha and H beta chemical shifts for other residues; (b) scalar coupling constants 3J alpha beta for nine side chains in methanol-d4 but only seven side chains in Me2SO-d6, due to chemical shift degeneracy; the Gln9 and Tyr10 side chains in methanol-d4 were only approximately analyzed; (c) a total spin-spin analysis of Pro5 in Me2SO-d6 and, partly by comparison, also in methanol-d4; (d) conversion of 3J alpha beta values to side-chain conformations for all residues in methanol-d4; comparisons, where possible, led to the conclusion that side-chain conformations are similar in methanol-d4 and Me2SO-d6; (e) an absolute conformational analysis of Pro5 from 3J values and a method of assigning all pro-R,S protons; Pro5 has a Ramachandran B, C2-Cexo-Cendo conformation; (f) chi 1, chi 2 conformations of several aromatic residues based upon proton-chromophore distance measurement from anomalous chemical shifts and Johnson-Bovey diagrams; (g) pro-R and pro-S assignments of H beta's from anomalous chemical shifts, high-temperature dependence of anomalous chemical shifts, and backbone side-chain nuclear Overhauser effects; (h) most tertiary conformations of the whole tyrocidine A molecule possessing residues 4--8 and 10 in highly preferred (ca. 90%) chi 1 conformations, but residues 1--3 and 9 having at least two chi 1 rotamers; (2) description of three topographical regions of the molecule--a hydrophobic region, a flat hydrophilic surface on the other side of the molecule, and a hydrophilic region consisting of two peptide backbone units and the side chains of Asn8, Gln9, and Tyr10; (j) proposed side chain, beta-turn, and beta-pleated sheet conformations that readily account for all "normal" and anomalous chemical shifts.

  8. Static dielectric constants and molecular dipole distributions of liquid water and ice-Ih investigated by the PAW-PBE exchange-correlation functional.

    PubMed

    Rusnak, Andrew J; Pinnick, Eric R; Calderon, Camilo E; Wang, Feng

    2012-07-21

    The static dielectric constants, ε(s), of ice-Ih and liquid water were calculated using density functional theory with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the projector-augmented-wave (PAW) approach. Proton disordered ice configurations and uncorrelated liquid configurations were sampled with the electrostatic switching method using force fields specially designed to facilitate the ab initio free energy perturbation calculations. Our results indicate that PAW-PBE underestimates the ε(s) of both ice-Ih and liquid water but predicts the ratio of ice and water ε(s) in good agreement with experimental measurements. PAW-PBE gives average water dipole moments of 2.50 D in ice-Ih and 2.48 D in the liquid. Our results show that the fixed-charge water models developed by adaptive force matching can reproduce the PAW-PBE dipole moments with an error of approximately 5%. The ice and liquid models created in this work have polarizabilities of 1.32 Å(3) and 1.30 Å(3), respectively, along the HOH bisector direction.

  9. Influence of electronic and steric effects on stability constants and electrochemical reversibility of divalent ion complexes with glycine and sarcosine. A glass electrode potentiometric, sampled direct current polarographic, virtual potentiometric, and molecular modelling study.

    PubMed

    Cukrowski, Ignacy; Marques, Helder M; Mkwizu, Tumaini S; Magampa, Philemon P; Serge, Claudette

    2007-05-08

    Cd(II) complexes with glycine (gly) and sarcosine (sar) were studied by glass electrode potentiometry, direct current polarography, virtual potentiometry, and molecular modelling. The electrochemically reversible Cd(II)-glycine-OH labile system was best described by a model consisting of M(HL), ML, ML2, ML3, ML(OH) and ML2(OH) (M = Cd(II), L = gly) with the overall stability constants, as log beta, determined to be 10.30+/-0.05, 4.21+/-0.03, 7.30+/-0.05, 9.84+/-0.04, 8.9+/-0.1, and 10.75+/-0.10, respectively. In case of the electrochemically quasi-reversible Cd(II)-sarcosine-OH labile system, only ML, ML2 and ML3 (M = Cd(II), L = sar) were found and their stability constants, as log beta, were determined to be 3.80+/-0.03, 6.91+/-0.07, and 8.9+/-0.4, respectively. Stability constants for the ML complexes, the prime focus of this work, were thus established with an uncertainty smaller than 0.05 log units. The observed departure from electrochemical reversibility for the Cd-sarcosine-OH system was attributed mainly to the decrease in the transfer coefficient alpha. The MM2 force field, supplemented by additional parameters, reproduced the reported crystal structures of diaqua-bis(glycinato-O,N)nickel(II) and fac-tri(glycinato)-nickelate(II) very well. These parameters were used to predict structures of all possible isomers of (i) [Ni(H2O)4(gly)]+ and [Ni(H2O)4(sar)]+; and (ii) [Ni(H2O)3(IDA)] and [Ni(H2O)3(MIDA)] (IDA = iminodiacetic acid, MIDA = N-methyl iminodiacetic acid) by molecular mechanics/simulated annealing methods. The change in strain energy, deltaU(str), that accompanies the substitution of one ligand by another (ML + L' --> ML' + L), was computed and a strain energy deltaU(str) = +0.28 kcal mol(-1) for the reaction [Ni(H2O)4(gly)]+ + sar --> [Ni(H2O)4(sar)]+ + gly was found. This predicts the monoglycine complex to be marginally more stable. By contrast, for the reaction [Ni(H2O)3IDA] + MIDA --> [Ni(H2O)3MIDA] + IDA, deltaU(str) = -0.64 kcal mol(-1

  10. 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

  11. BDflex: A method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from Brownian dynamics simulations

    PubMed Central

    Greives, Nicholas; Zhou, Huan-Xiang

    2012-01-01

    A method developed by Northrup [J. Chem. Phys. 80, 1517 (1984)]10.1063/1.446900 for calculating protein-ligand binding rate constants (ka) from Brownian dynamics (BD) simulations has been widely used for rigid molecules. Application to flexible molecules is limited by the formidable computational cost to treat conformational fluctuations during the long BD simulations necessary for ka calculation. Here, we propose a new method called BDflex for ka calculation that circumvents this problem. The basic idea is to separate the whole space into an outer region and an inner region, and formulate ka as the product of kE and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}\\bar \\eta _{\\rm d}\\end{equation*} \\end{document}η¯d, which are obtained by separately solving exterior and interior problems. kE is the diffusion-controlled rate constant for the ligand in the outer region to reach the dividing surface between the outer and inner regions; in this exterior problem conformational fluctuations can be neglected. \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}\\bar \\eta _{\\rm d}\\end{equation*} \\end{document}η¯d is the probability that the ligand, starting from the dividing surface, will react at the binding site rather than escape to infinity. The crucial step in reducing the determination of \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin

  12. 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.

  13. Accurate Methods for Large Molecular Systems (Preprint)

    DTIC Science & Technology

    2009-01-06

    Gaussian functions. These basis sets can be used in a systematic way to obtain results approaching the complete basis set ( CBS ) limit. However...convergence to the CBS limit. The high accuracy of these basis sets still comes at a significant computational cost, only feasible on relatively small...J. Chem. Phys. 2006, 124, 114103. (b) ccCA: DeYonker, N. J.; Grimes , T.; Yockel, S.; Dinescu, A.; Mintz, B.; Cundari, T. R.; Wilson, A. K. J. Chem

  14. Accurate Methods for Large Molecular Systems (Postprint)

    DTIC Science & Technology

    2009-01-06

    approaching the complete basis set ( CBS ) limit. However, increasingly large basis sets must be used, and the convergence tends to be slow. Werner has...recently introduced a series of F12 basis sets6 with improved convergence to the CBS limit. The high accuracy of these basis sets still comes at a...DeYonker, N. J.; Grimes , T.; Yockel, S.; Dinescu, A.; Mintz, B.; Cundari, T. R.; Wilson, A. K. J. Chem. Phys. 2006, 125, 104011. (c) ROCBS-QB3: Wood

  15. 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)

  16. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

    NASA Astrophysics Data System (ADS)

    Hu, Hao; Lu, Zhenyu; Parks, Jerry M.; Burger, Steven K.; Yang, Weitao

    2008-01-01

    To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics minimum free-energy path (QM/MM-MFEP) method. In the QM/MM-MFEP method, the thermodynamics of a complex reaction system is described by the potential of mean force (PMF) surface of the quantum mechanical (QM) subsystem with a small number of degrees of freedom, somewhat like describing a reaction process in the gas phase. The main computational cost of the QM/MM-MFEP method comes from the statistical sampling of conformations of the molecular mechanical (MM) subsystem required for the calculation of the QM PMF and its gradient. In our new sequential sampling and optimization approach, we aim to reduce the amount of MM sampling while still retaining the accuracy of the results by first carrying out MM phase-space sampling and then optimizing the QM subsystem in the fixed-size ensemble of MM conformations. The resulting QM optimized structures are then used to obtain more accurate sampling of the MM subsystem. This process of sequential MM sampling and QM optimization is iterated until convergence. The use of a fixed-size, finite MM conformational ensemble enables the precise evaluation of the QM potential of mean force and its gradient within the ensemble, thus circumventing the challenges associated with statistical averaging and significantly speeding up the convergence of the optimization process. To further improve the accuracy of the QM/MM-MFEP method, the reaction path potential method developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004)] is employed to describe the QM/MM electrostatic interactions in an approximate yet accurate way with a computational cost that is comparable to classical MM simulations. The new method was successfully applied to two example reaction processes, the

  17. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

    SciTech Connect

    Hu Hao; Lu Zhenyu; Parks, Jerry M.; Burger, Steven K.; Yang Weitao

    2008-01-21

    To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics minimum free-energy path (QM/MM-MFEP) method. In the QM/MM-MFEP method, the thermodynamics of a complex reaction system is described by the potential of mean force (PMF) surface of the quantum mechanical (QM) subsystem with a small number of degrees of freedom, somewhat like describing a reaction process in the gas phase. The main computational cost of the QM/MM-MFEP method comes from the statistical sampling of conformations of the molecular mechanical (MM) subsystem required for the calculation of the QM PMF and its gradient. In our new sequential sampling and optimization approach, we aim to reduce the amount of MM sampling while still retaining the accuracy of the results by first carrying out MM phase-space sampling and then optimizing the QM subsystem in the fixed-size ensemble of MM conformations. The resulting QM optimized structures are then used to obtain more accurate sampling of the MM subsystem. This process of sequential MM sampling and QM optimization is iterated until convergence. The use of a fixed-size, finite MM conformational ensemble enables the precise evaluation of the QM potential of mean force and its gradient within the ensemble, thus circumventing the challenges associated with statistical averaging and significantly speeding up the convergence of the optimization process. To further improve the accuracy of the QM/MM-MFEP method, the reaction path potential method developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004)] is employed to describe the QM/MM electrostatic interactions in an approximate yet accurate way with a computational cost that is comparable to classical MM simulations. The new method was successfully applied to two example reaction processes, the

  18. Cosmological constant, fine structure constant and beyond

    NASA Astrophysics Data System (ADS)

    Wei, Hao; Zou, Xiao-Bo; Li, Hong-Yu; Xue, Dong-Ze

    2017-01-01

    In the present work, we consider the cosmological constant model Λ ∝ α ^{-6}, which is well motivated from three independent approaches. As is well known, the hint of varying fine structure constant α was found in 1998. If Λ ∝ α ^{-6} is right, it means that the cosmological constant Λ should also be varying. Here, we try to develop a suitable framework to model this varying cosmological constant Λ ∝ α ^{-6}, in which we view it from an interacting vacuum energy perspective. Then we consider the observational constraints on these models by using the 293 Δ α /α data from the absorption systems in the spectra of distant quasars. We find that the model parameters can be tightly constrained to the very narrow ranges of O(10^{-5}) typically. On the other hand, we can also view the varying cosmological constant model Λ ∝ α ^{-6} from another perspective, namely it can be equivalent to a model containing "dark energy" and "warm dark matter", but there is no interaction between them. We find that this is also fully consistent with the observational constraints on warm dark matter.

  19. 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.

  20. 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.

  1. Prediction of nitroxide hyperfine coupling constants in solution from combined nanosecond scale simulations and quantum computations

    NASA Astrophysics Data System (ADS)

    Houriez, Céline; Ferré, Nicolas; Masella, Michel; Siri, Didier

    2008-06-01

    We present a combined theoretical approach based on analyzing molecular dynamics trajectories (at the nanosecond scale) generated by use of classical polarizable force fields and on quantum calculations to compute averaged hyperfine coupling constants. That method is used to estimate the constant of a prototypical nitroxide: the dimethylnitroxide. The molecule is embedded during the simulations in a cubic box containing about 500 water molecules and the molecular dynamics is generated using periodic conditions. Once the trajectories are achieved, the nitroxide and its first hydration shell molecules are extracted, and the coupling constants are computed by considering the latter aggregates by means of quantum computations. However, all the water molecules of the bulk are also accounted for during those computations by means of the electrostatic potential fitted method. Our results exhibit that in order to predict accurate and reliable coupling constants, one needs to describe carefully the out-of-plane motion of the nitroxide nitrogen and to sample trajectories with a time interval of 400 fs at least to generate an uncorrelated large set of nitroxide structures. Compared to Car-Parrinello molecular dynamics techniques, our approach can be used readily to compute hyperfine coupling constants of large systems, such as nitroxides of great size interacting with macromolecules such as proteins or polymers.

  2. Benchmarking singlet and triplet excitation energies of molecular semiconductors for singlet fission: Tuning the amount of HF exchange and adjusting local correlation to obtain accurate functionals for singlet-triplet gaps

    NASA Astrophysics Data System (ADS)

    Brückner, Charlotte; Engels, Bernd

    2017-01-01

    Vertical and adiabatic singlet and triplet excitation energies of molecular p-type semiconductors calculated with various DFT functionals and wave-function based approaches are benchmarked against MS-CASPT2/cc-pVTZ reference values. A special focus lies on the singlet-triplet gaps that are very important in the process of singlet fission. Singlet fission has the potential to boost device efficiencies of organic solar cells, but the scope of existing singlet-fission compounds is still limited. A computational prescreening of candidate molecules could enlarge it; yet it requires efficient methods accurately predicting singlet and triplet excitation energies. Different DFT formulations (Tamm-Dancoff approximation, linear response time-dependent DFT, Δ-SCF) and spin scaling schemes along with several ab initio methods (CC2, ADC(2)/MP2, CIS(D), CIS) are evaluated. While wave-function based methods yield rather reliable singlet-triplet gaps, many DFT functionals are shown to systematically underestimate triplet excitation energies. To gain insight, the impact of exact exchange and correlation is in detail addressed.

  3. 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.

  4. Molecular structure and conformational composition of 1,3-dihydroxyacetone studied by combined analysis of gas-phase electron diffraction data, rotational constants, and results of theoretical calculations. Ideal gas thermodynamic properties of 1,3-dihydroxyacetone.

    PubMed

    Dorofeeva, Olga V; Vogt, Natalja; Vogt, Jürgen; Popik, Mikhail V; Rykov, Anatolii N; Vilkov, Lev V

    2007-07-19

    The molecular structure of 1,3-dihydroxyacetone (DHA) has been studied by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) data, ab initio, and density functional theory calculations. The equilibrium re structure of DHA was determined by a joint analysis of the GED data and rotational constants taken from the literature. The anharmonic vibrational corrections to the internuclear distances (re-ra) and to the rotational constants (B(i)e-B(i)0) needed for the estimation of the re structure were calculated from the B3LYP/cc-pVTZ cubic force field. It was found that the experimental data are well reproduced by assuming that DHA consists of a mixture of three conformers. The most stable conformer of C2v symmetry has two hydrogen bonds, whereas the next two lowest energy conformers (Cs and C1 symmetry) have one hydrogen bond and their abundance is about 30% in total. A combined analysis of GED and MW data led to the following equilibrium structural parameters (re) of the most abundant conformer of DHA (the uncertainties in parentheses are 3 times the standard deviations): r(C=O)=1.215(2) A, r(C-C)=1.516(2) A, r(C-O)=1.393(2) A, r(C-H)=1.096(4) A, r(O-H)=0.967(4) A, angleC-C=O=119.9(2) degrees, angleC-C-O=111.0(2) degrees, angleC-C-H=108.2(7) degrees, angleC-O-H=106.5(7) degrees. These structural parameters reproduce the experimental B(i)0 values within 0.05 MHz. The experimental structural parameters are in good agreement with those obtained from theoretical calculations. Ideal gas thermodynamic functions (S degrees (T), C degrees p(T), and H degrees (T)-H degrees (0)) of DHA were calculated on the basis of experimental and theoretical molecular parameters obtained in this work. The enthalpy of formation of DHA, -523+/-4 kJ/mol, was calculated by the atomization procedure using the G3X method.

  5. 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.

  6. 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.

  7. "Recognizing Numerical Constants"

    NASA Technical Reports Server (NTRS)

    Bailey, David H.; Craw, James M. (Technical Monitor)

    1995-01-01

    The advent of inexpensive, high performance computer and new efficient algorithms have made possible the automatic recognition of numerically computed constants. In other words, techniques now exist for determining, within certain limits, whether a computed real or complex number can be written as a simple expression involving the classical constants of mathematics. In this presentation, some of the recently discovered techniques for constant recognition, notably integer relation detection algorithms, will be presented. As an application of these methods, the author's recent work in recognizing "Euler sums" will be described in some detail.

  8. Science Is Constantly Cool.

    ERIC Educational Resources Information Center

    Eichinger, John

    1996-01-01

    Presents an activity in which students attempt to keep water at a constant temperature. Helps students in grades three to six hone their skills in prediction, observation, measurement, data collection, graphing, data analysis, and communication. (JRH)

  9. 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

  10. 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.

  11. 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.

  12. Spatial and temporal variations of fundamental constants

    NASA Astrophysics Data System (ADS)

    Levshakov, S. A.; Agafonova, I. I.; Molaro, P.; Reimers, D.

    2010-11-01

    Spatial and temporal variations in the electron-to-proton mass ratio, μ, and in the fine-structure constant, α, are not present in the Standard Model of particle physics but they arise quite naturally in grant unification theories, multidimensional theories and in general when a coupling of light scalar fields to baryonic matter is considered. The light scalar fields are usually attributed to a negative pressure substance permeating the entire visible Universe and known as dark energy. This substance is thought to be responsible for a cosmic acceleration at low redshifts, z < 1. A strong dependence of μ and α on the ambient matter density is predicted by chameleon-like scalar field models. Calculations of atomic and molecular spectra show that different transitions have different sensitivities to changes in fundamental constants. Thus, measuring the relative line positions, Δ V, between such transitions one can probe the hypothetical variability of physical constants. In particular, interstellar molecular clouds can be used to test the matter density dependence of μ, since gas density in these clouds is ~15 orders of magnitude lower than that in terrestrial environment. We use the best quality radio spectra of the inversion transition of NH3 (J,K)=(1,1) and rotational transitions of other molecules to estimate the radial velocity offsets, Δ V ≡ Vrot - Vinv. The obtained value of Δ V shows a statistically significant positive shift of 23±4stat±3sys m s-1 (1σ). Being interpreted in terms of the electron-to-proton mass ratio variation, this gives Δμ/μ = (22±4stat±3sys)×10-9. A strong constraint on variation of the quantity F = α2/μ in the Milky Way is found from comparison of the fine-structure transition J=1-0 in atomic carbon C i with the low-J rotational lines in carbon monoxide 13CO arising in the interstellar molecular clouds: |Δ F/F| < 3×10-7. This yields |Δ α/α| < 1.5×10-7 at z = 0. Since extragalactic absorbers have gas densities

  13. Formation of the prebiotic molecule NH2CHO on astronomical amorphous solid water surfaces: accurate tunneling rate calculations† †Electronic supplementary information (ESI) available: Geometric details, lists of calculated rate constants. See DOI: 10.1039/c6cp05727f Click here for additional data file.

    PubMed Central

    Song, Lei

    2016-01-01

    Investigating how formamide forms in the interstellar medium is a hot topic in astrochemistry, which can contribute to our understanding of the origin of life on Earth. We have constructed a QM/MM model to simulate the hydrogenation of isocyanic acid on amorphous solid water surfaces to form formamide. The binding energy of HNCO on the ASW surface varies significantly between different binding sites, we found values between ∼0 and 100 kJ mol–1. The barrier for the hydrogenation reaction is almost independent of the binding energy, though. We calculated tunneling rate constants of H + HNCO → NH2CO at temperatures down to 103 K combining QM/MM with instanton theory. Tunneling dominates the reaction at such low temperatures. The tunneling reaction is hardly accelerated by the amorphous solid water surface compared to the gas phase for this system, even though the activation energy of the surface reaction is lower than the one of the gas-phase reaction. Both the height and width of the barrier affect the tunneling rate in practice. Strong kinetic isotope effects were observed by comparing to rate constants of D + HNCO → NHDCO. At 103 K we found a KIE of 231 on the surface and 146 in the gas phase. Furthermore, we investigated the gas-phase reaction NH2 + H2CO → NH2CHO + H and found it unlikely to occur at cryogenic temperatures. The data of our tunneling rate constants are expected to significantly influence astrochemical models. PMID:27731439

  14. Quantum electrodynamics and fundamental constants

    NASA Astrophysics Data System (ADS)

    Wundt, Benedikt Johannes Wilhelm

    The unprecedented precision achieved both in the experimental measurements as well as in the theoretical description of atomic bound states make them an ideal study object for fundamental physics and the determination of fundamental constants. This requires a careful study of the effects from quantum electrodynamics (QED) on the interaction between the electron and the nucleus. The two theoretical approaches for the evaluation of QED corrections are presented and discussed. Due to the presence of two energy scales from the binding potential and the radiation field, an overlapping parameter has to be used in both approaches in order to separate the energy scales. The different choices for the overlapping parameter in the two methods are further illustrated in a model example. With the nonrelativistic theory, relativistic corrections in order ( Zalpha)2 to the two-photon decay rate of ionic states are calculated, as well as the leading radiative corrections of alpha( Zalpha)2ln[(Zalpha)-2 ]. It is shown that the corrections is gauge-invariant under a "hybrid" gauge transformation between Coulomb and Yennie gauge. Furthermore, QED corrections for Rydberg states in one-electron ions are investigated. The smallness of the corrections and the absence of nuclear size corrections enable very accurate theoretical predictions. Measuring transition frequencies and comparing them to the theoretical predictions, QED theory can be tested more precisely. In turn, this could yield a more accurate value for the Rydberg constant. Using a transition in a nucleus with a well determined mass, acting as a reference, a comparison to transition in other nuclei can even allow to determined nuclear masses. Finally, in order to avoid an additional uncertainty in nuclei with non zero nuclear spin, QED self-energy corrections to the hyperfine structure up to order alpha(Zalpha)2Delta EHFS are determined for highly excited Rydberg states.

  15. Dielectric Constant of Suspensions

    NASA Astrophysics Data System (ADS)

    Mendelson, Kenneth S.; Ackmann, James J.

    1997-03-01

    We have used a finite element method to calculate the dielectric constant of a cubic array of spheres. Extensive calculations support preliminary conclusions reported previously (K. Mendelson and J. Ackmann, Bull. Am. Phys. Soc. 41), 657 (1996).. At frequencies below 100 kHz the real part of the dielectric constant (ɛ') shows oscillations as a function of the volume fraction of suspension. These oscillations disappear at low conductivities of the suspending fluid. Measurements of the dielectric constant (J. Ackmann, et al., Ann. Biomed. Eng. 24), 58 (1996). (H. Fricke and H. Curtis, J. Phys. Chem. 41), 729 (1937). are not sufficiently sensitive to show oscillations but appear to be consistent with the theoretical results.

  16. 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.

  17. Determination of second-order elastic constants of cyclotetramethylene tetranitramine (β-HMX) using impulsive stimulated thermal scattering

    NASA Astrophysics Data System (ADS)

    Sun, B.; Winey, J. M.; Gupta, Y. M.; Hooks, D. E.

    2009-09-01

    The second-order elastic constants for cyclotetramethylene tetranitramine (β-HMX) single crystals were determined using the impulsive stimulated thermal scattering (ISTS) method. Despite the low symmetry of these crystals, the complete set of 13 elastic constants were determined accurately from acoustic velocity measurements using samples cut parallel to three different crystal planes. Our acoustic velocities are consistent with the limited sound speed data available from ultrasonic measurements. However, significant differences are observed between the elastic constants determined from our experiments and those obtained previously using Brillouin scattering. Our results demonstrate the usefulness and efficiency of the ISTS method for determining the full set of elastic constants of low-symmetry molecular crystals, including energetic crystals.

  18. Impact of the molecular structure and adsorption mode of D-π-A dye sensitizers with a pyridyl group in dye-sensitized solar cells on the adsorption equilibrium constant for dye-adsorption on TiO2 surface.

    PubMed

    Ooyama, Yousuke; Yamaguchi, Naoya; Ohshita, Joji; Harima, Yutaka

    2016-12-07

    D-π-A dyes NI-4 bearing a pyridyl group, YNI-1 bearing two pyridyl groups and YNI-2 bearing two thienylpyridyl groups as the anchoring group on the TiO2 surface have been developed as dye sensitizers for dye-sensitized solar cells (DSSCs), where NI-4 and YNI-2 can adsorb onto the TiO2 electrode through the formation of the coordinate bond between the pyridyl group of the dye and the Lewis acid site (exposed Ti(n+) cations) on the TiO2 surface, but YNI-1 is predominantly adsorbed on the TiO2 electrode through the formation of the hydrogen bond between the pyridyl group of the dye and the Brønsted acid sites (surface-bound hydroxyl groups, Ti-OH) on the TiO2 surface. The difference in the dye-adsorption mode among the three dyes on the TiO2 surface has been investigated from the adsorption equilibrium constant (Kad) based on the Langmuir adsorption isotherms. It was found that the Kad values of YNI-1 and YNI-2 are higher than that of NI-4, and more interestingly, the Kad value of YNI-2 is higher than that of YNI-1. This work demonstrates that that for the D-π-A dye sensitizers with the pyridyl group as the anchoring group to the TiO2 surface the number of pyridyl groups and the dye-adsorption mode on the TiO2 electrode as well as the molecular structure of the dye sensitizer affect the Kad value for the adsorption of the dye to the TiO2 electrode, that is, resulting in a difference in the Kad value among the D-π-A dye sensitizers NI-4, YNI-1 and YNI-2.

  19. BIOACCESSIBILITY TESTS ACCURATELY ESTIMATE ...

    EPA Pesticide Factsheets

    Hazards of soil-borne Pb to wild birds may be more accurately quantified if the bioavailability of that Pb is known. To better understand the bioavailability of Pb to birds, we measured blood Pb concentrations in Japanese quail (Coturnix japonica) fed diets containing Pb-contaminated soils. Relative bioavailabilities were expressed by comparison with blood Pb concentrations in quail fed a Pb acetate reference diet. Diets containing soil from five Pb-contaminated Superfund sites had relative bioavailabilities from 33%-63%, with a mean of about 50%. Treatment of two of the soils with P significantly reduced the bioavailability of Pb. The bioaccessibility of the Pb in the test soils was then measured in six in vitro tests and regressed on bioavailability. They were: the “Relative Bioavailability Leaching Procedure” (RBALP) at pH 1.5, the same test conducted at pH 2.5, the “Ohio State University In vitro Gastrointestinal” method (OSU IVG), the “Urban Soil Bioaccessible Lead Test”, the modified “Physiologically Based Extraction Test” and the “Waterfowl Physiologically Based Extraction Test.” All regressions had positive slopes. Based on criteria of slope and coefficient of determination, the RBALP pH 2.5 and OSU IVG tests performed very well. Speciation by X-ray absorption spectroscopy demonstrated that, on average, most of the Pb in the sampled soils was sorbed to minerals (30%), bound to organic matter 24%, or present as Pb sulfate 18%. Ad

  20. Accurate equilibrium structures for piperidine and cyclohexane.

    PubMed

    Demaison, Jean; Craig, Norman C; Groner, Peter; Écija, Patricia; Cocinero, Emilio J; Lesarri, Alberto; Rudolph, Heinz Dieter

    2015-03-05

    Extended and improved microwave (MW) measurements are reported for the isotopologues of piperidine. New ground state (GS) rotational constants are fitted to MW transitions with quartic centrifugal distortion constants taken from ab initio calculations. Predicate values for the geometric parameters of piperidine and cyclohexane are found from a high level of ab initio theory including adjustments for basis set dependence and for correlation of the core electrons. Equilibrium rotational constants are obtained from GS rotational constants corrected for vibration-rotation interactions and electronic contributions. Equilibrium structures for piperidine and cyclohexane are fitted by the mixed estimation method. In this method, structural parameters are fitted concurrently to predicate parameters (with appropriate uncertainties) and moments of inertia (with uncertainties). The new structures are regarded as being accurate to 0.001 Å and 0.2°. Comparisons are made between bond parameters in equatorial piperidine and cyclohexane. Another interesting result of this study is that a structure determination is an effective way to check the accuracy of the ground state experimental rotational constants.

  1. Accurate spectral color measurements

    NASA Astrophysics Data System (ADS)

    Hiltunen, Jouni; Jaeaeskelaeinen, Timo; Parkkinen, Jussi P. S.

    1999-08-01

    Surface color measurement is of importance in a very wide range of industrial applications including paint, paper, printing, photography, textiles, plastics and so on. For a demanding color measurements spectral approach is often needed. One can measure a color spectrum with a spectrophotometer using calibrated standard samples as a reference. Because it is impossible to define absolute color values of a sample, we always work with approximations. The human eye can perceive color difference as small as 0.5 CIELAB units and thus distinguish millions of colors. This 0.5 unit difference should be a goal for the precise color measurements. This limit is not a problem if we only want to measure the color difference of two samples, but if we want to know in a same time exact color coordinate values accuracy problems arise. The values of two instruments can be astonishingly different. The accuracy of the instrument used in color measurement may depend on various errors such as photometric non-linearity, wavelength error, integrating sphere dark level error, integrating sphere error in both specular included and specular excluded modes. Thus the correction formulas should be used to get more accurate results. Another question is how many channels i.e. wavelengths we are using to measure a spectrum. It is obvious that the sampling interval should be short to get more precise results. Furthermore, the result we get is always compromise of measuring time, conditions and cost. Sometimes we have to use portable syste or the shape and the size of samples makes it impossible to use sensitive equipment. In this study a small set of calibrated color tiles measured with the Perkin Elmer Lamda 18 and the Minolta CM-2002 spectrophotometers are compared. In the paper we explain the typical error sources of spectral color measurements, and show which are the accuracy demands a good colorimeter should have.

  2. Redshift in Hubble's constant.

    NASA Astrophysics Data System (ADS)

    Temple-Raston, M.

    1997-01-01

    A topological field theory with Bogomol'nyi solitons is examined. The Bogomol'nyi solitons have much in common with the instanton in Yang-Mills theory; consequently the author called them 'topological instantons'. When periodic boundary conditions are imposed, the field theory comments indirectly on the speed of light within the theory. In this particular model the speed of light is not a universal constant. This may or may not be relevant to the current debate in astronomy and cosmology over the large values of the Hubble constant obtained by the latest generation of ground- and space-based telescopes. An experiment is proposed to detect spatial variation in the speed of light.

  3. 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.

  4. Percolation with Constant Freezing

    NASA Astrophysics Data System (ADS)

    Mottram, Edward

    2014-06-01

    We introduce and study a model of percolation with constant freezing ( PCF) where edges open at constant rate , and clusters freeze at rate independently of their size. Our main result is that the infinite volume process can be constructed on any amenable vertex transitive graph. This is in sharp contrast to models of percolation with freezing previously introduced, where the limit is known not to exist. Our interest is in the study of the percolative properties of the final configuration as a function of . We also obtain more precise results in the case of trees. Surprisingly the algebraic exponent for the cluster size depends on the degree, suggesting that there is no lower critical dimension for the model. Moreover, even for , it is shown that finite clusters have algebraic tail decay, which is a signature of self organised criticality. Partial results are obtained on , and many open questions are discussed.

  5. Solvent effects on zero-point vibrational corrections to optical rotations and nuclear magnetic resonance shielding constants

    NASA Astrophysics Data System (ADS)

    Kongsted, Jacob; Ruud, Kenneth

    2008-01-01

    We present a study of solvent effects on the zero-point vibrational corrections (ZPVC) to optical rotations and nuclear magnetic resonance shielding constants of solvated molecules. The model used to calculate vibrational corrections rely on an expansion of the potential and property surfaces around an effective molecular geometry and includes both harmonic and anharmonic corrections. Numerical examples are presented for ( S)-propylene oxide in various solvents as well as for acetone and the three diazene molecules. We find that solvent effects on the ZPVCs may be significant and in some cases crucial to accurately predict solvent shifts on molecular properties.

  6. Constant-pressure Blowers

    NASA Technical Reports Server (NTRS)

    Sorensen, E

    1940-01-01

    The conventional axial blowers operate on the high-pressure principle. One drawback of this type of blower is the relatively low pressure head, which one attempts to overcome with axial blowers producing very high pressure at a given circumferential speed. The Schicht constant-pressure blower affords pressure ratios considerably higher than those of axial blowers of conventional design with approximately the same efficiency.

  7. Universe of constant

    NASA Astrophysics Data System (ADS)

    Yongquan, Han

    2016-10-01

    The ideal gas state equation is not applicable to ordinary gas, it should be applied to the Electromagnetic ``gas'' that is applied to the radiation, the radiation should be the ultimate state of matter changes or initial state, the universe is filled with radiation. That is, the ideal gas equation of state is suitable for the Singular point and the universe. Maybe someone consider that, there is no vessel can accommodate radiation, it is because the Ordinary container is too small to accommodate, if the radius of your container is the distance that Light through an hour, would you still think it can't accommodates radiation? Modern scientific determinate that the radius of the universe now is about 1027 m, assuming that the universe is a sphere whose volume is approximately: V = 4.19 × 1081 cubic meters, the temperature radiation of the universe (cosmic microwave background radiation temperature of the universe, should be the closest the average temperature of the universe) T = 3.15k, radiation pressure P = 5 × 10-6 N / m 2, according to the law of ideal gas state equation, PV / T = constant = 6 × 1075, the value of this constant is the universe, The singular point should also equal to the constant Author: hanyongquan

  8. The Hubble Constant.

    PubMed

    Jackson, Neal

    2015-01-01

    I review the current state of determinations of the Hubble constant, which gives the length scale of the Universe by relating the expansion velocity of objects to their distance. There are two broad categories of measurements. The first uses individual astrophysical objects which have some property that allows their intrinsic luminosity or size to be determined, or allows the determination of their distance by geometric means. The second category comprises the use of all-sky cosmic microwave background, or correlations between large samples of galaxies, to determine information about the geometry of the Universe and hence the Hubble constant, typically in a combination with other cosmological parameters. Many, but not all, object-based measurements give H0 values of around 72-74 km s(-1) Mpc(-1), with typical errors of 2-3 km s(-1) Mpc(-1). This is in mild discrepancy with CMB-based measurements, in particular those from the Planck satellite, which give values of 67-68 km s(-1) Mpc(-1) and typical errors of 1-2 km s(-1) Mpc(-1). The size of the remaining systematics indicate that accuracy rather than precision is the remaining problem in a good determination of the Hubble constant. Whether a discrepancy exists, and whether new physics is needed to resolve it, depends on details of the systematics of the object-based methods, and also on the assumptions about other cosmological parameters and which datasets are combined in the case of the all-sky methods.

  9. Dielectric constant of water in the interface

    NASA Astrophysics Data System (ADS)

    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.

  10. Quantum electrodynamics, high-resolution spectroscopy and fundamental constants

    NASA Astrophysics Data System (ADS)

    Karshenboim, Savely G.; Ivanov, Vladimir G.

    2017-01-01

    Recent progress in high-resolution spectroscopy has delivered us a variety of accurate optical results, which can be used for the determination of the atomic fundamental constants and for constraining their possible time variation. We present a brief overview of the results discussing in particular, the determination of the Rydberg constant, the relative atomic weight of the electron and proton, their mass ratio and the fine structure constant. Many individual results on those constants are obtained with use of quantum electrodynamics, and we discuss which sectors of QED are involved. We derive constraints on a possible time variation of the fine structure constants and me/mp.

  11. 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.

  12. 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.

  13. 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).

  14. 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.

  15. 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.

  16. 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.

  17. New model accurately predicts reformate composition

    SciTech Connect

    Ancheyta-Juarez, J.; Aguilar-Rodriguez, E. )

    1994-01-31

    Although naphtha reforming is a well-known process, the evolution of catalyst formulation, as well as new trends in gasoline specifications, have led to rapid evolution of the process, including: reactor design, regeneration mode, and operating conditions. Mathematical modeling of the reforming process is an increasingly important tool. It is fundamental to the proper design of new reactors and revamp of existing ones. Modeling can be used to optimize operating conditions, analyze the effects of process variables, and enhance unit performance. Instituto Mexicano del Petroleo has developed a model of the catalytic reforming process that accurately predicts reformate composition at the higher-severity conditions at which new reformers are being designed. The new AA model is more accurate than previous proposals because it takes into account the effects of temperature and pressure on the rate constants of each chemical reaction.

  18. Accurate colorimetric feedback for RGB LED clusters

    NASA Astrophysics Data System (ADS)

    Man, Kwong; Ashdown, Ian

    2006-08-01

    We present an empirical model of LED emission spectra that is applicable to both InGaN and AlInGaP high-flux LEDs, and which accurately predicts their relative spectral power distributions over a wide range of LED junction temperatures. We further demonstrate with laboratory measurements that changes in LED spectral power distribution with temperature can be accurately predicted with first- or second-order equations. This provides the basis for a real-time colorimetric feedback system for RGB LED clusters that can maintain the chromaticity of white light at constant intensity to within +/-0.003 Δuv over a range of 45 degrees Celsius, and to within 0.01 Δuv when dimmed over an intensity range of 10:1.

  19. The Hubble Constant.

    PubMed

    Jackson, Neal

    2007-01-01

    I review the current state of determinations of the Hubble constant, which gives the length scale of the Universe by relating the expansion velocity of objects to their distance. In the last 20 years, much progress has been made and estimates now range between 60 and 75 km s(-1) Mpc(-1), with most now between 70 and 75 km s(-1) Mpc(-1), a huge improvement over the factor-of-2 uncertainty which used to prevail. Further improvements which gave a generally agreed margin of error of a few percent rather than the current 10% would be vital input to much other interesting cosmology. There are several programmes which are likely to lead us to this point in the next 10 years.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Molecular modeling of heterogeneous catalysis

    NASA Astrophysics Data System (ADS)

    Gislason, Jason Joseph

    A novel method for modeling heterogeneous catalysis was developed to further facilitate the understanding of catalytic reactor mechanisms. The method employs molecular dynamics simulations, statistical mechanical, and Unity Bond Index - Quadratic Exponential Potential (UBI-QEP) calculations to calculate the rate constants for reactions on metal surfaces. The primary difficulty of molecular dynamics simulations on metal surfaces has been the lack of reliable reactive potential energy surfaces. We have overcome this through the development of the Normalized Bond Index - Reactive Potential Function (NBI-RPF), which can accurately describe the reaction of adsorbates on metal surfaces. The first calculations of rate constants for a reaction on a metal surface using molecular dynamics simulations are presented. This method is applied to the determination of the mechanism for selective hydrogenation of acetylene in an ethylene rich flow. It was determined that the selectivity for acetylene hydrogenation is attributable to the higher reactivity of acetylene versus ethylene with respect to hydrogenation by molecular hydrogen. It was shown that hydrogen transfer from the carbonaceous layer to acetylene or ethylene is insignificant in the hydrogenation process. Molecular dynamics simulations and molecular mechanics calculations were used to determine the diffusion rate constants for dimethylnaphthalene isomers is mordenite. 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene were found to have similar diffusion rate constants. Grand canonical Monte Carlo calculations were performed on the competitive adsorption of 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene in type X zeolites exchanged individually with barium, calcium, potassium, and rubidium ions, calcium exchanged MCM-22, and hydrogen form mordenite (MOR), X zeolite, Y zeolite, hypBEB, ZSM- 12, and MCM-22. These calculations showed that barium exchanged X zeolite was the most selective toward 2

  5. 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

    2015-06-09

    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.

  6. 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.

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

    PubMed

    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.

  8. 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...

  9. 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.

  10. Benchmark calculations with correlated molecular wave functions. V. The determination of accurate [ital ab] [ital initio] intermolecular potentials for He[sub 2], Ne[sub 2], and Ar[sub 2

    SciTech Connect

    Woon, D.E. )

    1994-02-15

    Dimer interactions of helium, neon, and argon have been studied using the augmented correlation consistent basis sets of Dunning and co-workers. Two correlation methods have been employed throughout; Moller--Plesset perturbation theory through fourth-order (MP4) and single and double excitation coupled-cluster theory with perturbative treatment of triple excitations [CCSD(T)]. Full configuration interaction (FCI) calculations were performed on He[sub 2] for some basis sets. In general, only valence electrons were correlated, although some calculations which also correlated the [ital n]=2 shell of Ar[sub 2] were performed. Dimer potential energy curves were determined using the supermolecule method with and without the counterpoise correction. A series of additional basis sets beyond the augmented correlation consistent sets were explored in which the diffuse region of the radial function space has been systematically saturated. In combination with the systematic expansion across angular function space which is inherent to the correlation consistent prescription, this approach guarantees very accurate atomic polarizabilities and hyperpolarizabilities and should lead to an accurate description of dispersion forces. The best counterpoise-corrected MP4 values for the well depths of the three dimers are (in microhartrees, empirical values in parentheses) He[sub 2], 31.9 (34.6); Ne[sub 2], 123 (134); and Ar[sub 2], 430 (454). The corresponding CCSD(T) values are He[sub 2], 33.1; Ne[sub 2], 128; and Ar[sub 2], 417. Although these values are very good, the nearly exponential convergence of well depth as a function of basis quality afforded by using the various series of correlation consistent basis sets allows estimation of complete basis set (CBS) limiting values. The MP4 estimated CBS limits are He[sub 2], 32.2; Ne[sub 2], 126; and Ar[sub 2], 447.

  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. Accurate Evaluation of Quantum Integrals

    NASA Technical Reports Server (NTRS)

    Galant, D. C.; Goorvitch, D.; Witteborn, Fred C. (Technical Monitor)

    1995-01-01

    Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schrodinger's equation. Important results are that error estimates are provided, and that one can extrapolate expectation values rather than the wavefunctions to obtain highly accurate expectation values. We discuss the eigenvalues, the error growth in repeated Richardson's extrapolation, and show that the expectation values calculated on a crude mesh can be extrapolated to obtain expectation values of high accuracy.

  13. 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.

  14. 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

    2011-04-05

    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.

  15. Is Planck's quantization constant unique?

    NASA Astrophysics Data System (ADS)

    Livadiotis, George

    2016-07-01

    A cornerstone of Quantum Mechanics is the existence of a non-zero least action, the Planck constant. However, the basic concepts and theoretical developments of Quantum Mechanics are independent of its specific numerical value. A different constant h _{*}, similar to the Planck constant h, but ˜12 orders of magnitude larger, characterizes plasmas. The study of >50 different geophysical, space, and laboratory plasmas, provided the first evidence for the universality and the quantum nature of h _{*}, revealing that it is a new quantization constant. The recent results show the diagnostics for determining whether plasmas are characterized by the Planck or the new quantization constant, compounding the challenge to reconcile both quantization constants in quantum mechanics.

  16. Spectral curve fitting of dielectric constants

    NASA Astrophysics Data System (ADS)

    Ruzi, M.; Ennis, C.; Robertson, E. G.

    2017-01-01

    Optical constants are important properties governing the response of a material to incident light. It follows that they are often extracted from spectra measured by absorbance, transmittance or reflectance. One convenient method to obtain optical constants is by curve fitting. Here, model curves should satisfy Kramer-Kronig relations, and preferably can be expressed in closed form or easily calculable. In this study we use dielectric constants of three different molecular ices in the infrared region to evaluate four different model curves that are generally used for fitting optical constants: (1) the classical damped harmonic oscillator, (2) Voigt line shape, (3) Fourier series, and (4) the Triangular basis. Among these, only the classical damped harmonic oscillator model strictly satisfies the Kramer-Kronig relation. If considering the trade-off between accuracy and speed, Fourier series fitting is the best option when spectral bands are broad while for narrow peaks the classical damped harmonic oscillator and the Triangular basis fitting model are the best choice.

  17. QCD coupling constants and VDM

    SciTech Connect

    Erkol, G.; Ozpineci, A.; Zamiralov, V. S.

    2012-10-23

    QCD sum rules for coupling constants of vector mesons with baryons are constructed. The corresponding QCD sum rules for electric charges and magnetic moments are also derived and with the use of vector-meson-dominance model related to the coupling constants. The VDM role as the criterium of reciprocal validity of the sum rules is considered.

  18. 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.

  19. Multiscale reactive molecular dynamics

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    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.

  20. Time constants in thermal laser medicine: II. Distributions of time constants and thermal relaxation of tissue.

    PubMed

    van Gemert, M J; Lucassen, G W; Welch, A J

    1996-08-01

    The thermal response of a semi-infinite medium in air, irradiated by laser light in a cylindrical geometry, cannot accurately be approximately by single radial and axial time constants for heat conduction. This report presents an analytical analysis of hear conduction where the thermal response is expressed in terms of distributions over radial and axial time constants. The source term for heat production is written as the product of a Gaussian shaped radial term and an exponentially shaped axial term. The two terms are expanded in integrals over eigenfunctions of the radial and axial parts of the Laplace heat conduction operator. The result is a double integral over the coupled distributions of the two time constants to compute the temperature rise as a function of time and of axial and radial positions. The distribution of axial time constants is a homogeneous slowly decreasing function of spatial frequency (v) indicating that one single axial time constant cannot reasonably characterize axial heat conduction. The distribution of radial time constants is a function centred around a distinguished maximum in the spatial frequency (lambda) close to the single radial time constant value used previously. This suggests that one radial time constant to characterize radial heat conduction may be a useful concept. Special cases have been evaluated analytically, such as short and long irradiation times, axial or radial heat conduction (shallow or deep penetrating laser beams) and, especially, thermal relaxation (cooling) of the tissue. For shallow penetrating laser beams the asymptotic cooling rate is confirmed to be proportional to [(t)0.5-(t-tL)0.5] which approaches 1/t0.5 for t > tL, where t is the time and tL is the laser pulse duration. For deep penetrating beams this is proportional to 1/(t-tL). For intermediate penetration, i.e. penetration depths about equal to spot size diameters, this is proportional to 1/(t-tL)1.5. The double integral has been evaluated

  1. Constant-force approach to discontinuous potentials.

    PubMed

    Orea, Pedro; Odriozola, Gerardo

    2013-06-07

    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.

  2. Oxygen Michaelis constants for tyrosinase.

    PubMed Central

    Rodríguez-López, J N; Ros, J R; Varón, R; García-Cánovas, F

    1993-01-01

    The Michaelis constant of tyrosinase for oxygen in the presence of monophenols and o-diphenols, which generate a cyclizable o-quinone, has been studied. This constant depends on the nature of the monophenol and o-diphenol and is always lower in the presence of the former than of the latter. From the mechanism proposed for tyrosinase and from its kinetic analysis [Rodríguez-López, J. N., Tudela, J., Varón, R., García-Carmona, F. and García-Cánovas, F. (1992) J. Biol. Chem. 267, 3801-3810] a quantitative ratio has been established between the Michaelis constants for oxygen in the presence of monophenols and their o-diphenols. This ratio is used for the determination of the Michaelis constant for oxygen with monophenols when its value cannot be calculated experimentally. PMID:8352753

  3. Avogadro's Number and Avogadro's Constant

    ERIC Educational Resources Information Center

    Davies, R. O.

    1973-01-01

    Discusses three possible methods of thinking about the implications of the definitions of the Avogadro constant and number. Indicates that there is only one way to arrive at a simple and standard conclusion. (CC)

  4. Varying Constants, Gravitation and Cosmology.

    PubMed

    Uzan, Jean-Philippe

    2011-01-01

    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.

  5. Determining accurate distances to nearby galaxies

    NASA Astrophysics Data System (ADS)

    Bonanos, Alceste Zoe

    2005-11-01

    Determining accurate distances to nearby or distant galaxies is a very simple conceptually, yet complicated in practice, task. Presently, distances to nearby galaxies are only known to an accuracy of 10-15%. The current anchor galaxy of the extragalactic distance scale is the Large Magellanic Cloud, which has large (10-15%) systematic uncertainties associated with it, because of its morphology, its non-uniform reddening and the unknown metallicity dependence of the Cepheid period-luminosity relation. This work aims to determine accurate distances to some nearby galaxies, and subsequently help reduce the error in the extragalactic distance scale and the Hubble constant H 0 . In particular, this work presents the first distance determination of the DIRECT Project to M33 with detached eclipsing binaries. DIRECT aims to obtain a new anchor galaxy for the extragalactic distance scale by measuring direct, accurate (to 5%) distances to two Local Group galaxies, M31 and M33, with detached eclipsing binaries. It involves a massive variability survey of these galaxies and subsequent photometric and spectroscopic follow-up of the detached binaries discovered. In this work, I also present a catalog of variable stars discovered in one of the DIRECT fields, M31Y, which includes 41 eclipsing binaries. Additionally, we derive the distance to the Draco Dwarf Spheroidal galaxy, with ~100 RR Lyrae found in our first CCD variability study of this galaxy. A "hybrid" method of discovering Cepheids with ground-based telescopes is described next. It involves applying the image subtraction technique on the images obtained from ground-based telescopes and then following them up with the Hubble Space Telescope to derive Cepheid period-luminosity distances. By re-analyzing ESO Very Large Telescope data on M83 (NGC 5236), we demonstrate that this method is much more powerful for detecting variability, especially in crowded fields. I finally present photometry for the Wolf-Rayet binary WR 20a

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. Inconstant Planck’s constant

    NASA Astrophysics Data System (ADS)

    Mangano, Gianpiero; Lizzi, Fedele; Porzio, Alberto

    2015-12-01

    Motivated by the Dirac idea that fundamental constants are dynamical variables and by conjectures on quantum structure of space-time at small distances, we consider the possibility that Planck constant ℏ is a time depending quantity, undergoing random Gaussian fluctuations around its measured constant mean value, with variance σ2 and a typical correlation timescale Δt. We consider the case of propagation of a free particle and a one-dimensional harmonic oscillator coherent state, and show that the time evolution in both cases is different from the standard behavior. Finally, we discuss how interferometric experiments or exploiting coherent electromagnetic fields in a cavity may put effective bounds on the value of τ = σ2Δt.

  12. Contribution of molecular flexibility to the elastic-plastic properties of molecular crystal α-RDX

    NASA Astrophysics Data System (ADS)

    Pal, Anirban; Picu, Catalin R.

    2017-01-01

    We show in this work that the mechanical properties of molecular crystals are strongly affected by the flexibility of the constituent molecules. To this end, we explore several kinematically restrained models of the molecular crystal cyclotrimethylene trinitramine in the α phase. We evaluate the effect of gradually removing the flexibility of the molecule on various crystal-scale parameters such as the elastic constants, the lattice parameters, the thermal expansion coefficients, the stacking fault energy and the critical stress for the motion of a dislocation (the Peierls-Nabarro stress). The values of these parameters evaluated with the fully refined, fully flexible atomistic model of the crystal are taken as reference. It is observed that the elastic constants, the lattice parameters and their dependence on pressure, and the thermal expansion coefficient can be accurately predicted with models that consider the NO2 and CH2 groups rigid, and the N-N bonds and the bonds of the triazine ring inextensible. Eliminating the dihedral flexibility of the ring leads to larger errors. The model in which the entire molecule is considered rigid or is mapped to a blob leads to even larger errors. Only the fully flexible, reference model provides accurate values for the stacking fault energy and the Peierls-Nabarro critical stress. Removing any component of the molecular flexibility leads to large errors in these parameters. These results also provide guidance for the development of coarse grained models of molecular crystals.

  13. 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

  14. Cosmological constant from quantum spacetime

    NASA Astrophysics Data System (ADS)

    Majid, Shahn; Tao, Wen-Qing

    2015-06-01

    We show that a hypothesis that spacetime is quantum with coordinate algebra [xi,t ]=λPxi , and spherical symmetry under rotations of the xi, essentially requires in the classical limit that the spacetime metric is the Bertotti-Robinson metric, i.e., a solution of Einstein's equations with a cosmological constant and a non-null electromagnetic field. Our arguments do not give the value of the cosmological constant or the Maxwell field strength, but they cannot both be zero. We also describe the quantum geometry and the full moduli space of metrics that can emerge as classical limits from this algebra.

  15. On flows having constant vorticity

    NASA Astrophysics Data System (ADS)

    Roberts, Paul H.; Wu, Cheng-Chin

    2011-10-01

    Constant vorticity flows of a uniform fluid in a rigid ellipsoidal container rotating at a variable rate are considered. These include librationally driven and precessionally driven flows. The well-known Poincaré solution for precessionally driven flow in a spheroid is generalized to an ellipsoid with unequal principal axes. The dynamic stability of these flows is investigated, and of other flows in which the angular velocity of the container is constant in time. Solutions for the Chandler wobble are discussed. The role of an invariant, called here the Helmholtzian, is examined.

  16. Vibrational force constants for acetaldehyde

    NASA Astrophysics Data System (ADS)

    Nikolova, B.

    1990-05-01

    The vibrational force field of ethanal (acetaldehyde), CH 3CHO, is refined by using procedures with differential increments for the force constants (Commun. Dep. Chem., Bulg. Acad. Sci., 21/3 (1988) 433). The characteristics general valence force constants of the high-dimensional symmetry classes of ethanal, A' of tenth and A″ of fifth order, are determined for the experimental assignment of bands. The low barrier to hindered internal rotation about the single carbon—carbon bond is quantitatively estimated on the grounds of normal vibrational analysis.

  17. 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.

  18. 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

  19. On numerically accurate finite element

    NASA Technical Reports Server (NTRS)

    Nagtegaal, J. C.; Parks, D. M.; Rice, J. R.

    1974-01-01

    A general criterion for testing a mesh with topologically similar repeat units is given, and the analysis shows that only a few conventional element types and arrangements are, or can be made suitable for computations in the fully plastic range. Further, a new variational principle, which can easily and simply be incorporated into an existing finite element program, is presented. This allows accurate computations to be made even for element designs that would not normally be suitable. Numerical results are given for three plane strain problems, namely pure bending of a beam, a thick-walled tube under pressure, and a deep double edge cracked tensile specimen. The effects of various element designs and of the new variational procedure are illustrated. Elastic-plastic computation at finite strain are discussed.

  20. Energy conservation and constants variation.

    NASA Astrophysics Data System (ADS)

    Kraiselburd, L.; Miller Bertolami, M. M.; Sisterna, P.; Vucetich, H.

    If fundamental constants vary, the internal energy of macroscopic bodies should change. This should produce observable effects. It is shown that those effects can produce upper bounds on the variation of much lower than those coming from Eötvös experiments.

  1. Variations of the solar constant

    SciTech Connect

    Sofia, S.

    1981-12-01

    The variations in data received from rocket-borne and balloon-borne instruments are discussed. Indirect techniques to measure and monitor the solar constant are presented. Emphasis is placed on the correlation of data from the Solar Maximum Mission and the Nimbus 7 satellites. Abstracts of individual items from the workshop were prepared separately for the data base.

  2. Constant-bandwidth constant-temperature hot-wire anemometer.

    PubMed

    Ligeza, P

    2007-07-01

    A constant-temperature anemometer (CTA) enables the measurement of fast-changing velocity fluctuations. In the classical solution of CTA, the transmission band is a function of flow velocity. This is a minor drawback when the mean flow velocity does not significantly change, though it might lead to dynamic errors when flow velocity varies over a considerable range. A modification is outlined, whereby an adaptive controller is incorporated in the CTA system such that the anemometer's transmission band remains constant in the function of flow velocity. For that purpose, a second feedback loop is provided, and the output signal from the anemometer will regulate the controller's parameters such that the transmission bandwidth remains constant. The mathematical model of a CTA that has been developed and model testing data allow a through evaluation of the proposed solution. A modified anemometer can be used in measurements of high-frequency variable flows in a wide range of velocities. The proposed modification allows the minimization of dynamic measurement errors.

  3. 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%.

  4. Accurate ab Initio Spin Densities.

    PubMed

    Boguslawski, Katharina; Marti, Konrad H; Legeza, Ors; Reiher, Markus

    2012-06-12

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740].

  5. Dielectric-constant gas thermometry

    NASA Astrophysics Data System (ADS)

    Gaiser, Christof; Zandt, Thorsten; Fellmuth, Bernd

    2015-10-01

    The principles, techniques and results from dielectric-constant gas thermometry (DCGT) are reviewed. Primary DCGT with helium has been used for measuring T-T90 below the triple point of water (TPW), where T is the thermodynamic temperature and T90 is the temperature on the international temperature scale of 1990 (ITS-90), and, in an inverse regime with T as input quantity, for determining the Boltzmann constant at the TPW. Furthermore, DCGT allows the determination of several important material properties including the polarizability of neon and argon as well as the virial coefficients of helium, neon, and argon. With interpolating DCGT (IDCGT), the ITS-90 has been approximated in the temperature range from 4 K to 25 K. An overview and uncertainty budget for each of these applications of DCGT is provided, accompanied by corroborating evidence from the literature or, for IDCGT, a CIPM key comparison.

  6. 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.

  7. Renormalization constants from string theory.

    NASA Astrophysics Data System (ADS)

    di Vecchia, P.; Magnea, L.; Lerda, A.; Russo, R.; Marotta, R.

    The authors review some recent results on the calculation of renormalization constants in Yang-Mills theory using open bosonic strings. The technology of string amplitudes, supplemented with an appropriate continuation off the mass shell, can be used to compute the ultraviolet divergences of dimensionally regularized gauge theories. The results show that the infinite tension limit of string amplitudes corresponds to the background field method in field theory.

  8. 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.

  9. WHY IS THE SOLAR CONSTANT NOT A CONSTANT?

    SciTech Connect

    Li, K. J.; Xu, J. C.; Gao, P. X.; Yang, L. H.; Liang, H. F.; Zhan, L. S.

    2012-03-10

    In order to probe the mechanism of variations of the solar constant on the inter-solar-cycle scale, the total solar irradiance (TSI; the so-called solar constant) in the time interval of 1978 November 7 to 2010 September 20 is decomposed into three components through empirical mode decomposition and time-frequency analyses. The first component is the rotation signal, counting up to 42.31% of the total variation of TSI, which is understood to be mainly caused by large magnetic structures, including sunspot groups. The second is an annual-variation signal, counting up to 15.17% of the total variation, the origin of which is not known at this point in time. Finally, the third is the inter-solar-cycle signal, counting up to 42.52%, which is inferred to be caused by the network magnetic elements in quiet regions, whose magnetic flux ranges from (4.27-38.01) Multiplication-Sign 10{sup 19} Mx.

  10. Constant-pH Molecular Dynamics using Continuous Titration Coordinates

    DTIC Science & Technology

    2007-11-02

    examined in this study: turkey ovomucoid (1OMT),48 bovine trypsin inhibi- tor (1BPTI),49 hen egg white lysozyme (193L),50 and ribonuclease A (7RSA).51 For... lysozyme and RNase are presented in Tables V and VI. In Table V, we have included, for comparison, the averaged results of Bürgi et al.,21 which only...states and conformational states of a protein are sampled in an explicit solvent environment. Their simulation of lysozyme entailed the explicit treatment

  11. Constant-Frequency Pulsed Phase-Locked-Loop Measuring Device

    NASA Technical Reports Server (NTRS)

    Yost, William T.; Cantrell, John H.; Kushnick, Peter W.

    1992-01-01

    Constant-frequency pulsed phase-locked-loop measuring device is sensitive to small changes in phase velocity and easily automated. Based on use of fixed-frequency oscillator in measuring small changes in ultrasonic phase velocity when sample exposed to such changes in environment as changes in pressure and temperature. Automatically balances electrical phase shifts against acoustical phase shifts to obtain accurate measurements of acoustical phase shifts.

  12. 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.

  13. 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.

  14. 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

  15. Assessing uncertainty in physical constants

    NASA Astrophysics Data System (ADS)

    Henrion, Max; Fischhoff, Baruch

    1986-09-01

    Assessing the uncertainty due to possible systematic errors in a physical measurement unavoidably involves an element of subjective judgment. Examination of historical measurements and recommended values for the fundamental physical constants shows that the reported uncertainties have a consistent bias towards underestimating the actual errors. These findings are comparable to findings of persistent overconfidence in psychological research on the assessment of subjective probability distributions. Awareness of these biases could help in interpreting the precision of measurements, as well as provide a basis for improving the assessment of uncertainty in measurements.

  16. Tolman length and rigidity constants of the Lennard-Jones fluid.

    PubMed

    Wilhelmsen, Øivind; Bedeaux, Dick; Reguera, David

    2015-02-14

    It is well-known that the surface tension of small droplets and bubbles deviates significantly from that at the planar interface. In this work, we analyze the leading corrections in the curvature expansion of the surface tension, i.e., the Tolman length and the rigidity constants, using a "hybrid" square gradient theory, where the local Helmholtz energy density is described by an accurate equation of state. We particularize this analysis for the case of the truncated and shifted Lennard-Jones fluid, and are then able to reproduce the surface tensions and Tolman length from recent molecular dynamics simulations within their accuracy. The obtained constants in the curvature expansion depend little on temperature, except in the vicinity of the critical point. When the bubble/droplet radius becomes comparable to the interfacial width at coexistence, the critical bubble/droplet prefers to change its density, rather than to decrease its size, and the curvature expansion is no longer sufficient to describe the change in surface tension. We find that the radius of the bubble/droplet in this region is proportional to the correlation length between fluctuations in the liquid-phase.

  17. 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

  18. Cosmological constant and local gravity

    SciTech Connect

    Bernabeu, Jose; Espinoza, Catalina; Mavromatos, Nick E.

    2010-04-15

    We discuss the linearization of Einstein equations in the presence of a cosmological constant, by expanding the solution for the metric around a flat Minkowski space-time. We demonstrate that one can find consistent solutions to the linearized set of equations for the metric perturbations, in the Lorentz gauge, which are not spherically symmetric, but they rather exhibit a cylindrical symmetry. We find that the components of the gravitational field satisfying the appropriate Poisson equations have the property of ensuring that a scalar potential can be constructed, in which both contributions, from ordinary matter and {Lambda}>0, are attractive. In addition, there is a novel tensor potential, induced by the pressure density, in which the effect of the cosmological constant is repulsive. We also linearize the Schwarzschild-de Sitter exact solution of Einstein's equations (due to a generalization of Birkhoff's theorem) in the domain between the two horizons. We manage to transform it first to a gauge in which the 3-space metric is conformally flat and, then, make an additional coordinate transformation leading to the Lorentz gauge conditions. We compare our non-spherically symmetric solution with the linearized Schwarzschild-de Sitter metric, when the latter is transformed to the Lorentz gauge, and we find agreement. The resulting metric, however, does not acquire a proper Newtonian form in terms of the unique scalar potential that solves the corresponding Poisson equation. Nevertheless, our solution is stable, in the sense that the physical energy density is positive.

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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.

  5. Stability analysis of 4-species Aβ aggregation model: A novel approach to obtaining physically meaningful rate constants.

    PubMed

    Ghag, G; Ghosh, P; Mauro, A; Rangachari, V; Vaidya, A

    2013-11-01

    Protein misfolding and concomitant aggregation towards amyloid formation is the underlying biochemical commonality among a wide range of human pathologies. Amyloid formation involves the conversion of proteins from their native monomeric states (intrinsically disordered or globular) to well-organized, fibrillar aggregates in a nucleation-dependent manner. Understanding the mechanism of aggregation is important not only to gain better insight into amyloid pathology but also to simulate and predict molecular pathways. One of the main impediments in doing so is the stochastic nature of interactions that impedes thorough experimental characterization and the development of meaningful insights. In this study, we have utilized a well-known intermediate state along the amyloid-β peptide aggregation pathway called protofibrils as a model system to investigate the molecular mechanisms by which they form fibrils using stability and perturbation analysis. Investigation of protofibril aggregation mechanism limits both the number of species to be modeled (monomers, and protofibrils), as well as the reactions to two (elongation by monomer addition, and protofibril-protofibril lateral association). Our new model is a reduced order four species model grounded in mass action kinetics. Our prior study required 3200 reactions, which makes determining the reaction parameters prohibitively difficult. Using this model, along with a linear perturbation argument, we rigorously determine stable ranges of rate constants for the reactions and ensure they are physically meaningful. This was accomplished by finding the ranges in which the perturbations dieout in a five-parameter sweep, which includes the monomer and protofibril equilibrium concentrations and three of the rate constants. The results presented are a proof-of-concept method in determining meaningful rate constants that can be used as a bonafide way for determining accurate rate constants for other models involving complex

  6. Accurate Scientific Visualization in Research and Physics Teaching

    NASA Astrophysics Data System (ADS)

    Wendler, Tim

    2011-10-01

    Accurate visualization is key in the expression and comprehension of physical principles. Many 3D animation software packages come with built-in numerical methods for a variety of fundamental classical systems. Scripting languages give access to low-level computational functionality, thereby revealing a virtual physics laboratory for teaching and research. Specific examples will be presented: Galilean relativistic hair, energy conservation in complex systems, scattering from a central force, and energy transfer in bi-molecular reactions.

  7. Elasticity of crystalline molecular explosives

    DOE PAGES

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

    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

  8. 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.

  9. Dependence of rate constants on vibrational temperatures - An Arrhenius description

    NASA Technical Reports Server (NTRS)

    Ford, D. I.; Johnson, R. E.

    1988-01-01

    An interpretation of the variation of rate constants with vibrational temperature is proposed which introduces parameters analogous to those of the classical Arrhenius expression. The constancy of vibrational activation energy is studied for the dissociaton of NO, the ion-molecular reaction of O(+) with N2, and the atom exchange reaction of I with H2. It is found that when a Boltzmann distribution for vibrational states is applicable, the variation of the rate constant with the vibrational temperature can be used to define a vibrational activation energy. The method has application to exchange reactions where a vibrational energy threshold exists.

  10. When Rate Constants Are Not Enough.

    PubMed

    Barker, John R; Frenklach, Michael; Golden, David M

    2015-07-16

    Real-world chemical systems consisting of multiple isomers and multiple reaction channels often react significantly prior to attaining a steady state energy distribution (SED). Detailed elementary reaction models, which implicitly require SED conditions, may be invalid when non-steady-state energy distributions (NSED) exist. NSED conditions may result in reaction rates and product yields that are different from those expected for SED conditions, although this problem is to some extent reduced by using phenomenological models and rate constants. The present study defines pragmatic diagnostics useful for identifying NSED conditions in stochastic master equation simulations. A representative example is presented for each of four classes of common combustion species: RO2 radicals, aliphatic hydrocarbons, alkyl radicals, and polyaromatic radicals. An example selected from the seminal work of Tsang et al. demonstrates that stochastic simulations and eigenvalue methods for solving the master equation predict the same NSED effects. NSED effects are common under relatively moderate combustion conditions, and accurate simulations may require a master equation analysis.

  11. Constant magnification optical tracking system

    NASA Technical Reports Server (NTRS)

    Frazer, R. E. (Inventor)

    1982-01-01

    A constant magnification optical tracking system for continuously tracking of a moving object is described. In the tracking system, a traveling objective lens maintains a fixed relationship with an object to be optically tracked. The objective lens was chosen to provide a collimated light beam oriented in the direction of travel of the moving object. A reflective surface is attached to the traveling objective lens for reflecting an image of the moving object. The object to be tracked is a free-falling object which is located at the focal point of the objective lens for at least a portion of its free-fall path. A motor and control means is provided for mantaining the traveling objective lens in a fixed relationship relative to the free-falling object, thereby keeping the free-falling object at the focal point and centered on the axis of the traveling objective lens throughout its entire free-fall path.

  12. 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

  13. Omnidirectional antenna having constant phase

    DOEpatents

    Sena, Matthew

    2017-04-04

    Various technologies presented herein relate to constructing and/or operating an antenna having an omnidirectional electrical field of constant phase. The antenna comprises an upper plate made up of multiple conductive rings, a lower ground-plane plate, a plurality of grounding posts, a conical feed, and a radio frequency (RF) feed connector. The upper plate has a multi-ring configuration comprising a large outer ring and several smaller rings of equal size located within the outer ring. The large outer ring and the four smaller rings have the same cross-section. The grounding posts ground the upper plate to the lower plate while maintaining a required spacing/parallelism therebetween.

  14. 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

  15. 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.

  16. 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.

  17. Search for a Variation of Fundamental Constants

    NASA Astrophysics Data System (ADS)

    Ubachs, W.

    2013-06-01

    Since the days of Dirac scientists have speculated about the possibility that the laws of nature, and the fundamental constants appearing in those laws, are not rock-solid and eternal but may be subject to change in time or space. Such a scenario of evolving constants might provide an answer to the deepest puzzle of contemporary science, namely why the conditions in our local Universe allow for extreme complexity: the fine-tuning problem. In the past decade it has been established that spectral lines of atoms and molecules, which can currently be measured at ever-higher accuracies, form an ideal test ground for probing drifting constants. This has brought this subject from the realm of metaphysics to that of experimental science. In particular the spectra of molecules are sensitive for probing a variation of the proton-electron mass ratio μ, either on a cosmological time scale, or on a laboratory time scale. A comparison can be made between spectra of molecular hydrogen observed in the laboratory and at a high redshift (z=2-3), using the Very Large Telescope (Paranal, Chile) and the Keck telescope (Hawaii). This puts a constraint on a varying mass ratio Δμ/μ at the 10^{-5} level. The optical work can also be extended to include CO molecules. Further a novel direction will be discussed: it was discovered that molecules exhibiting hindered internal rotation have spectral lines in the radio-spectrum that are extremely sensitive to a varying proton-electron mass ratio. Such lines in the spectrum of methanol were recently observed with the radio-telescope in Effelsberg (Germany). F. van Weerdenburg, M.T. Murphy, A.L. Malec, L. Kaper, W. Ubachs, Phys. Rev. Lett. 106, 180802 (2011). A. Malec, R. Buning, M.T. Murphy, N. Milutinovic, S.L. Ellison, J.X. Prochaska, L. Kaper, J. Tumlinson, R.F. Carswell, W. Ubachs, Mon. Not. Roy. Astron. Soc. 403, 1541 (2010). E.J. Salumbides, M.L. Niu, J. Bagdonaite, N. de Oliveira, D. Joyeux, L. Nahon, W. Ubachs, Phys. Rev. A 86, 022510

  18. 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.

  19. Spin-rotation and NMR shielding constants in HCl

    NASA Astrophysics Data System (ADS)

    Jaszuński, Michał; Repisky, Michal; Demissie, Taye B.; Komorovsky, Stanislav; Malkin, Elena; Ruud, Kenneth; Garbacz, Piotr; Jackowski, Karol; Makulski, Włodzimierz

    2013-12-01

    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 1H35Cl are CCl = -53.914 kHz and CH = 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.

  20. Vibrational Constants for Triatomic Molecules from Fourth-Order Perturbation Theory

    NASA Astrophysics Data System (ADS)

    Matthews, Devin A.; Gong, Justin Z.; Stanton, John F.

    2013-06-01

    The second vibrational anharmonicity constants (y_{ijk}) for general non-linear triatomic molecules as derived from fourth-order Rayleigh-Schrödinger perturbation theory (VPT4) are presented. The derived constants include all force field and Coriolis terms from the Watson Hamiltonian except for the pseudopotential. The basic theory of VPT4 is discussed, particularly with application to molecular constants, as well as the computational methods used to derive the specific constants. Finally, the constants are analyzed in the context of model systems such as Morse and double-well potentials.

  1. Is There a Cosmological Constant?

    NASA Astrophysics Data System (ADS)

    Kochanek, Christopher

    2002-07-01

    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

  2. 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

  3. Determination of the Avogadro Constant by Counting the Atoms in a Si28 Crystal

    NASA Astrophysics Data System (ADS)

    Andreas, B.; Azuma, Y.; Bartl, G.; Becker, P.; Bettin, H.; Borys, M.; Busch, I.; Gray, M.; Fuchs, P.; Fujii, K.; Fujimoto, H.; Kessler, E.; Krumrey, M.; Kuetgens, U.; Kuramoto, N.; Mana, G.; Manson, P.; Massa, E.; Mizushima, S.; Nicolaus, A.; Picard, A.; Pramann, A.; Rienitz, O.; Schiel, D.; Valkiers, S.; Waseda, A.

    2011-01-01

    The Avogadro constant links the atomic and the macroscopic properties of matter. Since the molar Planck constant is well known via the measurement of the Rydberg constant, it is also closely related to the Planck constant. In addition, its accurate determination is of paramount importance for a definition of the kilogram in terms of a fundamental constant. We describe a new approach for its determination by counting the atoms in 1 kg single-crystal spheres, which are highly enriched with the Si28 isotope. It enabled isotope dilution mass spectroscopy to determine the molar mass of the silicon crystal with unprecedented accuracy. The value obtained, NA=6.02214078(18)×1023mol-1, is the most accurate input datum for a new definition of the kilogram.

  4. Determination of the Avogadro constant by counting the atoms in a 28Si crystal.

    PubMed

    Andreas, B; Azuma, Y; Bartl, G; Becker, P; Bettin, H; Borys, M; Busch, I; Gray, M; Fuchs, P; Fujii, K; Fujimoto, H; Kessler, E; Krumrey, M; Kuetgens, U; Kuramoto, N; Mana, G; Manson, P; Massa, E; Mizushima, S; Nicolaus, A; Picard, A; Pramann, A; Rienitz, O; Schiel, D; Valkiers, S; Waseda, A

    2011-01-21

    The Avogadro constant links the atomic and the macroscopic properties of matter. Since the molar Planck constant is well known via the measurement of the Rydberg constant, it is also closely related to the Planck constant. In addition, its accurate determination is of paramount importance for a definition of the kilogram in terms of a fundamental constant. We describe a new approach for its determination by counting the atoms in 1 kg single-crystal spheres, which are highly enriched with the 28Si isotope. It enabled isotope dilution mass spectroscopy to determine the molar mass of the silicon crystal with unprecedented accuracy. The value obtained, NA = 6.022,140,78(18) × 10(23) mol(-1), is the most accurate input datum for a new definition of the kilogram.

  5. Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.

    PubMed

    Wallace, Jason A; Wang, Yuhang; Shi, Chuanyin; Pastoor, Kevin J; Nguyen, Bao-Linh; Xia, Kai; Shen, Jana K

    2011-12-01

    Proton uptake or release controls many important biological processes, such as energy transduction, virus replication, and catalysis. Accurate pK(a) prediction informs about proton pathways, thereby revealing detailed acid-base mechanisms. Physics-based methods in the framework of molecular dynamics simulations not only offer pK(a) predictions but also inform about the physical origins of pK(a) shifts and provide details of ionization-induced conformational relaxation and large-scale transitions. One such method is the recently developed continuous constant pH molecular dynamics (CPHMD) method, which has been shown to be an accurate and robust pK(a) prediction tool for naturally occurring titratable residues. To further examine the accuracy and limitations of CPHMD, we blindly predicted the pK(a) values for 87 titratable residues introduced in various hydrophobic regions of staphylococcal nuclease and variants. The predictions gave a root-mean-square deviation of 1.69 pK units from experiment, and there were only two pK(a)'s with errors greater than 3.5 pK units. Analysis of the conformational fluctuation of titrating side-chains in the context of the errors of calculated pK(a) values indicate that explicit treatment of conformational flexibility and the associated dielectric relaxation gives CPHMD a distinct advantage. Analysis of the sources of errors suggests that more accurate pK(a) predictions can be obtained for the most deeply buried residues by improving the accuracy in calculating desolvation energies. Furthermore, it is found that the generalized Born implicit-solvent model underlying the current CPHMD implementation slightly distorts the local conformational environment such that the inclusion of an explicit-solvent representation may offer improvement of accuracy.

  6. THE POSSIBLE INTERSTELLAR ANION CH{sub 2}CN{sup -}: SPECTROSCOPIC CONSTANTS, VIBRATIONAL FREQUENCIES, AND OTHER CONSIDERATIONS

    SciTech Connect

    Fortenberry, Ryan C.; Lee, Timothy J.; Crawford, T. Daniel E-mail: Timothy.J.Lee@nasa.gov

    2013-01-10

    The A {sup 1}B{sub 1} Leftwards-Open-Headed-Arrow X-tilde{sup 1}A' excitation into the dipole-bound state of the cyanomethyl anion (CH{sub 2}CN{sup -}) has been hypothesized as the carrier for one diffuse 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 fields and second-order vibrational perturbation theory to compute accurate spectroscopic constants and fundamental vibrational frequencies for X-tilde{sup 1} A' CH{sub 2}CN{sup -} in order to assist in laboratory studies and astronomical observations.

  7. 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

  8. 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.

  9. 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.

  10. Equilibrium star formation in a constant Q disc: model optimization and initial tests

    NASA Astrophysics Data System (ADS)

    Zheng, Zheng; Meurer, Gerhardt R.; Heckman, Timothy M.; Thilker, David A.; Zwaan, Martin A.

    2013-10-01

    We develop a model for the distribution of the interstellar medium (ISM) and star formation in galaxies based on recent studies that indicate that galactic discs stabilize to a constant stability parameter, which we combine with prescriptions of how the phases of the ISM are determined and for the star formation law (SFL). The model predicts the gas surface mass density and star formation intensity of a galaxy given its rotation curve, stellar surface mass density and the gas velocity dispersion. This model is tested on radial profiles of neutral and molecular ISM surface mass density and star formation intensity of 12 galaxies selected from the H I Nearby Galaxy Survey sample. Our tests focus on intermediate radii (0.3 to 1 times the optical radius) because there are insufficient data to test the outer discs and the fits are less accurate in detail in the centre. Nevertheless, the model produces reasonable agreement with the ISM mass and star formation rate integrated over the central region in all but one case. To optimize the model, we evaluate four recipes for the stability parameter, three recipes for apportioning the ISM into molecular and neutral components, and eight versions of the SFL. We find no clear-cut best prescription for the two-fluid (gas and stars) stability parameter Q2f and therefore for simplicity, we use the Wang and Silk approximation (QWS). We found that an empirical scaling between the molecular-to-neutral ISM ratio (Rmol) and the stellar surface mass density proposed by Leroy et al. works marginally better than the other two prescriptions for this ratio in predicting the ISM profiles, and noticeably better in predicting the star formation intensity from the ISM profiles produced by our model with the SFLs we tested. Thus, in the context of our modelled ISM profiles, the linear molecular SFL and the two-component SFL work better than the other prescriptions we tested. We incorporate these relations into our `constant Q disc' model.

  11. 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.

  12. 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.

  13. Virtual Screening Using Molecular Simulations

    PubMed Central

    Yang, Tianyi; Wu, Johnny C.; Yan, Chunli; Wang, Yuanfeng; Luo, Ray; Gonzales, Michael B.; Dalby, Kevin N.; Ren, Pengyu

    2011-01-01

    Effective virtual screening relies on our ability to make accurate prediction of protein-ligand binding, which remains a great challenge. In this work, utilizing the molecular-mechanics Poisson-Boltzmann (or Generalized Born) Surface Area approach, we have evaluated the binding affinity of a set of 156 ligands to seven families of proteins, trypsin β, thrombin α, cyclin-dependent kinase (CDK), cAMP-dependent kinase (PKA), urokinase-type plasminogen activator, β-glucosidase A and coagulation factor Xa. The effect of protein dielectric constant in the implicit-solvent model on the binding free energy calculation is shown to be important. The statistical correlations between the binding energy calculated from the implicit-solvent approach and experimental free energy are in the range 0.56~0.79 across all the families. This performance is better than that of typical docking programs especially given that the latter is directly trained using known binding data while the molecular mechanics is based on general physical parameters. Estimation of entropic contribution remains the barrier to accurate free energy calculation. We show that the traditional rigid rotor harmonic oscillator approximation is unable to improve the binding free energy prediction. Inclusion of conformational restriction seems to be promising but requires further investigation. On the other hand, our preliminary study suggests that implicit-solvent based alchemical perturbation, which offers explicit sampling of configuration entropy, can be a viable approach to significantly improve the prediction of binding free energy. Overall, the molecular mechanics approach has the potential for medium to high-throughput computational drug discovery. PMID:21491494

  14. Measurements of the dielectric constants for planetary volatiles

    NASA Technical Reports Server (NTRS)

    Anicich, Vincent G.; Huntress, Wesley T., Jr.

    1987-01-01

    The model of Titan at present has the surface temperature, pressure, and composition such that there is a possibility of a binary ethane-methane ocean. Proposed experiments for future Titan flybys include microwave mappers. Very little has been measured of the dielectric properties of the small hydrocarbons at these radar frequencies. An experiment was conducted utilizing a slotted line to measure the dielectric properties of the hydrocarbons, methane to heptane, from room temperature to -180 C. Measurements of the real part of the dielectric constants are accurate to + or - 0.006 and the imaginary part (the loss tangent) of the liquids studied is less than or equal to 0.001. In order to verify this low loss tangent, the real part of the dielectric constant of hexane at 25 C was studied as a function of the frequency range of the slotted line system used. The dielectric constant of hexane at room temperature, between 500 MHz and 3 MHz, is constant within experimental error.

  15. Accurate van der Waals coefficients from density functional theory

    PubMed Central

    Tao, Jianmin; Perdew, John P.; Ruzsinszky, Adrienn

    2012-01-01

    The van der Waals interaction is a weak, long-range correlation, arising from quantum electronic charge fluctuations. This interaction affects many properties of materials. A simple and yet accurate estimate of this effect will facilitate computer simulation of complex molecular materials and drug design. Here we develop a fast approach for accurate evaluation of dynamic multipole polarizabilities and van der Waals (vdW) coefficients of all orders from the electron density and static multipole polarizabilities of each atom or other spherical object, without empirical fitting. Our dynamic polarizabilities (dipole, quadrupole, octupole, etc.) are exact in the zero- and high-frequency limits, and exact at all frequencies for a metallic sphere of uniform density. Our theory predicts dynamic multipole polarizabilities in excellent agreement with more expensive many-body methods, and yields therefrom vdW coefficients C6, C8, C10 for atom pairs with a mean absolute relative error of only 3%. PMID:22205765

  16. 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.

  17. 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.

  18. Harmonic undulator radiations with constant magnetic field

    NASA Astrophysics Data System (ADS)

    Jeevakhan, Hussain; Mishra, G.

    2015-01-01

    Harmonic undulators has been analysed in the presence of constant magnetic field along the direction of main undulator field. The spectrum modifications in harmonic undulator radiations and intensity degradation as a function of constant magnetic field magnitude at fundamental and third harmonics have been evaluated with a numerical integration method and generalised Bessel function. The role of harmonic field to overcome the intensity reduction due to constant magnetic field and energy spread in electron beam has also been demonstrated.

  19. 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.

  20. 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.

  1. On the calculation of resonances by means of analytic continuation in coupling constant

    NASA Astrophysics Data System (ADS)

    Horáček, J.; Paidarová, I.

    2010-11-01

    The method of analytic continuation in the coupling constant in combination with the use of statistical Padé approximation designed to determine resonance parameters is introduced. It is shown that standard quantum chemistry codes provide accurate data which can be used for the process of analytic continuation in coupling constant. Resonance parameters, both the energy and the width, can be inferred for real molecules with accuracy comparable to other more elaborated methods.

  2. Critical role of morphology on the dielectric constant of semicrystalline polyolefins.

    PubMed

    Misra, Mayank; Mannodi-Kanakkithodi, Arun; Chung, T C; Ramprasad, Rampi; Kumar, Sanat K

    2016-06-21

    A particularly attractive method to predict the dielectric properties of materials is density functional theory (DFT). While this method is very popular, its large computational requirements allow practical treatments of unit cells with just a small number of atoms in an ordered array, i.e., in a crystalline morphology. By comparing DFT and Molecular Dynamics (MD) simulations on the same ordered arrays of functional polyolefins, we confirm that both methodologies yield identical estimates for the dipole moments and hence the ionic component of the dielectric storage modulus. Additionally, MD simulations of more realistic semi-crystalline morphologies yield estimates for this polar contribution that are in good agreement with the limited experiments in this field. However, these predictions are up to 10 times larger than those for pure crystalline simulations. Here, we show that the constraints provided by the surrounding chains significantly impede dipolar relaxations in the crystalline regions, whereas amorphous chains must sample all configurations to attain their fully isotropic spatial distributions. These results, which suggest that the amorphous phase is the dominant player in the context, argue strongly that the proper polymer morphology needs to be modeled to ensure accurate estimates of the ionic component of the dielectric constant.

  3. The time constant of the somatogravic illusion.

    PubMed

    Correia Grácio, B J; de Winkel, K N; Groen, E L; Wentink, M; Bos, J E

    2013-02-01

    Without visual feedback, humans perceive tilt when experiencing a sustained linear acceleration. This tilt illusion is commonly referred to as the somatogravic illusion. Although the physiological basis of the illusion seems to be well understood, the dynamic behavior is still subject to discussion. In this study, the dynamic behavior of the illusion was measured experimentally for three motion profiles with different frequency content. Subjects were exposed to pure centripetal accelerations in the lateral direction and were asked to indicate their tilt percept by means of a joystick. Variable-radius centrifugation during constant angular rotation was used to generate these motion profiles. Two self-motion perception models were fitted to the experimental data and were used to obtain the time constant of the somatogravic illusion. Results showed that the time constant of the somatogravic illusion was on the order of two seconds, in contrast to the higher time constant found in fixed-radius centrifugation studies. Furthermore, the time constant was significantly affected by the frequency content of the motion profiles. Motion profiles with higher frequency content revealed shorter time constants which cannot be explained by self-motion perception models that assume a fixed time constant. Therefore, these models need to be improved with a mechanism that deals with this variable time constant. Apart from the fundamental importance, these results also have practical consequences for the simulation of sustained accelerations in motion simulators.

  4. Regularizing cosmological singularities by varying physical constants

    SciTech Connect

    Dąbrowski, Mariusz P.; Marosek, Konrad E-mail: k.marosek@wmf.univ.szczecin.pl

    2013-02-01

    Varying physical constant cosmologies were claimed to solve standard cosmological problems such as the horizon, the flatness and the Λ-problem. In this paper, we suggest yet another possible application of these theories: solving the singularity problem. By specifying some examples we show that various cosmological singularities may be regularized provided the physical constants evolve in time in an appropriate way.

  5. Water dimer equilibrium constant of saturated vapor

    NASA Astrophysics Data System (ADS)

    Malomuzh, N. P.; Mahlaichuk, V. N.; Khrapatyi, S. V.

    2014-08-01

    The value and temperature dependence of the dimerization constant for saturated water vapor are determined. A general expression that links the second virial coefficient and the dimerization constant is obtained. It is shown that the attraction between water monomers and dimers is fundamental, especially at T > 350 K. The range of application for the obtained results is determined.

  6. Cosmological constant from the emergent gravity perspective

    NASA Astrophysics Data System (ADS)

    Padmanabhan, T.; Padmanabhan, Hamsa

    2014-05-01

    Observations indicate that our universe is characterized by a late-time accelerating phase, possibly driven by a cosmological constant Λ, with the dimensionless parameter Λ {LP2} ˜= 10-122, where LP = (Għ/c3)1/2 is the Planck length. In this review, we describe how the emergent gravity paradigm provides a new insight and a possible solution to the cosmological constant problem. After reviewing the necessary background material, we identify the necessary and sufficient conditions for solving the cosmological constant problem. We show that these conditions are naturally satisfied in the emergent gravity paradigm in which (i) the field equations of gravity are invariant under the addition of a constant to the matter Lagrangian and (ii) the cosmological constant appears as an integration constant in the solution. The numerical value of this integration constant can be related to another dimensionless number (called CosMIn) that counts the number of modes inside a Hubble volume that cross the Hubble radius during the radiation and the matter-dominated epochs of the universe. The emergent gravity paradigm suggests that CosMIn has the numerical value 4π, which, in turn, leads to the correct, observed value of the cosmological constant. Further, the emergent gravity paradigm provides an alternative perspective on cosmology and interprets the expansion of the universe itself as a quest towards holographic equipartition. We discuss the implications of this novel and alternate description of cosmology.

  7. Acquisition of accurate data from intramolecular quenched fluorescence protease assays.

    PubMed

    Arachea, Buenafe T; Wiener, Michael C

    2017-04-01

    The Intramolecular Quenched Fluorescence (IQF) protease assay utilizes peptide substrates containing donor-quencher pairs that flank the scissile bond. Following protease cleavage, the dequenched donor emission of the product is subsequently measured. Inspection of the IQF literature indicates that rigorous treatment of systematic errors in observed fluorescence arising from inner-filter absorbance (IF) and non-specific intermolecular quenching (NSQ) is incompletely performed. As substrate and product concentrations vary during the time-course of enzyme activity, iterative solution of the kinetic rate equations is, generally, required to obtain the proper time-dependent correction to the initial velocity fluorescence data. Here, we demonstrate that, if the IQF assay is performed under conditions where IF and NSQ are approximately constant during the measurement of initial velocity for a given initial substrate concentration, then a simple correction as a function of initial substrate concentration can be derived and utilized to obtain accurate initial velocity data for analysis.

  8. 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.

  9. 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.

  10. Machine Learning of Parameters for Accurate Semiempirical Quantum Chemical Calculations

    PubMed Central

    2015-01-01

    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. PMID:26146493

  11. 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)

  12. 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

  13. 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.

  14. Machine Learning of Parameters for Accurate Semiempirical Quantum Chemical Calculations.

    PubMed

    Dral, Pavlo O; von Lilienfeld, O Anatole; Thiel, Walter

    2015-05-12

    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.

  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. 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.

  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. Elastic constant determination of hardwoods using ultrasonic insertion technique.

    PubMed

    Mat Daud, Anis Nazihah; Jaafar, Rosly; Ayop, Shahrul Kadri; Yaacob, Mohd Ikhwan Hadi; Rohani, Md Supar

    2017-03-01

    Ultrasonic insertion technique (IT) is an ultrasonic technique which involves sample immersion in a solution to determine its acoustic properties. IT is normally used to determine the acoustic properties of a medical phantom. We proposed the use of IT as an alternative technique to the common contact ultrasonic technique: through-transmission technique (TT) for determining the elastic constant of hardwoods in longitudinal, tangential and radial directions. The elastic constant of twelve rectangular-shaped Malaysian hardwoods from three different categories; heavy, medium and light with the density ranging from 602 to 992kgm(-3) were determined using IT and TT. Both techniques were carried out at 24.0°C surrounding temperature and utilized 2.25MHz ultrasonic transducers. Data from both techniques were compared to validate the use of the proposed technique. Findings indicated that IT offers consistent and accurate results for, tangential and radial elastic constants (TEC and REC) within 8.89% and 5.86% differences, respectively compared to TT for all tested hardwoods. IT offers an alternative technique for TEC and REC determinations of precious wood samples.

  19. 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).

  20. NMR shielding and spin-rotation constants in XCO (X = Ni, Pd, Pt) molecules

    NASA Astrophysics Data System (ADS)

    Demissie, Taye B.; Jaszuński, Michał; Malkin, Elena; Komorovský, Stanislav; Ruud, Kenneth

    2015-07-01

    Ab initio nonrelativistic and four-component relativistic DFT (density functional theory) methods are combined to study the spin-rotation and absolute nuclear magnetic resonance (NMR) shielding constants of group 10 transition metal monocarbonyls. Good agreement is obtained between the calculated and available experimental data for the spin-rotation constants and shielding spans for PdCO and PtCO. These data allow us to determine accurate absolute chemical shielding constants for all the nuclei, as well as for the unknown spin-rotation constants. We compare the four-component shielding constants with those obtained from the spin-orbit zeroth-order regular approximation, together with an assessment of the performance of different basis sets. For the first time, relativistically optimised basis sets for the heavy atoms used in the four-component calculations are shown to give converged results for both magnetic properties studied. We dedicate this article to the memory of Professor Nicholas C. Handy.

  1. 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.

  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. 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

    2009-03-07

    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

  4. The second acidic constant of salicylic acid.

    PubMed

    Porto, Raffaella; De Tommaso, Gaetano; Furia, Emilia

    2005-01-01

    The second dissociation constant of salicylic acid (H2L) has been determined, at 25 degrees C, in NaCl ionic media by UV spectrophotometric measurements. The investigated ionic strength values were 0.16, 0.25, 0.50, 1.0, 2.0 and 3.0 M. The protolysis constants calculated at the different ionic strengths yielded, with the Specific Interaction Theory, the infinite dilution constant, log beta1(0) = 13.62 +/- 0.03, for the equilibrium L2- + H+ <==> HL-. The interaction coefficient between Na+ and L2-, b(Na+, L2-) = 0.02 +/- 0.07, has been also calculated.

  5. 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.

  6. Improved Lebesgue constants on the triangle

    NASA Astrophysics Data System (ADS)

    Heinrichs, Wilhelm

    2005-08-01

    New sets of points with improved Lebesgue constants in the triangle are calculated. Starting with the Fekete points a direct minimization process for the Lebesgue constant leads to better results. The points and corresponding quadrature weigths are explicitly given. It is quite surprising that the optimal points are not symmetric. The points along the boundary of the triangle are the 1D Gauss-Lobatto points. For all degrees, our points yield the smallest Lebesgue constants currently known. Numerical examples are presented, which show the improved interpolation properties of our nodes.

  7. The cosmological constant and cold dark matter

    NASA Astrophysics Data System (ADS)

    Efstathiou, G.; Sutherland, W. J.; Maddox, S. J.

    1990-12-01

    It is argued here that the success of the cosmological cold dark matter (CDM) model can be retained and the new observations of very large scale cosmological structures can be accommodated in a spatially flat cosmology in which as much as 80 percent of the critical density is provided by a positive cosmological constant. In such a universe, expansion was dominated by CDM until a recent epoch, but is now governed by the cosmological constant. This constant can also account for the lack of fluctuations in the microwave background and the large number of certain kinds of objects found at high redshift.

  8. 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.

  9. Marshak waves: Constant flux vs constant T-a (slight) paradigm shift

    SciTech Connect

    Rosen, M.D.

    1994-12-22

    We review the basic scaling laws for Marshak waves and point out the differences in results for wall loss, albedo, and Marshak depth when a constant absorbed flux is considered as opposed to a constant absorbed temperature. Comparisons with LASNEX simulations and with data are presented that imply that a constant absorbed flux is a more appropriate boundary condition.

  10. 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

  11. Explicit equations for two-dimensional water waves with constant vorticity.

    PubMed

    Ruban, V P

    2008-03-01

    Governing equations for two-dimensional inviscid free-surface flows with constant vorticity over arbitrary nonuniform bottom profile are presented in exact and compact form using conformal variables. An efficient and very accurate numerical method for this problem is developed.

  12. 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.

  13. The Cosmological Constant in Quantum Cosmology

    SciTech Connect

    Wu Zhongchao

    2008-10-10

    Hawking proposed that the cosmological constant is probably zero in quantum cosmology in 1984. By using the right configuration for the wave function of the universe, a complete proof is found very recently.

  14. 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)

  15. 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)

  16. Beyond lensing by the cosmological constant

    NASA Astrophysics Data System (ADS)

    Faraoni, Valerio; Lapierre-Léonard, Marianne

    2017-01-01

    The long-standing problem of whether the cosmological constant affects directly the deflection of light caused by a gravitational lens is reconsidered. We use a new approach based on the Hawking quasilocal mass of a sphere grazed by light rays and on its splitting into local and cosmological parts. Previous literature restricted to the cosmological constant is extended to any form of dark energy accelerating the universe in which the gravitational lens is embedded.

  17. Low-Dielectric-Constant Polyimide Fibers

    NASA Technical Reports Server (NTRS)

    Dorogy, William E., Jr.; Proctor, K. Mason; St. Clair, Anne K.

    1994-01-01

    In experiments performed at NASA Langley Research Center, low-dielectric-constant polyimide fibers produced by use of resin extrusion. These fibers also have high thermal stability and good tensile properties. Useful in industrial and aerospace applications in which fibers required to have dielectric constants less than 3, high thermal stability, and tensile properties in range of those of standard textile fibers. Potential applications include use in printed circuit-boards and in aircraft composites.

  18. A theoretical study of the NMR spin-spin coupling constants of the complexes [(NC)(5)Pt-Tl(CN)(n)](n-) (n = 0-3) and [(NC)(5)Pt-Tl-Pt(CN)(5)](3-): a lesson on environmental effects.

    PubMed

    Autschbach, Jochen; Le Guennic, Boris

    2003-11-05

    The molecular geometries and the nuclear spin-spin coupling constants of the complexes [(NC)(5)Pt-Tl(CN)(n)](n-), n = 0-3, and the related system [(NC)(5)Pt-Tl-Pt(CN)(5)](3-) are studied. These complexes have received considerable interest since the first characterization of the n = 1 system by Glaser and co-workers in 1995 [J. Am. Chem. Soc. 1995, 117, 7550-7551]. For instance, these systems exhibit outstanding NMR properties, such as extremely large Pt-Tl spin-spin coupling constants. For the present work, all nuclear spin-spin coupling constants J(Pt-Tl), J(Pt-C), and J(Tl-C) have been computed by means of a two-component relativistic density functional approach. It is demonstrated by the application of increasingly accurate computational models that both the huge J(Pt-Tl) for the complex (NC)(5)Pt-Tl and the whole experimental trend among the series are entirely due to solvent effects. An approximate inclusion of the bulk solvent effects by means of a continuum model, in addition to the direct coordination, proves to be crucial. Similarly drastic effects are reported for the coupling constants between the heavy atoms and the carbon nuclei. A computational model employing the statistical average of orbital-dependent model potentials (SAOP) in addition to the solvent effects allows to accurately reproduce the experimental coupling constants within reasonable limits.

  19. 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…

  20. Inflation with a constant rate of roll

    SciTech Connect

    Motohashi, Hayato; Starobinsky, Alexei A.; Yokoyama, Jun'ichi E-mail: alstar@landau.ac.ru

    2015-09-01

    We consider an inflationary scenario where the rate of inflaton roll defined by {sup ··}φ/H φ-dot 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. An Accurate, Simplified Model Intrabeam Scattering

    SciTech Connect

    Bane, Karl LF

    2002-05-23

    Beginning with the general Bjorken-Mtingwa solution for intrabeam scattering (IBS) we derive an accurate, greatly simplified model of IBS, valid for high energy beams in normal storage ring lattices. In addition, we show that, under the same conditions, a modified version of Piwinski's IBS formulation (where {eta}{sub x,y}{sup 2}/{beta}{sub x,y} has been replaced by {Eta}{sub x,y}) asymptotically approaches the result of Bjorken-Mtingwa.

  7. An accurate registration technique for distorted images

    NASA Technical Reports Server (NTRS)

    Delapena, Michele; Shaw, Richard A.; Linde, Peter; Dravins, Dainis

    1990-01-01

    Accurate registration of International Ultraviolet Explorer (IUE) images is crucial because the variability of the geometrical distortions that are introduced by the SEC-Vidicon cameras ensures that raw science images are never perfectly aligned with the Intensity Transfer Functions (ITFs) (i.e., graded floodlamp exposures that are used to linearize and normalize the camera response). A technique for precisely registering IUE images which uses a cross correlation of the fixed pattern that exists in all raw IUE images is described.

  8. On accurate determination of contact angle

    NASA Technical Reports Server (NTRS)

    Concus, P.; Finn, R.

    1992-01-01

    Methods are proposed that exploit a microgravity environment to obtain highly accurate measurement of contact angle. These methods, which are based on our earlier mathematical results, do not require detailed measurement of a liquid free-surface, as they incorporate discontinuous or nearly-discontinuous behavior of the liquid bulk in certain container geometries. Physical testing is planned in the forthcoming IML-2 space flight and in related preparatory ground-based experiments.

  9. Analysis of laminated beams with a layer-wise constant shear theory

    NASA Astrophysics Data System (ADS)

    Davalos, Julio F.; Kim, Youngchan; Barbero, Ever J.

    Based on generalized laminate plate theory, the formulation of a one-dimensional beam finite element with layer-wise constant shear (BLCS) is presented. The linear layer-wise representation of in-plane displacements permit accurate computation of normal stresses and transverse shear stresses on each layer for laminated beams with dissimilar ply stiffnesses. The BLCS formulation is equivalent to a first-order shear deformation beam theory (Timoshenko beam theory) on each layer. For the accurate computation of interlaminar shear stresses, the layer-wise constant shear stresses obtained from constitutive relations are transformed into parabolic shear stress distributions in a post-processing operation described in detail. The accuracy of the BLCS element is demonstrated by solving several numerical examples reported in the literature. While retaining the simplicity of a laminated beam theory, the element predicts results as accurate as much more complex elasticity analyses, and it is suitable to model frame-type structures.

  10. Equilibrium morphologies and effective spring constants of capillary bridges.

    PubMed

    Kusumaatmaja, Halim; Lipowsky, Reinhard

    2010-12-21

    We theoretically study the behavior of a liquid bridge formed between a pair of rigid and parallel plates. The plates are smooth, they may either be homogeneous or decorated by circular patches of more hydrophilic domains, and they are generally not identical. We calculate the mechanical equilibrium distance of the liquid bridge as a function of liquid volume, contact angle, and radius of the chemical domain. We show that a liquid bridge can be an equilibrium configuration as long as the sum of the contact angles at the two walls is larger than 180°. When comparisons are possible, our results agree well with recent analytical and molecular dynamics simulation results. We also derive the effective spring constant of the liquid bridge as it is perturbed from its equilibrium distance. The spring constant diverges when the sum of the contact angles is 180° and is finite otherwise. The value of the spring constant decreases with increasing contact angle and volume, and the rate at which it decreases depends strongly on the properties of the two plates.

  11. 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

  12. Phototransformation rate constants of PAHs associated with soot particles.

    PubMed

    Kim, Daekyun; Young, Thomas M; Anastasio, Cort

    2013-01-15

    Photodegradation is a key process governing the residence time and fate of polycyclic aromatic hydrocarbons (PAHs) in particles, both in the atmosphere and after deposition. We have measured photodegradation rate constants of PAHs in bulk deposits of soot particles illuminated with simulated sunlight. The photodegradation rate constants at the surface (k(p)(0)), the effective diffusion coefficients (D(eff)), and the light penetration depths (z(0.5)) for PAHs on soot layers of variable thickness were determined by fitting experimental data with a model of coupled photolysis and diffusion. The overall disappearance rates of irradiated low molecular weight PAHs (with 2-3 rings) on soot particles were influenced by fast photodegradation and fast diffusion kinetics, while those of high molecular weight PAHs (with 4 or more rings) were apparently controlled by either the combination of slow photodegradation and slow diffusion kinetics or by very slow diffusion kinetics alone. The value of z(0.5) is more sensitive to the soot layer thickness than the k(p)(0) value. As the thickness of the soot layer increases, the z(0.5) values increase, but the k(p)(0) values are almost constant. The effective diffusion coefficients calculated from dark experiments are generally higher than those from the model fitting method for illumination experiments. Due to the correlation between k(p)(0) and z(0.5) in thinner layers, D(eff) should be estimated by an independent method for better accuracy. Despite some limitations of the model used in this study, the fitted parameters were useful for describing empirical results of photodegradation of soot-associated PAHs.

  13. 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.

  14. The role of the medium on the acid dissociation constants of some azo dyes in view of experimental and theoretical data

    NASA Astrophysics Data System (ADS)

    Ebead, Y. H.

    2010-10-01

    In this study, the p Ka values of some azo dyes derived from cyclohexane-1,3-dione in different organic solvent + water mixtures have been determined spectrophotometrically. The organic solvents used are ethanol, acetone and N, N-dimethylformamide (DMF). Thus, the nature and the proportion of the organic cosolvent effects as well as the molecular structure on acidity constants were evaluated. Furthermore, the proton-donating ability of N 10H reflected by thermodynamic parameters - Δ f,298Ho, Δ 298So and Δ f,298Go - for compounds 1- 4 has been estimated using AM1and PM6 methods in the gas and aqueous phases. The data obtained provides a complete and accurate picture of the acid-base properties of the compounds under study. The p Ka values predicted in aqueous phase by the previous methods were compared with the experimental values and the best agreement with the experimental data was obtained by AM1.

  15. (In)validity of the constant field and constant currents assumptions in theories of ion transport.

    PubMed Central

    Syganow, A; von Kitzing, E

    1999-01-01

    Constant electric fields and constant ion currents are often considered in theories of ion transport. Therefore, it is important to understand the validity of these helpful concepts. The constant field assumption requires that the charge density of permeant ions and flexible polar groups is virtually voltage independent. We present analytic relations that indicate the conditions under which the constant field approximation applies. Barrier models are frequently fitted to experimental current-voltage curves to describe ion transport. These models are based on three fundamental characteristics: a constant electric field, negligible concerted motions of ions inside the channel (an ion can enter only an empty site), and concentration-independent energy profiles. An analysis of those fundamental assumptions of barrier models shows that those approximations require large barriers because the electrostatic interaction is strong and has a long range. In the constant currents assumption, the current of each permeating ion species is considered to be constant throughout the channel; thus ion pairing is explicitly ignored. In inhomogeneous steady-state systems, the association rate constant determines the strength of ion pairing. Among permeable ions, however, the ion association rate constants are not small, according to modern diffusion-limited reaction rate theories. A mathematical formulation of a constant currents condition indicates that ion pairing very likely has an effect but does not dominate ion transport. PMID:9929480

  16. 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.

  17. 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).

  18. Second Yamabe constant on Riemannian products

    NASA Astrophysics Data System (ADS)

    Henry, Guillermo

    2017-04-01

    Let (Mm , g) be a closed Riemannian manifold (m ≥ 2) of positive scalar curvature and (Nn , h) any closed manifold. We study the asymptotic behaviour of the second Yamabe constant and the second N-Yamabe constant of (M × N , g + th) as t goes to + ∞. We obtain that lim t → + ∞Y2(M × N , [ g + th ]) =2 2/m+n Y(M ×Rn , [ g +ge ]) . If n ≥ 2, we show the existence of nodal solutions of the Yamabe equation on (M × N , g + th) (provided t large enough). When sg is constant, we prove that lim t → + ∞ YN2 (M × N , g + th) =2 2/m+n YRn(M ×Rn , g +ge) . Also we study the second Yamabe invariant and the second N-Yamabe invariant.

  19. Construction and experimental testing of the constant-bandwidth constant-temperature anemometer.

    PubMed

    Ligeza, P

    2008-09-01

    A classical constant-temperature hot-wire anemometer enables the measurement of fast-changing flow velocity fluctuations, although its transmission bandwidth is a function of measured velocity. This may be a source of significant dynamic errors. Incorporation of an adaptive controller into the constant-temperature system results in hot-wire anemometer operating with a constant transmission bandwidth. The construction together with the results of experimental testing of a constant-bandwidth hot-wire anemometer prototype are presented in this article. During the testing, an approximately constant transmission bandwidth of the anemometer was achieved. The constant-bandwidth hot-wire anemometer can be used in measurements of high-frequency variable flows characterized by a wide range of velocity changes.

  20. 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.

  1. Accurate measurement of unsteady state fluid temperature

    NASA Astrophysics Data System (ADS)

    Jaremkiewicz, Magdalena

    2017-03-01

    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.

  2. 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.

  3. 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.

  4. Accurate length control of supramolecular oligomerization: Vernier assemblies.

    PubMed

    Hunter, Christopher A; Tomas, Salvador

    2006-07-12

    Linear oligomeric supramolecular assemblies of defined length have been generated using the Vernier principle. Two molecules, containing a different number (n and m) of mutually complementary binding sites, separated by the same distance, interact with each other to form an assembly of length (n x m). The assembly grows in the same way as simple supramolecular polymers, but at a molecular stop signal, when the binding sites come into register, the assembly terminates giving an oligomer of defined length. This strategy has been realized using tin and zinc porphyrin oligomers as the molecular building blocks. In the presence of isonicotinic acid, a zinc porphyrin trimer and a tin porphyrin dimer form a 3:4 triple stranded Vernier assembly six porphyrins long. The triple strand Vernier architecture introduced here adds an additional level of cooperativity, yielding a stability and selectivity that cannot be achieved via a simple Vernier approach. The assembly properties of the system were characterized using fluorescence titrations and size-exclusion chromatography (SEC). Assembly of the Vernier complex is efficient at micromolar concentrations in nonpolar solvents, and under more competitive conditions, a variety of fragmentation assemblies can be detected, allowing determination of the stability constants for this system and detailed speciation profiles to be constructed.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Degravitation of the cosmological constant in bigravity

    NASA Astrophysics Data System (ADS)

    Platscher, Moritz; Smirnov, Juri

    2017-03-01

    In this article the phenomenon of degravitation of the cosmological constant is studied in the framework of bigravity. It is demonstrated that despite a sizable value of the cosmological constant its gravitational effect can be only mild. The bigravity framework is chosen for this demonstration as it leads to a consistent, ghost-free theory of massive gravity. We show that degravitation takes place in the limit where the physical graviton is dominantly a gauge invariant metric combination. We present and discuss several phenomenological consequences expected in this regime.

  14. Porous low dielectric constant materials for microelectronics.

    PubMed

    Baklanov, Mikhail R; Maex, Karen

    2006-01-15

    Materials with a low dielectric constant are required as interlayer dielectrics for the on-chip interconnection of ultra-large-scale integration devices to provide high speed, low dynamic power dissipation and low cross-talk noise. The selection of chemical compounds with low polarizability and the introduction of porosity result in a reduced dielectric constant. Integration of such materials into microelectronic circuits, however, poses a number of challenges, as the materials must meet strict requirements in terms of properties and reliability. These issues are the subject of the present paper.

  15. 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.

  16. Computational models of molecular self-organization in cellular environments.

    PubMed

    LeDuc, Philip; Schwartz, Russell

    2007-01-01

    The cellular environment creates numerous obstacles to efficient chemistry, as molecular components must navigate through a complex, densely crowded, heterogeneous, and constantly changing landscape in order to function at the appropriate times and places. Such obstacles are especially challenging to self-organizing or self-assembling molecular systems, which often need to build large structures in confined environments and typically have high-order kinetics that should make them exquisitely sensitive to concentration gradients, stochastic noise, and other non-ideal reaction conditions. Yet cells nonetheless manage to maintain a finely tuned network of countless molecular assemblies constantly forming and dissolving with a robustness and efficiency generally beyond what human engineers currently can achieve under even carefully controlled conditions. Significant advances in high-throughput biochemistry and genetics have made it possible to identify many of the components and interactions of this network, but its scale and complexity will likely make it impossible to understand at a global, systems level without predictive computational models. It is thus necessary to develop a clear understanding of how the reality of cellular biochemistry differs from the ideal models classically assumed by simulation approaches and how simulation methods can be adapted to accurately reflect biochemistry in the cell, particularly for the self-organizing systems that are most sensitive to these factors. In this review, we present approaches that have been undertaken from the modeling perspective to address various ways in which self-organization in the cell differs from idealized models.

  17. 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.

  18. Theoretical study of the nitrogen atom hyperfine coupling constant

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Chong, Delano P.

    1988-01-01

    The nitrogen-atom isotropic hyperfine coupling constant A(iso) is studied as a function of improvements in both the one-particle and n-particle basis sets. The study underscores the importance of diffuse basis functions. For example, the (9s 5p) primitive set of Huzinaga (1965) augmented with an even-tempered diffuse s function yields values for A(iso) that are virtually identical to an energy-optimized (23s 12p) even-tempered set. The A(iso) constant is found to converge relatively quickly with increasing l quantum numbers: d, f, and g functions are estimated to contribute 2.5 + or - 0.2, 0.4 + or - 0.1, and 0.05 + or - 0.05 MHz, respectively. Full CI calibration calculations indicate that very high levels of correlation treatment are required for quantitative results. In addition, a strong coupling is observed between the one-particle and n-particle requirements. The best result, 10.4 MHz, is in excellent agreement with the accurate experimental value of 10.4509 MHz.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. The Avogadro constant: determining the number of atoms in a single-crystal ²⁸Si sphere.

    PubMed

    Becker, Peter; Bettin, Horst

    2011-10-28

    The Avogadro constant, the number of entities in an amount of substance of one mole, links the atomic and the macroscopic properties of matter. Since the molar Planck constant--the product of the Planck constant and the Avogadro constant--is very well known via the measurement of the Rydberg constant, the Avogadro constant is also closely related to the Planck constant. In addition, its accurate determination is of paramount importance for a new definition of the kilogram in terms of a fundamental constant. Here, we describe a new and unique approach to determine the Avogadro constant from the number of atoms in 1 kg single-crystal spheres that are highly enriched with the (28)Si isotope. This approach has enabled us to apply isotope dilution mass spectroscopy to determine the molar mass of the silicon crystal with unprecedented accuracy. The value obtained, N(A)=6.022 140 82(18)×10(23) mol(-1), is now the most accurate input datum for a new definition of the kilogram.

  4. Calculation of Dielectric Response in Molecular Solids for High Capacitance Organic Dielectrics

    NASA Astrophysics Data System (ADS)

    Heitzer, Henry Matthew

    The dielectric response of a material is critically important in numerous scientific processes spanning the fields of biology, chemistry, materials science, and physics. While important across these fundamental disciplines, it remains difficult to determine theoretically the dielectric environment of a system. With recent advances in nanotechnology, biochemistry, and molecular electronics, it has become necessary to determine the dielectric response in molecular systems that are difficult to measure experimentally, such as nanoscale interfaces, highly disordered biological environments, or molecular materials that are difficult to synthesize. In these scenarios it is highly advantageous to determine the dielectric response through efficient and accurate calculations. A good example of where a theoretical prediction of dielectric response is critical is in the development of high capacitance molecular dielectrics. Molecular dielectrics offer the promise of cheap, flexible, and mass producible electronic devices when used in conjunction with organic semiconducting materials to form Organic Field Effect Transistors (OFETs). To date, molecular dielectrics suffer from poor dielectric properties resulting in low capacitances. A low capacitance dielectric material requires a much larger power source to operate the device in OFETs, leading to modest device performance. Development of better performing dielectric materials has been hindered due to the time it takes to synthesize and fabricate new molecular materials. An accurate and efficient theoretical technique could drastically decrease this time by screening potential dielectric materials and providing design rules for future molecular dielectrics. Here in, the methodology used to calculate dielectric properties of molecular materials is described. The validity of the technique is demonstrated on model systems, capturing the frequency dependence of the dielectric response and achieving quantitative accuracy compared

  5. 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).

  6. Accurate taxonomic assignment of short pyrosequencing reads.

    PubMed

    Clemente, José C; Jansson, Jesper; Valiente, Gabriel

    2010-01-01

    Ambiguities in the taxonomy dependent assignment of pyrosequencing reads are usually resolved by mapping each read to the lowest common ancestor in a reference taxonomy of all those sequences that match the read. This conservative approach has the drawback of mapping a read to a possibly large clade that may also contain many sequences not matching the read. A more accurate taxonomic assignment of short reads can be made by mapping each read to the node in the reference taxonomy that provides the best precision and recall. We show that given a suffix array for the sequences in the reference taxonomy, a short read can be mapped to the node of the reference taxonomy with the best combined value of precision and recall in time linear in the size of the taxonomy subtree rooted at the lowest common ancestor of the matching sequences. An accurate taxonomic assignment of short reads can thus be made with about the same efficiency as when mapping each read to the lowest common ancestor of all matching sequences in a reference taxonomy. We demonstrate the effectiveness of our approach on several metagenomic datasets of marine and gut microbiota.

  7. 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.

  8. Accurate pose estimation for forensic identification

    NASA Astrophysics Data System (ADS)

    Merckx, Gert; Hermans, Jeroen; Vandermeulen, Dirk

    2010-04-01

    In forensic authentication, one aims to identify the perpetrator among a series of suspects or distractors. A fundamental problem in any recognition system that aims for identification of subjects in a natural scene is the lack of constrains on viewing and imaging conditions. In forensic applications, identification proves even more challenging, since most surveillance footage is of abysmal quality. In this context, robust methods for pose estimation are paramount. In this paper we will therefore present a new pose estimation strategy for very low quality footage. Our approach uses 3D-2D registration of a textured 3D face model with the surveillance image to obtain accurate far field pose alignment. Starting from an inaccurate initial estimate, the technique uses novel similarity measures based on the monogenic signal to guide a pose optimization process. We will illustrate the descriptive strength of the introduced similarity measures by using them directly as a recognition metric. Through validation, using both real and synthetic surveillance footage, our pose estimation method is shown to be accurate, and robust to lighting changes and image degradation.

  9. Sparse and accurate high resolution SAR imaging

    NASA Astrophysics Data System (ADS)

    Vu, Duc; Zhao, Kexin; Rowe, William; Li, Jian

    2012-05-01

    We investigate the usage of an adaptive method, the Iterative Adaptive Approach (IAA), in combination with a maximum a posteriori (MAP) estimate to reconstruct high resolution SAR images that are both sparse and accurate. IAA is a nonparametric weighted least squares algorithm that is robust and user parameter-free. IAA has been shown to reconstruct SAR images with excellent side lobes suppression and high resolution enhancement. We first reconstruct the SAR images using IAA, and then we enforce sparsity by using MAP with a sparsity inducing prior. By coupling these two methods, we can produce a sparse and accurate high resolution image that are conducive for feature extractions and target classification applications. In addition, we show how IAA can be made computationally efficient without sacrificing accuracies, a desirable property for SAR applications where the size of the problems is quite large. We demonstrate the success of our approach using the Air Force Research Lab's "Gotcha Volumetric SAR Data Set Version 1.0" challenge dataset. Via the widely used FFT, individual vehicles contained in the scene are barely recognizable due to the poor resolution and high side lobe nature of FFT. However with our approach clear edges, boundaries, and textures of the vehicles are obtained.

  10. 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.

  11. Molecular processes in a high temperature shock layer

    NASA Technical Reports Server (NTRS)

    Guberman, S. L.

    1984-01-01

    Models of the shock layer encountered by an Aeroassisted Orbital Transfer Vehicle require as input accurate cross sections and rate constants for the atomic and molecular processes that characterize the shock radiation. From the estimated atomic and molecular densities in the shock layer and the expected residence time of 1 m/s, it can be expected that electron-ion collision processes will be important in the shock model. Electron capture by molecular ions followed by dissociation, e.g., O2(+) + e(-) yields 0 + 0, can be expected to be of major importance since these processes are known to have high rates (e.g., 10 to the -7th power cu/cm/sec) at room temperature. However, there have been no experimental measurements of dissociative recombination (DR) at temperatures ( 12000K) that are expected to characterize the shock layer. Indeed, even at room temperature, it is often difficult to perform experiments that determine the dependence of the translational energy and quantum yields of the product atoms on the electronic and vibrational state of the reactant molecular ions. Presented are ab initio quantum chemical studies of DR for molecular ions that are likely to be important in the atmospheric shock layer.

  12. 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…

  13. Spray Gun With Constant Mixing Ratio

    NASA Technical Reports Server (NTRS)

    Simpson, William G.

    1987-01-01

    Conceptual mechanism mounted in handle of spray gun maintains constant ratio between volumetric flow rates in two channels leading to spray head. With mechanism, possible to keep flow ratio near 1:1 (or another desired ratio) over range of temperatures, orifice or channel sizes, or clogging conditions.

  14. Variations of the Solar Constant. [conference

    NASA Technical Reports Server (NTRS)

    Sofia, S. (Editor)

    1981-01-01

    The variations in data received from rocket-borne and balloon-borne instruments are discussed. Indirect techniques to measure and monitor the solar constant are presented. Emphasis is placed on the correlation of data from the Solar Maximum Mission and the Nimbus 7 satellites.

  15. Teaching Nanochemistry: Madelung Constants of Nanocrystals

    ERIC Educational Resources Information Center

    Baker, Mark D.; Baker, A. David

    2010-01-01

    The Madelung constants for binary ionic nanoparticles are determined. The computational method described here sums the Coulombic interactions of each ion in the particle without the use of partial charges commonly used for bulk materials. The results show size-dependent lattice energies. This is a useful concept in teaching how properties such as…

  16. Sensing Position With Approximately Constant Contact Force

    NASA Technical Reports Server (NTRS)

    Sturdevant, Jay

    1996-01-01

    Computer-controlled electromechanical system uses number of linear variable-differential transformers (LVDTs) to measure axial positions of selected points on surface of lens, mirror, or other precise optical component with high finish. Pressures applied to pneumatically driven LVDTs adjusted to maintain small, approximately constant contact forces as positions of LVDT tips vary.

  17. A tunable CMOS constant current source

    NASA Technical Reports Server (NTRS)

    Thelen, D.

    1991-01-01

    A constant current source has been designed which makes use of on chip electrically erasable memory to adjust the magnitude and temperature coefficient of the output current. The current source includes a voltage reference based on the difference between enhancement and depletion transistor threshold voltages. Accuracy is +/- 3% over the full range of power supply, process variations, and temperature using eight bits for tuning.

  18. Can compactifications solve the cosmological constant problem?

    SciTech Connect

    Hertzberg, Mark P.; Masoumi, Ali

    2016-06-30

    Recently, there have been claims in the literature that the cosmological constant problem can be dynamically solved by specific compactifications of gravity from higher-dimensional toy models. These models have the novel feature that in the four-dimensional theory, the cosmological constant Λ is much smaller than the Planck density and in fact accumulates at Λ=0. Here we show that while these are very interesting models, they do not properly address the real cosmological constant problem. As we explain, the real problem is not simply to obtain Λ that is small in Planck units in a toy model, but to explain why Λ is much smaller than other mass scales (and combinations of scales) in the theory. Instead, in these toy models, all other particle mass scales have been either removed or sent to zero, thus ignoring the real problem. To this end, we provide a general argument that the included moduli masses are generically of order Hubble, so sending them to zero trivially sends the cosmological constant to zero. We also show that the fundamental Planck mass is being sent to zero, and so the central problem is trivially avoided by removing high energy physics altogether. On the other hand, by including various large mass scales from particle physics with a high fundamental Planck mass, one is faced with a real problem, whose only known solution involves accidental cancellations in a landscape.

  19. Unified Technical Concepts. Module 12: Time Constants.

    ERIC Educational Resources Information Center

    Technical Education Research Center, Waco, TX.

    This concept module on time constants is one of thirteen modules that provide a flexible, laboratory-based physics instructional package designed to meet the specialized needs of students in two-year, postsecondary technical schools. Each of the thirteen concept modules discusses a single physics concept and how it is applied to each energy…

  20. Man's Size in Terms of Fundamental Constants.

    ERIC Educational Resources Information Center

    Press, William H.

    1980-01-01

    Reviews calculations that derive an order of magnitude expression for the size of man in terms of fundamental constants, assuming that man satifies these three properties: he is made of complicated molecules; he requires an atmosphere which is not hydrogen and helium; he is as large as possible. (CS)

  1. The Elastic Constants for Wrought Aluminum Alloys

    NASA Technical Reports Server (NTRS)

    Templin, R L; Hartmann, E C

    1945-01-01

    There are several constants which have been devised as numerical representations of the behavior of metals under the action of loadings which stress the metal within the range of elastic action. Some of these constants, such as Young's modulus of elasticity in tension and compression, shearing modulus of elasticity, and Poisson's ratio, are regularly used in engineering calculations. Precise tests and experience indicate that these elastic constants are practically unaffected by many of the factors which influence the other mechanical properties of materials and that a few careful determinations under properly controlled conditions are more useful and reliable than many determinations made under less favorable conditions. It is the purpose of this paper to outline the methods employed by the Aluminum Research Laboratories for the determination of some of these elastic constants, to list the values that have been determined for some of the wrought aluminum alloys, and to indicate the variations in the values that may be expected for some of the commercial products of these alloys.

  2. Constant capacitance in nanopores of carbon monoliths.

    PubMed

    García-Gómez, Alejandra; Moreno-Fernández, Gelines; Lobato, Belén; Centeno, Teresa A

    2015-06-28

    The results obtained for binder-free electrodes made of carbon monoliths with narrow micropore size distributions confirm that the specific capacitance in the electrolyte (C2H5)4NBF4/acetonitrile does not depend significantly on the micropore size and support the foregoing constant result of 0.094 ± 0.011 F m(-2).

  3. When is the growth index constant?

    NASA Astrophysics Data System (ADS)

    Polarski, David; Starobinsky, Alexei A.; Giacomini, Hector

    2016-12-01

    The growth index γ is an interesting tool to assess the phenomenology of dark energy (DE) models, in particular of those beyond general relativity (GR). We investigate the possibility for DE models to allow for a constant γ during the entire matter and DE dominated stages. It is shown that if DE is described by quintessence (a scalar field minimally coupled to gravity), this behaviour of γ is excluded either because it would require a transition to a phantom behaviour at some finite moment of time, or, in the case of tracking DE at the matter dominated stage, because the relative matter density Ωm appears to be too small. An infinite number of solutions, with Ωm and γ both constant, are found with wDE = 0 corresponding to Einstein-de Sitter universes. For all modified gravity DE models satisfying Geff >= G, among them the f(R) DE models suggested in the literature, the condition to have a constant wDE is strongly violated at the present epoch. In contrast, DE tracking dust-like matter deep in the matter era, but with Ωm <1, requires Geff > G and an example is given using scalar-tensor gravity for a range of admissible values of γ. For constant wDE inside GR, departure from a quasi-constant value is limited until today. Even a large variation of wDE may not result in a clear signature in the change of γ. The change however is substantial in the future and the asymptotic value of γ is found while its slope with respect to Ωm (and with respect to z) diverges and tends to ‑∞.

  4. A New Method for Determining the Optical Constants of Highly Transparent Solids.

    PubMed

    Li, Xingcan; Wang, Chengchao; Zhao, Junming; Liu, Linhua

    2017-01-01

    Highly transparent substrates are of interest for a variety of applications, but it is difficult to measure their optical constants precisely, especially the absorption index in the transparent spectral region. In this paper, a combination technique (DOPTM-EM) using both the double optical pathlength transmission method (DOPTM) and the ellipsometry method (EM) is presented to obtain the optical constants of highly transparent substrates, which overcomes the deficiencies of both the two methods. The EM cannot give accurate result of optical constants when the absorption index is very weak. The DOPTM is suitable to retrieve the weak absorption index; however, two sets of solutions exist for the retrieved refractive index and absorption index, and only one is the true value that needs to be identified. In the DOPTM-EM, the optical constants are measured first by using the EM and set as the initial value in the gradient-based inverse method used in the DOPTM, which ensures only the true optical constants are retrieved. The new method simultaneously obtains the refractive index and the absorption index of highly transparent substrate without relying on the Kramers-Kronig relation. The optical constants of three highly transparent substrates (polycrystalline BaF2, CaF2, and MgF2) were experimentally determined within wavelength range from ultraviolet to infrared regions (0.2-14 µm). The presented method will facilitate the measurement of optical constants for highly transparent materials.

  5. Apparatus for accurately measuring high temperatures

    DOEpatents

    Smith, D.D.

    The present invention is a thermometer used for measuring furnace temperatures in the range of about 1800/sup 0/ to 2700/sup 0/C. The thermometer comprises a broadband multicolor thermal radiation sensor positioned to be in optical alignment with the end of a blackbody sight tube extending into the furnace. A valve-shutter arrangement is positioned between the radiation sensor and the sight tube and a chamber for containing a charge of high pressure gas is positioned between the valve-shutter arrangement and the radiation sensor. A momentary opening of the valve shutter arrangement allows a pulse of the high gas to purge the sight tube of air-borne thermal radiation contaminants which permits the radiation sensor to accurately measure the thermal radiation emanating from the end of the sight tube.

  6. Apparatus for accurately measuring high temperatures

    DOEpatents

    Smith, Douglas D.

    1985-01-01

    The present invention is a thermometer used for measuring furnace temperaes in the range of about 1800.degree. to 2700.degree. C. The thermometer comprises a broadband multicolor thermal radiation sensor positioned to be in optical alignment with the end of a blackbody sight tube extending into the furnace. A valve-shutter arrangement is positioned between the radiation sensor and the sight tube and a chamber for containing a charge of high pressure gas is positioned between the valve-shutter arrangement and the radiation sensor. A momentary opening of the valve shutter arrangement allows a pulse of the high gas to purge the sight tube of air-borne thermal radiation contaminants which permits the radiation sensor to accurately measure the thermal radiation emanating from the end of the sight tube.

  7. LSM: perceptually accurate line segment merging

    NASA Astrophysics Data System (ADS)

    Hamid, Naila; Khan, Nazar

    2016-11-01

    Existing line segment detectors tend to break up perceptually distinct line segments into multiple segments. We propose an algorithm for merging such broken segments to recover the original perceptually accurate line segments. The algorithm proceeds by grouping line segments on the basis of angular and spatial proximity. Then those line segment pairs within each group that satisfy unique, adaptive mergeability criteria are successively merged to form a single line segment. This process is repeated until no more line segments can be merged. We also propose a method for quantitative comparison of line segment detection algorithms. Results on the York Urban dataset show that our merged line segments are closer to human-marked ground-truth line segments compared to state-of-the-art line segment detection algorithms.

  8. Highly accurate articulated coordinate measuring machine

    DOEpatents

    Bieg, Lothar F.; Jokiel, Jr., Bernhard; Ensz, Mark T.; Watson, Robert D.

    2003-12-30

    Disclosed is a highly accurate articulated coordinate measuring machine, comprising a revolute joint, comprising a circular encoder wheel, having an axis of rotation; a plurality of marks disposed around at least a portion of the circumference of the encoder wheel; bearing means for supporting the encoder wheel, while permitting free rotation of the encoder wheel about the wheel's axis of rotation; and a sensor, rigidly attached to the bearing means, for detecting the motion of at least some of the marks as the encoder wheel rotates; a probe arm, having a proximal end rigidly attached to the encoder wheel, and having a distal end with a probe tip attached thereto; and coordinate processing means, operatively connected to the sensor, for converting the output of the sensor into a set of cylindrical coordinates representing the position of the probe tip relative to a reference cylindrical coordinate system.

  9. Practical aspects of spatially high accurate methods

    NASA Technical Reports Server (NTRS)

    Godfrey, Andrew G.; Mitchell, Curtis R.; Walters, Robert W.

    1992-01-01

    The computational qualities of high order spatially accurate methods for the finite volume solution of the Euler equations are presented. Two dimensional essentially non-oscillatory (ENO), k-exact, and 'dimension by dimension' ENO reconstruction operators are discussed and compared in terms of reconstruction and solution accuracy, computational cost and oscillatory behavior in supersonic flows with shocks. Inherent steady state convergence difficulties are demonstrated for adaptive stencil algorithms. An exact solution to the heat equation is used to determine reconstruction error, and the computational intensity is reflected in operation counts. Standard MUSCL differencing is included for comparison. Numerical experiments presented include the Ringleb flow for numerical accuracy and a shock reflection problem. A vortex-shock interaction demonstrates the ability of the ENO scheme to excel in simulating unsteady high-frequency flow physics.

  10. Toward Accurate and Quantitative Comparative Metagenomics

    PubMed Central

    Nayfach, Stephen; Pollard, Katherine S.

    2016-01-01

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  11. Obtaining accurate translations from expressed sequence tags.

    PubMed

    Wasmuth, James; Blaxter, Mark

    2009-01-01

    The genomes of an increasing number of species are being investigated through the generation of expressed sequence tags (ESTs). However, ESTs are prone to sequencing errors and typically define incomplete transcripts, making downstream annotation difficult. Annotation would be greatly improved with robust polypeptide translations. Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects. As part of our ongoing EST programs investigating these "neglected" genomes, we have developed a polypeptide prediction pipeline, prot4EST. It incorporates freely available software to produce final translations that are more accurate than those derived from any single method. We describe how this integrated approach goes a long way to overcoming the deficit in training data.

  12. Micron Accurate Absolute Ranging System: Range Extension

    NASA Technical Reports Server (NTRS)

    Smalley, Larry L.; Smith, Kely L.

    1999-01-01

    The purpose of this research is to investigate Fresnel diffraction as a means of obtaining absolute distance measurements with micron or greater accuracy. It is believed that such a system would prove useful to the Next Generation Space Telescope (NGST) as a non-intrusive, non-contact measuring system for use with secondary concentrator station-keeping systems. The present research attempts to validate past experiments and develop ways to apply the phenomena of Fresnel diffraction to micron accurate measurement. This report discusses past research on the phenomena, and the basis of the use Fresnel diffraction distance metrology. The apparatus used in the recent investigations, experimental procedures used, preliminary results are discussed in detail. Continued research and equipment requirements on the extension of the effective range of the Fresnel diffraction systems is also described.

  13. Accurate radio positions with the Tidbinbilla interferometer

    NASA Technical Reports Server (NTRS)

    Batty, M. J.; Gulkis, S.; Jauncey, D. L.; Rayner, P. T.

    1979-01-01

    The Tidbinbilla interferometer (Batty et al., 1977) is designed specifically to provide accurate radio position measurements of compact radio sources in the Southern Hemisphere with high sensitivity. The interferometer uses the 26-m and 64-m antennas of the Deep Space Network at Tidbinbilla, near Canberra. The two antennas are separated by 200 m on a north-south baseline. By utilizing the existing antennas and the low-noise traveling-wave masers at 2.29 GHz, it has been possible to produce a high-sensitivity instrument with a minimum of capital expenditure. The north-south baseline ensures that a good range of UV coverage is obtained, so that sources lying in the declination range between about -80 and +30 deg may be observed with nearly orthogonal projected baselines of no less than about 1000 lambda. The instrument also provides high-accuracy flux density measurements for compact radio sources.

  14. Magnetic ranging tool accurately guides replacement well

    SciTech Connect

    Lane, J.B.; Wesson, J.P. )

    1992-12-21

    This paper reports on magnetic ranging surveys and directional drilling technology which accurately guided a replacement well bore to intersect a leaking gas storage well with casing damage. The second well bore was then used to pump cement into the original leaking casing shoe. The repair well bore kicked off from the surface hole, bypassed casing damage in the middle of the well, and intersected the damaged well near the casing shoe. The repair well was subsequently completed in the gas storage zone near the original well bore, salvaging the valuable bottom hole location in the reservoir. This method would prevent the loss of storage gas, and it would prevent a potential underground blowout that could permanently damage the integrity of the storage field.

  15. The high cost of accurate knowledge.

    PubMed

    Sutcliffe, Kathleen M; Weber, Klaus

    2003-05-01

    Many business thinkers believe it's the role of senior managers to scan the external environment to monitor contingencies and constraints, and to use that precise knowledge to modify the company's strategy and design. As these thinkers see it, managers need accurate and abundant information to carry out that role. According to that logic, it makes sense to invest heavily in systems for collecting and organizing competitive information. Another school of pundits contends that, since today's complex information often isn't precise anyway, it's not worth going overboard with such investments. In other words, it's not the accuracy and abundance of information that should matter most to top executives--rather, it's how that information is interpreted. After all, the role of senior managers isn't just to make decisions; it's to set direction and motivate others in the face of ambiguities and conflicting demands. Top executives must interpret information and communicate those interpretations--they must manage meaning more than they must manage information. So which of these competing views is the right one? Research conducted by academics Sutcliffe and Weber found that how accurate senior executives are about their competitive environments is indeed less important for strategy and corresponding organizational changes than the way in which they interpret information about their environments. Investments in shaping those interpretations, therefore, may create a more durable competitive advantage than investments in obtaining and organizing more information. And what kinds of interpretations are most closely linked with high performance? Their research suggests that high performers respond positively to opportunities, yet they aren't overconfident in their abilities to take advantage of those opportunities.

  16. Time place learning and activity profile under constant light and constant dark in zebrafish (Danio rerio).

    PubMed

    Moura, Clarissa de Almeida; Lima, Jéssica Polyana da Silva; Silveira, Vanessa Augusta Magalhães; Miguel, Mário André Leocadio; Luchiari, Ana Carolina

    2017-05-01

    The ability to learn about the signs of variability in space and time is known as time place learning (TPL). To adjust their circadian rhythms, animals use stimuli that change regularly, such as the light-dark cycle, temperature, food availability or even social stimuli. Because light-dark cycle is the most important environmental temporal cue, we asked how a diurnal animal would perform TPL if this cue was removed. Zebrafish has been extensively studied in the chronobiology area due to it diurnal chronotype, thus, we studied the effects of constant light and constant dark on the time-place learning and activity profile in zebrafish. Our data show that while under constant light and dark condition zebrafish was not able of TPL, after 30days under the constant conditions, constant light led to higher activity level and less significant (robust) 24h rhythm.

  17. Surface tensions, viscosities, and diffusion constants in mixed component single aerosol particles

    NASA Astrophysics Data System (ADS)

    Bzdek, Bryan; Marshall, Frances; Song, Young-Chul; Haddrell, Allen; Reid, Jonathan

    2016-04-01

    Surface tension and viscosity are important aerosol properties but are challenging to measure on individual particles owing to their small size and mass. Aerosol viscosity impacts semivolatile partitioning from the aerosol phase, molecular diffusion in the bulk of the particle, and reaction kinetics. Aerosol surface tension impacts how particles activate to serve as cloud condensation nuclei. Knowledge of these properties and how they change under different conditions hinders accurate modelling of aerosol physical state and atmospheric impacts. We present measurements made using holographic optical tweezers to directly determine the viscosity and surface tension of optically trapped droplets containing ~1-4 picolitres of material (corresponding to radii of ~5-10 micrometres). Two droplets are captured in the experimental setup, equilibrated to a relative humidity, and coalesced through manipulation of the relative trap positions. The moment of coalescence is captured using camera imaging as well as from elastically backscattered light connected to an oscilloscope. For lower viscosity droplets, the relaxation in droplet shape to a sphere follows the form of a damped oscillator and gives the surface tension and viscosity. For high viscosity droplets, the relaxation results in a slow merging of the two droplets to form a sphere and the timescale of that process permits determination of viscosity. We show that droplet viscosity and surface tension can be quantitatively determined to within <10% of the expected value for low viscosity droplets and to better than 1 order of magnitude for high viscosity droplets. Examples illustrating how properties such as surface tension can change in response to environmental conditions will be discussed. Finally, a study of the relationship between viscosity, diffusion constants, vapour pressures, and reactive uptake coefficients for a mixed component aerosol undergoing oxidation and volatilisation will be discussed.

  18. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    NASA Astrophysics Data System (ADS)

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  19. Atomic force microscopy: Loading position dependence of cantilever spring constants and detector sensitivity

    NASA Astrophysics Data System (ADS)

    Vakarelski, Ivan U.; Edwards, Scott A.; Dagastine, Raymond R.; Chan, Derek Y. C.; Stevens, Geoffrey W.; Grieser, Franz

    2007-11-01

    A simple and accurate experimental method is described for determining the effective cantilever spring constant and the detector sensitivity of atomic force microscopy cantilevers on which a colloidal particle is attached. By attaching large (approximately 85μm diameter) latex particles at various positions along the V-shaped cantilevers, we demonstrate how the normal and lateral spring constants as well as the sensitivity vary with loading position. Comparison with an explicit point-load theoretical model has also been used to verify the accuracy of the method.

  20. Atomic force microscopy: loading position dependence of cantilever spring constants and detector sensitivity.

    PubMed

    Vakarelski, Ivan U; Edwards, Scott A; Dagastine, Raymond R; Chan, Derek Y C; Stevens, Geoffrey W; Grieser, Franz

    2007-11-01

    A simple and accurate experimental method is described for determining the effective cantilever spring constant and the detector sensitivity of atomic force microscopy cantilevers on which a colloidal particle is attached. By attaching large (approximately 85 microm diameter) latex particles at various positions along the V-shaped cantilevers, we demonstrate how the normal and lateral spring constants as well as the sensitivity vary with loading position. Comparison with an explicit point-load theoretical model has also been used to verify the accuracy of the method.

  1. Precise atomic force microscope cantilever spring constant calibration using a reference cantilever array.

    PubMed

    Gates, Richard S; Reitsma, Mark G

    2007-08-01

    A method for calibrating the stiffness of atomic force microscope (AFM) cantilevers is demonstrated using an array of uniform microfabricated reference cantilevers. A series of force-displacement curves was obtained using a commercial AFM test cantilever on the reference cantilever array, and the data were analyzed using an implied Euler-Bernoulli model to extract the test cantilever spring constant from linear regression fitting. The method offers a factor of 5 improvement over the precision of the usual reference cantilever calibration method and, when combined with the Systeme International traceability potential of the cantilever array, can provide very accurate spring constant calibrations.

  2. Accurate simulation of optical properties in dyes.

    PubMed

    Jacquemin, Denis; Perpète, Eric A; Ciofini, Ilaria; Adamo, Carlo

    2009-02-17

    Since Antiquity, humans have produced and commercialized dyes. To this day, extraction of natural dyes often requires lengthy and costly procedures. In the 19th century, global markets and new industrial products drove a significant effort to synthesize artificial dyes, characterized by low production costs, huge quantities, and new optical properties (colors). Dyes that encompass classes of molecules absorbing in the UV-visible part of the electromagnetic spectrum now have a wider range of applications, including coloring (textiles, food, paintings), energy production (photovoltaic cells, OLEDs), or pharmaceuticals (diagnostics, drugs). Parallel to the growth in dye applications, researchers have increased their efforts to design and synthesize new dyes to customize absorption and emission properties. In particular, dyes containing one or more metallic centers allow for the construction of fairly sophisticated systems capable of selectively reacting to light of a given wavelength and behaving as molecular devices (photochemical molecular devices, PMDs).Theoretical tools able to predict and interpret the excited-state properties of organic and inorganic dyes allow for an efficient screening of photochemical centers. In this Account, we report recent developments defining a quantitative ab initio protocol (based on time-dependent density functional theory) for modeling dye spectral properties. In particular, we discuss the importance of several parameters, such as the methods used for electronic structure calculations, solvent effects, and statistical treatments. In addition, we illustrate the performance of such simulation tools through case studies. We also comment on current weak points of these methods and ways to improve them.

  3. Networks in Neuroscience: The Problem of Stability in the Face of Constant Change

    DTIC Science & Technology

    2006-11-01

    Networks in neuroscience • Every individual neuron contains complex networks of interacting biochemical and molecular processes • The nervous system...How is function maintained while the nervous system is constantly rebuilding itself? PD, Alexa 568 hydrazide Bucher D, Prinz AA, Marder E (2005) J

  4. Higher order accurate partial implicitization: An unconditionally stable fourth-order-accurate explicit numerical technique

    NASA Technical Reports Server (NTRS)

    Graves, R. A., Jr.

    1975-01-01

    The previously obtained second-order-accurate partial implicitization numerical technique used in the solution of fluid dynamic problems was modified with little complication to achieve fourth-order accuracy. The Von Neumann stability analysis demonstrated the unconditional linear stability of the technique. The order of the truncation error was deduced from the Taylor series expansions of the linearized difference equations and was verified by numerical solutions to Burger's equation. For comparison, results were also obtained for Burger's equation using a second-order-accurate partial-implicitization scheme, as well as the fourth-order scheme of Kreiss.

  5. Rate constants from instanton theory via a microcanonical approach

    NASA Astrophysics Data System (ADS)

    McConnell, Sean R.; Löhle, Andreas; Kästner, Johannes

    2017-02-01

    Microcanonical instanton theory offers the promise of providing rate constants for chemical reactions including quantum tunneling of atoms over the whole temperature range. We discuss different rate expressions, which require the calculation of stability parameters of the instantons. The traditional way of obtaining these stability parameters is shown to be numerically unstable in practical applications. We provide three alternative algorithms to obtain such stability parameters for non-separable systems, i.e., systems in which the vibrational modes perpendicular to the instanton path couple to movement along the path. We show the applicability of our algorithms on two molecular systems: H2 + OH → H2O + H using a fitted potential energy surface and HNCO + H → NH2CO using a potential obtained on-the-fly from density functional calculations.

  6. Brownian dynamics of charged particles in a constant magnetic field

    SciTech Connect

    Hou, L. J.; Piel, A.; Miskovic, Z. L.; Shukla, P. K.

    2009-05-15

    Numerical algorithms are proposed for simulating the Brownian dynamics of charged particles in an external magnetic field, taking into account the Brownian motion of charged particles, damping effect, and the effect of magnetic field self-consistently. Performance of these algorithms is tested in terms of their accuracy and long-time stability by using a three-dimensional Brownian oscillator model with constant magnetic field. Step-by-step recipes for implementing these algorithms are given in detail. It is expected that these algorithms can be directly used to study particle dynamics in various dispersed systems in the presence of a magnetic field, including polymer solutions, colloidal suspensions, and, particularly, complex (dusty) plasmas. The proposed algorithms can also be used as thermostat in the usual molecular dynamics simulation in the presence of magnetic field.

  7. Divided Saddle Theory: A New Idea for Rate Constant Calculation.

    PubMed

    Daru, János; Stirling, András

    2014-03-11

    We present a theory of rare events and derive an algorithm to obtain rates from postprocessing the numerical data of a free energy calculation and the corresponding committor analysis. The formalism is based on the division of the saddle region of the free energy profile of the rare event into two adjacent segments called saddle domains. The method is built on sampling the dynamics within these regions: auxiliary rate constants are defined for the saddle domains and the absolute forward and backward rates are obtained by proper reweighting. We call our approach divided saddle theory (DST). An important advantage of our approach is that it requires only standard computational techniques which are available in most molecular dynamics codes. We demonstrate the potential of DST numerically on two examples: rearrangement of alanine-dipeptide (CH3CO-Ala-NHCH3) conformers and the intramolecular Cope reaction of the fluxional barbaralane molecule.

  8. Gladstone-Dale constant for CF4

    NASA Astrophysics Data System (ADS)

    Burner, A. W., Jr.; Goad, W. K.

    1980-05-01

    The Gladstone-Dale constant, which relates the refractive index to density, was measured for CF4 by counting fringes of a two-beam interferometer, one beam of which passes through a cell containing the test gas. The experimental approach and sources of systematic and imprecision errors are discussed. The constant for CF4 was measured at several wavelengths in the visible region of the spectrum. A value of 0.122 cu cm/g with an uncertainty of plus or minus 0.001 cu cm/g was determined for use in the visible region. A procedure for noting the departure of the gas density from the ideal-gas law is discussed.

  9. On determining dose rate constants spectroscopically

    SciTech Connect

    Rodriguez, M.; Rogers, D. W. O.

    2013-01-15

    Purpose: To investigate several aspects of the Chen and Nath spectroscopic method of determining the dose rate constants of {sup 125}I and {sup 103}Pd seeds [Z. Chen and R. Nath, Phys. Med. Biol. 55, 6089-6104 (2010)] including the accuracy of using a line or dual-point source approximation as done in their method, and the accuracy of ignoring the effects of the scattered photons in the spectra. Additionally, the authors investigate the accuracy of the literature's many different spectra for bare, i.e., unencapsulated {sup 125}I and {sup 103}Pd sources. Methods: Spectra generated by 14 {sup 125}I and 6 {sup 103}Pd seeds were calculated in vacuo at 10 cm from the source in a 2.7 Multiplication-Sign 2.7 Multiplication-Sign 0.05 cm{sup 3} voxel using the EGSnrc BrachyDose Monte Carlo code. Calculated spectra used the initial photon spectra recommended by AAPM's TG-43U1 and NCRP (National Council of Radiation Protection and Measurements) Report 58 for the {sup 125}I seeds, or TG-43U1 and NNDC(2000) (National Nuclear Data Center, 2000) for {sup 103}Pd seeds. The emitted spectra were treated as coming from a line or dual-point source in a Monte Carlo simulation to calculate the dose rate constant. The TG-43U1 definition of the dose rate constant was used. These calculations were performed using the full spectrum including scattered photons or using only the main peaks in the spectrum as done experimentally. Statistical uncertainties on the air kerma/history and the dose rate/history were Less-Than-Or-Slanted-Equal-To 0.2%. The dose rate constants were also calculated using Monte Carlo simulations of the full seed model. Results: The ratio of the intensity of the 31 keV line relative to that of the main peak in {sup 125}I spectra is, on average, 6.8% higher when calculated with the NCRP Report 58 initial spectrum vs that calculated with TG-43U1 initial spectrum. The {sup 103}Pd spectra exhibit an average 6.2% decrease in the 22.9 keV line relative to the main peak when

  10. Optical constants of liquid and solid methane

    NASA Technical Reports Server (NTRS)

    Martonchik, John V.; Orton, Glenn S.

    1994-01-01

    The optical constants n(sub r) + in(sub i) of liquid methane and phase 1 solid methane were determined over the entire spectral range by the use of various data sources published in the literature. Kramers-Kronig analyses were performed on the absorption spectra of liquid methane at the boiling point (111 K) and the melting point (90 K) and on the absorption spectra of phase 1 solid methane at the melting point and at 30 K. Measurements of the static dielectric constant at these temperatures and refractive indices determined over limited spectral ranges were used as constraints in the analyses. Applications of methane optical properties to studies of outer solar system bodies are described.

  11. Constant envelope chirped OFDM power efficiency

    NASA Astrophysics Data System (ADS)

    Dida, Mussa A.; Hao, Huan; Anjum, M. R.; Ran, Tao

    2016-10-01

    Fractional Fourier OFDM or simply chirped OFDM performs better in time-frequency selective channel than its convectional OFDM. Although chirped OFDM outperforms OFDM it still inherits Peak to Average Power Ratio (PAPR) drawback as a convectional OFDM. To eliminate PAPR drawback Constant Envelope OFDM was developed and for better performance in time frequency selective channel Constant Envelope Fractional Fourier OFDM (CE-COFDM) is used. Its BER performance is analyzed and compared to chirped OFDM and OFDM in AWGN and Rayleigh channel. The simulations show the BER performance of CE-COFDM is the same as chirped OFDM and OFDM. The power efficiency of CE-COFDM is also studied and different simulations performed shows CE-COFDM is more power efficient than chirped OFDM and convectional OFDM for class A and class B Linear Power Amplifier (LPA).

  12. BOREAS RSS-17 Dielectric Constant Profile Measurements

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G. (Editor); Nickeson, Jaime (Editor); McDonald, Kyle C.; Zimmerman, Reiner; Way, JoBea

    2000-01-01

    The BOREAS RSS-17 team acquired and analyzed imaging radar data from the ESA's ERS-1 over a complete annual cycle at the BOREAS sites in Canada in 1994 to detect shifts in radar backscatter related to varying environmental conditions. This data set consists of dielectric constant profile measurements from selected trees at various BOREAS flux tower sites. The relative dielectric constant was measured at C-band (frequency = 5 GHz) as a function of depth into the trunk of three trees at each site, Measurements were made during April 1994 with an Applied Microwave Corporation field PDP fitted with a 0.358-cm (0.141-inch) diameter coaxial probe tip. The data are available in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  13. Some Dynamical Effects of the Cosmological Constant

    NASA Astrophysics Data System (ADS)

    Axenides, M.; Floratos, E. G.; Perivolaropoulos, L.

    Newton's law gets modified in the presence of a cosmological constant by a small repulsive term (antigravity) that is proportional to the distance. Assuming a value of the cosmological constant consistent with the recent SnIa data (Λ~=10-52 m-2), we investigate the significance of this term on various astrophysical scales. We find that on galactic scales or smaller (less than a few tens of kpc), the dynamical effects of the vacuum energy are negligible by several orders of magnitude. On scales of 1 Mpc or larger however we find that the vacuum energy can significantly affect the dynamics. For example we show that the velocity data in the local group of galaxies correspond to galactic masses increased by 35% in the presence of vacuum energy. The effect is even more important on larger low density systems like clusters of galaxies or superclusters.

  14. Fast Constant Weight Codeword to Index Converter

    DTIC Science & Technology

    2011-08-01

    en.wikipedia.org/wiki/Side_channel_attack. [5] D. E. Knuth , The Art of Computer Programming, “Generating all com- binations and partitions,” Vol. 4...Fast Constant Weight Codeword to Index Converter J. T. Butler T. Sasao Department of Electrical and Computer Engineering Department of Computer ...represen- tation. The middle column shows how this value is computed according to (1). The rightmost column of Table I shows the corresponding 6 bit

  15. Mars Pathfinder Project: Planetary Constants and Models

    NASA Technical Reports Server (NTRS)

    Vaughan, Robin

    1995-01-01

    This document provides a common set of astrodynamic constants and planetary models for use by the Mars Pathfinder Project. It attempts to collect in a single reference all the quantities and models in use across the project during development and for mission operations. These models are central to the navigation and mission design functions, but they are also used in other aspects of the project such as science observation planning and data reduction.

  16. Gravitational constant in multiple field gravity

    SciTech Connect

    Abedi, Habib; Abbassi, Amir M. E-mail: amabasi@khayam.ut.ac.ir

    2015-05-01

    In the present study, we consider general form of the Lagrangian  f(R, φ{sup I}, X) , that is a function of the Ricci scalar, multiple scalar fields and non-canonical kinetic terms. We obtain the effective Newton's constant deep inside the Hubble radius. We use Jordan and Einstein frames, and study the conservation of energy-momentum tensor.

  17. High Dielectric Constant Polymer Film Capacitors (PREPRINT)

    DTIC Science & Technology

    2010-02-01

    film, and the test of our first generation prototype capacitors . High-K Polymeric Dielectrics Commercial polypropylene (PP) capacitor film has a...1994). 2. Maurizio Rabuffi and Guido Picci, “Status Quo and Future Prospects for Metallized Polypropylene Energy Storage Capacitors ”, IEEE Trans...AFRL-RZ-WP-TP-2010-2126 HIGH DIELECTRIC CONSTANT POLYMER FILM CAPACITORS (PREPRINT) Shihai Zhang, Brian Zellers, Dean Anderson, Paul

  18. Variational solutions by the use of stepwise constant functions. I - Linear case.

    NASA Technical Reports Server (NTRS)

    Yoshikawa, K. K.

    1972-01-01

    Demonstration that accurate solutions to the integral equation or to the extremal function can be easily obtained by the variational method in many cases when a stepwise constant function is used for the trial function. The evaluation procedure is simple and straightforward; integrals of the kernel function can be evaluated analytically; the method provides, when the solution involves singularities, the best mean value across the singularity; the results are accurate in both the detailed physical quantities and their averages; the resultant solution can be further integrated analytically over the parameters associated with the problem; and the method can be readily applied to nonlinear integral equations.

  19. Borehole measurement of the Newtonian gravitational constant

    NASA Astrophysics Data System (ADS)

    Hsui, Albert T.

    1987-08-01

    Gravimetric measurements in a borehole within the Michigan Basin, obtained in September 1983, were utilized to estimate the Newtonian gravitational constant. Gravitational constants are computed using gravity measurements from two stations along the same vertical and by knowing the total rock mass sandwiched between these two stations. The calculation of rock formation density using a gamma-gamma density log is described. The gravity values are analyzed in terms of reference surface values, and it is observed that the gravity increases with depth. Borehole measurement determined gravity constant values ranged from 6.6901 + or - 0.0668 x 10 to the -11th cu m/kg sec sq (at station separation 264.5 + or - 0.5 m) to 6.7000 + or - 0.0650 x 10 to the -11th cu m/kg sec sq (at 1163.5 + or - 0.5 m), which are higher than the laboratory value of Luther and Towler (1982) of 6.672 + or - 0.0004 x 10 to the -11th cu m/kg sec sq. It is noted that the data correlate well with the values of Stacey (1981).

  20. Cosmological constant, near brane behavior and singularities

    NASA Astrophysics Data System (ADS)

    Gautason, Fridrik Freyr; Junghans, Daniel; Zagermann, Marco

    2013-09-01

    We show that the classical cosmological constant in type II flux compactifications can be written as a sum of terms from the action of localized sources plus a specific contribution from non-trivial background fluxes. Exploiting two global scaling symmetries of the classical supergravity action, we find that the flux contribution can in many interesting cases be set to zero such that the cosmological constant is fully determined by the boundary conditions of the fields in the near-source region. This generalizes and makes more explicit previous arguments in the literature. We then discuss the problem of putting -branes at the tip of the Klebanov-Strassler throat glued to a compact space in type IIB string theory so as to engineer a de Sitter solution. Our result for the cosmological constant and a simple global argument indicate that inserting a fully localized and backreacting -brane into such a background yields a singular energy density for the NSNS and RR 3-form field strengths at the -brane. This argument does not rely on partial smearing of the -brane or a linearization of field equations, but on a few general assumptions that we also discuss carefully.