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. PMID:24182003
Accurate lineshape spectroscopy and the Boltzmann constant
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
Accurate lineshape spectroscopy and the Boltzmann constant.
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
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
History and progress on accurate measurements of the Planck constant.
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
Accurate Molecular Polarizabilities Based on Continuum Electrostatics
Truchon, Jean-François; Nicholls, Anthony; Iftimie, Radu I.; Roux, Benoît; Bayly, Christopher I.
2013-01-01
A novel approach for representing the intramolecular polarizability as a continuum dielectric is introduced to account for molecular electronic polarization. It is shown, using a finite-difference solution to the Poisson equation, that the Electronic Polarization from Internal Continuum (EPIC) model yields accurate gas-phase molecular polarizability tensors for a test set of 98 challenging molecules composed of heteroaromatics, alkanes and diatomics. The electronic polarization originates from a high intramolecular dielectric that produces polarizabilities consistent with B3LYP/aug-cc-pVTZ and experimental values when surrounded by vacuum dielectric. In contrast to other approaches to model electronic polarization, this simple model avoids the polarizability catastrophe and accurately calculates molecular anisotropy with the use of very few fitted parameters and without resorting to auxiliary sites or anisotropic atomic centers. On average, the unsigned error in the average polarizability and anisotropy compared to B3LYP are 2% and 5%, respectively. The correlation between the polarizability components from B3LYP and this approach lead to a R2 of 0.990 and a slope of 0.999. Even the F2 anisotropy, shown to be a difficult case for existing polarizability models, can be reproduced within 2% error. In addition to providing new parameters for a rapid method directly applicable to the calculation of polarizabilities, this work extends the widely used Poisson equation to areas where accurate molecular polarizabilities matter. PMID:23646034
Molecular dynamics at constant temperature and pressure
NASA Astrophysics Data System (ADS)
Toxvaerd, S.
1993-01-01
Algorithms for molecular dynamics (MD) at constant temperature and pressure are investigated. The ability to remain in a regular orbit in an intermittent chaotic regime is used as a criterion for long-time stability. A simple time-centered algorithm (leap frog) is found to be the most stable of the commonly used algorithms in MD. A model of N one-dimensional dimers with a double-well intermolecular potential, for which the distribution functions at constant temperature T and pressure P can be calculated, is used to investigate MD-NPT dynamics. A time-centered NPT algorithm is found to sample correctly and to be very robust with respect to volume scaling.
Molecular dynamics at constant Cauchy stress
NASA Astrophysics Data System (ADS)
Miller, Ronald E.; Tadmor, Ellad B.; Gibson, Joshua S.; Bernstein, Noam; Pavia, Fabio
2016-05-01
The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress.
Molecular dynamics at constant Cauchy stress.
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. PMID:27179471
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).
Quick and accurate estimation of the elastic constants using the minimum image method
NASA Astrophysics Data System (ADS)
Tretiakov, Konstantin V.; Wojciechowski, Krzysztof W.
2015-04-01
A method for determining the elastic properties using the minimum image method (MIM) is proposed and tested on a model system of particles interacting by the Lennard-Jones (LJ) potential. The elastic constants of the LJ system are determined in the thermodynamic limit, N → ∞, using the Monte Carlo (MC) method in the NVT and NPT ensembles. The simulation results show that when determining the elastic constants, the contribution of long-range interactions cannot be ignored, because that would lead to erroneous results. In addition, the simulations have revealed that the inclusion of further interactions of each particle with all its minimum image neighbors even in case of small systems leads to results which are very close to the values of elastic constants in the thermodynamic limit. This enables one for a quick and accurate estimation of the elastic constants using very small samples.
Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang
2015-01-01
Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson’s ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers. PMID:26510769
Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang
2015-01-01
Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers. PMID:26510769
NASA Astrophysics Data System (ADS)
Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang
2015-10-01
Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson’s ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.
NASA Astrophysics Data System (ADS)
Gates, Richard S.; Osborn, William A.; Shaw, Gordon A.
2015-06-01
Calibration of the flexural spring constant for atomic force microscope (AFM) colloid probe cantilevers provides significant challenges. The presence of a large attached spherical added mass complicates many of the more common calibration techniques such as reference cantilever, Sader, and added mass. Even the most promising option, AFM thermal calibration, can encounter difficulties during the optical lever sensitivity measurement due to strong adhesion and friction between the sphere and a surface. This may cause buckling of the end of the cantilever and hysteresis in the approach-retract curves resulting in increased uncertainty in the calibration. Most recently, a laser Doppler vibrometry thermal method has been used to accurately calibrate the normal spring constant of a wide variety of tipped and tipless commercial cantilevers. This paper describes a variant of the technique, scanning laser Doppler vibrometry, optimized for colloid probe cantilevers and capable of spring constant calibration uncertainties near ±1%.
Accurate measurements of the dielectric constant of seawater at L band
NASA Astrophysics Data System (ADS)
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°C to 35°C in 5°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.
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.
Developing accurate molecular mechanics force fields for conjugated molecular systems.
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. PMID:26349916
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%.
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.
Effect of molecular orientation on the elastic constants of polypropylene.
Kumar, S. R.; Renusch, D. P.; Grimsditch, M.; Materials Science Division; Amoco Polymers Research & Development
2000-03-07
The Brillouin spectroscopic measurements of elastic properties of polypropylene films fabricated by different processing techniques are described. We find that the elastic symmetry and the associated elastic constants are dependent on the molecular orientation brought about by the processing conditions used to produce the films. We have shown that Brillouin scattering techniques can successfully be used to track the molecular orientation induced by uniaxial stretching. We find a direct correspondence between the Brillouin measurements and optical birefringence measurements, illustrating that molecular orientation plays a dominant role in determining the mechanical anisotropy in these materials.
Huang, Xinchuan; Taylor, Peter R; Lee, Timothy J
2011-05-19
High levels of theory have been used to compute quartic force fields (QFFs) for the cyclic and linear forms of the C(3)H(3)(+) molecular cation, referred to as c-C(3)H(3)(+) and l-C(3)H(3)(+). Specifically, the singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations, CCSD(T), has been used in conjunction with extrapolation to the one-particle basis set limit, and corrections for scalar relativity and core correlation have been included. The QFFs have been used to compute highly accurate fundamental vibrational frequencies and other spectroscopic constants by use of both vibrational second-order perturbation theory and variational methods to solve the nuclear Schrödinger equation. Agreement between our best computed fundamental vibrational frequencies and recent infrared photodissociation experiments is reasonable for most bands, but there are a few exceptions. Possible sources for the discrepancies are discussed. We determine the energy difference between the cyclic and linear forms of C(3)H(3)(+), obtaining 27.9 kcal/mol at 0 K, which should be the most reliable available. It is expected that the fundamental vibrational frequencies and spectroscopic constants presented here for c-C(3)H(3)(+) and l-C(3)H(3)(+) are the most reliable available for the free gas-phase species, and it is hoped that these will be useful in the assignment of future high-resolution laboratory experiments or astronomical observations. PMID:21510653
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.
A robust and accurate formulation of molecular and colloidal electrostatics.
Sun, Qiang; Klaseboer, Evert; Chan, Derek Y C
2016-08-01
This paper presents a re-formulation of the boundary integral method for the Debye-Hückel model of molecular and colloidal electrostatics that removes the mathematical singularities that have to date been accepted as an intrinsic part of the conventional boundary integral equation method. The essence of the present boundary regularized integral equation formulation consists of subtracting a known solution from the conventional boundary integral method in such a way as to cancel out the singularities associated with the Green's function. This approach better reflects the non-singular physical behavior of the systems on boundaries with the benefits of the following: (i) the surface integrals can be evaluated accurately using quadrature without any need to devise special numerical integration procedures, (ii) being able to use quadratic or spline function surface elements to represent the surface more accurately and the variation of the functions within each element is represented to a consistent level of precision by appropriate interpolation functions, (iii) being able to calculate electric fields, even at boundaries, accurately and directly from the potential without having to solve hypersingular integral equations and this imparts high precision in calculating the Maxwell stress tensor and consequently, intermolecular or colloidal forces, (iv) a reliable way to handle geometric configurations in which different parts of the boundary can be very close together without being affected by numerical instabilities, therefore potentials, fields, and forces between surfaces can be found accurately at surface separations down to near contact, and (v) having the simplicity of a formulation that does not require complex algorithms to handle singularities will result in significant savings in coding effort and in the reduction of opportunities for coding errors. These advantages are illustrated using examples drawn from molecular and colloidal electrostatics. PMID:27497538
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.
Molecular structure, spectral constants, and fermi resonances in chlorine nitrate
NASA Astrophysics Data System (ADS)
Petkie, Douglas T.; Butler, Rebecca A. H.; Helminger, Paul; De Lucia, Frank C.
2004-06-01
Chlorine nitrate has two low-lying vibrational modes that lead to a series of Fermi resonances in the 9 υ97 υ7 family of levels that include the 9 2⇔7 1 and 9 3⇔7 19 1 dyads and the 9 4⇔9 27 1⇔7 2 and 9 5⇔9 37 1⇔9 17 2 triads. These states, along with the ground and 9 1 vibrational states, have been previously analyzed with millimeter and submillimeter wave spectroscopy and provide a substantial body of data for the investigation of these resonances and their impact on calculated spectroscopic constants and structural parameters. Due to fitting indeterminacies, these previous analyses did not include the main Fermi resonance interaction term. Consequently, the fitted rotational constants are linear combinations of the unmixed rotational constants of the basis vibrational states. In this paper, we have calculated the contributions of the Fermi resonances to the observed rotational constants in a model that determines the vibrational-rotational constants, the Fermi term and the mixing between interacting vibrational states, the cubic potential constant ( φ997) that connects interacting levels through a Fermi resonance, and the inertial defects. These results agree with predictions from ab initio and harmonic force field calculations and provide further experimental information for the determination of the fundamental molecular properties of chlorine nitrate.
A general, accurate procedure for calculating molecular interaction force.
Yang, Pinghai; Qian, Xiaoping
2009-09-15
The determination of molecular interaction forces, e.g., van der Waals force, between macroscopic bodies is of fundamental importance for understanding sintering, adhesion and fracture processes. In this paper, we develop an accurate, general procedure for van der Waals force calculation. This approach extends a surface formulation that converts a six-dimensional (6D) volume integral into a 4D surface integral for the force calculation. It uses non-uniform rational B-spline (NURBS) surfaces to represent object surfaces. Surface integrals are then done on the parametric domain of the NURBS surfaces. It has combined advantages of NURBS surface representation and surface formulation, including (1) molecular interactions between arbitrary-shaped objects can be represented and evaluated by the NURBS model further common geometries such as spheres, cones, planes can be represented exactly and interaction forces are thus calculated accurately; (2) calculation efficiency is improved by converting the volume integral to the surface integral. This approach is implemented and validated via its comparison with analytical solutions for simple geometries. Calculation of van der Waals force between complex geometries with surface roughness is also demonstrated. A tutorial on the NURBS approach is given in Appendix A. PMID:19596335
Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency
NASA Astrophysics Data System (ADS)
Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao
2008-05-01
Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.
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.
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.
Microsatellites Are Molecular Clocks That Support Accurate Inferences about History
Mullikin, James C.; Patterson, Nick; Reich, David E.
2009-01-01
Microsatellite length mutations are often modeled using the generalized stepwise mutation process, which is a type of random walk. If this model is sufficiently accurate, one can estimate the coalescence time between alleles of a locus after a mathematical transformation of the allele lengths. When large-scale microsatellite genotyping first became possible, there was substantial interest in using this approach to make inferences about time and demography, but that interest has waned because it has not been possible to empirically validate the clock by comparing it with data in which the mutation process is well understood. We analyzed data from 783 microsatellite loci in human populations and 292 loci in chimpanzee populations, and compared them with up to one gigabase of aligned sequence data, where the molecular clock based upon nucleotide substitutions is believed to be reliable. We empirically demonstrate a remarkable linearity (r2 > 0.95) between the microsatellite average square distance statistic and sequence divergence. We demonstrate that microsatellites are accurate molecular clocks for coalescent times of at least 2 million years (My). We apply this insight to confirm that the African populations San, Biaka Pygmy, and Mbuti Pygmy have the deepest coalescent times among populations in the Human Genome Diversity Project. Furthermore, we show that microsatellites support unbiased estimates of population differentiation (FST) that are less subject to ascertainment bias than single nucleotide polymorphism (SNP) FST. These results raise the prospect of using microsatellite data sets to determine parameters of population history. When genotyped along with SNPs, microsatellite data can also be used to correct for SNP ascertainment bias. PMID:19221007
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.
Molecular adsorption at Pt(111). How accurate are DFT functionals?
Gautier, Sarah; Steinmann, Stephan N; Michel, Carine; Fleurat-Lessard, Paul; Sautet, Philippe
2015-11-21
Molecular chemisorption at a metal surface is a key step for many processes, such as catalysis, electrochemistry, surface treatment, tribology and friction. Modeling with density functional theory is largely used on these systems. From a detailed comparison with accurate micro-calorimetric data on ten systems (involving ethylene, cyclohexene, benzene, naphthalene, CO, O2, H2, methane, ethane), we study the accuracy, for chemisorption on Pt(111), of five exchange-correlation functionals including one generalized gradient approximation functional (PBE) and four functionals that take into account van der Waals interactions (optPBE-vdW, optB86b-vdW, BEEF-vdW, PBE-dDsC). If the functionals used provide very similar geometries and electronic structures, as shown by projected density of states, they give strikingly different results for the adsorption energy of molecules on Pt(111). Among the set of chemisorption data, the lowest mean absolute deviations (MAD) are obtained with the optPBE-vdW and PBE-dDsC functionals (∼0.2 eV) while PBE and optB86b-vdW give twice larger MAD (∼0.45 eV). BEEF-vdW is intermediate with a MAD of 0.33 eV. For laterally π-bound unsaturated hydrocarbons (cyclohexene, benzene, naphthalene) the PBE and the BEEF-vdW functionals are severally under-bound, while optPBE-vdW and PBE-dDsC provide a good match with experiments. Hence both the incorporation of van der Waals dispersive forces and the choice of the exchange functional have a key influence on the chemisorption energy. Vertically bound ethylidyne and CO are in contrast over-bound with all functionals, the best agreement being obtained with BEEF-vdW. None of the selected functionals hence provides a universally accurate treatment of chemisorption energies. PMID:26455444
Accurate calculations of the high-pressure elastic constants based on the first-principles
NASA Astrophysics Data System (ADS)
Wang, Chen-Ju; Gu, Jian-Bing; Kuang, Xiao-Yu; Yang, Xiang-Dong
2015-08-01
The energy term corresponding to the first order of the strain in Taylor series expansion of the energy with respect to strain is always ignored when high-pressure elastic constants are calculated. Whether the modus operandi would affect the results of the high-pressure elastic constants is still unsolved. To clarify this query, we calculate the high-pressure elastic constants of tantalum and rhenium when the energy term mentioned above is considered and neglected, respectively. Results show that the neglect of the energy term corresponding to the first order of the strain indeed would influence the veracity of the high-pressure elastic constants, and this influence becomes larger with pressure increasing. Therefore, the energy term corresponding to the first-order of the strain should be considered when the high-pressure elastic constants are calculated. Project supported by the National Natural Science Foundation of China (Grant No. 11274235), the Young Scientist Fund of the National Natural Science Foundation of China (Grant No. 11104190), and the Doctoral Education Fund of Education Ministry of China (Grant Nos. 20100181110086 and 20110181120112).
Song, Yunpeng; Wu, Sen; Xu, Linyan; Fu, Xing
2015-01-01
Measurement of force on a micro- or nano-Newton scale is important when exploring the mechanical properties of materials in the biophysics and nanomechanical fields. The atomic force microscope (AFM) is widely used in microforce measurement. The cantilever probe works as an AFM force sensor, and the spring constant of the cantilever is of great significance to the accuracy of the measurement results. This paper presents a normal spring constant calibration method with the combined use of an electromagnetic balance and a homemade AFM head. When the cantilever presses the balance, its deflection is detected through an optical lever integrated in the AFM head. Meanwhile, the corresponding bending force is recorded by the balance. Then the spring constant can be simply calculated using Hooke’s law. During the calibration, a feedback loop is applied to control the deflection of the cantilever. Errors that may affect the stability of the cantilever could be compensated rapidly. Five types of commercial cantilevers with different shapes, stiffness, and operating modes were chosen to evaluate the performance of our system. Based on the uncertainty analysis, the expanded relative standard uncertainties of the normal spring constant of most measured cantilevers are believed to be better than 2%. PMID:25763650
Stresses and elastic constants of crystalline sodium, from molecular dynamics
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.
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.
Highly accurate analytical energy of a two-dimensional exciton in a constant magnetic field
NASA Astrophysics Data System (ADS)
Hoang, Ngoc-Tram D.; Nguyen, Duy-Anh P.; Hoang, Van-Hung; Le, Van-Hoang
2016-08-01
Explicit expressions are given for analytically describing the dependence of the energy of a two-dimensional exciton on magnetic field intensity. These expressions are highly accurate with the precision of up to three decimal places for the whole range of the magnetic field intensity. The results are shown for the ground state and some excited states; moreover, we have all formulae to obtain similar expressions of any excited state. Analysis of numerical results shows that the precision of three decimal places is maintained for the excited states with the principal quantum number of up to n=100.
NASA Astrophysics Data System (ADS)
Teale, Andrew M.; Lutnæs, Ola B.; Helgaker, Trygve; Tozer, David J.; Gauss, Jürgen
2013-01-01
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)], 10.1063/1.3242081, 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.
Fang, Tao; Li, Wei; Gu, Fangwei; Li, Shuhua
2015-01-13
We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals. PMID:26574207
Constant pressure and temperature discrete-time Langevin molecular dynamics.
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. PMID:25416875
Constant pressure and temperature discrete-time Langevin molecular dynamics
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.
Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting
Khan, Tarik A.; Friedensohn, Simon; de Vries, Arthur R. Gorter; Straszewski, Jakub; Ruscheweyh, Hans-Joachim; Reddy, Sai T.
2016-01-01
High-throughput antibody repertoire sequencing (Ig-seq) provides quantitative molecular information on humoral immunity. However, Ig-seq is compromised by biases and errors introduced during library preparation and sequencing. By using synthetic antibody spike-in genes, we determined that primer bias from multiplex polymerase chain reaction (PCR) library preparation resulted in antibody frequencies with only 42 to 62% accuracy. Additionally, Ig-seq errors resulted in antibody diversity measurements being overestimated by up to 5000-fold. To rectify this, we developed molecular amplification fingerprinting (MAF), which uses unique molecular identifier (UID) tagging before and during multiplex PCR amplification, which enabled tagging of transcripts while accounting for PCR efficiency. Combined with a bioinformatic pipeline, MAF bias correction led to measurements of antibody frequencies with up to 99% accuracy. We also used MAF to correct PCR and sequencing errors, resulting in enhanced accuracy of full-length antibody diversity measurements, achieving 98 to 100% error correction. Using murine MAF-corrected data, we established a quantitative metric of recent clonal expansion—the intraclonal diversity index—which measures the number of unique transcripts associated with an antibody clone. We used this intraclonal diversity index along with antibody frequencies and somatic hypermutation to build a logistic regression model for prediction of the immunological status of clones. The model was able to predict clonal status with high confidence but only when using MAF error and bias corrected Ig-seq data. Improved accuracy by MAF provides the potential to greatly advance Ig-seq and its utility in immunology and biotechnology. PMID:26998518
Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting.
Khan, Tarik A; Friedensohn, Simon; Gorter de Vries, Arthur R; Straszewski, Jakub; Ruscheweyh, Hans-Joachim; Reddy, Sai T
2016-03-01
High-throughput antibody repertoire sequencing (Ig-seq) provides quantitative molecular information on humoral immunity. However, Ig-seq is compromised by biases and errors introduced during library preparation and sequencing. By using synthetic antibody spike-in genes, we determined that primer bias from multiplex polymerase chain reaction (PCR) library preparation resulted in antibody frequencies with only 42 to 62% accuracy. Additionally, Ig-seq errors resulted in antibody diversity measurements being overestimated by up to 5000-fold. To rectify this, we developed molecular amplification fingerprinting (MAF), which uses unique molecular identifier (UID) tagging before and during multiplex PCR amplification, which enabled tagging of transcripts while accounting for PCR efficiency. Combined with a bioinformatic pipeline, MAF bias correction led to measurements of antibody frequencies with up to 99% accuracy. We also used MAF to correct PCR and sequencing errors, resulting in enhanced accuracy of full-length antibody diversity measurements, achieving 98 to 100% error correction. Using murine MAF-corrected data, we established a quantitative metric of recent clonal expansion-the intraclonal diversity index-which measures the number of unique transcripts associated with an antibody clone. We used this intraclonal diversity index along with antibody frequencies and somatic hypermutation to build a logistic regression model for prediction of the immunological status of clones. The model was able to predict clonal status with high confidence but only when using MAF error and bias corrected Ig-seq data. Improved accuracy by MAF provides the potential to greatly advance Ig-seq and its utility in immunology and biotechnology. PMID:26998518
Accurate molecular classification of cancer using simple rules
Wang, Xiaosheng; Gotoh, Osamu
2009-01-01
Background One intractable problem with using microarray data analysis for cancer classification is how to reduce the extremely high-dimensionality gene feature data to remove the effects of noise. Feature selection is often used to address this problem by selecting informative genes from among thousands or tens of thousands of genes. However, most of the existing methods of microarray-based cancer classification utilize too many genes to achieve accurate classification, which often hampers the interpretability of the models. For a better understanding of the classification results, it is desirable to develop simpler rule-based models with as few marker genes as possible. Methods We screened a small number of informative single genes and gene pairs on the basis of their depended degrees proposed in rough sets. Applying the decision rules induced by the selected genes or gene pairs, we constructed cancer classifiers. We tested the efficacy of the classifiers by leave-one-out cross-validation (LOOCV) of training sets and classification of independent test sets. Results We applied our methods to five cancerous gene expression datasets: leukemia (acute lymphoblastic leukemia [ALL] vs. acute myeloid leukemia [AML]), lung cancer, prostate cancer, breast cancer, and leukemia (ALL vs. mixed-lineage leukemia [MLL] vs. AML). Accurate classification outcomes were obtained by utilizing just one or two genes. Some genes that correlated closely with the pathogenesis of relevant cancers were identified. In terms of both classification performance and algorithm simplicity, our approach outperformed or at least matched existing methods. Conclusion In cancerous gene expression datasets, a small number of genes, even one or two if selected correctly, is capable of achieving an ideal cancer classification effect. This finding also means that very simple rules may perform well for cancerous class prediction. PMID:19874631
Accurate and molecular-size-tolerant NMR quantitation of diverse components in solution
Okamura, Hideyasu; Nishimura, Hiroshi; Nagata, Takashi; Kigawa, Takanori; Watanabe, Takashi; Katahira, Masato
2016-01-01
Determining the amount of each component of interest in a mixture is a fundamental first step in characterizing the nature of the solution and to develop possible means of utilization of its components. Similarly, determining the composition of units in complex polymers, or polymer mixtures, is crucial. Although NMR is recognized as one of the most powerful methods to achieve this and is widely used in many fields, variation in the molecular sizes or the relative mobilities of components skews quantitation due to the size-dependent decay of magnetization. Here, a method to accurately determine the amount of each component by NMR was developed. This method was validated using a solution that contains biomass-related components in which the molecular sizes greatly differ. The method is also tolerant of other factors that skew quantitation such as variation in the one-bond C–H coupling constant. The developed method is the first and only way to reliably overcome the skewed quantitation caused by several different factors to provide basic information on the correct amount of each component in a solution. PMID:26883279
Williams, Sarah L; Blachly, Patrick G; McCammon, J Andrew
2011-12-01
A constant pH molecular dynamics method has been used in the blind prediction of pK(a) 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 pK(a) of solvent-exposed residues. For residues in the protein interior, the CpHMD method encounters some difficulties in reaching convergence and predicting the pK(a) 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 pK(a) values consistent with experimental results. PMID:22072520
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.
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…
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)
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.
Constant pH Molecular Dynamics of Proteins in Explicit Solvent with Proton Tautomerism
Goh, Garrett B.; Hulbert, Benjamin S.; Zhou, Huiqing; Brooks, Charles L.
2015-01-01
pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMDMSλD). In the CPHMDMSλD framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMDMSλD simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMDMSλD framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules – proteins and nucleic acids is now possible. PMID:24375620
Efficient implementation of constant pH molecular dynamics on modern graphics processors.
Arthur, Evan J; Brooks, Charles L
2016-09-15
The treatment of pH sensitive ionization states for titratable residues in proteins is often omitted from molecular dynamics (MD) simulations. While static charge models can answer many questions regarding protein conformational equilibrium and protein-ligand interactions, pH-sensitive phenomena such as acid-activated chaperones and amyloidogenic protein aggregation are inaccessible to such models. Constant pH molecular dynamics (CPHMD) coupled with the Generalized Born with a Simple sWitching function (GBSW) implicit solvent model provide an accurate framework for simulating pH sensitive processes in biological systems. Although this combination has demonstrated success in predicting pKa values of protein structures, and in exploring dynamics of ionizable side-chains, its speed has been an impediment to routine application. The recent availability of low-cost graphics processing unit (GPU) chipsets with thousands of processing cores, together with the implementation of the accurate GBSW implicit solvent model on those chipsets (Arthur and Brooks, J. Comput. Chem. 2016, 37, 927), provide an opportunity to improve the speed of CPHMD and ionization modeling greatly. Here, we present a first implementation of GPU-enabled CPHMD within the CHARMM-OpenMM simulation package interface. Depending on the system size and nonbonded force cutoff parameters, we find speed increases of between one and three orders of magnitude. Additionally, the algorithm scales better with system size than the CPU-based algorithm, thus allowing for larger systems to be modeled in a cost effective manner. We anticipate that the improved performance of this methodology will open the door for broad-spread application of CPHMD in its modeling pH-mediated biological processes. © 2016 Wiley Periodicals, Inc. PMID:27405884
NASA Astrophysics Data System (ADS)
Yogurtcu, Osman N.; Johnson, Margaret E.
2015-08-01
The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute
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.
Frictional Response of Molecularly Thin Liquid Polymer Films Subject to Constant Shear Stress
NASA Astrophysics Data System (ADS)
Tschirhart, Charles; Troian, Sandra
2014-03-01
Measurements of the frictional response of nanoscale viscous films are typically obtained using the surface force apparatus in which a fluid layer is confined between smooth solid substrates approaching at constant speed or force. The squeezing pressure causes lateral flow from which the shear viscosity can be deduced. Under these conditions however, molecularly thin films tend to solidify wholly or partially and estimates of the shear viscosity can exceed those in macroscale films by many orders of magnitude. This problem can be avoided altogether by examining the response of an initially flat, supported, free surface film subject to comparable values of surface shear stress by application of an external inert gas stream. This method was first conceived by Derjaguin in 1944; more recent studies by Mate et al. at IBM Almaden on complex polymeric systems have uncovered fluid layering and other interesting behaviors. The only drawback is that this alternative technique requires an accurate model for interface distortion. We report on ellipsometric measurements of ultrathin polymeric films in efforts to determine whether the usual interface equations for free surface films based purely on continuum models can be properly extended to nanoscale films. Supported by a Fred and Jean Felberg Fellowship and G. W. Housner Student Discovery Fund.
NASA Astrophysics Data System (ADS)
Richardi, Johannes; Krienke, Hartmut; Fries, Pascal H.
1997-07-01
Kirkwood factors, yielding dielectric constants, are calculated from pair correlation functions, which are numerical solutions of the hypernetted-chain approximation of molecular Ornstein-Zernike (MOZ) theory. The combined influence of the molecular polarizability and the hydrogen bond strength is investigated. Using a reasonable diameter for the hydrogen size in the amide group, the MOZ Kirkwood factors and dielectric constants are in good agreement with the experimental values. This is explained by the statistical correlations between the orientations of two near molecules. This is consistent with hydrogen bonds, forming networks in formamide and chains in N-methylformamide.
NASA Astrophysics Data System (ADS)
Orkin, V. L.; Khamaganov, V. G.; Martynova, L. E.; Kurylo, M. J.
2013-12-01
Reactions with hydroxyl radicals and photolysis are the main processes dictating the compound residence time in the atmosphere for a majority of trace gases. In case of very short lived compounds their reaction with OH dictates both the atmospheric lifetime and active halogen release. Therefore, the accuracy of OH kinetic data is of primary importance for the purpose of comprehensive atmospheric modeling of compound's impact on the atmosphere, such as in ozone depletion (ODP) and climate change (GWP). The currently recommended uncertainties of OH reaction rate constants (NASA/JPL Publications and IUPAC Publications) exceed 10% at room temperature for the majority of compounds to be larger at lower temperatures of atmospheric interest. Thus, uncertainties in the photochemical properties of potential and current atmospheric trace gases obtained under controlled laboratory conditions may constitute a major source of uncertainty in estimating the compound's environmental impact. We will present the higher accuracy results of OH reaction rate constant determinations between 220 K and 370 K. A statistical analysis of the data will be discussed. The high precision of kinetic measurements performed at low temperatures allows reliable determination of temperature dependences of the rate constants. This is especially important because we found that many OH reactions exhibit the curvature of the Arrhenius plots. A detailed inventory of sources of instrumental uncertainties related to our experiment proves a total uncertainty of the OH reaction rate constant to be as small as ~2-3%. The estimation of the atmospheric lifetime of a compound based on its OH reaction rate constant will be discussed.
NASA Astrophysics Data System (ADS)
Mozafari, E.; Shulumba, N.; Steneteg, P.; Alling, B.; Abrikosov, Igor A.
2016-08-01
We present a theoretical scheme to calculate the elastic constants of magnetic materials in the high-temperature paramagnetic state. Our approach is based on a combination of disordered local moments picture and ab initio molecular dynamics (DLM-MD). Moreover, we investigate a possibility to enhance the efficiency of the simulations of elastic properties using the recently introduced method: symmetry imposed force constant temperature-dependent effective potential (SIFC-TDEP). We have chosen cubic paramagnetic CrN as a model system. This is done due to its technological importance and its demonstrated strong coupling between magnetic and lattice degrees of freedom. We have studied the temperature-dependent single-crystal and polycrystalline elastic constants of paramagentic CrN up to 1200 K. The obtained results at T = 300 K agree well with the experimental values of polycrystalline elastic constants as well as the Poisson ratio at room temperature. We observe that the Young's modulus is strongly dependent on temperature, decreasing by ˜14 % from T = 300 K to 1200 K. In addition we have studied the elastic anisotropy of CrN as a function of temperature and we observe that CrN becomes substantially more isotropic as the temperature increases. We demonstrate that the use of Birch law may lead to substantial errors for calculations of temperature induced changes of elastic moduli. The proposed methodology can be used for accurate predictions of mechanical properties of magnetic materials at temperatures above their magnetic order-disorder phase transition.
Use of hydrophobic constants of molecular fragments for characterizing analytical systems
Tselik, E.I.; Polvektov, N.S.
1985-06-10
The authors attempt to clarify the applicability of the proposed hydrophobicity parameters to a description of the behavior of complex compounds with organic ligands in extractional systems, and to establish quantitative relationships between the properties of the complex and hydrophobicity of the ligand. It was found that the stability constants of the ionic associates of lanthanum, neodymium, and erbium with certain derivatives of salicylic acid, dihalogenated derivatives of 8-hydroxyquinoline, and Rhodamine B correlate with the hydrophobicity of the ligands. The quantitative expressions of these serve as empirical hydrophobic constants of molecular fragments of organic compounds.
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.
Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre
2015-06-04
Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less
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.
Kim, Yong-Hyun; Kim, Ki-Hyun
2016-01-01
A novel technique is developed to determine the Henry's law constants (HLCs) of seven volatile fatty acids (VFAs) with significantly high solubility using a combined application of thermal desorber/gas chromatography/mass spectrometry (TD/GC/MS). In light of the strong sorptive properties of these semi-volatile organic compounds (SVOCs), their HLCs were determined by properly evaluating the fraction lost on the surface of the materials used to induce equilibrium (vial, gas-tight syringe, and sorption tube). To this end, a total of nine repeated experiments were conducted in a closed (static) system at three different gas/liquid volume ratios. The best estimates for HLCs (M/atm) were thus 7,200 (propionic acid), 4,700 (i-butyric acid), 4,400 (n-butyric acid), 2,700 (i-valeric acid), 2,400 (n-valeric acid), 1,000 (hexanoic acid), and 1,500 (heptanoic acid). The differences in the HLC values between this study and previous studies, if assessed in terms of the percent difference, ranged from 9.2% (n-valeric acid) to 55.7% (i-valeric acid). We overcame the main cause of errors encountered in previous studies by performing the proper correction of the sorptive losses of the SVOCs that inevitably took place, particularly on the walls of the equilibration systems (mainly the headspace vial and/or the glass tight syringe). PMID:26577086
Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations
NASA Astrophysics Data System (ADS)
Grønbech-Jensen, Niels; Hayre, Natha Robert; Farago, Oded
2014-02-01
A new Langevin-Verlet thermostat that preserves the fluctuation-dissipation relationship for discrete time steps is applied to molecular modeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as an example that can be easily simulated by all three packages. Contrary to existing methods, the new thermostat exhibits no detectable changes in the sampling statistics as the time step is varied in the entire numerical stability range. The simple form of the method, which we express in the three common forms (Velocity-Explicit, Störmer-Verlet, and Leap-Frog), allows for easy implementation within existing molecular simulation packages to achieve faster and more accurate results with no cost in either computing time or programming complexity.
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. PMID:25056524
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.
NASA Astrophysics Data System (ADS)
Sellers, Michael; Lisal, Martin; Brennan, John
2015-06-01
Investigating the ability of a molecular model to accurately represent a real material is crucial to model development and use. When the model simulates materials in extreme conditions, one such property worth evaluating is the phase transition point. However, phase transitions are often overlooked or approximated because of difficulty or inaccuracy when simulating them. Techniques such as super-heating or super-squeezing a material to induce a phase change suffer from inherent timescale limitations leading to ``over-driving,'' and dual-phase simulations require many long-time runs to seek out what frequently results in an inexact location of phase-coexistence. We present a compilation of methods for the determination of solid-solid and solid-liquid phase transition points through the accurate calculation of the chemical potential. The methods are applied to the Smith-Bharadwaj atomistic potential's representation of cyclotrimethylene trinitramine (RDX) to accurately determine its melting point (Tm) and the alpha to gamma solid phase transition pressure. We also determine Tm for a coarse-grain model of RDX, and compare its value to experiment and atomistic counterpart. All methods are employed via the LAMMPS simulator, resulting in 60-70 simulations that total 30-50 ns. Approved for public release. Distribution is unlimited.
NASA Astrophysics Data System (ADS)
Mills, Andrew A.; Ford, Kyle B.; Kreckel, Holger; Perera, Manori; Crabtree, Kyle N.; McCall, Benjamin J.
2009-06-01
With the advent of Herschel and SOFIA, laboratory methods capable of providing molecular rest frequencies in the terahertz and sub-millimeter regime are increasingly important. As of yet, it has been difficult to perform spectroscopy in this wavelength region due to the limited availability of radiation sources, optics, and detectors. Our goal is to provide accurate THz rest frequencies for molecular ions by combining previously recorded microwave transitions with combination differences obtained from high precision mid-IR spectroscopy. We are constructing a Sensitive Resolved Ion Beam Spectroscopy setup which will harness the benefits of kinematic compression in a molecular ion beam to enable very high resolution spectroscopy. This ion beam is interrogated by continuous-wave cavity ringdown spectroscopy using a home-made widely tunable difference frequency laser that utilizes two near-IR lasers and a periodically-poled lithium niobate crystal. Here, we report our efforts to optimize our ion beam spectrometer and to perform high-precision and high-accuracy frequency measurements using an optical frequency comb. footnote
A large catalog of accurate distances to molecular clouds from PS1 photometry
Schlafly, E. F.; Rix, H.-W.; Martin, N. F.; Green, G.; Finkbeiner, D. P.; Bell, E. F.; Burgett, W. S.; Chambers, K. C.; Hodapp, K. W.; Kaiser, N.; Magnier, E. A.; Tonry, J. L.; Draper, P. W.; Metcalfe, N.; Price, P. A.
2014-05-01
Distance measurements to molecular clouds are important but are often made separately for each cloud of interest, employing very different data and techniques. We present a large, homogeneous catalog of distances to molecular clouds, most of which are of unprecedented accuracy. We determine distances using optical photometry of stars along lines of sight toward these clouds, obtained from PanSTARRS-1. We simultaneously infer the reddenings and distances to these stars, tracking the full probability distribution function using a technique presented in Green et al. We fit these star-by-star measurements using a simple dust screen model to find the distance to each cloud. We thus estimate the distances to almost all of the clouds in the Magnani et al. catalog, as well as many other well-studied clouds, including Orion, Perseus, Taurus, Cepheus, Polaris, California, and Monoceros R2, avoiding only the inner Galaxy. Typical statistical uncertainties in the distances are 5%, though the systematic uncertainty stemming from the quality of our stellar models is about 10%. The resulting catalog is the largest catalog of accurate, directly measured distances to molecular clouds. Our distance estimates are generally consistent with available distance estimates from the literature, though in some cases the literature estimates are off by a factor of more than two.
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.
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
Elastic Constants of Superconducting MgB2 from Molecular Dynamics Simulations with Shell Model
NASA Astrophysics Data System (ADS)
Guo, Yun-Dong; Chen, Xiang-Rong; Yang, Xiang-Dong; Gou, Qing-Quan
2005-11-01
The elastic constants of superconducting MgB2 are calculated using a molecular dynamics method (MD) with shell model. The lattice parameters, five independent elastic constants, equations of state (EOS), Debye temperature, and bulk modulus of MgB2 are obtained. Meanwhile, the dependence of the bulk modulus B, the lattice parameters a and c, and the unit cell volume V on the applied pressure are presented. It is demonstrated that the method introduced here can well reproduce the experimental results with a reasonable accuracy. The project supported by National Natural Science Foundation of China under Grant No. 60436010 and the Scientific Research Foundation for the Returned Overseas Chinese Scholars, the Ministry of Education of China under Grant No. 2004176-6-4
A molecular site-site integral equation that yields the dielectric constant
NASA Astrophysics Data System (ADS)
Dyer, Kippi M.; Perkyns, John S.; Stell, George; Pettitt, B. Montgomery
2008-09-01
Our recent derivation [K. M. Dyer et al., J. Chem. Phys. 127, 194506 (2007)] of a diagrammatically proper, site-site, integral equation theory using molecular angular expansions is extended to polar fluids. With the addition of atomic site charges we take advantage of the formal long-ranged potential field cancellations before renormalization to generate a set of numerically stable equations. Results for calculations in a minimal (spherical) angular basis set are presented for the radial distribution function, the first dipolar (110) projection, and the dielectric constant for two model diatomic systems. All results, when compared to experiment and simulation, are a significant quantitative and qualitative improvement over previous site-site theories. More importantly, the dielectric constant is not trivial and close to simulation and experiment.
Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes
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.
Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes
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
Accurate force fields and methods for modelling organic molecular crystals at finite temperatures.
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. PMID:27230942
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
Surface electron density models for accurate ab initio molecular dynamics with electronic friction
NASA Astrophysics Data System (ADS)
Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.
2016-06-01
Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.
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).
NASA Astrophysics Data System (ADS)
Orkin, V. L.; Khamaganov, V. G.; Martynova, L. E.; Kurylo, M. J.
2012-12-01
The emissions of halogenated (Cl, Br containing) organics of both natural and anthropogenic origin contribute to the balance of and changes in the stratospheric ozone concentration. The associated chemical cycles are initiated by the photochemical decomposition of the portion of source gases that reaches the stratosphere. Reactions with hydroxyl radicals and photolysis are the main processes dictating the compound lifetime in the troposphere and release of active halogen in the stratosphere for a majority of halogen source gases. Therefore, the accuracy of photochemical data is of primary importance for the purpose of comprehensive atmospheric modeling and for simplified kinetic estimations of global impacts on the atmosphere, such as in ozone depletion (i.e., the Ozone Depletion Potential, ODP) and climate change (i.e., the Global Warming Potential, GWP). The sources of critically evaluated photochemical data for atmospheric modeling, NASA/JPL Publications and IUPAC Publications, recommend uncertainties within 10%-60% for the majority of OH reaction rate constants with only a few cases where uncertainties lie at the low end of this range. These uncertainties can be somewhat conservative because evaluations are based on the data from various laboratories obtained during the last few decades. Nevertheless, even the authors of the original experimental works rarely estimate the total combined uncertainties of the published OH reaction rate constants to be less than ca. 10%. Thus, uncertainties in the photochemical properties of potential and current atmospheric trace gases obtained under controlled laboratory conditions still may constitute a major source of uncertainty in estimating the compound's environmental impact. One of the purposes of the presentation is to illustrate the potential for obtaining accurate laboratory measurements of the OH reaction rate constant over the temperature range of atmospheric interest. A detailed inventory of accountable sources of
Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free Energies
2015-01-01
In protein–ligand binding, the electrostatic environments of the two binding partners may vary significantly in bound and unbound states, which may lead to protonation changes upon binding. In cases where ligand binding results in a net uptake or release of protons, the free energy of binding is pH-dependent. Nevertheless, conventional free energy calculations and molecular docking protocols typically do not rigorously account for changes in protonation that may occur upon ligand binding. To address these shortcomings, we present a simple methodology based on Wyman’s binding polynomial formalism to account for the pH dependence of binding free energies and demonstrate its use on cucurbit[7]uril (CB[7]) host–guest systems. Using constant pH molecular dynamics and a reference binding free energy that is taken either from experiment or from thermodynamic integration computations, the pH-dependent binding free energy is determined. This computational protocol accurately captures the large pKa shifts observed experimentally upon CB[7]:guest association and reproduces experimental binding free energies at different levels of pH. We show that incorrect assignment of fixed protonation states in free energy computations can give errors of >2 kcal/mol in these host–guest systems. Use of the methods presented here avoids such errors, thus suggesting their utility in computing proton-linked binding free energies for protein–ligand complexes. PMID:25134690
Casciola, Maura; Kasimova, Marina A; Rems, Lea; Zullino, Sara; Apollonio, Francesca; Tarek, Mounir
2016-06-01
Molecular dynamics (MD) simulations have become a powerful tool to study electroporation (EP) in atomic detail. In the last decade, numerous MD studies have been conducted to model the effect of pulsed electric fields on membranes, providing molecular models of the EP process of lipid bilayers. Here we extend these investigations by modeling for the first time conditions comparable to experiments using long (μs-ms) low intensity (~kV/cm) pulses, by studying the characteristics of pores formed in lipid bilayers maintained at a constant surface tension and subject to constant charge imbalance. This enables the evaluation of structural (size) and electrical (conductance) properties of the pores formed, providing information hardly accessible directly by experiments. Extensive simulations of EP of simple phosphatidylcholine bilayers in 1M NaCl show that hydrophilic pores with stable radii (1-2.5nm) form under transmembrane voltages between 420 and 630mV, allowing for ionic conductance in the range of 6.4-29.5nS. We discuss in particular these findings and characterize both convergence and size effects in the MD simulations. We further extend these studies in a follow-up paper (Rems et al., Bioelectrochemistry, Submitted), by proposing an improved continuum model of pore conductance consistent with the results from the MD simulations. PMID:26883056
Partial hessian fitting for determining force constant parameters in molecular mechanics.
Wang, Ruixing; Ozhgibesov, Mikhail; Hirao, Hajime
2016-10-01
We present a new protocol for deriving force constant parameters that are used in molecular mechanics (MM) force fields to describe the bond-stretching, angle-bending, and dihedral terms. A 3 × 3 partial matrix is chosen from the MM Hessian matrix in Cartesian coordinates according to a simple rule and made as close as possible to the corresponding partial Hessian matrix computed using quantum mechanics (QM). This partial Hessian fitting (PHF) is done analytically and thus rapidly in a least-squares sense, yielding force constant parameters as the output. We herein apply this approach to derive force constant parameters for the AMBER-type energy expression. Test calculations on several different molecules show good performance of the PHF parameter sets in terms of how well they can reproduce QM-calculated frequencies. When soft bonds are involved in the target molecule as in the case of secondary building units of metal-organic frameworks, the MM-optimized geometry sometimes deviates significantly from the QM-optimized one. We show that this problem is rectified effectively by use of a simple procedure called Katachi that modifies the equilibrium bond distances and angles in bond-stretching and angle-bending terms. © 2016 Wiley Periodicals, Inc. PMID:27497261
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.
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.
Accurate calculation of binding energies for molecular clusters - Assessment of different models
NASA Astrophysics Data System (ADS)
Friedrich, Joachim; Fiedler, Benjamin
2016-06-01
In this work we test different strategies to compute high-level benchmark energies for medium-sized molecular clusters. We use the incremental scheme to obtain CCSD(T)/CBS energies for our test set and carefully validate the accuracy for binding energies by statistical measures. The local errors of the incremental scheme are <1 kJ/mol. Since they are smaller than the basis set errors, we obtain higher total accuracy due to the applicability of larger basis sets. The final CCSD(T)/CBS benchmark values are ΔE = - 278.01 kJ/mol for (H2O)10, ΔE = - 221.64 kJ/mol for (HF)10, ΔE = - 45.63 kJ/mol for (CH4)10, ΔE = - 19.52 kJ/mol for (H2)20 and ΔE = - 7.38 kJ/mol for (H2)10 . Furthermore we test state-of-the-art wave-function-based and DFT methods. Our benchmark data will be very useful for critical validations of new methods. We find focal-point-methods for estimating CCSD(T)/CBS energies to be highly accurate and efficient. For foQ-i3CCSD(T)-MP2/TZ we get a mean error of 0.34 kJ/mol and a standard deviation of 0.39 kJ/mol.
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.
Lee, Myung Won; Meuwly, Markus
2013-12-14
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. PMID:24170171
Wijma, Hein J; Marrink, Siewert J; Janssen, Dick B
2014-07-28
Computational approaches could decrease the need for the laborious high-throughput experimental screening that is often required to improve enzymes by mutagenesis. Here, we report that using multiple short molecular dynamics (MD) simulations makes it possible to accurately model enantioselectivity for large numbers of enzyme-substrate combinations at low computational costs. We chose four different haloalkane dehalogenases as model systems because of the availability of a large set of experimental data on the enantioselective conversion of 45 different substrates. To model the enantioselectivity, we quantified the frequency of occurrence of catalytically productive conformations (near attack conformations) for pairs of enantiomers during MD simulations. We found that the angle of nucleophilic attack that leads to carbon-halogen bond cleavage was a critical variable that limited the occurrence of productive conformations; enantiomers for which this angle reached values close to 180° were preferentially converted. A cluster of 20-40 very short (10 ps) MD simulations allowed adequate conformational sampling and resulted in much better agreement to experimental enantioselectivities than single long MD simulations (22 ns), while the computational costs were 50-100 fold lower. With single long MD simulations, the dynamics of enzyme-substrate complexes remained confined to a conformational subspace that rarely changed significantly, whereas with multiple short MD simulations a larger diversity of conformations of enzyme-substrate complexes was observed. PMID:24916632
Lattice constant and substitutional composition of GeSn alloys grown by molecular beam epitaxy
NASA Astrophysics Data System (ADS)
Bhargava, Nupur; Coppinger, Matthew; Prakash Gupta, Jay; Wielunski, Leszek; Kolodzey, James
2013-07-01
Single crystal epitaxial Ge1-xSnx alloys with atomic fractions of tin up to x = 0.145 were grown by solid source molecular beam epitaxy on Ge (001) substrates. The Ge1-xSnx alloys formed high quality, coherent, strained layers at growth temperatures below 250 °C, as shown by high resolution X-ray diffraction. The amount of Sn that was on lattice sites, as determined by Rutherford backscattering spectrometry channeling, was found to be above 90% substitutional in all alloys. The degree of strain and the dependence of the effective unstrained bulk lattice constant of Ge1-xSnx alloys versus the composition of Sn have been determined.
Recent development and application of constant pH molecular dynamics
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. PMID:25309035
Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method.
Chen, Yunjie; Roux, Benoît
2015-08-11
A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys. 2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD-MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD-MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems. PMID:26300709
Molecular properties of alternative refrigerants derived from dielectric-constant measurements
Barao, M.T.; Castro, C.A.N. de; Mardolcar, U.V.
1997-03-01
A review of the current work in Lisbon on the measurement of the dielectric constant of the liquid phase of some environmentally acceptable refrigerants proposed as alternative replacements of the chlorofluorocarbons (CFCs), responsible for the destruction of the ozone layer, is presented. Measurements on HCFC 141b, HCFC 142b, HCFC 123, HFC 134a, HFC 152a, and HFC 32 samples of stated purities of 99.8 mass % or better were performed as a function of pressure and temperature, in the temperature range from 200 to 300 K and at pressures up to 20 MPa. The ratio of the capacitances of a cell filled with the sample and under vacuum was measured with a direct capacitance method. The dielectric-constant measurements have a repeatability of 0.003% and an accuracy of 0.1%. The theory developed by Vedam et al. based on the Eulerian Strain and the Kirkwood equation for the variation of the modified molar polarization with temperature and density were applied to obtain the dipole moments of the refrigerants in the liquid state, to obtain a physical insight of the molecular behavior, and to understand the equilibrium configuration of these liquids.
Sutter, Kiplangat; Truflandier, Lionel A; Autschbach, Jochen
2011-06-01
Solvent effects on J((195)Pt-(15)N) one-bond nuclear spin-spin coupling constants (J(PtN)) of cisplatin [cis-diamminedichloroplatinum(II)] and three cisplatin derivatives are investigated using a combination of density functional theory (DFT) based ab initio molecular dynamics (aiMD) and all-electron relativistic DFT NMR calculations employing the two-component relativistic zeroth-order regular approximation (ZORA). Good agreement with experiment is obtained when explicit solvent molecules are considered and when the computations are performed with a hybrid functional. Spin-orbit coupling causes only small effects on J(PtN) . Key factors contributing to the magnitude of coupling constants are elucidated, with the most significant being the presence of solvent as well as the quality of the density functional and basis set combination. The solvent effects are of the same magnitude as J(PtN) calculated for gas-phase geometries. However, the trends of J(PtN) among the complexes are already present in the gas phase. Results obtained with a continuum solvent model agree quite well with the aiMD results, provided that the Pt solvent-accessible radius is carefully chosen. The aiMD results support the existence of a partial hydrogen-bond-like inverse-hydration-type interaction affording a weak (1)J(Pt⋅⋅⋅H(w)) coupling between the complexes and the coordinating water molecule. PMID:21381179
NASA Astrophysics Data System (ADS)
Masunov, Artëm E.; Gangopadhyay, Shruba
2015-12-01
New method to eliminate the spin-contamination in broken symmetry density functional theory (BS DFT) calculations is introduced. Unlike conventional spin-purification correction, this method is based on canonical Natural Orbitals (NO) for each high/low spin coupled electron pair. We derive an expression to extract the energy of the pure singlet state given in terms of energy of BS DFT solution, the occupation number of the bonding NO, and the energy of the higher spin state built on these bonding and antibonding NOs (not self-consistent Kohn-Sham orbitals of the high spin state). Compared to the other spin-contamination correction schemes, spin-correction is applied to each correlated electron pair individually. We investigate two binuclear Mn(IV) molecular magnets using this pairwise correction. While one of the molecules is described by magnetic orbitals strongly localized on the metal centers, and spin gap is accurately predicted by Noodleman and Yamaguchi schemes, for the other one the gap is predicted poorly by these schemes due to strong delocalization of the magnetic orbitals onto the ligands. We show our new correction to yield more accurate results in both cases.
Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations.
Soares, Rosemberg O; Torres, Pedro H M; da Silva, Manuela L; Pascutti, Pedro G
2016-08-01
The active site of HIV protease (HIV-PR) is covered by two flaps. These flaps are known to be essential for the catalytic activity of the HIV-PR, but their exact conformations at the different stages of the enzymatic pathway remain subject to debate. Understanding the correct functional dynamics of the flaps might aid the development of new HIV-PR inhibitors. It is known that, the HIV-PR catalytic efficiency is pH-dependent, likely due to the influence of processes such as charge transfer and protonation/deprotonation of ionizable residues. Several Molecular Dynamics (MD) simulations have reported information about the HIV-PR flaps. However, in MD simulations the protonation of a residue is fixed and thus it is not possible to study the correlation between conformation and protonation state. To address this shortcoming, this work attempts to capture, through Constant pH Molecular Dynamics (CpHMD), the conformations of the apo, substrate-bound and inhibitor-bound HIV-PR, which differ drastically in their flap arrangements. The results show that the HIV-PR flaps conformations are defined by the protonation of the catalytic residues Asp25/Asp25' and that these residues are sensitive to pH changes. This study suggests that the catalytic aspartates can modulate the opening of the active site and substrate binding. PMID:27291071
2015-01-01
We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The pKa values estimated with the EDS-HREX method agree well with the experimental pKa values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 pKa units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 pKa units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated pKa values. PMID:25061443
NASA Astrophysics Data System (ADS)
Campbell, H. M.; Boardman, B. M.; DeVore, T. C.; Havey, D. K.
2012-12-01
This article describes an undergraduate laboratory exercise that uses optical spectroscopy to determine the magnitude and the uncertainty of the Boltzmann constant kb. The more accurate approach uses photoacoustic spectroscopy to measure the Doppler-broadened line profile of individual spectral lines of N2O to extract kb. Measurements and estimates of the uncertainties in the quantities needed to calculate kb from the line profiles are then used to estimate the uncertainty in kb. This experiment is unusual in that it uses advanced laser-based spectroscopy techniques to emphasize standard practices of uncertainty analysis. The core instrumentation is modular and relatively affordable; it requires a tunable single-mode laser, photoreceiver, optical cell, and vacuum pump. If this instrumentation is not available, an alternate approach can be performed which uses the intensity of each rotational transition of an infrared band to measure kb. Although there is more uncertainty using the alternate approach, low concentrations of CO2, DCl, or N2O give reasonable results for the magnitude of kb. Student assessment results indicate retention and mastery of the concept of combined measurement uncertainty.
NASA Astrophysics Data System (ADS)
Ansari, R.; Mirnezhad, M.; Sahmani, S.
2015-04-01
Molecular mechanics theory has been widely used to investigate the mechanical properties of nanostructures analytically. However, there is a limited number of research in which molecular mechanics model is utilized to predict the elastic properties of boron nitride nanotubes (BNNTs). In the current study, the mechanical properties of chiral single-walled BNNTs are predicted analytically based on an accurate molecular mechanics model. For this purpose, based upon the density functional theory (DFT) within the framework of the generalized gradient approximation (GGA), the exchange correlation of Perdew-Burke-Ernzerhof is adopted to evaluate force constants used in the molecular mechanics model. Afterwards, based on the principle of molecular mechanics, explicit expressions are given to calculate surface Young's modulus and Poisson's ratio of the single-walled BNNTs for different values of tube diameter and types of chirality. Moreover, the values of surface Young's modulus, Poisson's ratio and bending stiffness of boron nitride sheets are obtained via the DFT as byproducts. The results predicted by the present model are in reasonable agreement with those reported by other models in the literature.
Capturing molten globule state of α-lactalbumin through constant pH molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Bhattacharjee, Nicholus; Rani, Pooja; Biswas, Parbati
2013-03-01
The recently developed methods of constant pH molecular dynamics directly captures the correlation between protonation and conformation to probe protein structure, function, and dynamics. In this work, we investigate the effect of pH on the conformational properties of the protein human α-lactalbumin. Constant pH simulations at both acidic and alkaline medium indicate the formation of the molten globule state, which is in accordance with the previous experimental observations (especially, in acidic medium). The size of the protein measured by its radius of gyration (RG) exhibits a marked increase in both acidic and alkaline medium, which matches with the corresponding experimentally observed value of RG found in the molten globule. The probability of native contacts is also considerably reduced at acidic and basic pH as compared to that of native structure crystallized at neutral pH. The mean fractal dimension D2 of the protein records a sharp increase in basic medium as compared to those in neutral and acidic solutions implying a significant pH induced conformational change. The mean square fluctuations of all residues of the entire protein are found to increase by several folds in both acidic and basic medium, which may be correlated with the normalized solvent accessibility of the residues indicating role of solvent accessible surface area on protein internal dynamics. The helices comprising the α-domain of the protein are moderately preserved in the acidic and alkaline pH. However, the β-sheet structures present in the β-domain are completely disrupted in both acidic as well as basic pH.
Perspective: Tipping the scales: Search for drifting constants from molecular spectra
Jansen, Paul; Bethlem, Hendrick L.; Ubachs, Wim
2014-01-07
Transitions in atoms and molecules provide an ideal test ground for constraining or detecting a possible variation of the fundamental constants of nature. In this perspective, we review molecular species that are of specific interest in the search for a drifting proton-to-electron mass ratio μ. In particular, we outline the procedures that are used to calculate the sensitivity coefficients for transitions in these molecules and discuss current searches. These methods have led to a rate of change in μ bounded to 6 × 10{sup −14}/yr from a laboratory experiment performed in the present epoch. On a cosmological time scale, the variation is limited to |Δμ/μ| < 10{sup −5} for look-back times of 10–12× 10{sup 9} years and to |Δμ/μ| < 10{sup −7} for look-back times of 7× 10{sup 9} years. The last result, obtained from high-redshift observation of methanol, translates into μ{sup .}/μ=(1.4±1.4)×10{sup −17}/yr if a linear rate of change is assumed.
Perspective: tipping the scales: search for drifting constants from molecular spectra.
Jansen, Paul; Bethlem, Hendrick L; Ubachs, Wim
2014-01-01
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. PMID:24410211
Costandy, Joseph; Michalis, Vasileios K; Tsimpanogiannis, Ioannis N; Stubos, Athanassios K; Economou, Ioannis G
2016-03-28
We introduce a simple correction to the calculation of the lattice constants of fully occupied structure sI methane or carbon dioxide pure hydrates that are obtained from classical molecular dynamics simulations using the TIP4PQ/2005 water force field. The obtained corrected lattice constants are subsequently used in order to obtain isobaric thermal expansion coefficients of the pure gas hydrates that exhibit a trend that is significantly closer to the experimental behavior than previously reported classical molecular dynamics studies. PMID:27036466
NASA Astrophysics Data System (ADS)
Grenev, I. V.; Gavrilov, V. Yu.
2014-01-01
Adsorption isotherms of molecular hydrogen are measured at 77 K in a series of AlPO alumophosphate zeolites with different microchannel sizes. The potential of the intermolecular interaction of H2 is calculated within the model of a cylindrical channel of variable size. Henry constants are calculated for this model for arbitrary orientations of the adsorbate molecules in microchannels. The experimental and calculated values of the Henry adsorption constant of H2 are compared at 77 K on AlPO zeolites. The constants of intermolecular interaction are determined for the H2-AlPO system.
Predicting Extreme pKa Shifts in Staphylococcal Nuclease Mutants with Constant pH Molecular Dynamics
Arthur, Evan J.; Yesselman, Joseph D.; Brooks, Charles L.
2011-01-01
Accurate computational methods of determining protein and nucleic acid pKa values are vital to understanding pH-dependent processes in biological systems. In this paper we use the recently developed method constant pH molecular dynamics (CPHMD) to explore the calculation of highly-perturbed pKa values in variants of staphylococcal nuclease (SNase). Simulations were performed using the replica exchange (REX) protocol for improved conformational sampling with eight temperature windows, and yielded converged proton populations in a total sampling time of 4 ns. Our REX-CPHMD simulations resulted in calculated pKa values with an average unsigned error (AUE) of 0.75 pK units for the acidic residues in Δ+PHS, a hyperstable variant of SNase. For highly pKa-perturbed SNase mutants with known crystal structures, our calculations yielded an AUE of 1.5 pK units and for those mutants based on modeled structures an AUE of 1.4 pK units was found. Although a systematic underestimate of pK shifts was observed in most of the cases for the highly perturbed pK mutants, correlations between conformational rearrangement and plasticity associated with the mutation and error in pKa prediction was not evident in the data. This study further extends the scope of electrostatic environments explored using the REX-CPHMD methodology and suggests it is a reliable tool for rapidly characterizing ionizable amino acids within proteins even when modeled structures are employed. PMID:22002886
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.
NASA Astrophysics Data System (ADS)
Meng, Qingyong; Chen, Jun; Zhang, Dong H.
2015-09-01
The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.
Nayak, Malaya K.; Chaudhuri, Rajat K.
2011-02-15
The spin-rotational Hamiltonian parameters A{sub ||} and A{sub perpendicular} for the BaF molecule are calculated using four-component relativistic spinors at the second-order many-body perturbation theory (MBPT) level via the Z-vector technique. The second-order MBPT is applied to assess the accuracy of the computed hyperfine-structure constants before studying the problem with the state-of-the-artcoupled cluster with single and double excitations (CCSD) method which is highly accurate but computationally more expensive than MBPT. The hyperfine-structure constants A and A{sub d} resulted from these calculations agree favorably well with experimental findings and with other correlated calculations. The convergence behavior of A and A{sub d} with respect to the number of active orbitals used in the perturbative calculations suggests that our estimated A and A{sub d} values should be accurate.
Fast and accurate modeling of molecular atomization energies with machine learning.
Rupp, Matthias; Tkatchenko, Alexandre; Müller, Klaus-Robert; von Lilienfeld, O Anatole
2012-02-01
We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schrödinger equation is mapped onto a nonlinear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross validation over more than seven thousand organic molecules yields a mean absolute error of ∼10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves. PMID:22400967
Chocholousová, Jana; Feig, Michael
2006-04-30
Different integrator time steps in NVT and NVE simulations of protein and nucleic acid systems are tested with the GBMV (Generalized Born using Molecular Volume) and GBSW (Generalized Born with simple SWitching) methods. The simulation stability and energy conservation is investigated in relation to the agreement with the Poisson theory. It is found that very close agreement between generalized Born methods and the Poisson theory based on the commonly used sharp molecular surface definition results in energy drift and simulation artifacts in molecular dynamics simulation protocols with standard 2-fs time steps. New parameters are proposed for the GBMV method, which maintains very good agreement with the Poisson theory while providing energy conservation and stable simulations at time steps of 1 to 1.5 fs. PMID:16518883
NASA Astrophysics Data System (ADS)
Xin, Cui; Di-Yu, Zhang; Gao, Chen; Ji-Gen, Chen; Si-Liang, Zeng; Fu-Ming, Guo; Yu-Jun, Yang
2016-03-01
We demonstrate that the interference minima in the linear molecular harmonic spectra can be accurately predicted by a modified two-center model. Based on systematically investigating the interference minima in the linear molecular harmonic spectra by the strong-field approximation (SFA), it is found that the locations of the harmonic minima are related not only to the nuclear distance between the two main atoms contributing to the harmonic generation, but also to the symmetry of the molecular orbital. Therefore, we modify the initial phase difference between the double wave sources in the two-center model, and predict the harmonic minimum positions consistent with those simulated by SFA. Project supported by the National Basic Research Program of China (Grant No. 2013CB922200) and the National Natural Science Foundation of China (Grant Nos. 11274001, 11274141, 11304116, 11247024, and 11034003), and the Jilin Provincial Research Foundation for Basic Research, China (Grant Nos. 20130101012JC and 20140101168JC).
Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul
2015-03-14
Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online. PMID:25770527
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.
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.
Machuqueiro, Miguel; Baptista, António M
2011-12-01
In this study, we investigate two factors that can hinder the performance of constant-pH molecular dynamics methods in predicting protein pK(a) values, using hen egg white lysozyme as a test system. The first factor is related to the molecular definition and pK(a) value of model compounds in the Poisson-Boltzmann framework. We address this by defining the model compound as a molecular fragment with an associated pK(a) value that is calibrated against experimental data, which results in a decrease of 0.12 units in pK(a) errors. The second addressed factor is the possibility that detrimental structural distortions are being introduced in the simulations by the underlying molecular mechanics force field. This issue is investigated by analyzing how the gradual structural rearrangements affect the predicted pK(a) values. The two GROMOS force fields studied here (43A1 and 53A6) yield good pK(a) predictions, although a time-dependent performance is observed: 43A1 performs better after a few nanoseconds of structural reorganization (pK(a) errors of ~0.45), while 53A6 gives the best prediction right at the first nanosecond (pK(a) errors of 0.42). These results suggest that the good performance of constant-pH molecular dynamics methods could be further improved if these force field limitations were overcome. PMID:22072522
Huang, Xinchuan; Valeev, Edward F; Lee, Timothy J
2010-12-28
One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H(2)O, N(2)H(+), NO(2)(+), and C(2)H(2) molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N(2)H(+) where it is concluded that basis set extrapolation is still preferred. The differences for H(2)O and NO(2)(+) are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C(2)H(2), however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)(R12), incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N(2)H(+) and NO(2)(+) were computed, including basis set extrapolation, core-correlation, scalar
NASA Astrophysics Data System (ADS)
Morishita, Tetsuya
2001-09-01
Pressure-induced phase transitions in liquid phosphorus have been studied by constant-pressure first-principles molecular dynamics simulations. By compressing a low-pressure liquid which consists of the tetrahedral P4 molecules, a structural phase transition from the molecular to polymeric liquid (a high-pressure phase) observed in the recent experiment by Katayama et al. [Nature (London) 403, 170 (2000)] was successfully realized. It is found that this transition is caused by a breakup of the tetrahedral molecules with large volume contraction. The same transition is also realized by heating. This indicates that only the polymeric liquid can stably exist at high temperature.
NASA Astrophysics Data System (ADS)
Flores-Ruiz, Hugo M.; Naumis, Gerardo G.
2009-10-01
Using molecular dynamics at constant pressure, the relationship between the excess of low frequency vibrational modes (known as the boson peak) and the glass transition is investigated for a truncated Lennard-Jones potential. It is observed that the quadratic mean displacement is enhanced by such modes, as predicted using a harmonic Hamiltonian for metastable states. As a result, glasses loose mechanical stability at lower temperatures than the corresponding crystal, since the Lindemann criteria are observed, as is also deduced from density functional theory. Finally, we found that the average force and elastic constant are reduced in the glass due to such excess of modes. The ratio between average elastic constants can be approximated using the 2/3 rule between melting and glass transition temperatures.
Molecular Detection of Foodborne Pathogens: A Rapid and Accurate Answer to Food Safety.
Mangal, Manisha; Bansal, Sangita; Sharma, Satish K; Gupta, Ram K
2016-07-01
Food safety is a global health concern. For the prevention and recognition of problems related to health and safety, detection of foodborne pathogen is of utmost importance at all levels of food production chain. For several decades, a lot of research has been targeted at the development of rapid methodology as reducing the time needed to complete pathogen detection tests has been the primary goal of food microbiologists. With the result, food microbiology laboratories now have a wide array of detection methods and automated technologies such as enzyme immunoassay, polymerase chain reaction, and microarrays, which can cut test times considerably. Nucleic acid amplification strategies and advances in amplicon detection methodologies have been the key factors in the progress of molecular microbiology. A comprehensive literature survey has been carried out to give an overview in the field of foodborne pathogen detection. In this paper, we describe the conventional methods, as well as recent developments in food pathogen detection, identification, and quantification, with a major emphasis on molecular detection methods. PMID:25830555
Accurate decay-constant ratios fB*/fB and fBs*/fBs from Borel QCD sum rules
NASA Astrophysics Data System (ADS)
Lucha, Wolfgang; Melikhov, Dmitri; Simula, Silvano
2015-06-01
We present our analysis of the decay constants of the beauty vector mesons B* and Bs* within the framework of dispersive sum rules for the two-point correlator of vector currents in QCD. While the decay constants of the vector mesons fB* and fBs* —similar to the decay constants of the pseudoscalar mesons fB and fBs—individuallyhave large uncertainties induced by theory parameters not known with a satisfactory precision, these uncertainties almost entirely cancel out in the ratios of vector over pseudoscalar decay constants. These ratios, thus, may be predicted with very high accuracy due to the good control over the systematic uncertainties of the decay constants gained upon application of our hadron-parameter extraction algorithm. Our final results read fB*/fB=0.944 ±0.01 1OPE±0.01 8syst and fBs*/fB s=0.947 ±0.02 3OPE±0.02 0syst . Thus, both fB*/fB and fBs*/fBs are less than unity at 2.5 σ and 2 σ level, respectively.
A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat.
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. PMID:27421393
Hepburn, I; Chen, W; De Schutter, E
2016-08-01
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification. PMID:27497550
NASA Astrophysics Data System (ADS)
Hepburn, I.; Chen, W.; De Schutter, E.
2016-08-01
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.
NASA Technical Reports Server (NTRS)
Boughner, Robert E.
1986-01-01
A method for calculating the photodissociation rates needed for photochemical modeling of the stratosphere, which includes the effects of molecular scattering, is described. The procedure is based on Sokolov's method of averaging functional correction. The radiation model and approximations used to calculate the radiation field are examined. The approximated diffuse fields and photolysis rates are compared with exact data. It is observed that the approximate solutions differ from the exact result by 10 percent or less at altitudes above 15 km; the photolysis rates differ from the exact rates by less than 5 percent for altitudes above 10 km and all zenith angles, and by less than 1 percent for altitudes above 15 km.
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.
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).
Accurate description of phase diagram of clathrate hydrates at the molecular level
NASA Astrophysics Data System (ADS)
Belosludov, Rodion V.; Subbotin, Oleg S.; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki; Belosludov, Vladimir R.
2009-12-01
In order to accurately estimate the thermodynamic properties of hydrogen clathrate hydrates, we developed a method based on the solid solution theory of van der Waals and Platteeuw. This model allows one to take into account the influence of guest molecules on the host lattice and guest-guest interactions—especially when more than one guest molecule occupies a cage. The free energies, equations of state, and chemical potentials of hydrogen and mixed propane-hydrogen clathrate hydrates of cubic structure II with different cage fillings have been estimated using this approach. Moreover, the proposed theory has been used for construction p -T phase diagrams of hydrogen hydrate and mixed hydrogen-propane hydrates in a wide range of pressures and temperatures. For the systems with well defined interactions the calculated curves of "guest gas-hydrate-ice Ih" equilibrium agree with the available experimental data. We also believe that the present model allows one not only to calculate the hydrogen storage ability of known hydrogen hydrate but also predict this value for structures that have not yet been realized by experiment.
Microbial transformation rate constants for a series of phenols were correlated with a property of the substituents, van der Waal's radius. Transformation products were the corresponding catecols, with the exception of p-hydroxybenzoic acid, the product of p-acetylphenol. A diffe...
Estimation of Henry's Law Constant for a Diverse Set of Organic Compounds from Molecular Structure
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...
Accurate Photodissociation in UV and X-ray Irradiated Molecular Gas
NASA Astrophysics Data System (ADS)
Stancil, Phillip C.; Gay, C. D.; Cieszewski, R. M.; el-Qadi, W.; Kuri, A.; Miyake, S.; Abel, N.; Porter, R. L.; Shaw, G.; Ferland, G. J.; van Hoof, P. A. M.
2011-05-01
Molecules are primarily destroyed in diffuse and translucent regions, in protoplanetary disks, in cool stellar atmospheres, in photodissociation regions, and in x-ray dominated regions via photodissociation (PD) due to the incident radiation field. The majority of astrochemical/spectral modeling codes available today use pre-computed exponentially-attenuated photorates based on dust scattering/absorption for an ``average" interstellar cloud. Since there is clearly a large scatter in the dust properties and local radiation field for various environments in the Galaxy and beyond, the adoption of such pre-computed photorates can lead to considerable errors in predicted abundances. To improve current modeling capabilities, we are computing new rovibrationally-resolved PD cross sections for H_2, HD, HeH+, NH, C_2, CN, and CS and implementing the cross sections in the spectral simulation code Cloudy for explicit computation of local photorates. We present model results using the new photodissociation cross sections for a variety of environments emphasizing differences in total and state-specific molecular column densities. This work was partially supported by NASA grants NNG06GJ11G and HST-AR-11776.01-A, NSF grant AST-0607733, and the PRODEX Programme of ESA.
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.
NASA Astrophysics Data System (ADS)
Morishita, Tetsuya
2001-12-01
Constant-pressure first-principles molecular dynamics simulations have been carried out to study structural phase transitions of liquid black phosphorus. By compressing the tetrahedral molecular liquid (a low-pressure phase), a structural phase transition from the molecular to polymeric liquid (a high-pressure phase) was successfully realized just as observed in the recent experiment by Katayama et al. [Nature 170 (2000) 403]. Structural properties in the polymeric liquid were investigated and it is found that the covalent p-state bonds are dominant within the first nearest neighbors of each atom. However, further compression of the polymeric liquid shows that the covalent bonding is weakened as pressure is increased. As a result, liquid phosphorus becomes similar to the simple liquid in which atoms form a close-packed structure at very high pressure.
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.
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. PMID:25573553
NASA Astrophysics Data System (ADS)
Luo, Ye; Sorella, Sandro
2014-03-01
We introduce a general and efficient method for the calculation of vibrational frequencies of electronic systems, ranging from molecules to solids. By performing damped molecular dynamics with ab initio forces, we show that quantum vibrational frequencies can be evaluated by diagonalizing the time averaged position-position or force-force correlation matrices, although the ionic motion is treated on the classical level within the Born-Oppenheimer approximation. The novelty of our approach is to evaluate atomic forces with QMC by means of a highly accurate and correlated variational wave function which is optimized simultaneously during the dynamics. QMC is an accurate and promising many-body technique for electronic structure calculation thanks to massively parallel computers. However, since infinite statistics is not feasible, property evaluation may be affected by large noise that is difficult to harness. Our approach controls the QMC stochastic bias systematically and gives very accurate results with moderate computational effort, namely even with noisy forces. We prove the accuracy and efficiency of our method on the water monomer[A. Zen et al., JCTC 9 (2013) 4332] and dimer. We are currently working on the challenging problem of simulating liquid water at ambient conditions.
NASA Astrophysics Data System (ADS)
Álvarez-Bajo, O.; Sánchez-Castellanos, M.; Amezcua-Eccius, C. A.; Lemus, R.
2006-06-01
A connection between the unitary group approach U ( ν + 1) and the traditional description in configuration space of vibrational excitations is proposed. Local operators bˆi†(b) satisfying the su (2) commutation relations are used to establish approximate algebraic expansions of the local coordinates and momenta. The use of the proposed relations allows to obtain an algebraic representation of traditional Hamiltonians in terms of the U ( ν + 1) model. This approach provides in natural form the connection between the spectroscopic parameters and force constants. Using the linear expansion of the coordinates in terms of the bˆi†(b) operators, an approach to study local dipole transition intensities based on traditional descriptions is proposed. A closed general analytical expression for the local dipole operators is obtained. The analysis of the stretching vibrational excitations of arsine is taken as an example for the determination of both force constants and the description of dipole transition intensities.
NASA Astrophysics Data System (ADS)
Mohapatra, Himansu; Eckhardt, Craig J.
2007-03-01
Polymorphism is the property of a compound to crystallize in two or more crystalline phases containing different arrangements and/or conformations of the molecules in the crystal lattice. The Phenomenon of polymorphism is a major issue in the pharmaceutical industry especially in relation to drug uptake in the body, tablet processing and growth. This has led to considerable interest in predicting and understanding properties of drug polymorphs, and more recently the mechanical properties of the polymorphs. In this work, Brillouin scattering is used to probe the acoustic phonons of the monoclinic (P21/c) polymorph of the drug, carbamazepine (CBZ). By sampling a variety of acoustic phonons, the complete elastic constant tensor has been determined for this CBZ polymorph. The observed trend in the elastic constants: C11< C22˜C33 is qualitatively associated with the crystal growth pattern seen in CBZ. Investigation into the anisotropy of the intermolecular interactions has been investigated further by calculation of linear compressibilities.
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. PMID:26930445
Deridder, Sander; Desmet, Gert
2012-02-01
Using computational fluid dynamics (CFD), the effective B-term diffusion constant γ(eff) has been calculated for four different random sphere packings with different particle size distributions and packing geometries. Both fully porous and porous-shell sphere packings are considered. The obtained γ(eff)-values have subsequently been used to determine the value of the three-point geometrical constant (ζ₂) appearing in the 2nd-order accurate effective medium theory expression for γ(eff). It was found that, whereas the 1st-order accurate effective medium theory expression is accurate to within 5% over most part of the retention factor range, the 2nd-order accurate expression is accurate to within 1% when calculated with the best-fit ζ₂-value. Depending on the exact microscopic geometry, the best-fit ζ₂-values typically lie in the range of 0.20-0.30, holding over the entire range of intra-particle diffusion coefficients typically encountered for small molecules (0.1 ≤ D(pz)/D(m) ≤ 0.5). These values are in agreement with the ζ₂-value proposed by Thovert et al. for the random packing they considered. PMID:22236565
NASA Astrophysics Data System (ADS)
Desforges, Jean; Deschamps, Clément; Gauvin, Serge
2015-08-01
The determination of the complex refractive index of thin films usually requires the highest accuracy. In this paper, we report on a new and accurate method based on a spectral rectifying process of a single transmittance curve. The agreements with simulated and real experimental data show the helpfulness of the method. The case of materials having arbitrary absorption bands at midpoint in spectral range, such as pigments in guest-host polymers, is also encompassed by this method.
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.
NASA Astrophysics Data System (ADS)
Huang, Xinchuan; Fortenberry, Ryan C.; Lee, Timothy J.
2013-05-01
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 → 3) and growing as J increases, the assignment of the observed rotational lines from the Horsehead nebula to l-C3H+ is questionable.
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.
2015-01-01
By utilizing Graphics Processing Units, we show that constant pH molecular dynamics simulations (CpHMD) run in Generalized Born (GB) implicit solvent for long time scales can yield poor pKa predictions as a result of sampling unrealistic conformations. To address this shortcoming, we present a method for performing constant pH molecular dynamics simulations (CpHMD) in explicit solvent using a discrete protonation state model. The method involves standard molecular dynamics (MD) being propagated in explicit solvent followed by protonation state changes being attempted in GB implicit solvent at fixed intervals. Replica exchange along the pH-dimension (pH-REMD) helps to obtain acceptable titration behavior with the proposed method. We analyzed the effects of various parameters and settings on the titration behavior of CpHMD and pH-REMD in explicit solvent, including the size of the simulation unit cell and the length of the relaxation dynamics following protonation state changes. We tested the method with the amino acid model compounds, a small pentapeptide with two titratable sites, and hen egg white lysozyme (HEWL). The proposed method yields superior predicted pKa values for HEWL over hundreds of nanoseconds of simulation relative to corresponding predicted values from simulations run in implicit solvent. PMID:24803862
Mackie, Cameron J; Candian, Alessandra; Huang, Xinchuan; Lee, Timothy J; Tielens, Alexander G G M
2015-06-28
A full derivation of the analytic transformation of the quadratic, cubic, and quartic force constants from normal coordinates to Cartesian coordinates is given. Previous attempts at this transformation have resulted in non-linear transformations; however, for the first time, a simple linear transformation is presented here. Two different approaches have been formulated and implemented, one of which does not require prior knowledge of the translation-rotation eigenvectors from diagonalization of the Hessian matrix. The validity of this method is tested using two molecules H2O and c-C3H2D(+). PMID:26133410
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).
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.
Hughes, Steven J.; Xi, Liqiang; Raja, Siva; Gooding, William; Cole, David J.; Gillanders, William E.; Mikhitarian, Keidi; McCarty, Kenneth; Silver, Susan; Ching, Jesus; McMillan, William; Luketich, James D.; Godfrey, Tony E.
2006-01-01
Objective: To develop a fully automated, rapid, molecular-based assay that accurately and objectively evaluates sentinel lymph nodes (SLN) from breast cancer patients. Summary Background Data: Intraoperative analysis for the presence of metastatic cancer in SLNs from breast cancer patients lacks sensitivity. Even with immunohistochemical staining (IHC) and time-consuming review, alarming discordance in the interpretation of SLN has been observed. Methods: A total of 43 potential markers were evaluated for the ability to accurately characterize lymph node specimens from breast cancer patients as compared with complete histologic analysis including IHC. Selected markers then underwent external validation on 90 independent SLN specimens using rapid, multiplex quantitative reverse transcription-polymerase chain reaction (QRT-PCR) assays. Finally, 18 SLNs were analyzed using a completely automated RNA isolation, reverse transcription, and quantitative PCR instrument (GeneXpert). Results: Following analysis of potential markers, promising markers were evaluated to establish relative level of expression cutoff values that maximized classification accuracy. A validation set of 90 SLNs from breast cancer patients was prospectively characterized using 4 markers individually or in combinations, and the results compared with histologic analysis. A 2-marker assay was found to be 97.8% accurate (94% sensitive, 100% specific) compared with histologic analysis. The fully automated GeneXpert instrument produced comparable and reproducible results in less than 35 minutes. Conclusions: A rapid, fully automated QRT-PCR assay definitively characterizes breast cancer SLN with accuracy equal to conventional pathology. This approach is superior to intraoperative SLN analysis and can provide standardized, objective results to assist in pathologic diagnosis. PMID:16495705
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.).
Filizola, Marta
2009-01-01
For years conventional drug design at G-protein coupled receptors (GPCRs) has mainly focused on the inhibition of a single receptor at a usually well-defined ligand-binding site. The recent discovery of more and more physiologically relevant GPCR dimers/oligomers suggests that selectively targeting these complexes or designing small molecules that inhibit receptor-receptor interactions might provide new opportunities for novel drug discovery. To uncover the fundamental mechanisms and dynamics governing GPCR dimerization/oligomerization, it is crucial to understand the dynamic process of receptor-receptor association, and to identify regions that are suitable for selective drug binding. This minireview highlights current progress in the development of increasingly accurate dynamic molecular models of GPCR oligomers based on structural, biochemical, and biophysical information that has recently appeared in the literature. In view of this new information, there has never been a more exciting time for computational research into GPCRs than at present. Information-driven modern molecular models of GPCR complexes are expected to efficiently guide the rational design of GPCR oligomer-specific drugs, possibly allowing researchers to reach for the high-hanging fruits in GPCR drug discovery, i.e. more potent and selective drugs for efficient therapeutic interventions. PMID:19465029
Molecular dynamics simulation of dextran extension by constant force in single molecule AFM.
Neelov, Igor M; Adolf, David B; McLeish, Tom C B; Paci, Emanuele
2006-11-15
The extension of 1-6 polysaccharides has been studied in a series of recent single molecule AFM experiments. For dextran, a key finding was the existence of a plateau in the force-extension curve at forces between 700 and 1000 pN. We studied the extension of the dextran 10-mer under constant force using atomistic simulation with various force fields. All the force fields reproduce the experimental plateau on the force-extension curve. With AMBER94 and AMBER-GLYCAM04 force fields the plateau can be explained by a transition of the glucopyranose rings in the dextran monomers from the chair ((4)C(1)) to the inverted chair ((1)C(4)) conformation while other processes occur at smaller (rotation around C5-C6 bond) or higher (chairs to boat transitions) forces. The CHARMM force field provides a different picture which associates the occurrence of the plateau to chair-boat transitions of the glucopyranose rings. PMID:16950842
NASA Astrophysics Data System (ADS)
Yu, Bingwu; van Ingen, Hugo; Freedberg, Darón I.
2013-03-01
Strong 1H-1H coupling can significantly reduce the accuracy of 1JCH measured from frequency differences in coupled HSQC spectra. Although accurate 1JCH values can be extracted from spectral simulation, it would be more convenient if the same accurate 1JCH values can be obtained experimentally. Furthermore, simulations reach their limit for residual dipolar coupling (RDC) measurement, as many significant, but immeasurable RDCs are introduced into the spin system when a molecule is weakly aligned, thus it is impossible to have a model spin system that truly represents the real spin system. Here we report a new J modulated method, constant-time INEPT CT-HSQC (CTi-CT-HSQC), to accurately measure one-bond scalar coupling constant and RDCs without strong coupling interference. In this method, changing the spacing between the two 180° pulses during a constant time INEPT period selectively modulates heteronuclear coupling in quantitative J fashion. Since the INEPT delays for measuring one-bond carbon-proton spectra are short compared to 3JHH, evolution due to (strong) 1H-1H coupling is marginal. The resulting curve shape is practically independent of 1H-1H coupling and only correlated to the heteronuclear coupling evolution. Consequently, an accurate 1JCH can be measured even in the presence of strong coupling. We tested this method on N-acetyl-glucosamine and mannose whose apparent isotropic 1JCH values are significantly affected by strong coupling with other methods. Agreement to within 0.5 Hz or better is found between 1JCH measured by this method and previously published simulation data. We further examined the strong coupling effects on RDC measurements and observed an error up to 100% for one bond RDCs using coupled HSQC in carbohydrates. We demonstrate that RDCs can be obtained with higher accuracy by CTi-CT-HSQC, which compensates the limitation of simulation method.
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...
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.}
Rate Constant Change of Photo Reaction of Bacteriorhodopsin Observed in Trimeric Molecular System.
Tsujiuchi, Yutaka; Masumoto, Hiroshi; Goto, Takashi
2016-04-01
To elucidate the time evolution of photo reaction of bacteriorhodopsin in glycerol mixed purple membrane at around 196 K under irradiation by red light, a kinetic model was constructed. The change of absorption with irradiation at times of 560 nm and 412 nm was analyzed for the purpose of determining reaction rates of photo reaction of bacteriorhodopsin and its product M intermediate. In this study it is shown that reaction rates of conversion from bacteriorhodopsin to the M intermediate can be explained by a set of linear differential equations. This model analysis concludes that bacteriorhodopsin in which constitutes a trimer unit with other two bacteriorhodopsin molecules changes into M intermediates in the 1.73 of reaction rate, in the initial step, and according to the number of M intermediate in a trimer unit, from three to one, the reaction rate of bacteriorhodopsin into M intermediates smaller as 1.73, 0.80, 0.19 which caused by influence of inter-molecular interaction between bacteriorhodopsin. PMID:27451646
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
Ovchinnikov, Victor; Nam, Kwangho; Karplus, Martin
2016-08-25
A method is developed to obtain simultaneously free energy profiles and diffusion constants from restrained molecular simulations in diffusive systems. The method is based on low-order expansions of the free energy and diffusivity as functions of the reaction coordinate. These expansions lead to simple analytical relationships between simulation statistics and model parameters. The method is tested on 1D and 2D model systems; its accuracy is found to be comparable to or better than that of the existing alternatives, which are briefly discussed. An important aspect of the method is that the free energy is constructed by integrating its derivatives, which can be computed without need for overlapping sampling windows. The implementation of the method in any molecular simulation program that supports external umbrella potentials (e.g., CHARMM) requires modification of only a few lines of code. As a demonstration of its applicability to realistic biomolecular systems, the method is applied to model the α-helix ↔ β-sheet transition in a 16-residue peptide in implicit solvent, with the reaction coordinate provided by the string method. Possible modifications of the method are briefly discussed; they include generalization to multidimensional reaction coordinates [in the spirit of the model of Ermak and McCammon (Ermak, D. L.; McCammon, J. A. J. Chem. Phys. 1978, 69, 1352-1360)], a higher-order expansion of the free energy surface, applicability in nonequilibrium systems, and a simple test for Markovianity. In view of the small overhead of the method relative to standard umbrella sampling, we suggest its routine application in the cases where umbrella potential simulations are appropriate. PMID:27135391
Bai, Fang; Liao, Sha; Gu, Junfeng; Jiang, Hualiang; Wang, Xicheng; Li, Honglin
2015-04-27
Metalloproteins, particularly zinc metalloproteins, are promising therapeutic targets, and recent efforts have focused on the identification of potent and selective inhibitors of these proteins. However, the ability of current drug discovery and design technologies, such as molecular docking and molecular dynamics simulations, to probe metal-ligand interactions remains limited because of their complicated coordination geometries and rough treatment in current force fields. Herein we introduce a robust, multiobjective optimization algorithm-driven metalloprotein-specific docking program named MpSDock, which runs on a scheme similar to consensus scoring consisting of a force-field-based scoring function and a knowledge-based scoring function. For this purpose, in this study, an effective knowledge-based zinc metalloprotein-specific scoring function based on the inverse Boltzmann law was designed and optimized using a dynamic sampling and iteration optimization strategy. This optimization strategy can dynamically sample and regenerate decoy poses used in each iteration step of refining the scoring function, thus dramatically improving both the effectiveness of the exploration of the binding conformational space and the sensitivity of the ranking of the native binding poses. To validate the zinc metalloprotein-specific scoring function and its special built-in docking program, denoted MpSDockZn, an extensive comparison was performed against six universal, popular docking programs: Glide XP mode, Glide SP mode, Gold, AutoDock, AutoDock4Zn, and EADock DSS. The zinc metalloprotein-specific knowledge-based scoring function exhibited prominent performance in accurately describing the geometries and interactions of the coordination bonds between the zinc ions and chelating agents of the ligands. In addition, MpSDockZn had a competitive ability to sample and identify native binding poses with a higher success rate than the other six docking programs. PMID:25746437
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.
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.
Barone, Vincenzo; Biczysko, Malgorzata Bloino, Julien; Puzzarini, Cristina
2014-07-21
Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been evaluated by means of high-level quantum-chemical calculations at the coupled-cluster level including single and double excitations together with a perturbative treatment of triples (CCSD(T)). Extrapolation to the complete basis-set limit as well as core-correlation effects have also been taken into account. Anharmonic contributions have been computed at the CCSD(T)/cc-pVTZ level for trans-2,3-dideuterooxirane. These data can serve as references to evaluate the accuracy of less expensive computational approaches rooted in the density functional theory (DFT). The latter have been used within hybrid CC/DFT approaches, which have been applied to simulate fully anharmonic infrared (IR) spectra. Finally, the best theoretical estimates of the equilibrium structures and vibrational wavenumbers are compared to the most accurate experimental data and show in all cases very good agreement, i.e., within 0.001 Å, 0.1 deg, 10 cm{sup −1}, and 0.5 km mol{sup −1}, for bond lengths, angles, wavenumbers, and IR intensities, respectively.
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
Timr, Štěpán; Brabec, Jiří; Bondar, Alexey; Ryba, Tomáš; Železný, Miloš; Lazar, Josef; Jungwirth, Pavel
2015-07-30
Several methods based on single- and two-photon fluorescence detected linear dichroism have recently been used to determine the orientational distributions of fluorescent dyes in lipid membranes. However, these determinations relied on simplified descriptions of nonlinear anisotropic properties of the dye molecules, using a transition dipole-moment-like vector instead of an absorptivity tensor. To investigate the validity of the vector approximation, we have now carried out a combination of computer simulations and polarization microscopy experiments on two representative fluorescent dyes (DiI and F2N12S) embedded in aqueous phosphatidylcholine bilayers. Our results indicate that a simplified vector-like treatment of the two-photon transition tensor is applicable for molecular geometries sampled in the membrane at ambient conditions. Furthermore, our results allow evaluation of several distinct polarization microscopy techniques. In combination, our results point to a robust and accurate experimental and computational treatment of orientational distributions of DiI, F2N12S, and related dyes (including Cy3, Cy5, and others), with implications to monitoring physiologically relevant processes in cellular membranes in a novel way. PMID:26146848
Colmenares, Pedro J; López, Floralba; Olivares-Rivas, Wilmer
2009-12-01
We carried out a molecular-dynamics (MD) study of the self-diffusion tensor of a Lennard-Jones-type fluid, confined in a slit pore with attractive walls. We developed Bayesian equations, which modify the virtual layer sampling method proposed by Liu, Harder, and Berne (LHB) [P. Liu, E. Harder, and B. J. Berne, J. Phys. Chem. B 108, 6595 (2004)]. Additionally, we obtained an analytical solution for the corresponding nonhomogeneous Langevin equation. The expressions found for the mean-squared displacement in the layers contain naturally a modification due to the mean force in the transverse component in terms of the anisotropic diffusion constants and mean exit time. Instead of running a time consuming dual MD-Langevin simulation dynamics, as proposed by LHB, our expression was used to fit the MD data in the entire survival time interval not only for the parallel but also for the perpendicular direction. The only fitting parameter was the diffusion constant in each layer. PMID:20365134
NASA Astrophysics Data System (ADS)
Colmenares, Pedro J.; López, Floralba; Olivares-Rivas, Wilmer
2009-12-01
We carried out a molecular-dynamics (MD) study of the self-diffusion tensor of a Lennard-Jones-type fluid, confined in a slit pore with attractive walls. We developed Bayesian equations, which modify the virtual layer sampling method proposed by Liu, Harder, and Berne (LHB) [P. Liu, E. Harder, and B. J. Berne, J. Phys. Chem. B 108, 6595 (2004)]. Additionally, we obtained an analytical solution for the corresponding nonhomogeneous Langevin equation. The expressions found for the mean-squared displacement in the layers contain naturally a modification due to the mean force in the transverse component in terms of the anisotropic diffusion constants and mean exit time. Instead of running a time consuming dual MD-Langevin simulation dynamics, as proposed by LHB, our expression was used to fit the MD data in the entire survival time interval not only for the parallel but also for the perpendicular direction. The only fitting parameter was the diffusion constant in each layer.
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.
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.
Hayes, Malcolm; Peckova, Kvetoslava; Martinek, Petr; Hora, Milan; Kalusova, Kristyna; Straka, Lubomir; Daum, Ondrej; Kokoskova, Bohuslava; Rotterova, Pavla; Pivovarčikova, Kristyna; Branzovsky, Jindrich; Dubova, Magdalena; Vesela, Pavla; Michal, Michal; Hes, Ondrej
2015-03-01
tumours can only be sub-classified accurately by multi-parameter molecular-genetic analysis. PMID:25544614
Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors.
Ellis, Christopher R; Tsai, Cheng-Chieh; Hou, Xinjun; Shen, Jana
2016-03-17
Targeting β-secretase (BACE1) with small-molecule inhibitors offers a promising route for treatment of Alzheimer's disease. However, the intricate pH dependence of BACE1 function and inhibitor efficacy has posed major challenges for structure-based drug design. Here we investigate two structurally similar BACE1 inhibitors that have dramatically different inhibitory activity using continuous constant pH molecular dynamics (CpHMD). At high pH, both inhibitors are stably bound to BACE1; however, within the enzyme active pH range, only the iminopyrimidinone-based inhibitor remains bound, while the aminothiazine-based inhibitor becomes partially dissociated following the loss of hydrogen bonding with the active site and change of the 10s loop conformation. The drastically lower activity of the second inhibitor is due to the protonation of a catalytic aspartate and the lack of a propyne tail. This work demonstrates that CpHMD can be used for screening pH-dependent binding profiles of small-molecule inhibitors, providing a new tool for structure-based drug design and optimization. PMID:26905811
NASA Astrophysics Data System (ADS)
Ma, Zhonghua; Zhang, Yanli; Tuckerman, Mark E.
2012-07-01
It is generally believed that studies of liquid water using the generalized gradient approximation to density functional theory require dispersion corrections in order to obtain reasonably accurate structural and dynamical properties. Here, we report on an ab initio molecular dynamics study of water in the isothermal-isobaric ensemble using a converged discrete variable representation basis set and an empirical dispersion correction due to Grimme [J. Comp. Chem. 27, 1787 (2006)], 10.1002/jcc.20495. At 300 K and an applied pressure of 1 bar, the density obtained without dispersion corrections is approximately 0.92 g/cm3 while that obtained with dispersion corrections is 1.07 g/cm3, indicating that the empirical dispersion correction overestimates the density by almost as much as it is underestimated without the correction for this converged basis. Radial distribution functions exhibit a loss of structure in the second solvation shell. Comparison of our results with other studies using the same empirical correction suggests the cause of the discrepancy: the Grimme dispersion correction is parameterized for use with a particular basis set; this parameterization is sensitive to this choice and, therefore, is not transferable to other basis sets.
Kim, Yong-Hyun; Kim, Ki-Hyun
2014-05-16
Accurate values for the Henry's law constants are essential to describe the environmental dynamics of a solute, but substantial errors are recognized in many reported data due to practical difficulties in measuring solubility and/or vapor pressure. Despite such awareness, validation of experimental approaches has scarcely been made. An experimental approach based on thermal desorption-gas chromatography-mass spectrometery (TD-GC-MS) method was developed to concurrently allow the accurate determination of target compounds from the headspace and aqueous samples in closed equilibrated system. The analysis of six aromatics and eight non-aromatic oxygenates was then carried out in a static headspace mode. An estimation of the potential bias and mass balance (i.e., sum of mass measured individually from gas and liquid phases vs. the mass initially added to the system) demonstrates compound-specific phase dependency so that the best results are obtained by aqueous (less soluble aromatics) and headspace analysis (more soluble non-aromatics). Accordingly, we were able to point to the possible sources of biases in previous studies and provide the best estimates for the Henry's constants (Matm(-1)): benzene (0.17), toluene (0.15), p-xylene (0.13), m-xylene (0.13), o-xylene (0.19), styrene (0.27); propionaldehyde (9.26), butyraldehyde (6.19), isovaleraldehyde (2.14), n-valeraldehyde (3.98), methyl ethyl ketone (10.5), methyl isobutyl ketone (3.93), n-butyl acetate (2.41), and isobutyl alcohol (22.2). PMID:24704185
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
Fohlmeister, Jürgen F
2015-06-01
The structural similarity between the primary molecules of voltage-gated Na and K channels (alpha subunits) and activation gating in the Hodgkin-Huxley model is brought into full agreement by increasing the model's sodium kinetics to fourth order (m(3) → m(4)). Both structures then virtually imply activation gating by four independent subprocesses acting in parallel. The kinetics coalesce in four-dimensional (4D) cubic diagrams (16 states, 32 reversible transitions) that show the structure to be highly failure resistant against significant partial loss of gating function. Rate constants, as fitted in phase plot data of retinal ganglion cell excitation, reflect the molecular nature of the gating transitions. Additional dimensions (6D cubic diagrams) accommodate kinetically coupled sodium inactivation and gating processes associated with beta subunits. The gating transitions of coupled sodium inactivation appear to be thermodynamically irreversible; response to dielectric surface charges (capacitive displacement) provides a potential energy source for those transitions and yields highly energy-efficient excitation. A comparison of temperature responses of the squid giant axon (apparently Arrhenius) and mammalian channel gating yields kinetic Q10 = 2.2 for alpha unit gating, whose transitions are rate-limiting at mammalian temperatures; beta unit kinetic Q10 = 14 reproduces the observed non-Arrhenius deviation of mammalian gating at low temperatures; the Q10 of sodium inactivation gating matches the rate-limiting component of activation gating at all temperatures. The model kinetics reproduce the physiologically large frequency range for repetitive firing in ganglion cells and the physiologically observed strong temperature dependence of recovery from inactivation. PMID:25867741
NASA Astrophysics Data System (ADS)
Velazquez, Hector A.; Hamelberg, Donald
2015-02-01
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.
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...
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.
The cosmological constant problem
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.
Kanai, Y; Takeuchi, N
2009-10-14
We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.
NASA Astrophysics Data System (ADS)
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 7×10-4 Ha/Bohr.
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.
O'Brien, Leah C.; Cao, Hong; O'Brien, James J.
2001-05-01
High-resolution intracavity laser spectroscopy (ILS) absorption measurements have been made on the b-X oxygen electronic transition (the A-band) which has bandheads occurring in the region of 13 165 cm(-1). The positions of the lines were determined to an accuracy that is based on calibration with I(2) absorption lines using the Laboratoire Aimé Cotton (Orsay) Atlas as reference. Based on the ILS measurements and the more accurately determined positions given by L. R. Brown and C. Plymate (J. Mol. Spectrosc. 199, 166-179 (2000)) and with the (3)Sigma(g)(-) ground state molecular constants fixed at the values determined by G. Rouillé et al. (J. Mol. Spectrosc. 154, 372-382 (1992)), the following values (in cm(-1)) were found for the molecular constants: T(0)=13122.2524(1); B(0)=1.391244(2); D(0)=5.352(4)x10(-6); and H(0)=-1.2(2)x10(-11). These results are compared with values derived from fits of the line positions listed in several other studies of this transition. Copyright 2001 Academic Press. PMID:11336527
NASA Astrophysics Data System (ADS)
Wang, Jie-Min; Feng, Heng-Qiang; Sun, Jin-Feng; Shi, De-Heng
2012-02-01
The potential energy curves (PECs) of three low-lying electronic states (X1Σg+, w3Δu, and W1Δu) of P2 molecule are investigated using the full valence complete active space self-consistent field (CASSCF) method followed by the highly accurate valence internally contracted multireference configuration interaction (MRCI) approach in conjunction with the correlation-consistent basis set in the valence range. The PECs of the electronic states involved are modified by the Davidson correction and extrapolated to the complete basis set (CBS) limit. With these PECs, the spectroscopic parameters of the three electronic states are determined and compared in detail with the experimental data. The comparison shows that excellent agreement exists between the present results and the available experimental data. The complete vibrational states are computed for the w3Δu and W1Δu electronic states when the rotational quantum number J equals zero and the vibrational level G(υ), the inertial rotation constant Bυ, and the centrifugal distortion constant Dυ of the first 30 vibrational states are reported, which accord well with the experimental data. The present results show that the two-point extrapolation scheme can obviously improve the quality of spectroscopic parameters and molecular constants.
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.
NASA Astrophysics Data System (ADS)
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-03-01
We present a truly scalable First-Principles Molecular Dynamics algorithm with O(N) complexity and fully controllable accuracy, capable of simulating systems of sizes that were previously impossible with this degree of accuracy. By avoiding global communication, we have extended W. Kohn's condensed matter ``nearsightedness'' principle to a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wavefunctions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 100,000 atoms on 100,000 processors, with a wall-clock time of the order of one minute per molecular dynamics time step. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
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.
Rustad, J.R.; Felmy, A.R.; Hay, B.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-{Delta}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{sub 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 K{sup int} 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. 39 refs., 8 figs., 4 tabs.
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. PMID:24354624
Just, Pierre-Alexandre; Cazes, Aurélie; Audebourg, Anne; Cessot, Anatole; Pallier, Karine; Danel, Claire; Vacher-Lavenu, Marie-Cécile; Laurent-Puig, Pierre; Terris, Benoît; Blons, Hélène
2012-06-01
EML4-ALK adenocarcinomas constitute a new molecular subgroup of lung tumours that respond very well to crizotinib, an ALK inhibitor. However, the diagnosis of ALK rearrangement in lung cancer is challenging. The aim of this study was to compare the diagnostic accuracy of five different methods in a series of 20 EGFR(wt/wt) lung adenocarcinomas from non- or light- smokers. Multiplex RT-PCR was considered as gold standard and identified four ALK-rearranged tumours among the 20 tested tumours. qRT-PCR got an interpretability rate of 100% and accurately typed all 20 tumours. qRT-PCR from corresponding formalin-fixed paraffin-embedded (FFPE) specimens got an interpretability rate of 65%. Out of the four previously identified ALK-rearranged cases, three were interpretable and two were retrieved using FFPE qRT-PCR. ALK break-apart FISH got an interpretability rate of 60% and accurately typed all of the twelve remaining cases. Anti-ALK immunohistochemistry (IHC) accurately typed all twenty tumours using a cut-off value of strong staining of 100% tumour cells. The 16 non ALK-rearranged tumours got no/light staining in 13 cases, and a moderate staining of 80-100% tumour cells in 3 cases. We then analysed four solid signet-ring lung adenocarcinomas. FFPE qRT-PCR, FISH and immunohistochemistry were concordant in three cases, with positive and negative results in respectively one and two cases. The fourth case, which was positive by FISH and immunohistochemistry but negative by RT-PCR, was shown to have a non-EML4-ALK ALK-rearrangement. As various factors such as RNA quality, fixation quality and type of ALK rearrangement may impede ALK screening, we propose a combined FISH/molecular biology diagnostic algorithm in which anti-ALK immunohistochemistry is used as a pre-screening step. PMID:22153831
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.
Jia, Lijuan; Shen, Zhemin; Su, Pingru
2016-05-01
Fenton oxidation is a promising water treatment method to degrade organic pollutants. In this study, 30 different organic compounds were selected and their reaction rate constants (k) were determined for the Fenton oxidation process. Gaussian09 and Material Studio software sets were used to carry out calculations and obtain values of 10 different molecular descriptors for each studied compound. Ferric-oxyhydroxide coagulation experiments were conducted to determine the coagulation percentage. Based upon the adsorption capacity, all of the investigated organic compounds were divided into two groups (Group A and Group B). The percentage adsorption of organic compounds in Group A was less than 15% (wt./wt.) and that in the Group B was higher than 15% (wt./wt.). For Group A, removal of the compounds by oxidation was the dominant process while for Group B, removal by both oxidation and coagulation (as a synergistic process) took place. Results showed that the relationship between the rate constants (k values) and the molecular descriptors of Group A was more pronounced than for Group B compounds. For the oxidation-dominated process, EHOMO and Fukui indices (f(0)x, f(-)x, f(+)x) were the most significant factors. The influence of bond order was more significant for the synergistic process of oxidation and coagulation than for the oxidation-dominated process. The influences of all other molecular descriptors on the synergistic process were weaker than on the oxidation-dominated process. PMID:27155432
NASA Astrophysics Data System (ADS)
Lee, Sanghun; Park, Sung Soo
2013-01-01
Using non-polarizable and polarizable molecular dynamics simulations, binary mixtures of propylene carbonate + dimethyl carbonate and propylene carbonate + ethylene carbonate with various compositions were investigated. The polarizable model produces more reasonable estimation of dielectric constants than the non-polarizable model; however, combining the electronic continuum model with the non-polarizable MD improves the comparison between the two models. Fair agreement was found between the results from these simulations and available experimental data. In addition, for a better understanding of the mixing behaviour, the excess dielectric constants over the entire composition were calculated. By comparison of the two mixtures in various mole fractions, distinctive mixing behaviours of propylene carbonate + dimethyl carbonate (poorly symmetric mixture) and propylene carbonate + ethylene carbonate (highly symmetric mixture) were observed.
Scurlock, R.D.; Ogilby, P.R.
1987-08-13
Relative rate constants for the radiative deactivation (k/sub r/) of singlet molecular oxygen (/sup 3/Sigma/sub g//sup -/O/sub 2/ reverse arrow /sup 1/..delta../sub g/O/sub 2/) have been determined in 15 solvents. A substantial solvent effect is observed. Changes in the value of k/sub r/ can exceed a factor of 20. A reasonably good correlation exists between the solvent polarizability, defined as a function of the solvent refractive index, and the radiative rate constant. We suggest that our data support a model in which /sup 1/..delta../sub g/O/sub 2/ is perturbed through the formation of a discrete oxygen-solvent collision complex.
Zhang, Peili; Wang, Mei; Yang, Yong; Yao, Tianyi; Sun, Licheng
2014-12-01
The copper complex [(bztpen)Cu](BF4)2 (bztpen=N-benzyl-N,N',N'-tris(pyridin-2-ylmethyl)ethylenediamine) displays high catalytic activity for electrochemical proton reduction in acidic aqueous solutions, with a calculated hydrogen-generation rate constant (k(obs)) of over 10000 s(-1). A turnover frequency (TOF) of 7000 h(-1) cm(-2) and a Faradaic efficiency of 96% were obtained from a controlled potential electrolysis (CPE) experiment with [(bztpen)Cu](2+) in pH 2.5 buffer solution at -0.90 V versus the standard hydrogen electrode (SHE) over two hours using a glassy carbon electrode. A mechanism involving two proton-coupled reduction steps was proposed for the dihydrogen generation reaction catalyzed by [(bztpen)Cu](2+). PMID:25314646
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.
Rosskopf, Joachim; Paul-Yuan, Korbinian; Plenio, Martin B; Michaelis, Jens
2016-08-01
Analyzing the physical and chemical properties of single DNA-based molecular machines such as polymerases and helicases requires to track stepping motion on the length scale of base pairs. Although high-resolution instruments have been developed that are capable of reaching that limit, individual steps are oftentimes hidden by experimental noise which complicates data processing. Here we present an effective two-step algorithm which detects steps in a high-bandwidth signal by minimizing an energy-based model (energy-based step finder, EBS). First, an efficient convex denoising scheme is applied which allows compression to tuples of amplitudes and plateau lengths. Second, a combinatorial clustering algorithm formulated on a graph is used to assign steps to the tuple data while accounting for prior information. Performance of the algorithm was tested on Poissonian stepping data simulated based on published kinetics data of RNA polymerase II (pol II). Comparison to existing step-finding methods shows that EBS is superior in speed while providing competitive step-detection results, especially in challenging situations. Moreover, the capability to detect backtracked intervals in experimental data of pol II as well as to detect stepping behavior of the Phi29 DNA packaging motor is demonstrated. PMID:27627346
Fukuda, Ikuo; Kamiya, Narutoshi; Yonezawa, Yasushige; Nakamura, Haruki
2012-08-01
The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys. 134, 164107 (2011)], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a cutoff length longer than 13 Å for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical cutoff distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the molecular system we
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.
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
Friesner, Richard A.; Baik, Mu-Hyun; Gherman, Benjamin F.; Guallar, Victor; Wirstam, Maria E.; Murphy, Robert B.; Lippard, Stephen J.
2003-03-01
Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C-H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.
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.
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
Accurate far-infrared rotational frequencies of carbon monoxide
NASA Technical Reports Server (NTRS)
Varberg, Thomas D.; Evenson, Kenneth M.
1992-01-01
This study presents high-resolution measurements of the pure rotational absorption spectrum of CO in its ground state for the range J arcsec - 5-37. A least-squares fit to this data set, augmented by previous microwave measurements of the J arcsec = 0-4 rotational transitions in the literature, determined accurate values for the molecular constants. A table of calculated CO rotational frequencies is provided for the range J arcsec = 0-45.
Fahrenholz, Timothy; Wolle, Mesay Mulugeta; Kingston, H M Skip; Faber, Scott; Kern, John C; Pamuku, Matt; Miller, Logan; Chatragadda, Hemasudha; Kogelnik, Andreas
2015-01-20
Novel protocols were developed to accurately quantify reduced (GSH), oxidized (GSSG) and total (tGSH) glutathione in biological samples using molecular speciated isotope dilution mass spectrometry (SIDMS). For GSH and GSSG measurement, the sample was spiked with isotopically enriched analogues of the analytes ((310)GSH and (616)GSSG), along with N-ethylmaleimide (NEM), and treated with acetonitrile to solubilize the endogenous analytes via protein precipitation and equilibrate them with the spikes. The supernatant was analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the analytes were quantified with simultaneous tracking and correction for auto-oxidation of GSH to GSSG. For tGSH assay, a (310)GSH-spiked sample was treated with dithiothreitol (DTT) to convert disulfide-bonded glutathione to GSH. After removing the protein, the supernatant was analyzed by LC-MS/MS and the analyte was quantified by single-spiking isotope dilution mass spectrometry (IDMS). The mathematical relationships in IDMS and SIDMS quantifications are based on isotopic ratios and do not involve calibration curves. The protocols were validated using spike recovery tests and by analyzing synthetic standard solutions. Red blood cell (RBC) and saliva samples obtained from healthy subjects, and whole blood samples collected and shipped from a remote location were analyzed. The concentrations of tGSH in the RBC and whole blood samples were 2 orders of magnitude higher than those found in saliva. The fractions of GSSG were 0.2-2.2% (RBC and blood) and 15-47% (saliva) of the free glutathione (GSH + 2xGSSG) in the corresponding samples. Up to 3% GSH was auto-oxidized to GSSG during sample workup; the highest oxidations (>1%) were in the saliva samples. PMID:25519489
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
Chen, Qinghai; Wu, Nan; Xie, Meng; Zhang, Bo; Chen, Ming; Li, Jianjun; Zhuo, Lisha; Kuang, Hong; Fu, Weiling
2012-01-01
Summary The accurate and high-throughput detection of drug resistance-related multiple point mutations remains a challenge. Although the combination of molecular beacons with bio-immobilization technology, such as microarray, is promising, its application is difficult due to the ineffective immobilization of molecular beacons on the chip surface. Here, we propose a novel asymmetric-loop molecular beacon in which the loop consists of 2 parts. One is complementary to a target, while the other is complementary to an oligonucleotide probe immobilized on the chip surface. With this novel probe, a two-phase hybridization assay can be used for simultaneously detecting multiple point mutations. This assay will have advantages, such as easy probe availability, multiplex detection, low background, and high-efficiency hybridization, and may provide a new avenue for the immobilization of molecular beacons and high-throughput detection of point mutations. PMID:22460100
Formulas for determining rotational constants
NASA Astrophysics Data System (ADS)
Guelachvili, G.
This document is part of Subvolume B `Linear Triatomic Molecules', Part 9, of Volume 20 `Molecular Constants mostly from Infrared Spectroscopy' of Landolt-Börnstein Group II `Molecules and Radicals'. Part of the introduction, it states formulas for determining rotational constants, band center, band origin, and quadrupole coupling. Specific comments relate to BHO (HBO) and COS (OCS).
On the importance of having accurate data for astrophysical modelling
NASA Astrophysics Data System (ADS)
Lique, Francois
2016-06-01
The Herschel telescope and the ALMA and NOEMA interferometers have opened new windows of observation for wavelengths ranging from far infrared to sub-millimeter with spatial and spectral resolutions previously unmatched. To make the most of these observations, an accurate knowledge of the physical and chemical processes occurring in the interstellar and circumstellar media is essential.In this presentation, I will discuss what are the current needs of astrophysics in terms of molecular data and I will show that accurate molecular data are crucial for the proper determination of the physical conditions in molecular clouds.First, I will focus on collisional excitation studies that are needed for molecular lines modelling beyond the Local Thermodynamic Equilibrium (LTE) approach. In particular, I will show how new collisional data for the HCN and HNC isomers, two tracers of star forming conditions, have allowed solving the problem of their respective abundance in cold molecular clouds. I will also present the last collisional data that have been computed in order to analyse new highly resolved observations provided by the ALMA interferometer.Then, I will present the calculation of accurate rate constants for the F+H2 → HF+H and Cl+H2 ↔ HCl+H reactions, which have allowed a more accurate determination of the physical conditions in diffuse molecular clouds. I will also present the recent work on the ortho-para-H2 conversion due to hydrogen exchange that allow more accurate determination of the ortho-to-para-H2 ratio in the universe and that imply a significant revision of the cooling mechanism in astrophysical media.
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.
Connecting Fundamental Constants
Di Mario, D.
2008-05-29
A model for a black hole electron is built from three basic constants only: h, c and G. The result is a description of the electron with its mass and charge. The nature of this black hole seems to fit the properties of the Planck particle and new relationships among basic constants are possible. The time dilation factor in a black hole associated with a variable gravitational field would appear to us as a charge; on the other hand the Planck time is acting as a time gap drastically limiting what we are able to measure and its dimension will appear in some quantities. This is why the Planck time is numerically very close to the gravitational/electric force ratio in an electron: its difference, disregarding a {pi}{radical}(2) factor, is only 0.2%. This is not a coincidence, it is always the same particle and the small difference is between a rotating and a non-rotating particle. The determination of its rotational speed yields accurate numbers for many quantities, including the fine structure constant and the electron magnetic moment.
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.
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.
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
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. PMID:26851912
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.
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
Tully, R B
1993-06-01
Five methods of estimating distances have demonstrated internal reproducibility at the level of 5-20% rms accuracy. The best of these are the cepheid (and RR Lyrae), planetary nebulae, and surface-brightness fluctuation techniques. Luminosity-line width and Dn-sigma methods are less accurate for an individual case but can be applied to large numbers of galaxies. The agreement is excellent between these five procedures. It is determined that Hubble constant H0 = 90 +/- 10 km.s-1.Mpc-1 [1 parsec (pc) = 3.09 x 10(16) m]. It is difficult to reconcile this value with the preferred world model even in the low-density case. The standard model with Omega = 1 may be excluded unless there is something totally misunderstood about the foundation of the distance scale or the ages of stars. PMID:11607391
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
Deshpande, Amol A; Madhavan, P; Deshpande, Girish R; Chandel, Ravi Kumar; Yarbagi, Kaviraj M; Joshi, Alok R; Moses Babu, J; Murali Krishna, R; Rao, I M
2016-01-01
Fondaparinux sodium is a synthetic low-molecular-weight heparin (LMWH). This medication is an anticoagulant or a blood thinner, prescribed for the treatment of pulmonary embolism and prevention and treatment of deep vein thrombosis. Its determination in the presence of related impurities was studied and validated by a novel ion-pair HPLC method. The separation of the drug and its degradation products was achieved with the polymer-based PLRPs column (250 mm × 4.6 mm; 5 μm) in gradient elution mode. The mixture of 100 mM n-hexylamine and 100 mM acetic acid in water was used as buffer solution. Mobile phase A and mobile phase B were prepared by mixing the buffer and acetonitrile in the ratio of 90:10 (v/v) and 20:80 (v/v), respectively. Mobile phases were delivered in isocratic mode (2% B for 0-5 min) followed by gradient mode (2-85% B in 5-60 min). An Evaporative Light Scattering Detector (ELSD) was connected to the LC system to detect the responses of chromatographic separation. Further, the drug was subjected to stress studies for acidic, basic, oxidative, photolytic, and thermal degradations as per ICH guidelines and the drug was found to be labile in acid, base hydrolysis, and oxidation, while stable in neutral, thermal, and photolytic degradation conditions. The method provided linear responses over the concentration range of the LOQ to 0.30% for each impurity with respect to the analyte concentration of 12.5 mg/mL, and regression analysis showed a correlation coefficient value (r(2)) of more than 0.99 for all the impurities. The LOD and LOQ were found to be 1.4 µg/mL and 4.1 µg/mL, respectively, for fondaparinux. The developed ion-pair method was validated as per ICH guidelines with respect to accuracy, selectivity, precision, linearity, and robustness. PMID:27110496
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
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.
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
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.
Accurate equilibrium structures of fluoro- and chloroderivatives of methane
NASA Astrophysics Data System (ADS)
Vogt, Natalja; Demaison, Jean; Rudolph, Heinz Dieter
2014-11-01
This work is a systematic study of molecular structure of fluoro-, chloro-, and fluorochloromethanes. For the first time, the accurate ab initio structure is computed for 10 molecules (CF4, CClF3, CCl2F2, CCl3F, CHClF2, CHCl2F, CH2F2, CH2ClF, CH2Cl2, and CCl4) at the coupled cluster level of electronic structure theory including single and double excitations augmented by a perturbational estimate of the effects of connected triple excitations [CCSD(T)] with all electrons being correlated and Gaussian basis sets of at least quadruple-ζ quality. Furthermore, when possible, namely for the molecules CH2F2, CH2Cl2, CH2ClF, CHClF2, and CCl2F2, accurate semi-experimental equilibrium (rSEe) structure has also been determined. This is achieved through a least-squares structural refinement procedure based on the equilibrium rotational constants of all available isotopomers, determined by correcting the experimental ground-state rotational constants with computed ab initio vibration-rotation interaction constants and electronic g-factors. The computed and semi-experimental equilibrium structures are in excellent agreement with each other, but the rSEe structure is generally more accurate, in particular for the CF and CCl bond lengths. The carbon-halogen bond length is discussed within the framework of the ligand close-packing model as a function of the atomic charges. For this purpose, the accurate equilibrium structures of some other molecules with alternative ligands, such as CH3Li, CF3CCH, and CF3CN, are also computed.
Kutateladze, Andrei G; Mukhina, Olga A
2014-09-01
Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min. PMID:25158224
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
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
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)
A priori predictions of the rotational constants for protonated formaldehyde and protonated methanol
NASA Technical Reports Server (NTRS)
Defrees, D. J.; Mclean, A. D.
1986-01-01
Protonated formaldehyde and protonated methanol are candidate interstellar molecules and models for classes of protonated oxygen compounds. Ab initio molecular orbital theory has been used to compute rotational constants to guide spectroscopic searches both in the laboratory and in space. The ab initio results are empirically correct to account for systematic deficiencies in the theory and zero-point vibrational effects; they are expected to be accurate to about + or - 2 percent. For H2COH(+) the resultant constants are (in GHz) A = 194.3, B = 34.28, and C = 29.14; for H3COH2(+) A = 103.7, B = 21.18, and C = 20.30.
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.
Houriez, Céline; Ferré, Nicolas; Masella, Michel; Siri, Didier
2008-06-28
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. PMID:18601346
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.
Solar constant secular changes
NASA Technical Reports Server (NTRS)
Schatten, Kenneth H.; Orosz, Jerome A.
1990-01-01
A recent model for solar constant secular changes is used to calculate a 'proxy' solar constant for: (1) the past four centuries, based upon the sunspot record, (2) the past nine centuries, based upon C-14 observations and their relation to solar activity, and (3) the next decade, based upon a dynamo theory model for the solar cycle. The proxy solar constant data is tabulated as it may be useful for climate modelers studying global climate changes.
Optical constants of concentrated aqueous ammonium sulfate.
NASA Technical Reports Server (NTRS)
Remsberg, E. E.
1973-01-01
Using experimental data obtained from applying spectroscopy to a 39-wt-% aqueous ammonium sulfate solution, it is shown that, even though specific aerosol optical constants appear quite accurate, spectral variations may exist as functions of material composition or concentration or both. Prudent users of optical constant data must then include liberal data error estimates when performing calculations or in interpreting spectroscopic surveys of collected aerosol material.
ERIC Educational Resources Information Center
Rom, Mark Carl
2011-01-01
Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…
NASA Astrophysics Data System (ADS)
1995-08-01
about the distances to galaxies and thereby about the expansion rate of the Universe. A simple way to determine the distance to a remote galaxy is by measuring its redshift, calculate its velocity from the redshift and divide this by the Hubble constant, H0. For instance, the measured redshift of the parent galaxy of SN 1995K (0.478) yields a velocity of 116,000 km/sec, somewhat more than one-third of the speed of light (300,000 km/sec). From the universal expansion rate, described by the Hubble constant (H0 = 20 km/sec per million lightyears as found by some studies), this velocity would indicate a distance to the supernova and its parent galaxy of about 5,800 million lightyears. The explosion of the supernova would thus have taken place 5,800 million years ago, i.e. about 1,000 million years before the solar system was formed. However, such a simple calculation works only for relatively ``nearby'' objects, perhaps out to some hundred million lightyears. When we look much further into space, we also look far back in time and it is not excluded that the universal expansion rate, i.e. the Hubble constant, may have been different at earlier epochs. This means that unless we know the change of the Hubble constant with time, we cannot determine reliable distances of distant galaxies from their measured redshifts and velocities. At the same time, knowledge about such change or lack of the same will provide unique information about the time elapsed since the Universe began to expand (the ``Big Bang''), that is, the age of the Universe and also its ultimate fate. The Deceleration Parameter q0 Cosmologists are therefore eager to determine not only the current expansion rate (i.e., the Hubble constant, H0) but also its possible change with time (known as the deceleration parameter, q0). Although a highly accurate value of H0 has still not become available, increasing attention is now given to the observational determination of the second parameter, cf. also the Appendix at the
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.
Wang, Ting; Yin, Hongyun; Wang, Dunyou; Valiev, Marat
2012-02-16
The bimolecular nucleophilic substitution reaction of CCl{sub 4} and OH{sup -} in aqueous solution was investigated on the basis of a combined quantum mechanical and molecular mechanics method. A multilayered representation approach is employed to achieve high accuracy results at the CCSD(T) level of theory. The potential of mean force calculations at the DFT level and CCSD(T) level of theory yield reaction barrier heights of 22.7 and 27.9 kcal/mol, respectively. Both the solvation effects and the solvent-induced polarization effect have significant contributions to the reaction energetics, for example, the solvation effect raises the saddle point by 10.6 kcal/mol. The calculated rate constant coefficient is 8.6 x 10{sup -28} cm{sup 3} molecule{sup -1} s{sup -1} at the standard state condition, which is about 17 orders magnitude smaller than that in the gas phase. Among the four chloromethanes (CH{sub 3}Cl, CH{sub 2}Cl{sub 2}, CHCl{sub 3}, and CCl{sub 4}), CCl{sub 4} has the lowest free energy activation barrier for the reaction with OH{sup -1} in aqueous solution, confirming the trend that substitution of Cl by H in chloromethanes diminishes the reactivity.
Tang, W-R; Shioya, N; Eguchi, T; Ebata, T; Matsui, J; Takenouchi, H; Honma, D; Yasue, H; Takagaki, Y; Enosawa, S; Itagaki, M; Taguchi, T; Kiyokawa, N; Amemiya, H; Fujimoto, J
2005-01-10
A battery of mouse monoclonal antibodies (mAbs) reactive with porcine peripheral blood (PB) leukocytes was generated. Among the mAbs, 6F10 was found to react probably with cluster of differentiation (CD)8 alpha-chain, while 7G3 and 3E12 were found to recognize gammadelta T-cells, as revealed by two-color flow cytometric and immunoprecipitation studies. 7G3 was shown to react with the constant (C) region of the T-cell receptor (TCR) delta-chain by the following facts: (1) 7G3 immunoprecipitated full-length TCR delta-chain protein fused with glutathione S-transferase (GST) produced by Esherichia coli and (2) 7G3 reacted with TCR delta-chain expressing Cos-7 cells transfected with either full-length or N-terminal deleted mutant cDNA, but did not react with Cos-7 cells transfected with C-terminal deleted mutant TCR delta-chain cDNA. All three mAbs produced high-quality immunostaining results on frozen sections, revealing a distinct distribution of gammadelta T-cells and CD8(+) cells. This report precisely characterizes mAbs against porcine TCR for the first time, facilitating molecular biological investigations of the porcine immune system. PMID:15626467
Experimental rovibrational constants and equilibrium structure of phosphorus trifluoride
NASA Astrophysics Data System (ADS)
Najib, Hamid
2014-11-01
Thanks to recent high-resolution Fourier transform infrared (FTIR) and pure rotational (RF/CM/MMW) measurements, several experimental values of the rotation-vibration parameters of the oblate molecule PF3 have been extracted, contributing thus to the knowledge of the molecular potential of phosphorus trifluoride. The data used are those of the fundamental, overtone and combination bands studied in the 300-1500 cm-1 range. The new values are in good agreement with ones determined at low resolution, but significantly more accurate. The agreement is excellent with the available values determined by ab initio HF-SCF calculations employing the TZP/TZ2P triple-zeta basis. From the recent experimental rovibrational interaction constants αC and αB, new accurate equilibrium rotational constants Ce and Be have been derived for the symmetric top molecule PF3, which were used to derive the equilibrium geometry of this molecule: re(F-P) = 1.560986 (43) Å; θe(FPF) = 97.566657 (64)°.
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.
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.
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
A novel single-molecule study to determine protein--protein association constants.
Ratcliff, G C; Erie, D A
2001-06-20
Atomic force microscopy (AFM) is traditionally used as an imaging technique to gain qualitative information for a biological system. We have successfully used the imaging capabilities of the AFM to determine protein-protein association constants. We have developed a method to measure the molecular weight of a protein based on its volume determined from AFM images. Our volume determination method allows for rapid, accurate analysis of large protein populations. On the basis of the measured volume, the fraction of monomers as dimers was determined for the DNA helicase UvrD, and the dissociation constant (K(d)) for the helicase was calculated. We determined a K(d) for UvrD of 1.4 microM, which is in good agreement with published K(d) data obtained from analytical ultracentrifugation (AUC) studies. Our method provides a rapid method for determining protein-protein association constants. PMID:11403593
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.
NASA Astrophysics Data System (ADS)
Buryak, Ilya; Vigasin, Andrey A.
2015-12-01
The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.
Space Shuttle astrodynamical constants
NASA Technical Reports Server (NTRS)
Cockrell, B. F.; Williamson, B.
1978-01-01
Basic space shuttle astrodynamic constants are reported for use in mission planning and construction of ground and onboard software input loads. The data included here are provided to facilitate the use of consistent numerical values throughout the project.
Constant potential pulse polarography
Christie, J.H.; Jackson, L.L.; Osteryoung, R.A.
1976-01-01
The new technique of constant potential pulse polarography, In which all pulses are to be the same potential, is presented theoretically and evaluated experimentally. The response obtained is in the form of a faradaic current wave superimposed on a constant capacitative component. Results obtained with a computer-controlled system exhibit a capillary response current similar to that observed In normal pulse polarography. Calibration curves for Pb obtained using a modified commercial pulse polarographic instrument are in good accord with theoretical predictions.
Absolute radiometry and the solar constant
NASA Technical Reports Server (NTRS)
Willson, R. C.
1974-01-01
A series of active cavity radiometers (ACRs) are described which have been developed as standard detectors for the accurate measurement of irradiance in absolute units. It is noted that the ACR is an electrical substitution calorimeter, is designed for automatic remote operation in any environment, and can make irradiance measurements in the range from low-level IR fluxes up to 30 solar constants with small absolute uncertainty. The instrument operates in a differential mode by chopping the radiant flux to be measured at a slow rate, and irradiance is determined from two electrical power measurements together with the instrumental constant. Results are reported for measurements of the solar constant with two types of ACRs. The more accurate measurement yielded a value of 136.6 plus or minus 0.7 mW/sq cm (1.958 plus or minus 0.010 cal/sq cm per min).
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
NASA Astrophysics Data System (ADS)
Itano, Wayne M.; Ramsey, Norman F.
1993-07-01
The paper discusses current methods for accurate measurements of time by conventional atomic clocks, with particular attention given to the principles of operation of atomic-beam frequency standards, atomic hydrogen masers, and atomic fountain and to the potential use of strings of trapped mercury ions as a time device more stable than conventional atomic clocks. The areas of application of the ultraprecise and ultrastable time-measuring devices that tax the capacity of modern atomic clocks include radio astronomy and tests of relativity. The paper also discusses practical applications of ultraprecise clocks, such as navigation of space vehicles and pinpointing the exact position of ships and other objects on earth using the GPS.
Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.
Puzzarini, Cristina
2015-11-25
The structures, relative stabilities, and rotational and vibrational parameters of the Z-C-, E-C-, and N-cyanomethanimine isomers have been evaluated using state-of-the-art quantum-chemical approaches. Equilibrium geometries have been calculated by means of a composite scheme based on coupled-cluster calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The latter approach is proved to provide molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled-cluster theory, including up to single, double, triple, and quadruple excitations, and corrected for core-electron correlation and anharmonic zero-point vibrational energy, have been used to accurately determine relative energies and the Z-E isomerization barrier with an accuracy of about 1 kJ/mol. Vibrational and rotational spectroscopic parameters have been investigated by means of hybrid schemes that allow us to obtain rotational constants accurate to about a few megahertz and vibrational frequencies with a mean absolute error of ∼1%. Where available, for all properties considered, a very good agreement with experimental data has been observed. PMID:26529434
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.
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.
2005-06-20
This application (XrayOpticsConstants) is a tool for displaying X-ray and Optical properties for a given material, x-ray photon energy, and in the case of a gas, pressure. The display includes fields such as the photo-electric absorption attenuation length, density, material composition, index of refraction, and emission properties (for scintillator materials).
Prediction of Rate Constant for Supramolecular Systems with Multiconfigurations.
Guo, Tao; Li, Haiyan; Wu, Li; Guo, Zhen; Yin, Xianzhen; Wang, Caifen; Sun, Lixin; Shao, Qun; Gu, Jingkai; York, Peter; Zhang, Jiwen
2016-02-25
The control of supramolecular systems requires a thorough understanding of their dynamics, especially on a molecular level. It is extremely difficult to determine the thermokinetic parameters of supramolecular systems, such as drug-cyclodextrin complexes with fast association/dissociation processes by experimental techniques. In this paper, molecular modeling combined with novel mathematical relationships integrating the thermodynamic/thermokinetic parameters of a series of isomeric multiconfigurations to predict the overall parameters in a range of pH values have been employed to study supramolecular dynamics at the molecular level. A suitable form of Eyring's equation was derived and a two-stage model was introduced. The new approach enabled accurate prediction of the apparent dissociation/association (koff/kon) and unbinding/binding (k-r/kr) rate constants of the ubiquitous multiconfiguration complexes of the supramolecular system. The pyronine Y (PY) was used as a model system for the validation of the presented method. Interestingly, the predicted koff value ((40 ± 1) × 10(5) s(-1), 298 K) of PY is largely in agreement with that previously determined by fluorescence correlation spectroscopy ((5 ± 3) × 10(5) s(-1), 298 K). Moreover, the koff/kon and k-r/kr for flurbiprofen-β-cylcodextrin and ibuprofen-β-cyclodextrin systems were also predicted and suggested that the association processes are diffusion-controlled. The methodology is considered to be especially useful in the design and selection of excipients for a supramolecular system with preferred association and dissociation rate constants and understanding their mechanisms. It is believed that this new approach could be applicable to a wide range of ligand-receptor supramolecular systems and will surely help in understanding their complex mechanism. PMID:26840799
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.
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.
Renormalization of Newton's constant
NASA Astrophysics Data System (ADS)
Falls, Kevin
2015-12-01
The problem of obtaining a gauge independent beta function for Newton's constant is addressed. By a specific parametrization of metric fluctuations a gauge independent functional integral is constructed for the semiclassical theory around an arbitrary Einstein space. The effective action then has the property that only physical polarizations of the graviton contribute, while all other modes cancel with the functional measure. We are then able to compute a gauge independent beta function for Newton's constant in d dimensions to one-loop order. No Landau pole is present provided Ng<18 , where Ng=d (d -3 )/2 is the number of polarizations of the graviton. While adding a large number of matter fields can change this picture, the absence of a pole persists for the particle content of the standard model in four spacetime dimensions.
Varying constants quantum cosmology
Leszczyńska, Katarzyna; Balcerzak, Adam; Dabrowski, Mariusz P. E-mail: abalcerz@wmf.univ.szczecin.pl
2015-02-01
We discuss minisuperspace models within the framework of varying physical constants theories including Λ-term. In particular, we consider the varying speed of light (VSL) theory and varying gravitational constant theory (VG) using the specific ansätze for the variability of constants: c(a) = c{sub 0} a{sup n} and G(a)=G{sub 0} a{sup q}. We find that most of the varying c and G minisuperspace potentials are of the tunneling type which allows to use WKB approximation of quantum mechanics. Using this method we show that the probability of tunneling of the universe ''from nothing'' (a=0) to a Friedmann geometry with the scale factor a{sub t} is large for growing c models and is strongly suppressed for diminishing c models. As for G varying, the probability of tunneling is large for G diminishing, while it is small for G increasing. In general, both varying c and G change the probability of tunneling in comparison to the standard matter content (cosmological term, dust, radiation) universe models.
NASA Astrophysics Data System (ADS)
Jackson, Neal
2015-09-01
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 H_0 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.
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.
Dielectric constant of water in the interface.
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. PMID:27394114
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.
Temperature dependent effective potential method for accurate free energy calculations of solids
NASA Astrophysics Data System (ADS)
Hellman, Olle; Steneteg, Peter; Abrikosov, I. A.; Simak, S. I.
2013-03-01
We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on ab initio molecular dynamics followed by a mapping onto a model Hamiltonian that describes the lattice dynamics. The formalism and the numerical aspects of the technique are described in detail. A number of practical examples are given, and results are presented, which confirm the usefulness of TDEP within ab initio and classical molecular dynamics frameworks. In particular, we examine from first principles the behavior of force constants upon the dynamical stabilization of the body centered phase of Zr, and show that they become more localized. We also calculate the phase diagram for 4He modeled with the Aziz potential and obtain results which are in favorable agreement both with respect to experiment and established techniques.
Effective optical constants of anisotropic materials
NASA Technical Reports Server (NTRS)
Aronson, J. R.; Emslie, A. G.
1980-01-01
The applicability of a technique for determining the optical constants of soil or aerosol components on the basis of measurements of the reflectance or transmittance of inhomogeneous samples of component material is investigated. Optical constants for a sample of very pure quartzite were obtained by a specular reflection technique and line parameters were calculated by classical dispersion theory. Predictions of the reflectance of powdered quartz were then derived from optical constants measured for the anisotropic quartz and for pure quartz crystals, and compared with experimental measurements. The calculated spectra are found to resemble each other moderately well in shape, however the reflectance level calculated from the psuedo-optical constants (quartzite) is consistently below that calculated from quartz values. The spectrum calculated from the quartz optical constants is also shown to represent the experimental nonrestrahlen features more accurately. It is thus concluded that although optical constants derived from inhomogeneous materials may represent the spectral features of a powdered sample qualitatively a quantitative fit to observed data is not likely.
RNA structure and scalar coupling constants
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.
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).
New model accurately predicts reformate composition
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.
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.
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.
Unitaxial constant velocity microactuator
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.
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.
Ustinov, E A
2014-10-01
Commensurate-incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs-Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton-graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton-carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas-solid and solid-solid system. PMID:25296827
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.
An accurate and simple quantum model for liquid water.
Paesani, Francesco; Zhang, Wei; Case, David A; Cheatham, Thomas E; Voth, Gregory A
2006-11-14
The path-integral molecular dynamics and centroid molecular dynamics methods have been applied to investigate the behavior of liquid water at ambient conditions starting from a recently developed simple point charge/flexible (SPC/Fw) model. Several quantum structural, thermodynamic, and dynamical properties have been computed and compared to the corresponding classical values, as well as to the available experimental data. The path-integral molecular dynamics simulations show that the inclusion of quantum effects results in a less structured liquid with a reduced amount of hydrogen bonding in comparison to its classical analog. The nuclear quantization also leads to a smaller dielectric constant and a larger diffusion coefficient relative to the corresponding classical values. Collective and single molecule time correlation functions show a faster decay than their classical counterparts. Good agreement with the experimental measurements in the low-frequency region is obtained for the quantum infrared spectrum, which also shows a higher intensity and a redshift relative to its classical analog. A modification of the original parametrization of the SPC/Fw model is suggested and tested in order to construct an accurate quantum model, called q-SPC/Fw, for liquid water. The quantum results for several thermodynamic and dynamical properties computed with the new model are shown to be in a significantly better agreement with the experimental data. Finally, a force-matching approach was applied to the q-SPC/Fw model to derive an effective quantum force field for liquid water in which the effects due to the nuclear quantization are explicitly distinguished from those due to the underlying molecular interactions. Thermodynamic and dynamical properties computed using standard classical simulations with this effective quantum potential are found in excellent agreement with those obtained from significantly more computationally demanding full centroid molecular dynamics
Strauch, Matthias; Bonsa, Anne-Marie; Golub, Benjamin; Overbeck, Viviane; Michalik, Dirk; Paschek, Dietmar; Ludwig, Ralf
2016-07-21
We describe a method for the accurate determination of deuteron quadrupole coupling constants χD for N-D bonds in triethylammonium-based protic ionic liquids (PILs). This approach was first introduced by Wendt and Farrar for O-D bonds in molecular liquids, and is based on the linear relationship between the deuteron quadrupole coupling constants χD, and the proton chemical shifts δ(1)H, as obtained from DFT calculated properties in differently sized clusters of the compounds. Thus the measurement of δ(1)H provides an accurate estimate for χD, which can then be used for deriving reorientational correlation-times τND, by means of NMR deuteron quadrupole relaxation time measurements. The method is applied to pure PILs including differently strong interacting anions. The obtained χD values vary between 152 and 204 kHz, depending on the cation-anion interaction strength, intensified by H-bonding. We find that considering dispersion corrections in the DFT-calculations leads to only slightly decreasing χD values. The determined reorientational correlation times indicate that the extreme narrowing condition is fulfilled for these PILs. The τc values along with the measured viscosities provide an estimate for the volume/size of the clusters present in solution. In addition, the correlation times τc, and the H-bonded aggregates were also characterized by molecular dynamics (MD) simulations. PMID:27067640
Accurate phase-shift velocimetry in rock.
Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M
2016-06-01
Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models. PMID:27111139
Accurate phase-shift velocimetry in rock
NASA Astrophysics Data System (ADS)
Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.
2016-06-01
Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.
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.
ESTIMATION OF CARBOXYLIC ACID ESTER HYDROLYSIS RATE CONSTANTS
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...
Levin, M.B.; Snegov, M.I.; Cherkasov, A.S.
1987-03-01
A method of determining the average lifetime tau of the products responsible for inverse induced absorption in aqueous--micellar solutions of rhodamine 6G (R6G) on lamp pumping based on a comparison of threshold intensities of excitation (W/sub th/) in the resonators of a laser with a different Q is proposed. Using the value of tau found (0.2 ..mu..sec) and experimental data on the change in W/sub th/ with the concentration of cyclooctatetraene (COT) added to the solution the rate constant of quenching of the absorbing products by COT molecules (K/sub q/ = 2.6 x 10/sup 7/ M/sup -1/sec/sup -1/) was determined. In the assumption that the absorbing products are triplet dye molecules, the value of the rate constant of interconversion (K/sub 32/) of R6G into an aqueous--micellar solution (K/sub 32/ = 1.3 x 10/sup 7/ sec/sup -1/) was determined. A comparison was made of the values of the constants found with the corresponding values known from the literature.
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.
Gleisner, Heike; Einax, Jürgen W; Morés, Silvane; Welz, Bernhard; Carasek, Eduardo
2011-04-01
A fast and reliable method has been developed for the determination of total and soluble fluorine in toothpaste, important quality control parameters in dentifrices. The method is based on the molecular absorption of gallium mono-fluoride, GaF, using a commercially available high-resolution continuum source atomic absorption spectrometer. Transversely heated platform tubes with zirconium as permanent chemical modifier were used throughout. Before each sample injection, a palladium and zirconium modifier solution and a gallium reagent were deposited onto the graphite platform and thermally pretreated to transform them into their active forms. The samples were only diluted and introduced directly into the graphite tube together with additional gallium reagent. Under these conditions the fluoride was stable up to a pyrolysis temperature of 550 °C, and the optimum vaporization (molecule formation) temperature was 1550 °C. The GaF molecular absorption was measured at 211.248 nm, and the limits of detection and quantification were 5.2 pg and 17 pg, respectively, corresponding to a limit of quantification of about 30 μg g(-1) (ppm) F in the original toothpaste. The proposed method was used for the determination of total and soluble fluorine content in toothpaste samples from different manufactures. The samples contained different ionic fluoride species and sodium monofluorophosphate (MFP) with covalently bonded fluorine. The results for total fluorine were compared with those obtained with a modified conventional headspace gas chromatographic procedure. Accuracy and precision of the two procedures were comparable, but the proposed procedure was much less labor-intensive, and about five times faster than the latter one. PMID:21215545
Planck Constant Determination from Power Equivalence
NASA Astrophysics Data System (ADS)
Newell, David B.
2000-04-01
Equating mechanical to electrical power links the kilogram, the meter, and the second to the practical realizations of the ohm and the volt derived from the quantum Hall and the Josephson effects, yielding an SI determination of the Planck constant. The NIST watt balance uses this power equivalence principle, and in 1998 measured the Planck constant with a combined relative standard uncertainty of 8.7 x 10-8, the most accurate determination to date. The next generation of the NIST watt balance is now being assembled. Modification to the experimental facilities have been made to reduce the uncertainty components from vibrations and electromagnetic interference. A vacuum chamber has been installed to reduce the uncertainty components associated with performing the experiment in air. Most of the apparatus is in place and diagnostic testing of the balance should begin this year. Once a combined relative standard uncertainty of one part in 10-8 has been reached, the power equivalence principle can be used to monitor the possible drift in the artifact mass standard, the kilogram, and provide an accurate alternative definition of mass in terms of fundamental constants. *Electricity Division, Electronics and Electrical Engineering Laboratory, Technology Administration, U.S. Department of Commerce. Contribution of the National Institute of Standards and Technology, not subject to copyright in the U.S.
Piezoelectric constants for ZnO calculated using classical polarizable core-shell potentials
NASA Astrophysics Data System (ADS)
Dai, Shuangxing; Dunn, Martin L.; Park, Harold S.
2010-11-01
We demonstrate the feasibility of using classical atomistic simulations, i.e. molecular dynamics and molecular statics, to study the piezoelectric properties of ZnO using core-shell interatomic potentials. We accomplish this by reporting the piezoelectric constants for ZnO as calculated using two different classical interatomic core-shell potentials: that originally proposed by Binks and Grimes (1994 Solid State Commun. 89 921-4), and that proposed by Nyberg et al (1996 J. Phys. Chem. 100 9054-63). We demonstrate that the classical core-shell potentials are able to qualitatively reproduce the piezoelectric constants as compared to benchmark ab initio calculations. We further demonstrate that while the presence of the shell is required to capture the electron polarization effects that control the clamped ion part of the piezoelectric constant, the major shortcoming of the classical potentials is a significant underprediction of the clamped ion term as compared to previous ab initio results. However, the present results suggest that overall, these classical core-shell potentials are sufficiently accurate to be utilized for large scale atomistic simulations of the piezoelectric response of ZnO nanostructures.
Vibrational Averaging of the Isotropic Hyperfine Coupling Constants for the Methyl Radical
NASA Astrophysics Data System (ADS)
Adam, Ahmad; Jensen, Per; Yachmenev, Andrey; Yurchenko, Sergei N.
2014-06-01
Electronic contributions to molecular properties are often considered as the major factor and usually reported in the literature without ro-vibrational corrections. However, there are many cases where the nuclear motion contributions are significant and even larger than the electronic contribution. In order to obtain accurate theoretical predictions, nuclear motion effects on molecular properties need to be taken into account. The computed isotropic hyperfine coupling constants for the nonvibrating methyl radical CH_3 are far from the experimental values. For CH_3, we have calculated the vibrational-state-dependence of the isotropic hyperfine coupling constant in the electronic ground state. The vibrational wavefunctions used in the averaging procedure were obtained variationally with the TROVE program. Analytical representations for the potential energy surfaces and the hyperfine coupling constant surfaces are obtained in least-squares fitting procedures. Thermal averaging has been carried out for molecules in thermal equilibrium, i.e., with Boltzmann-distributed populations. The calculation methods and the results will be discussed in detail.
NNLOPS accurate associated HW production
NASA Astrophysics Data System (ADS)
Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia
2016-06-01
We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.
Are Kohn-Sham conductances accurate?
Mera, H; Niquet, Y M
2010-11-19
We use Fermi-liquid relations to address the accuracy of conductances calculated from the single-particle states of exact Kohn-Sham (KS) density functional theory. We demonstrate a systematic failure of this procedure for the calculation of the conductance, and show how it originates from the lack of renormalization in the KS spectral function. In certain limits this failure can lead to a large overestimation of the true conductance. We also show, however, that the KS conductances can be accurate for single-channel molecular junctions and systems where direct Coulomb interactions are strongly dominant. PMID:21231333
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.
Multiscale reactive molecular dynamics
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-01-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062
How to accurately bypass damage
Broyde, Suse; Patel, Dinshaw J.
2016-01-01
Ultraviolet radiation can cause cancer through DNA damage — specifically, by linking adjacent thymine bases. Crystal structures show how the enzyme DNA polymerase η accurately bypasses such lesions, offering protection. PMID:20577203
Accurate Evaluation of Quantum Integrals
NASA Technical Reports Server (NTRS)
Galant, David C.; Goorvitch, D.
1994-01-01
Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schr\\"{o}dinger'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.
Damping constant estimation in magnetoresistive readers
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.
Damping constant estimation in magnetoresistive readers
NASA Astrophysics Data System (ADS)
Stankiewicz, Andrzej; Hernandez, Stephanie
2015-05-01
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.
Accurate Mass Measurements in Proteomics
Liu, Tao; Belov, Mikhail E.; Jaitly, Navdeep; Qian, Weijun; Smith, Richard D.
2007-08-01
To understand different aspects of life at the molecular level, one would think that ideally all components of specific processes should be individually isolated and studied in details. Reductionist approaches, i.e., studying one biological event at a one-gene or one-protein-at-a-time basis, indeed have made significant contributions to our understanding of many basic facts of biology. However, these individual “building blocks” can not be visualized as a comprehensive “model” of the life of cells, tissues, and organisms, without using more integrative approaches.1,2 For example, the emerging field of “systems biology” aims to quantify all of the components of a biological system to assess their interactions and to integrate diverse types of information obtainable from this system into models that could explain and predict behaviors.3-6 Recent breakthroughs in genomics, proteomics, and bioinformatics are making this daunting task a reality.7-14 Proteomics, the systematic study of the entire complement of proteins expressed by an organism, tissue, or cell under a specific set of conditions at a specific time (i.e., the proteome), has become an essential enabling component of systems biology. While the genome of an organism may be considered static over short timescales, the expression of that genome as the actual gene products (i.e., mRNAs and proteins) is a dynamic event that is constantly changing due to the influence of environmental and physiological conditions. Exclusive monitoring of the transcriptomes can be carried out using high-throughput cDNA microarray analysis,15-17 however the measured mRNA levels do not necessarily correlate strongly with the corresponding abundances of proteins,18-20 The actual amount of functional proteins can be altered significantly and become independent of mRNA levels as a result of post-translational modifications (PTMs),21 alternative splicing,22,23 and protein turnover.24,25 Moreover, the functions of expressed
Accurate spring constant calibration for very stiff atomic force microscopy cantilevers
Grutzik, Scott J.; Zehnder, Alan T.; Gates, Richard S.; Gerbig, Yvonne B.; Smith, Douglas T.; Cook, Robert F.
2013-11-15
There are many atomic force microscopy (AFM) applications that rely on quantifying the force between the AFM cantilever tip and the sample. The AFM does not explicitly measure force, however, so in such cases knowledge of the cantilever stiffness is required. In most cases, the forces of interest are very small, thus compliant cantilevers are used. A number of methods have been developed that are well suited to measuring low stiffness values. However, in some cases a cantilever with much greater stiffness is required. Thus, a direct, traceable method for calibrating very stiff (approximately 200 N/m) cantilevers is presented here. The method uses an instrumented and calibrated nanoindenter to determine the stiffness of a reference cantilever. This reference cantilever is then used to measure the stiffness of a number of AFM test cantilevers. This method is shown to have much smaller uncertainty than previously proposed methods. An example application to fracture testing of nanoscale silicon beam specimens is included.
Accurate, conformation-dependent predictions of solvent effects on protein ionization constants
Barth, P.; Alber, T.; Harbury, P. B.
2007-01-01
Predicting how aqueous solvent modulates the conformational transitions and influences the pKa values that regulate the biological functions of biomolecules remains an unsolved challenge. To address this problem, we developed FDPB_MF, a rotamer repacking method that exhaustively samples side chain conformational space and rigorously calculates multibody protein–solvent interactions. FDPB_MF predicts the effects on pKa values of various solvent exposures, large ionic strength variations, strong energetic couplings, structural reorganizations and sequence mutations. The method achieves high accuracy, with root mean square deviations within 0.3 pH unit of the experimental values measured for turkey ovomucoid third domain, hen lysozyme, Bacillus circulans xylanase, and human and Escherichia coli thioredoxins. FDPB_MF provides a faithful, quantitative assessment of electrostatic interactions in biological macromolecules. PMID:17360348
NASA Astrophysics Data System (ADS)
Ćopuroǧlu, Ebru; Mamedov, Bahtiyar A.
2016-08-01
By the use of Löwdin- α radial function, an alternative method is introduced for two-center overlap integral over Slater type orbitals (STOs) at same screening constants (SSC). Notice that the overlap integrals with SSC have an important role in accurate evaluation of multicenter multielectron molecular integrals arising in combined Hartree-Fock-Roothaan (CHFR) theory. This approximation provides us simple and efficient expression for the two-center overlap integrals. To show the effectiveness of established formula we have compared our results with available literature data. The method ensures high performance with a very short CPU time.
A procedure for computing accurate ab initio quartic force fields: Application to HO2+ and H2O
NASA Astrophysics Data System (ADS)
Huang, Xinchuan; Lee, Timothy J.
2008-07-01
A procedure for the calculation of molecular quartic force fields (QFFs) is proposed and investigated. The goal is to generate highly accurate ab initio QFFs that include many of the so-called ``small'' effects that are necessary to achieve high accuracy. The small effects investigated in the present study include correlation of the core electrons (core correlation), extrapolation to the one-particle basis set limit, correction for scalar relativistic contributions, correction for higher-order correlation effects, and inclusion of diffuse functions in the one-particle basis set. The procedure is flexible enough to allow for some effects to be computed directly, while others may be added as corrections. A single grid of points is used and is centered about an initial reference geometry that is designed to be as close as possible to the final ab initio equilibrium structure (with all effects included). It is shown that the least-squares fit of the QFF is not compromised by the added corrections, and the balance between elimination of contamination from higher-order force constants while retaining energy differences large enough to yield meaningful quartic force constants is essentially unchanged from the standard procedures we have used for many years. The initial QFF determined from the least-squares fit is transformed to the exact minimum in order to eliminate gradient terms and allow for the use of second-order perturbation theory for evaluation of spectroscopic constants. It is shown that this step has essentially no effect on the quality of the QFF largely because the initial reference structure is, by design, very close to the final ab initio equilibrium structure. The procedure is used to compute an accurate, purely ab initio QFF for the H2O molecule, which is used as a benchmark test case. The procedure is then applied to the ground and first excited electronic states of the HO2+ molecular cation. Fundamental vibrational frequencies and spectroscopic
New Quasar Studies Keep Fundamental Physical Constant Constant
NASA Astrophysics Data System (ADS)
2004-03-01
Very Large Telescope sets stringent limit on possible variation of the fine-structure constant over cosmological time Summary Detecting or constraining the possible time variations of fundamental physical constants is an important step toward a complete understanding of basic physics and hence the world in which we live. A step in which astrophysics proves most useful. Previous astronomical measurements of the fine structure constant - the dimensionless number that determines the strength of interactions between charged particles and electromagnetic fields - suggested that this particular constant is increasing very slightly with time. If confirmed, this would have very profound implications for our understanding of fundamental physics. New studies, conducted using the UVES spectrograph on Kueyen, one of the 8.2-m telescopes of ESO's Very Large Telescope array at Paranal (Chile), secured new data with unprecedented quality. These data, combined with a very careful analysis, have provided the strongest astronomical constraints to date on the possible variation of the fine structure constant. They show that, contrary to previous claims, no evidence exist for assuming a time variation of this fundamental constant. PR Photo 07/04: Relative Changes with Redshift of the Fine Structure Constant (VLT/UVES) A fine constant To explain the Universe and to represent it mathematically, scientists rely on so-called fundamental constants or fixed numbers. The fundamental laws of physics, as we presently understand them, depend on about 25 such constants. Well-known examples are the gravitational constant, which defines the strength of the force acting between two bodies, such as the Earth and the Moon, and the speed of light. One of these constants is the so-called "fine structure constant", alpha = 1/137.03599958, a combination of electrical charge of the electron, the Planck constant and the speed of light. The fine structure constant describes how electromagnetic forces hold
Simple liquid models with corrected dielectric constants.
Fennell, Christopher J; Li, Libo; Dill, Ken A
2012-06-14
Molecular simulations often use explicit-solvent models. Sometimes explicit-solvent models can give inaccurate values for basic liquid properties, such as the density, heat capacity, and permittivity, as well as inaccurate values for molecular transfer free energies. Such errors have motivated the development of more complex solvents, such as polarizable models. We describe an alternative here. We give new fixed-charge models of solvents for molecular simulations--water, carbon tetrachloride, chloroform, and dichloromethane. Normally, such solvent models are parametrized to agree with experimental values of the neat liquid density and enthalpy of vaporization. Here, in addition to those properties, our parameters are chosen to give the correct dielectric constant. We find that these new parametrizations also happen to give better values for other properties, such as the self-diffusion coefficient. We believe that parametrizing fixed-charge solvent models to fit experimental dielectric constants may provide better and more efficient ways to treat solvents in computer simulations. PMID:22397577
QCD coupling constants and VDM
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.
Extended temperature dependence of elastic constants in cubic crystals.
Telichko, A V; Sorokin, B P
2015-08-01
To extend the theory of the temperature dependence of the elastic constants in cubic crystals beyond the second- and third-order elastic constants, the fourth-order elastic constants, as well as the non-linearity in the thermal expansion temperature dependence, have been taken into account. Theoretical results were represented as temperature functions of the effective elastic constants and compared with experimental data for a number of cubic crystals, such as alkali metal halides, and elements gold and silver. The relations obtained give a more accurate description of the experimental temperature dependences of second-order elastic constants for a number of cubic crystals, including deviations from linear behavior. A good agreement between theoretical estimates and experimental data has been observed. PMID:25819879
Constant-force approach to discontinuous potentials.
Orea, Pedro; Odriozola, Gerardo
2013-06-01
Aiming to approach the thermodynamical properties of hard-core systems by standard molecular dynamics simulation, we propose setting a repulsive constant-force for overlapping particles. That is, the discontinuity of the pair potential is replaced by a linear function with a large negative slope. Hence, the core-core repulsion, usually modeled with a power function of distance, yields a large force as soon as the cores slightly overlap. This leads to a quasi-hardcore behavior. The idea is tested for a triangle potential of short range. The results obtained by replica exchange molecular dynamics for several repulsive forces are contrasted with the ones obtained for the discontinuous potential and by means of replica exchange Monte Carlo. We found remarkable agreements for the vapor-liquid coexistence densities as well as for the surface tension. PMID:23758356
The thermodynamic cost of accurate sensory adaptation
NASA Astrophysics Data System (ADS)
Tu, Yuhai
2015-03-01
Living organisms need to obtain and process environment information accurately in order to make decisions critical for their survival. Much progress have been made in identifying key components responsible for various biological functions, however, major challenges remain to understand system-level behaviors from the molecular-level knowledge of biology and to unravel possible physical principles for the underlying biochemical circuits. In this talk, we will present some recent works in understanding the chemical sensory system of E. coli by combining theoretical approaches with quantitative experiments. We focus on addressing the questions on how cells process chemical information and adapt to varying environment, and what are the thermodynamic limits of key regulatory functions, such as adaptation.
USING THE STATIC HEADSPACE METHOD TO DETERMINE HENRY'S LAW CONSTANTS
A new, accurate, and experimentally simple method has been developed to determine dimensionless Henry's law constants using the static headspace method. he method appears applicable to a wide range of volatile and semivolatile organic compounds. he method work well even for methy...
The calculation of elastic constants from displacement fluctuations
NASA Astrophysics Data System (ADS)
Meyers, M. T.; Rickman, J. M.; Delph, T. J.
2005-09-01
We present a methodology for the accurate and efficient extraction of elastic constants in homogeneous solids via the calculation of the atomic displacement correlation function. This approach is validated for cubic solids parametrized by both Lennard-Jones and embedded-atom method potentials. Finally, we also discuss the extension of this method to obtain the elastic properties of inhomogeneous solids.
QSPR prediction of the hydroxyl radical rate constant of water contaminants.
Borhani, Tohid Nejad Ghaffar; Saniedanesh, Mohammadhossein; Bagheri, Mehdi; Lim, Jeng Shiun
2016-07-01
In advanced oxidation processes (AOPs), the aqueous hydroxyl radical (HO) acts as a strong oxidant to react with organic contaminants. The hydroxyl radical rate constant (kHO) is important for evaluating and modelling of the AOPs. In this study, quantitative structure-property relationship (QSPR) method is applied to model the hydroxyl radical rate constant for a diverse dataset of 457 water contaminants from 27 various chemical classes. The constricted binary particle swarm optimization and multiple-linear regression (BPSO-MLR) are used to obtain the best model with eight theoretical descriptors. An optimized feed forward neural network (FFNN) is developed to investigate the complex performance of the selected molecular parameters with kHO. Although the FFNN prediction results are more accurate than those obtained using BPSO-MLR, the application of the latter is much more convenient. Various internal and external validation techniques indicate that the obtained models could predict the logarithmic hydroxyl radical rate constants of a large number of water contaminants with less than 4% absolute relative error. Finally, the above-mentioned proposed models are compared to those reported earlier and the structural factors contributing to the AOP degradation efficiency are discussed. PMID:27124124
Computing the dielectric constant of liquid water at constant dielectric displacement
NASA Astrophysics Data System (ADS)
Zhang, Chao; Sprik, Michiel
2016-04-01
The static dielectric constant of liquid water is computed using classical force field based molecular dynamics simulation at fixed electric displacement D . The method to constrain the electric displacement is the finite-temperature classical variant of the constant D method developed by Stengel, Spaldin, and Vanderbilt [Nat. Phys. 5, 304 (2009), 10.1038/nphys1185]. There is also a modification of this scheme imposing fixed values of the macroscopic field E . The method is applied to the popular SPC/E model of liquid water. We compare four different estimates of the dielectric constant, two obtained from fluctuations of the polarization at D =0 and E =0 and two from the variation of polarization with finite D and E . It is found that all four estimates agree when properly converged. The computational effort to achieve convergence varies, however, with constant D calculations being substantially more efficient. We attribute this difference to the much shorter relaxation time of longitudinal polarization compared to transverse polarization accelerating constant D calculations.
Constant Communities in Complex Networks
NASA Astrophysics Data System (ADS)
Chakraborty, Tanmoy; Srinivasan, Sriram; Ganguly, Niloy; Bhowmick, Sanjukta; Mukherjee, Animesh
2013-05-01
Identifying community structure is a fundamental problem in network analysis. Most community detection algorithms are based on optimizing a combinatorial parameter, for example modularity. This optimization is generally NP-hard, thus merely changing the vertex order can alter their assignments to the community. However, there has been less study on how vertex ordering influences the results of the community detection algorithms. Here we identify and study the properties of invariant groups of vertices (constant communities) whose assignment to communities are, quite remarkably, not affected by vertex ordering. The percentage of constant communities can vary across different applications and based on empirical results we propose metrics to evaluate these communities. Using constant communities as a pre-processing step, one can significantly reduce the variation of the results. Finally, we present a case study on phoneme network and illustrate that constant communities, quite strikingly, form the core functional units of the larger communities.
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.
Thermodynamic binding constants for gallium transferrin
Harris, W.R.; Pecoraro, V.L.
1983-01-18
Gallium-67 is widely used as an imaging agent for tumors and inflammatory abscesses. It is well stablished that Ga/sup 3 +/ travels through the circulatory system bound to the serum iron transport protein transferrin and that this protein binding is an essential step in tumor localization. However, there have been conflicting reports on the magnitude of the gallium-transferrin binding constants. Therefore, thermodynamic binding constants for gallium complexation at the two specific metal binding sites of human serum transferrin at pH 7.4 and 5 mM NaHCO/sub 3/ have been determined by UV difference spectroscopy. The conditional constants calculated for 27 mM NaHCO/sub 3/ are log K/sub 1/* = 20.3 and log K/sub 2/* = 19.3. These results are discussed in relation to the thermodynamics of transferrin binding of Fe/sup 3 +/ and to previous reports on gallium binding. The strength of transferrin complexation is also compared to that of a series of low molecular weight ligands by using calculated pM values (pM = -log (Ga(H/sub 2/O)/sub 6/)) to express the effective binding strength at pH 7.4.
NASA Astrophysics Data System (ADS)
Moiseev, N. Ya.
2011-04-01
An approach to the construction of high-order accurate monotone difference schemes for solving gasdynamic problems by Godunov's method with antidiffusion is proposed. Godunov's theorem on monotone schemes is used to construct a new antidiffusion flux limiter in high-order accurate difference schemes as applied to linear advection equations with constant coefficients. The efficiency of the approach is demonstrated by solving linear advection equations with constant coefficients and one-dimensional gasdynamic equations.
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.
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.
How fundamental are fundamental constants?
NASA Astrophysics Data System (ADS)
Duff, M. J.
2015-01-01
I argue that the laws of physics should be independent of one's choice of units or measuring apparatus. This is the case if they are framed in terms of dimensionless numbers such as the fine structure constant, ?. For example, the standard model of particle physics has 19 such dimensionless parameters whose values all observers can agree on, irrespective of what clock, rulers or scales? they use to measure them. Dimensional constants, on the other hand, such as ?, c, G, e and k ?, are merely human constructs whose number and values differ from one choice of units to the next. In this sense, only dimensionless constants are 'fundamental'. Similarly, the possible time variation of dimensionless fundamental 'constants' of nature is operationally well defined and a legitimate subject of physical enquiry. By contrast, the time variation of dimensional constants such as ? or ? on which a good many (in my opinion, confusing) papers have been written, is a unit-dependent phenomenon on which different observers might disagree depending on their apparatus. All these confusions disappear if one asks only unit-independent questions. We provide a selection of opposing opinions in the literature and respond accordingly.
Predict amine solution properties accurately
Cheng, S.; Meisen, A.; Chakma, A.
1996-02-01
Improved process design begins with using accurate physical property data. Especially in the preliminary design stage, physical property data such as density viscosity, thermal conductivity and specific heat can affect the overall performance of absorbers, heat exchangers, reboilers and pump. These properties can also influence temperature profiles in heat transfer equipment and thus control or affect the rate of amine breakdown. Aqueous-amine solution physical property data are available in graphical form. However, it is not convenient to use with computer-based calculations. Developed equations allow improved correlations of derived physical property estimates with published data. Expressions are given which can be used to estimate physical properties of methyldiethanolamine (MDEA), monoethanolamine (MEA) and diglycolamine (DGA) solutions.
Accurate thickness measurement of graphene
NASA Astrophysics Data System (ADS)
Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.
2016-03-01
Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.
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
Accurate Relations Between the Neutron Current Densities and the Neutron Fluxes
Ronen, Yigal
2004-02-15
Accurate relations between neutron current densities and neutron flux are obtained using the integral transport equation. Using these relations and Fick's Law, diffusion constants can be calculated. These diffusion constants are better than those usually used for the cases in which {sigma}{sub a}/{sigma}{sub s} is not small.
Cosmologies with variable gravitational constant
NASA Astrophysics Data System (ADS)
Narlikar, 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.
Constant-amplitude RC oscillator
NASA Technical Reports Server (NTRS)
Kerwin, W. J.; Westbrook, R. M.
1970-01-01
Sinusoidal oscillator has a frequency determined by resistance-capacitance /RC/ values of two charge control devices and a constant-amplitude voltage independent of frequency and RC values. RC elements provide either voltage-control, resistance-control, or capacitance-control of the frequency.
The 1% concordance Hubble constant
Bennett, C. L.; Larson, D.; Weiland, J. L.; Hinshaw, G.
2014-10-20
The determination of the Hubble constant has been a central goal in observational astrophysics for nearly a hundred years. Extraordinary progress has occurred in recent years on two fronts: the cosmic distance ladder measurements at low redshift and cosmic microwave background (CMB) measurements at high redshift. The CMB is used to predict the current expansion rate through a best-fit cosmological model. Complementary progress has been made with baryon acoustic oscillation (BAO) measurements at relatively low redshifts. While BAO data do not independently determine a Hubble constant, they are important for constraints on possible solutions and checks on cosmic consistency. A precise determination of the Hubble constant is of great value, but it is more important to compare the high and low redshift measurements to test our cosmological model. Significant tension would suggest either uncertainties not accounted for in the experimental estimates or the discovery of new physics beyond the standard model of cosmology. In this paper we examine in detail the tension between the CMB, BAO, and cosmic distance ladder data sets. We find that these measurements are consistent within reasonable statistical expectations and we combine them to determine a best-fit Hubble constant of 69.6 ± 0.7 km s{sup –1} Mpc{sup –1}. This value is based upon WMAP9+SPT+ACT+6dFGS+BOSS/DR11+H {sub 0}/Riess; we explore alternate data combinations in the text. The combined data constrain the Hubble constant to 1%, with no compelling evidence for new physics.
Optical constants of solid methane
Khare, B.N.; Thompson, W.R.; Sagan, C. . Lab. for Planetary Studies); Arakawa, E.T.; Bruel, C.; Judish, J.P. ); Khanna, R.K. . Dept. of Chemistry and Biochemistry); Pollack, J.B. . Ames Research Center)
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 CH{sub 4} 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. We present preliminary results of the optical constants of solid methane for the 0.4 {mu}m to 2.6 {mu}m region. We report k for both the amorphous and the crystalline (annealed) states. Using our previously measured values of the real part of the refractive index, n, of liquid methane at 110{degree}K (Bull. Am. Phys. Soc.31, 700 (1986)) we compute n 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 CH{sub 4}. 33 refs., 6 figs., 2 tabs.
Dose rate constant and energy spectrum of interstitial brachytherapy sources.
Chen, Z; Nath, R
2001-01-01
In the past two years, several new manufacturers have begun to market low-energy interstitial brachytherapy seeds containing 125I and 103Pd. Parallel to this development, the National Institute of Standards and Technology (NIST) has implemented a modification to the air-kerma strength (S(K)) standard for 125I seeds and has also established an S(K) standard for 103Pd seeds. These events have generated a considerable number of investigations on the determination of the dose rate constants (inverted V) of interstitial brachytherapy seeds. The aim of this work is to study the general properties underlying the determination of dose rate constant and to develop a simple method for a quick and accurate estimation of dose rate constant. As the dose rate constant of clinical seeds is defined at a fixed reference point, we postulated that dose rate constant may be calculated by treating the seed as an effective point source when the seed's source strength is specified in S(K) and its source characteristics are specified by the photon energy spectrum measured in air at the reference point. Using a semi-analytic approach, an analytic expression for dose rate constant was derived for point sources with known photon energy spectra. This approach enabled a systematic study of dose rate constant as a function of energy. Using the measured energy spectra, the calculated dose rate constant for 125I model 6711 and 6702 seeds and for 192Ir seed agreed with the AAPM recommended values within +/-1%. For the 103Pd model 200 seed, the agreement was 5% with a recently measured value (within the +/-7% experimental uncertainty) and was within 1% with the Monte Carlo simulations. The analytic expression for dose rate constant proposed here can be evaluated using a programmable calculator or a simple spreadsheet and it provides an efficient method for checking the measured dose rate constant for any interstitial brachytherapy seed once the energy spectrum of the seed is known. PMID:11213926
Accurate ab Initio Spin Densities
2012-01-01
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]. PMID:22707921
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
Elasticity of crystalline molecular explosives
Hooks, Daniel E.; Ramos, Kyle J.; Bolme, C. A.; Cawkwell, Marc J.
2015-04-14
Crystalline molecular explosives are key components of engineered explosive formulations. In precision applications a high degree of consistency and predictability is desired under a range of conditions to a variety of stimuli. Prediction of behaviors from mechanical response and failure to detonation initiation and detonation performance of the material is linked to accurate knowledge of the material structure and first stage of deformation: elasticity. The elastic response of pentaerythritol tetranitrate (PETN), cyclotrimethylene trinitramine (RDX), and cyclotetramethylene tetranitramine (HMX), including aspects of material and measurement variability, and computational methods are described in detail. Experimental determinations of elastic tensors are compared, andmore » an evaluation of sources of error is presented. Furthermore, computed elastic constants are also compared for these materials and for triaminotrinitrobenzene (TATB), for which there are no measurements.« less
Elasticity of crystalline molecular explosives
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.
Corrections to fundamental constants from photoelectric observations of lunar occultations
NASA Astrophysics Data System (ADS)
Rossello, G.
1982-12-01
A catalog of photoelectric occultations, which are more accurate than visual observations, is presented along with an analysis of the occultations intended to correct the FK4 stellar reference frame and lunar theory constants. A constant correction at the epoch 1969.0 of plus 0.87 plus or minus 0.06 to the FK4 system is consistent with those obtained by other authors, and the corrections to the semidiameter and parallactic inequality are in accord with values recently obtained by Morrison and Appleby (1981).
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%.
Quaternions as astrometric plate constants
NASA Technical Reports Server (NTRS)
Jefferys, William H.
1987-01-01
A new method for solving problems in relative astrometry is proposed. In it, the relationship between the measured quantities and the components of the position vector of a star is modeled using quaternions, in effect replacing the plate constants of a standard four-plate-constant solution with the four components of a quaternion. The method allows a direct solution for the position vectors of the stars, and hence for the equatorial coordinates. Distortions, magnitude, and color effects are readily incorporated into the formalism, and the method is directly applicable to overlapping-plate problems. The advantages of the method include the simplicity of the resulting equations, their freedom from singularities, and the fact that trigonometric functions and tangential point transformations are not needed to model the plate material. A global solution over the entire sky is possible.
Confinement from constant field condensates
NASA Astrophysics Data System (ADS)
Gaete, Patricio; Guendelman, Eduardo; Spallucci, Euro
2007-01-01
For (2 + 1)- and (3 + 1)-dimensional reformulated SU (2) Yang-Mills theory, we compute the interaction potential within the framework of the gauge-invariant but path-dependent variables formalism. This reformulation is due to the presence of a constant gauge field condensate. Our results show that the interaction energy contains a linear term leading to the confinement of static probe charges. This result is equivalent to that of the massive Schwinger model.
Simulating Supercapacitors: Can We Model Electrodes As Constant Charge Surfaces?
Merlet, Céline; Péan, Clarisse; Rotenberg, Benjamin; Madden, Paul A; Simon, Patrice; Salanne, Mathieu
2013-01-17
Supercapacitors based on an ionic liquid electrolyte and graphite or nanoporous carbon electrodes are simulated using molecular dynamics. We compare a simplified electrode model in which a constant, uniform charge is assigned to each carbon atom with a realistic model in which a constant potential is applied between the electrodes (the carbon charges are allowed to fluctuate). We show that the simulations performed with the simplified model do not provide a correct description of the properties of the system. First, the structure of the adsorbed electrolyte is partly modified. Second, dramatic differences are observed for the dynamics of the system during transient regimes. In particular, upon application of a constant applied potential difference, the increase in the temperature, due to the Joule effect, associated with the creation of an electric current across the cell follows Ohm's law, while unphysically high temperatures are rapidly observed when constant charges are assigned to each carbon atom. PMID:26283432
Star polymers rupture induced by constant forces
NASA Astrophysics Data System (ADS)
García, N. A.; Febbo, M.; Vega, D. A.; Milchev, A.
2014-10-01
In this work, we study the breakage process of an unknotted three-arm star-shaped polymer when it is pulled from its free ends by a constant force. The star polymer configuration is described through an array of monomers coupled by anharmonic bonds, while the rupture process is tracked in three-dimensional space by means of Langevin Molecular Dynamics simulations. The interaction between monomers is described by a Morse potential, while a Weeks-Chandler-Anderson energetic contribution accounts for the excluded volume interaction. We explore the effect of the molecular architecture on the distributions of rupture times over a broad interval of pulling forces and star configurations. It was found that the rupture time distribution of the individual star arms is strongly affected by the star configuration imposed by the pulling forces and the length of the arms. We also observed that for large pulling forces the rupture time distributions resemble the dominant features observed for linear polymer chains. The model introduced here provides the basic ingredients to describe the effects of tensile forces on stress-induced degradation of branched macromolecules and polymer networks.
Bellili, A; Linguerri, R; Hochlaf, M; Puzzarini, C
2015-11-14
In an effort to provide an accurate structural and spectroscopic characterization of acetyl cyanide, its two enolic isomers and the corresponding cationic species, state-of-the-art computational methods, and approaches have been employed. The coupled-cluster theory including single and double excitations together with a perturbative treatment of triples has been used as starting point in composite schemes accounting for extrapolation to the complete basis-set limit as well as core-valence correlation effects to determine highly accurate molecular structures, fundamental vibrational frequencies, and rotational parameters. The available experimental data for acetyl cyanide allowed us to assess the reliability of our computations: structural, energetic, and spectroscopic properties have been obtained with an overall accuracy of about, or better than, 0.001 Å, 2 kcal/mol, 1-10 MHz, and 11 cm(-1) for bond distances, adiabatic ionization potentials, rotational constants, and fundamental vibrational frequencies, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and/or astronomical observations. PMID:26567669
Strong resetting of the mammalian clock by constant light followed by constant darkness
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
NASA Astrophysics Data System (ADS)
Kisiel, Z.; Desyatnyk, O.; Pszczółkowski, L.; Charnley, S. B.; Ehrenfreund, P.
2003-01-01
Rotational spectra of quinoline and of isoquinoline have been observed in the centimeter- and millimeter-wave regions. The spectra were assigned on the basis of bands formed by high- J transitions, which were measured up to J″⩽128 and ν⩽234 GHz. Complementary measurements were also made on low- J, centimeter-wave spectra observed in supersonic expansion and with fully resolved nuclear quadrupole hyperfine structure. Accurate rotational, centrifugal distortion and hyperfine splitting constants for the ground states of both molecules are reported. The electric dipole moments for the two molecules were also determined from Stark effect measurements and are μa=0.14355(19), μb=2.0146(17), μtot=2.0197(17) D for quinoline, and μa=2.3602(21), μb=0.9051(14), μtot=2.5278(20) D for isoquinoline. The experimental observables were found to be rather accurately predicted by MP2/6-31G** ab initio calculations, and corresponding molecular geometries are also reported.
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...
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...
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...
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...
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...
Henry's law constants of polyols
NASA Astrophysics Data System (ADS)
Compernolle, S.; Müller, J.-F.
2014-05-01
Henry's law constants (HLC) are derived for several polyols bearing between 2 and 6 hydroxyl groups, based on literature data for water activity, vapour pressure and/or solubility. Depending on the case, infinite dilution activity coefficients (IDACs), solid state pressures or activity coefficient ratios are obtained as intermediary results. For most compounds, these are the first values reported, while others compare favourably with literature data in most cases. Using these values and those from a previous work (Compernolle and Müller, 2014), an assessment is made on the partitioning of polyols, diacids and hydroxy acids to droplet and aqueous aerosol.
Markov constant and quantum instabilities
NASA Astrophysics Data System (ADS)
Pelantová, Edita; Starosta, Štěpán; Znojil, Miloslav
2016-04-01
For a qualitative analysis of spectra of certain two-dimensional rectangular-well quantum systems several rigorous methods of number theory are shown productive and useful. These methods (and, in particular, a generalization of the concept of Markov constant known in Diophantine approximation theory) are shown to provide a new mathematical insight in the phenomenologically relevant occurrence of anomalies in the spectra. Our results may inspire methodical innovations ranging from the description of the stability properties of metamaterials and of certain hiddenly unitary quantum evolution models up to the clarification of the mechanisms of occurrence of ghosts in quantum cosmology.
NASA Astrophysics Data System (ADS)
Faller, Alan J.
2001-05-01
It has been found that the generation of swirl by a continuous rotary oscillation of a right-circular cylinder partially filled with water can leave a vortex with a radially constant tangential velocity, V, i.e. [partial partial differential]V/[partial partial differential]r = 0, excepting a small central core and the sidewall boundary layer. This vortex maintains [partial partial differential]V/[partial partial differential]r = 0 during viscous decay by the turbulent bottom boundary layer, a fact that suggests that [partial partial differential]V/[partial partial differential]r = 0 is a stable condition for a decaying vortex.
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.
NASA Astrophysics Data System (ADS)
Sunaga, A.; Abe, M.; Hada, M.; Das, B. P.
2016-04-01
The scalar-pseudoscalar (S-PS) interaction, which has been predicted between the electrons and nuclei of atoms and molecules, violates parity- (P -) and time- (T -) reversal symmetries. The electric dipole moment of the electron (eEDM) and the S-PS interaction together give rise to an energy shift in paramagnetic polar molecules, which in principle can be measured. The determination of the S-PS interaction constant, ks ,A, for an atom A could be a sensitive probe of physics beyond the standard model. The upper limit for it can be obtained by combining the results of the measured energy shift mentioned above and the accurate quantum chemical calculation of the S-PS coefficient, Ws ,A. In this work, we use a method based on the four-component relativistic coupled-cluster singles and doubles (RCCSD) method to calculate this coefficient for YbF, one of the most promising candidates for the search of the eEDM and the S-PS interaction. We obtain Ws ,Yb=-40.5 (kHz ) with an estimated error of less than 10% for YbF. We also calculate the effective electric field (Eeff), the molecular dipole moment, and the parallel component of the hyperfine coupling constant (A∥) by the RCCSD method. The discrepancies in the results of these calculations with those of accurate measurements are used to estimate the accuracy of our calculation of Ws ,Yb.
Photoelastic constants of germanate glasses containing lead and bismuth oxides
Rabukhin, A.I.
1995-07-01
Regression equations which accurately approximate the concentration curves of the photoelastic constants of lead bismuth germanate glasses were obtained and the isolines of the photoelastic constants were plotted and graphically illustrate the change in the properties of the glasses in almost the entire glass-formation region of the PbO-Bi{sub 2}O{sub 3}-GeO{sub 2} system. The partial values of the photoelastic constants of the oxides, components of these glasses, were determined and are in agreement with the values established for glasses of other systems. The data obtained can be used in planning the compositions of effective optical media for fabrication of light and acoustic lines for acousto-optic instruments and glasses with a zero optical stress coefficient.
Correction for instrument time constant in determination of reaction kinetics.
Chilton, Marie; Clark, Jared; Thomas, Nathan; Nicholson, Allen; Hansen, Lee D.; Hansen, Clifford W.; Hansen, Jaron
2010-02-01
Rates of reactions can be expressed as dn/dt = kcf(n) where n is moles of reaction, k is a rate constant, c is a proportionality constant, and f(n) is a function of the properties of the sample. When the instrument time constant, ?, and k are sufficiently comparable that measured rates are significantly affected by instrument response, correction for instrument response must be done to obtain accurate reaction kinetics. Correction for instrument response has previously been done by truncating early data or by use of the Tian equation. Both methods can lead to significant errors. We describe a method for simultaneous determination of ?, k, and c by fitting equations describing the combined instrument response and rate law to rates observed as a function of time. The method was tested with data on the heat rate from acid-catalyzed hydrolysis of sucrose.
Atomic force microscopy spring constant determination in viscous liquids
Pirzer, Tobias; Hugel, Thorsten
2009-03-15
The spring constant of cantilever in atomic force microscopy (AFM) is often calibrated from thermal noise spectra. Essential for accurate implementation of this 'thermal noise method' is an appropriate fitting function and procedure. Here, we survey the commonly used fitting functions and examine their applicability in a range of environments. We find that viscous liquid environments are extremely problematic due to the frequency dependent nature of the damping coefficient. The deviations from the true spring constant were sometimes more than 100% when utilizing the fit routines built into the three investigated commercial AFM instruments; similar problems can arise with homebuilt AFMs. We discuss the reasons for this problem, especially the limits of the fitting process. Finally, we present a thermal noise based procedure and an improved fit function to determine the spring constant with AFMs in fluids of various viscosities.
Atomic force microscopy spring constant determination in viscous liquids.
Pirzer, Tobias; Hugel, Thorsten
2009-03-01
The spring constant of cantilever in atomic force microscopy (AFM) is often calibrated from thermal noise spectra. Essential for accurate implementation of this "thermal noise method" is an appropriate fitting function and procedure. Here, we survey the commonly used fitting functions and examine their applicability in a range of environments. We find that viscous liquid environments are extremely problematic due to the frequency dependent nature of the damping coefficient. The deviations from the true spring constant were sometimes more than 100% when utilizing the fit routines built into the three investigated commercial AFM instruments; similar problems can arise with homebuilt AFMs. We discuss the reasons for this problem, especially the limits of the fitting process. Finally, we present a thermal noise based procedure and an improved fit function to determine the spring constant with AFMs in fluids of various viscosities. PMID:19334955
Rate constant for the reaction of atomic chlorine with methane
NASA Technical Reports Server (NTRS)
Lin, C. L.; Leu, M. T.; Demore, W. B.
1978-01-01
The rate constant and temperature dependence of the Cl + CH4 reaction have been investigated by the techniques of competitive chlorination of CH4/C2H6 mixtures and by discharge-flow/mass spectroscopy. The objectives were to determine an accurate value for the rate constant for use in stratospheric modeling, and to clarify discrepancies in results previously obtained by different techniques. The results deduced from the competitive chlorination study are in good agreement with the absolute values measured by the mass spectrometric method, and at temperatures above 300 K are in good agreement with measurements by other techniques based on resonance fluorescence detection of atomic chlorine. However, in the 220-300 K region, the competitive experiments indicate lower rate constants than those obtained by resonance fluorescence methods, and do not reproduce the curved Arrhenius plots seen in some of those studies.
Stability constant estimator user`s guide
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.
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.
Note: Spring constant calibration of nanosurface-engineered atomic force microscopy cantilevers
Ergincan, O. Palasantzas, G.; Kooi, B. J.
2014-02-15
The determination of the dynamic spring constant (k{sub d}) of atomic force microscopy cantilevers is of crucial importance for converting cantilever deflection to accurate force data. Indeed, the non-destructive, fast, and accurate measurement method of the cantilever dynamic spring constant by Sader et al. [Rev. Sci. Instrum. 83, 103705 (2012)] is confirmed here for plane geometry but surface modified cantilevers. It is found that the measured spring constants (k{sub eff}, the dynamic one k{sub d}), and the calculated (k{sub d,1}) are in good agreement within less than 10% error.
Virtual Screening Using Molecular Simulations
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
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.
Henry's law constants of polyols
NASA Astrophysics Data System (ADS)
Compernolle, S.; Müller, J.-F.
2014-12-01
Henry's law constants (HLC) are derived for several polyols bearing between 2 and 6 hydroxyl groups, based on literature data for water activity, vapour pressure and/or solubility. While deriving HLC and depending on the case, also infinite dilution activity coefficients (IDACs), solid state vapour pressures or activity coefficient ratios are obtained as intermediate results. An error analysis on the intermediate quantities and the obtained HLC is included. For most compounds, these are the first values reported, while others compare favourably with literature data in most cases. Using these values and those from a previous work (Compernolle and Müller, 2014), an assessment is made on the partitioning of polyols, diacids and hydroxy acids to droplet and aqueous aerosol.
Philicities, Fugalities, and Equilibrium Constants.
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
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.
Determination of the Hubble constant.
Freedman, W L; Feng, L L
1999-09-28
Establishing accurate extragalactic distances has provided an immense challenge to astronomers since the 1920s. The situation has improved dramatically as better detectors have become available, and as several new, promising techniques have been developed. For the first time in the history of this difficult field, relative distances to galaxies are being compared on a case-by-case basis, and their quantitative agreement is being established. New instrumentation, the development of new techniques for measuring distances, and recent measurements with the Hubble Space telescope all have resulted in new distances to galaxies with precision at the +/-5-20% level. The current statistical uncertainty in some methods for measuring H(0) is now only a few percent; with systematic errors, the total uncertainty is approaching +/-10%. Hence, the historical factor-of-two uncertainty in the value of the H(0) is now behind us. PMID:10500124
Determination of the Hubble constant
Freedman, Wendy L.; Feng, Long Long
1999-01-01
Establishing accurate extragalactic distances has provided an immense challenge to astronomers since the 1920s. The situation has improved dramatically as better detectors have become available, and as several new, promising techniques have been developed. For the first time in the history of this difficult field, relative distances to galaxies are being compared on a case-by-case basis, and their quantitative agreement is being established. New instrumentation, the development of new techniques for measuring distances, and recent measurements with the Hubble Space telescope all have resulted in new distances to galaxies with precision at the ±5–20% level. The current statistical uncertainty in some methods for measuring H0 is now only a few percent; with systematic errors, the total uncertainty is approaching ±10%. Hence, the historical factor-of-two uncertainty in the value of the H0 is now behind us. PMID:10500124
Richter, Martin; Mai, Sebastian; González, Leticia
2014-01-01
Ab initio molecular dynamics simulations have been performed in order to investigate the relaxation dynamics of uracil after UV excitation in gas phase. Intersystem crossing (ISC) has been included for the first time into time-dependent simulations of uracil, allowing the system to relax in the singlet as well as in the triplet states. The results show a qualitatively different picture than similar simulations that include singlet states only. The inclusion of ISC effectively quenches the relaxation to the singlet ground state and instead privileges transitions from the low-lying nπ* state (S1) to a ππ* triplet state (T2) followed by rapid internal conversion to the lowest triplet state. PMID:25301389
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
Spin-rotation and NMR shielding constants in HCl
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.
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.
Ionization constants for 214 dye molecules were calculated from molecular structures using the chemical reactivity models developed in SPARC (SPARC Performs Automated Reasoning in Chemistry). hese models used fundamental chemical structure theory to predict chemical reactivities ...
Quantitative structure-activity relationships (QSARs) are developed relating initial and final pseudo-first-order disappearance rate constants of 45 halogenated aromatic hydrocarbons in anoxic sediments to four readily available molecular descriptors: the carbon-halogen bond stre...
Violation of fundamental symmetries and variation of fundamental constants in atomic phenomena
Flambaum, V. V.
2007-06-13
We present a review of recent works on variation of fundamental constants and violation of parity in atoms and nuclei.Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental 'constants' in expanding Universe. The spatial variation can explain fine tuning of the fundamental constants which allows humans (and any life) to appear. We appeared in the area of the Universe where the values of the fundamental constants are consistent with our existence.We describe recent works devoted to the variation of the fine structure constant {alpha}, strong interaction and fundamental masses (Higgs vacuum). There are some hints for the variation in quasar absorption spectra, Big Bang nucleosynthesis, and Oklo natural nuclear reactor data.A very promising method to search for the variation consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transitions between very close atomic and molecular energy levels. A new idea is to build a 'nuclear' clock based on UV transition in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude. Measurements of violation of fundamental symmetries, parity (P) and time reversal (T), in atoms allows one to test unification theories in atomic experiments. We have developed an accurate method of many-body calculations - all-orders summation of dominating diagrams in residual e-e interaction. To calculate QED radiative corrections to energy levels and electromagnetic amplitudes in many-electron atoms and molecules we derived the ''radiative potential'' and the low-energy theorem. This method is simple and can be easily incorporated into any many-body theory approach. Using the radiative correction and many-body calculations we obtained the PNC amplitude EPNC = -0.898(1 {+-} 0.5%) x 10-11ieaB(-QW/N). From the measurements of the PNC amplitude we extracted the Cs weak charge QW = -72.66(29)exp(36)theor. The
Determination of the Avogadro constant by counting the atoms in a 28Si crystal.
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. PMID:21405263
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
Spectroscopic Constants of the Known Electronic States of Lead Monofluoride
McRaven, C.P.; Sivakumar, P.; Shafer-Ray, N.E.; Hall, G.E.; Sears, T.J.
2010-08-01
Based on measurements made by mass-resolved 1 + 1{prime} + 1{double_prime} resonance-enhanced multiphoton ionization spectroscopy, we have determined new molecular constants describing the rotational and fine structure levels of the B, D, E, and F states of the most abundant isotopic variant {sup 208}Pb{sup 19}F, and we summarize the spectroscopic constants for all the know electronic states of the radical. Many spectroscopic constants for the isotopologues {sup 206}Pb{sup 19}F and {sup 207}Pb{sup 19}F have also been determined. The symmetry of the D-state is found to be {sup 2}{pi}{sub 1/2}, and the F-state is found to be an {Omega} = 3/2 state.
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.
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.
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.
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
High voltage compliance constant current ballast
NASA Technical Reports Server (NTRS)
Rosenthal, L. A.
1976-01-01
A ballast circuit employing a constant current diode and a vacuum tube that can provide a constant current over a voltage range of 1000 volts. The simple circuit can prove useful in studying voltage breakdown characteristics.
ESR melting under constant voltage conditions
Schlienger, M.E.
1997-02-01
Typical industrial ESR melting practice includes operation at a constant current. This constant current operation is achieved through the use of a power supply whose output provides this constant current characteristic. Analysis of this melting mode indicates that the ESR process under conditions of constant current is inherently unstable. Analysis also indicates that ESR melting under the condition of a constant applied voltage yields a process which is inherently stable. This paper reviews the process stability arguments for both constant current and constant voltage operation. Explanations are given as to why there is a difference between the two modes of operation. Finally, constant voltage process considerations such as melt rate control, response to electrode anomalies and impact on solidification will be discussed.
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.
Accurate theoretical chemistry with coupled pair models.
Neese, Frank; Hansen, Andreas; Wennmohs, Frank; Grimme, Stefan
2009-05-19
Quantum chemistry has found its way into the everyday work of many experimental chemists. Calculations can predict the outcome of chemical reactions, afford insight into reaction mechanisms, and be used to interpret structure and bonding in molecules. Thus, contemporary theory offers tremendous opportunities in experimental chemical research. However, even with present-day computers and algorithms, we cannot solve the many particle Schrodinger equation exactly; inevitably some error is introduced in approximating the solutions of this equation. Thus, the accuracy of quantum chemical calculations is of critical importance. The affordable accuracy depends on molecular size and particularly on the total number of atoms: for orientation, ethanol has 9 atoms, aspirin 21 atoms, morphine 40 atoms, sildenafil 63 atoms, paclitaxel 113 atoms, insulin nearly 800 atoms, and quaternary hemoglobin almost 12,000 atoms. Currently, molecules with up to approximately 10 atoms can be very accurately studied by coupled cluster (CC) theory, approximately 100 atoms with second-order Møller-Plesset perturbation theory (MP2), approximately 1000 atoms with density functional theory (DFT), and beyond that number with semiempirical quantum chemistry and force-field methods. The overwhelming majority of present-day calculations in the 100-atom range use DFT. Although these methods have been very successful in quantum chemistry, they do not offer a well-defined hierarchy of calculations that allows one to systematically converge to the correct answer. Recently a number of rather spectacular failures of DFT methods have been found-even for seemingly simple systems such as hydrocarbons, fueling renewed interest in wave function-based methods that incorporate the relevant physics of electron correlation in a more systematic way. Thus, it would be highly desirable to fill the gap between 10 and 100 atoms with highly correlated ab initio methods. We have found that one of the earliest (and now
Fundamental Constants and Tests with Simple Atoms
NASA Astrophysics Data System (ADS)
Tan, Joseph
2015-05-01
Precise measurements with simple atoms provide stringent tests of physical laws, improving the accuracy of fundamental constants--a set of which will be selected to fully define the proposed New International System of Units. This talk focuses on the atomic constants (namely, the Rydberg constant, the fine-structure constant, and the proton charge radius), discussing the impact of the proton radius obtained from the Lamb-shift measurements in muonic hydrogen. Significant discrepancies persist despite years of careful examination: the slightly smaller proton radius obtained from muonic hydrogen requires the Rydberg constant and the fine-structure constant to have values that disagree significantly with the CODATA recommendations. After giving a general overview, I will discuss our effort to produce one-electron ions in Rydberg states, to enable a different test of theory and measurement of the Rydberg constant.
Mud handling improved with a constant-volume riser
Baker, R.J. )
1990-09-24
Marine risers currently deployed by floating drilling units incorporate a telescopic joint to accommodate vessel movement, primarily heave. This vertical telescopic movement changes the internal volume of the riser and causes fluctuations in the return-mud flow rate. Flow fluctuations make accurate measurement of the return mud difficult. The significance is that these measurements are vital for the early detection of well bore influx or downhole mud losses. Erratic mud flow also adversely affects the efficiency of the solids-removal equipment and potentially increases the risk of discharging whole mud to the environment. To overcome these adverse effects, a design for a telescopic joint is proposed (constant volume riser or CVR) in which the internal riser volume remains constant, irrespective of movement, thus permitting a uniform flow rate of mud returns.
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.
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.
Remote balance weighs accurately amid high radiation
NASA Technical Reports Server (NTRS)
Eggenberger, D. N.; Shuck, A. B.
1969-01-01
Commercial beam-type balance, modified and outfitted with electronic controls and digital readout, can be remotely controlled for use in high radiation environments. This allows accurate weighing of breeder-reactor fuel pieces when they are radioactively hot.
Understanding the Code: keeping accurate records.
Griffith, Richard
2015-10-01
In his continuing series looking at the legal and professional implications of the Nursing and Midwifery Council's revised Code of Conduct, Richard Griffith discusses the elements of accurate record keeping under Standard 10 of the Code. This article considers the importance of accurate record keeping for the safety of patients and protection of district nurses. The legal implications of records are explained along with how district nurses should write records to ensure these legal requirements are met. PMID:26418404
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).
Leveraging Two Kinect Sensors for Accurate Full-Body Motion Capture
Gao, Zhiquan; Yu, Yao; Zhou, Yu; Du, Sidan
2015-01-01
Accurate motion capture plays an important role in sports analysis, the medical field and virtual reality. Current methods for motion capture often suffer from occlusions, which limits the accuracy of their pose estimation. In this paper, we propose a complete system to measure the pose parameters of the human body accurately. Different from previous monocular depth camera systems, we leverage two Kinect sensors to acquire more information about human movements, which ensures that we can still get an accurate estimation even when significant occlusion occurs. Because human motion is temporally constant, we adopt a learning analysis to mine the temporal information across the posture variations. Using this information, we estimate human pose parameters accurately, regardless of rapid movement. Our experimental results show that our system can perform an accurate pose estimation of the human body with the constraint of information from the temporal domain. PMID:26402681
Leveraging Two Kinect Sensors for Accurate Full-Body Motion Capture.
Gao, Zhiquan; Yu, Yao; Zhou, Yu; Du, Sidan
2015-01-01
Accurate motion capture plays an important role in sports analysis, the medical field and virtual reality. Current methods for motion capture often suffer from occlusions, which limits the accuracy of their pose estimation. In this paper, we propose a complete system to measure the pose parameters of the human body accurately. Different from previous monocular depth camera systems, we leverage two Kinect sensors to acquire more information about human movements, which ensures that we can still get an accurate estimation even when significant occlusion occurs. Because human motion is temporally constant, we adopt a learning analysis to mine the temporal information across the posture variations. Using this information, we estimate human pose parameters accurately, regardless of rapid movement. Our experimental results show that our system can perform an accurate pose estimation of the human body with the constraint of information from the temporal domain. PMID:26402681
[Molecular genetics and determination of time since death - short communication].
Šaňková, Markéta; Račanská, Michaela
2016-01-01
Estimation of time since death, i.e. the post-mortem interval (PMI), is one of the most problematic issues in forensic practice. Accurate determination of the PMI still remains very complicated task even for an experienced forensic pathologist.Physical changes including algor, livor and rigor mortis can be observed already during the first hours after death of an individual. Unfortunately, the estimation of PMI on the basis of these changes is often burdened with a certain degree of inaccuracy, which is caused by the temperature of surrounding environment, constitution of the body, cause of the death, location of the body, drug abuse etc.Accurate PMI estimation requires assessment of such parameters, which change constantly from the moment of death, but independently on ambient factors. According to current research in the field of molecular biology, it appears that a post-mortem degradation of nucleic acids (both DNA and RNA) will correspond to this definition. PMID:27526264
Emergent cosmological constant from colliding electromagnetic waves
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.
Constant voltage electro-slag remelting control
Schlienger, Max E.
1996-01-01
A system for controlling electrode gap in an electro-slag remelt furnace has a constant regulated voltage and an eletrode which is fed into the slag pool at a constant rate. The impedance of the circuit through the slag pool is directly proportional to the gap distance. Because of the constant voltage, the system current changes are inversely proportional to changes in gap. This negative feedback causes the gap to remain stable.
Constant voltage electro-slag remelting control
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.
Cosmological Constant and Axions in String Theory
Svrcek, Peter; /Stanford U., Phys. Dept. /SLAC
2006-08-18
String theory axions appear to be promising candidates for explaining cosmological constant via quintessence. In this paper, we study conditions on the string compactifications under which axion quintessence can happen. For sufficiently large number of axions, cosmological constant can be accounted for as the potential energy of axions that have not yet relaxed to their minima. In compactifications that incorporate unified models of particle physics, the height of the axion potential can naturally fall close to the observed value of cosmological constant.
Dielectric constant microscopy for biological materials
NASA Astrophysics Data System (ADS)
Valavade, A. V.; Kothari, D. C.; Löbbe, C.
2013-02-01
This paper describes the work on the development of Dielectric Constant Microscopy for biological materials using double pass amplitude modulation method. The dielectric constant information can be obtained at nanometer scales using this technique. Electrostatic force microscopy images of biological materials are presented. The images obtained from the EFM technique mode clearly show inversion contrast and gives the spatial variation of tip-sample capacitance. The EFM images are further processed to obtain dielectric constant information at nanometer scales.
Exploring accurate Poisson–Boltzmann methods for biomolecular simulations
Wang, Changhao; Wang, Jun; Cai, Qin; Li, Zhilin; Zhao, Hong-Kai; Luo, Ray
2013-01-01
Accurate and efficient treatment of electrostatics is a crucial step in computational analyses of biomolecular structures and dynamics. In this study, we have explored a second-order finite-difference numerical method to solve the widely used Poisson–Boltzmann equation for electrostatic analyses of realistic bio-molecules. The so-called immersed interface method was first validated and found to be consistent with the classical weighted harmonic averaging method for a diversified set of test biomolecules. The numerical accuracy and convergence behaviors of the new method were next analyzed in its computation of numerical reaction field grid potentials, energies, and atomic solvation forces. Overall similar convergence behaviors were observed as those by the classical method. Interestingly, the new method was found to deliver more accurate and better-converged grid potentials than the classical method on or nearby the molecular surface, though the numerical advantage of the new method is reduced when grid potentials are extrapolated to the molecular surface. Our exploratory study indicates the need for further improving interpolation/extrapolation schemes in addition to the developments of higher-order numerical methods that have attracted most attention in the field. PMID:24443709
Machine learning of parameters for accurate semiempirical quantum chemical calculations
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
Machine learning of parameters for accurate semiempirical quantum chemical calculations
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 C_{7}H_{10}O_{2}, 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.
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)
Modification of the characteristic gravitational constants
NASA Astrophysics Data System (ADS)
Vujičić, V. A.
2006-08-01
In the educational and scientific literature the numerical values of gravitational constants are seen as only approximately correct. The numerical values are different in work by various researchers, as also are the formulae and definitions of constants employed. In this paper, on the basis of Newton’s laws and Kepler’s laws we prove that it is necessary to modify the characteristic gravitational constants and their definitions. The formula for the geocentric gravitational constant of the satellites Kosmos N and the Moon are calculated.
A natural cosmological constant from chameleons
NASA Astrophysics Data System (ADS)
Nastase, Horatiu; Weltman, Amanda
2015-07-01
We present a simple model where the effective cosmological constant appears from chameleon scalar fields. For a Kachru-Kallosh-Linde-Trivedi (KKLT)-inspired form of the potential and a particular chameleon coupling to the local density, patches of approximately constant scalar field potential cluster around regions of matter with density above a certain value, generating the effect of a cosmological constant on large scales. This construction addresses both the cosmological constant problem (why Λ is so small, yet nonzero) and the coincidence problem (why Λ is comparable to the matter density now).
On the Utility of the Molecular Oxygen Dayglow Emissions as Proxies for Middle Atmospheric Ozone
NASA Technical Reports Server (NTRS)
Mlynczak, Martin G.; Olander, Daphne S.
1995-01-01
Molecular oxygen dayglow emissions arise in part from processes related to the Hartley band photolysis of ozone. It is therefore possible to derive daytime ozone concentrations from measurements of the volume emission rate of either dayglow. The accuracy to which the ozone concentration can be inferred depends on the accuracy to which numerous kinetic and spectroscopic rate constants are known, including rates which describe the excitation of molecular oxygen by processes that are not related to the ozone concentration. We find that several key rate constants must be known to better than 7 percent accuracy in order to achieve an inferred ozone concentration accurate to 15 percent from measurements of either dayglow. Currently, accuracies for various parameters typically range from 5 to 100 percent.
Heavy-meson decay constants from QCD sum rules
Lucha, Wolfgang; Melikhov, Dmitri; Simula, Silvano
2010-12-22
We sketch a recent sum-rule extraction of the decay constants of the heavy pseudoscalar mesons D, D{sub s}, B, and B{sub s} from the two-point correlator of heavy-light pseudoscalar currents. Our main emphasis lies on the control over all the uncertainties in the decay constants, related both to the input QCD parameters and to the limited accuracy of the method of sum rules. Gaining this control has become possible by application of our new procedure of extracting hadron observables based on a dual threshold depending on the Borel parameter. For the charmed-meson decay constants, we find fD = (206.2{+-}7.3{sub (OPE)}{+-}5.1{sub (syst)}) MeV, fD{sub s} = (245.3{+-}15.7{sub (OPE)}{+-}4.5{sub (syst)}) MeV. For the beauty mesons, the decay constants turn out to be extremely sensitive to the precise value of the {ovr MS} mass of the b-quark, {bar m}{sub b}({bar m}{sub b}). By requiring our sum-rule estimate to match the average of the lattice determinations of f{sub B}, we extract the rather accurate value {bar m}{sub b}({bar m}{sub b}) = (4.245{+-}0.025) GeV. Feeding this parameter value into our sum-rule formalism leads to the beauty-meson decay constants fB = (193.4{+-}12.3{sub (OPE)}{+-}4.3{sub (syst)}) MeV, fB{sub s} = (232.5{+-}18.6{sub (OPE)}{+-}2.4{sub (syst)}) MeV.
Accurate measure by weight of liquids in industry
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.
Accurate measure by weight of liquids in industry. Final report
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.
A highly accurate interatomic potential for argon
NASA Astrophysics Data System (ADS)
Aziz, Ronald A.
1993-09-01
A modified potential based on the individually damped model of Douketis, Scoles, Marchetti, Zen, and Thakkar [J. Chem. Phys. 76, 3057 (1982)] is presented which fits, within experimental error, the accurate ultraviolet (UV) vibration-rotation spectrum of argon determined by UV laser absorption spectroscopy by Herman, LaRocque, and Stoicheff [J. Chem. Phys. 89, 4535 (1988)]. Other literature potentials fail to do so. The potential also is shown to predict a large number of other properties and is probably the most accurate characterization of the argon interaction constructed to date.
Measuring the Hubble Constant with the Hubble Space Telescope
NASA Astrophysics Data System (ADS)
Freedman, Wendy
1996-05-01
In a uniform and isotropic Universe, the relative expansion velocity v is proportional to the relative distance r such that v = H × r. Thus a determination of the present-day value of the Hubble constant H0 determines both the expansion timescale and the size scale of the Universe. The Hubble constant also provides constraints on the density of baryons produced in the Big Bang, the amount of dark matter, and how structure formed in the early Universe. The most accurate means of measuring the distances to nearby galaxies has proved to be the application of a relationship between the period and the luminosity for a class of supergiant variable stars known as classical Cepheids. Unfortunately the Cepheid variables are not intrinsically luminous enough to be measured out to distances where the velocities of recession of galaxies are a few thousand km/sec and thus dominate the peculiar velocities due to the gravitational interactions between galaxies (typically a few hundred km/sec). The Hubble Space Telescope Key Project on the Extragalactic Distance has been designed to measure a value of the Hubble constant accurate to ±10% [random + systematic]. The program has been designed to use Cepheid variables to determine the distances to a representative sample of about 20 galaxies both inside and out of small groups and in major clusters. These galaxies are being used to tie into methods with high internal precision ( ~ ±5%) that operate at greater distances, thereby allowing an accurate absolute calibration and an intercomparison of several independent techniques. Our preliminary result is that the value of the Hubble constant is 80 ± 17 km/sec/Mpc footnote Freedman, W. L. et al., Nature, 371, 757, (1994) New results will be presented based on observations of several new galaxies, including NGC 1365 in the nearby Fornax cluster. My collaborators on the HST Key Project team are R. Kennicutt, J. Mould, F. Bresolin, L. Ferrarese, H. Ford, J. Graham, M. Han, P. Harding, J
Vacuum energy and the cosmological constant
NASA Astrophysics Data System (ADS)
Bass, Steven D.
2015-06-01
The accelerating expansion of the Universe points to a small positive value for the cosmological constant or vacuum energy density. We discuss recent ideas that the cosmological constant plus Large Hadron Collider (LHC) results might hint at critical phenomena near the Planck scale.
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.
Performance of a constant torque pedal device.
Sherwin, K.
1979-01-01
A constant-torque oscillatory pedal-crank device using vertical movement of the feet is described and its performance compared to a conventional rotational cycle. Using a generator to measure the power output the constant-torque device produced 33% less power and thus has no practical value as an alternative to the conventional pedal-crank system. Images Figure 3 PMID:526783
Regularizing cosmological singularities by varying physical constants
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.
The method of constant stimuli is inefficient
NASA Technical Reports Server (NTRS)
Watson, Andrew B.; Fitzhugh, Andrew
1990-01-01
Simpson (1988) has argued that the method of constant stimuli is as efficient as adaptive methods of threshold estimation and has supported this claim with simulations. It is shown that Simpson's simulations are not a reasonable model of the experimental process and that more plausible simulations confirm that adaptive methods are much more efficient that the method of constant stimuli.
Air kerma rate constants for radionuclides.
Wasserman, H; Groenewald, W
1988-01-01
Conversion to SI units requires that the exposure rate constant which was usually quoted in R.h-1.mCi-1.cm2 be replaced by the air kerma rate constant with units m2.Gy.Bq-1.s-1. The conversion factor is derived and air kerma rate constants for 30 radionuclides used in nuclear medicine and brachytherapy are listed. A table for calculation of air kerma rates for other radionuclides is also given. To calculate absorbed dose to tissue, the air kerma rate has to be multiplied by approximately 1.1. A dose equivalent rate constant is thus listed which allows direct calculation of dose equivalent rate to soft tissue without resorting to exposure rate constants tabulated in the special units R.m2.mCi-1.h-1 which should no longer be used. PMID:3208786
Elastic constants of layers in isotropic laminates.
Heyliger, Paul R; Ledbetter, Hassel; Kim, Sudook; Reimanis, Ivar
2003-11-01
The individual laminae elastic constants in multilayer laminates composed of dissimilar isotropic layers were determined using ultrasonic-resonance spectroscopy and the linear theory of elasticity. Ultrasonic resonance allows one to measure the free-vibration response spectrum of a traction-free solid under periodic vibration. These frequencies depend on pointwise density, laminate dimensions, layer thickness, and layer elastic constants. Given a material with known mass but unknown constitution, this method allows one to extract the elastic constants and density of the constituent layers. This is accomplished by measuring the frequencies and then minimizing the differences between these and those calculated using the theory of elasticity for layered media to select the constants that best replicate the frequency-response spectrum. This approach is applied to a three-layer, unsymmetric laminate of WpCu, and very good agreement is found with the elastic constants of the two constituent materials. PMID:14649998
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. PMID:20820304
Parameter identification of material constants in a composite shell structure
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.
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.
Accelerated molecular dynamics methods
Perez, Danny
2011-01-04
The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.
Improved in situ spring constant calibration for colloidal probe atomic force microscopy
McBride, Sean P.; Law, Bruce M.
2010-11-15
In colloidal probe atomic force microscopy (AFM) surface forces cannot be measured without an accurate determination of the cantilever spring constant. The effective spring constant k depends upon the cantilever geometry and therefore should be measured in situ; additionally, k may be coupled to other measurement parameters. For example, colloidal probe AFM is frequently used to measure the slip length b at solid/liquid boundaries by comparing the measured hydrodynamic force with Vinogradova slip theory (V-theory). However, in this measurement k and b are coupled, hence, b cannot be accurately determined without knowing k to high precision. In this paper, a new in situ spring constant calibration method based upon the residuals, namely, the difference between experimental force-distance data and V-theory is presented and contrasted with two other popular spring constant determination methods. In this residuals calibration method, V-theory is fitted to the experimental force-distance data for a range of systematically varied spring constants where the only adjustable parameter in V-theory is the slip length b. The optimal spring constant k is that value where the residuals are symmetrically displaced about zero for all colloidal probe separations. This residual spring constant calibration method is demonstrated by studying three different liquids (n-decanol, n-hexadecane, and n-octane) and two different silane coated colloidal probe-silicon wafer systems (n-hexadecyltrichlorosilane and n-dodecyltrichlorosilane).
ERIC Educational Resources Information Center
Strauss, Michael J.; Levine, Shellie H.
1985-01-01
Describes an extremely simple technique (using only Dreiding or Framework molecular models, a flashlight, small sheets of glass, and a piece of cardboard) which produces extremely accurate line drawings of stereoscopic images. Advantages of using the system are noted. (JN)
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…
Direct expressions for magnetic anisotropy constants
NASA Astrophysics Data System (ADS)
Miura, Daisuke; Sasaki, Ryo; Sakuma, Akimasa
2015-11-01
Direct expressions for the magnetic anisotropy constants are given at a finite temperature from a microscopic viewpoint. The present derivation assumes that the Hamiltonian is a linear function with respect to the magnetization direction. We discuss in detail the first-order anisotropy constant K1 and show that our present results reproduce previous results. We applied our method to Nd2Fe14B compounds and confirmed that the present method can reproduce the temperature dependence of the magnetocrystalline anisotoropy constants K1, K2, and K3 well.
Latest rocket measurements of the solar constant
NASA Technical Reports Server (NTRS)
Duncan, C. H.; Willson, R. C.; Kendall, J. M.; Harrison, R. G.; Hickey, J. R.
1982-01-01
Three rocket flights which carried a payload of absolute radiometers to measure the solar constant with an accuracy of plus or minus 0.5 per cent have been accomplished. Several of the rocket radiometers were duplicates of those aboard the Solar Maximum Mission and Nimbus spacecrafts. The values for the solar constant obtained by the rocket sensors for the three flight dates indicate an increase between the first and latter two flights approximately equivalent to the uncertainty of the measurements. The values for the solar constant for the three flights are 1367, 1372 and 1374 W/sq m.
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…
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
Marshak waves: Constant flux vs constant T-a (slight) paradigm shift
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.
The effect of receptor clustering on diffusion-limited forward rate constants.
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
Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi
2012-06-01
One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected byfeedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On day 1, participants performed a golf putting task under one of two conditions: one group received feedback on the most accurate trials, whereas another group received feedback on the least accurate trials. On day 2, participants completed an anxiety questionnaire and performed a retention test. Shin conductance level, as a measure of arousal, was determined. The results indicated that feedback about more accurate trials resulted in more effective learning as well as increased self-confidence. Also, activation was a predictor of performance. PMID:22808705
Kutateladze, Andrei G; Mukhina, Olga A
2015-05-15
We previously developed a reliable method for multiparametric scaling of Fermi contacts to achieve fast and accurate prediction of proton-proton spin-spin coupling constants (SSCC) in (1)H NMR. We now report that utilization of NBO hybridization coefficients for carbon atoms in the involved C-H bonds allows for a significant simplification of this parametric scheme, requiring only four general types of SSCCs: geminal, vicinal, 1,3-, and long-range constants. The method is optimized for inexpensive B3LYP/6-31G(d) molecular geometries. A new DU8 basis set, based on a training set of 475 experimental spin-spin coupling constants, is developed for hydrogen and common non-hydrogen atoms (Li, B, C, N, O, F, Si, P, S, Cl, Se, Br, I) to calculate Fermi contacts. On a test set of 919 SSCCs from a diverse collection of natural products and complex synthetic molecules the method gave excellent accuracy of 0.29 Hz (rmsd) with the maximum unsigned error not exceeding 1 Hz. PMID:25885091
Accurate mask model for advanced nodes
NASA Astrophysics Data System (ADS)
Zine El Abidine, Nacer; Sundermann, Frank; Yesilada, Emek; Ndiaye, El Hadji Omar; Mishra, Kushlendra; Paninjath, Sankaranarayanan; Bork, Ingo; Buck, Peter; Toublan, Olivier; Schanen, Isabelle
2014-07-01
Standard OPC models consist of a physical optical model and an empirical resist model. The resist model compensates the optical model imprecision on top of modeling resist development. The optical model imprecision may result from mask topography effects and real mask information including mask ebeam writing and mask process contributions. For advanced technology nodes, significant progress has been made to model mask topography to improve optical model accuracy. However, mask information is difficult to decorrelate from standard OPC model. Our goal is to establish an accurate mask model through a dedicated calibration exercise. In this paper, we present a flow to calibrate an accurate mask enabling its implementation. The study covers the different effects that should be embedded in the mask model as well as the experiment required to model them.
Accurate guitar tuning by cochlear implant musicians.
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
Two highly accurate methods for pitch calibration
NASA Astrophysics Data System (ADS)
Kniel, K.; Härtig, F.; Osawa, S.; Sato, O.
2009-11-01
Among profiles, helix and tooth thickness pitch is one of the most important parameters of an involute gear measurement evaluation. In principle, coordinate measuring machines (CMM) and CNC-controlled gear measuring machines as a variant of a CMM are suited for these kinds of gear measurements. Now the Japan National Institute of Advanced Industrial Science and Technology (NMIJ/AIST) and the German national metrology institute the Physikalisch-Technische Bundesanstalt (PTB) have each developed independently highly accurate pitch calibration methods applicable to CMM or gear measuring machines. Both calibration methods are based on the so-called closure technique which allows the separation of the systematic errors of the measurement device and the errors of the gear. For the verification of both calibration methods, NMIJ/AIST and PTB performed measurements on a specially designed pitch artifact. The comparison of the results shows that both methods can be used for highly accurate calibrations of pitch standards.
Accurate modeling of parallel scientific computations
NASA Technical Reports Server (NTRS)
Nicol, David M.; Townsend, James C.
1988-01-01
Scientific codes are usually parallelized by partitioning a grid among processors. To achieve top performance it is necessary to partition the grid so as to balance workload and minimize communication/synchronization costs. This problem is particularly acute when the grid is irregular, changes over the course of the computation, and is not known until load time. Critical mapping and remapping decisions rest on the ability to accurately predict performance, given a description of a grid and its partition. This paper discusses one approach to this problem, and illustrates its use on a one-dimensional fluids code. The models constructed are shown to be accurate, and are used to find optimal remapping schedules.
Accurate Guitar Tuning by Cochlear Implant Musicians
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
Zhang, Chao; Hutter, Jürg; Sprik, Michiel
2016-07-21
In his classic 1939 paper, Kirkwood linked the macroscopic dielectric constant of polar liquids to the local orientational order as measured by the g-factor (later named after him) and suggested that the corresponding dielectric constant at short-range is effectively equal to the macroscopic value just after "a distance of molecular magnitude" [ Kirkwood, J. Chem. Phys., 1939, 7, 911 ]. Here, we show a simple approach to extract the short-ranged Kirkwood g-factor from molecular dynamics (MD) simulation by superposing the outcomes of constant electric field E and constant electric displacement D simulations [ Zhang and Sprik, Phys. Rev. B: Condens. Matter Mater. Phys., 2016, 93, 144201 ]. Rather than from the notoriously slow fluctuations of the dipole moment of the full MD cell, the dielectric constant can now be estimated from dipole fluctuations at short-range, accelerating the convergence. Exploiting this feature, we computed the bulk dielectric constant of liquid water modeled in the generalized gradient approximation (PBE) to density functional theory and found it to be at least 40% larger than the experimental value. PMID:27352038
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.
The Cosmological Constant in Quantum Cosmology
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.
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)
How the cosmological constant affects gravastar formation
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.
Constant-amplitude, frequency- independent phase shifter
NASA Technical Reports Server (NTRS)
Deboo, G. J.
1971-01-01
Electronic circuit using operational amplifiers provides output with constant phase shift amplitude, with respect to sinusoidal input, over wide range of frequencies. New circuit includes field effect transistor, Q, operational amplifiers, A1 and A2, and phase detector.
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)
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.
Accurate maser positions for MALT-45
NASA Astrophysics Data System (ADS)
Jordan, Christopher; Bains, Indra; Voronkov, Maxim; Lo, Nadia; Jones, Paul; Muller, Erik; Cunningham, Maria; Burton, Michael; Brooks, Kate; Green, James; Fuller, Gary; Barnes, Peter; Ellingsen, Simon; Urquhart, James; Morgan, Larry; Rowell, Gavin; Walsh, Andrew; Loenen, Edo; Baan, Willem; Hill, Tracey; Purcell, Cormac; Breen, Shari; Peretto, Nicolas; Jackson, James; Lowe, Vicki; Longmore, Steven
2013-10-01
MALT-45 is an untargeted survey, mapping the Galactic plane in CS (1-0), Class I methanol masers, SiO masers and thermal emission, and high frequency continuum emission. After obtaining images from the survey, a number of masers were detected, but without accurate positions. This project seeks to resolve each maser and its environment, with the ultimate goal of placing the Class I methanol maser into a timeline of high mass star formation.
Holographic dark energy with varying gravitational constant
NASA Astrophysics Data System (ADS)
Jamil, Mubasher; Saridakis, Emmanuel N.; Setare, M. R.
2009-08-01
We investigate the holographic dark energy scenario with a varying gravitational constant, in flat and non-flat background geometry. We extract the exact differential equations determining the evolution of the dark energy density-parameter, which include G-variation correction terms. Performing a low-redshift expansion of the dark energy equation of state, we provide the involved parameters as functions of the current density parameters, of the holographic dark energy constant and of the G-variation.
Simple constant-current-regulated power supply
NASA Technical Reports Server (NTRS)
Priebe, D. H. E.; Sturman, J. C.
1977-01-01
Supply incorporates soft-start circuit that slowly ramps current up to set point at turn-on. Supply consists of full-wave rectifier, regulating pass transistor, current feedback circuit, and quad single-supply operational-amplifier circuit providing control. Technique is applicable to any system requiring constant dc current, such as vacuum tube equipment, heaters, or battery charges; it has been used to supply constant current for instrument calibration.
A model for solar constant secular changes
NASA Technical Reports Server (NTRS)
Schatten, Kenneth H.
1988-01-01
In this paper, contrast models for solar active region and global photospheric features are used to reproduce the observed Active Cavity Radiometer and Earth Radiation Budget secular trends in reasonably good fashion. A prediction for the next decade of solar constant variations is made using the model. Secular trends in the solar constant obtained from the present model support the view that the Maunder Minimum may be related to the Little Ice Age of the 17th century.
Divergences and involution-dependent constants
Nagao, G.
1989-01-01
The authors show the cancellation of the dilation divergence in the 1-loop open bosonic string vacuum and N-tachyon scattering amplitude depends upon a set of involution-dependent constants. Such a set of constants exists at each loop level and thus provides a means with which to study the connection between the cancellation of divergences and anomalies for the gauge group SO(2/sup D/2/).
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.
Accurate Determination of Conformational Transitions in Oligomeric Membrane Proteins
Sanz-Hernández, Máximo; Vostrikov, Vitaly V.; Veglia, Gianluigi; De Simone, Alfonso
2016-01-01
The structural dynamics governing collective motions in oligomeric membrane proteins play key roles in vital biomolecular processes at cellular membranes. In this study, we present a structural refinement approach that combines solid-state NMR experiments and molecular simulations to accurately describe concerted conformational transitions identifying the overall structural, dynamical, and topological states of oligomeric membrane proteins. The accuracy of the structural ensembles generated with this method is shown to reach the statistical error limit, and is further demonstrated by correctly reproducing orthogonal NMR data. We demonstrate the accuracy of this approach by characterising the pentameric state of phospholamban, a key player in the regulation of calcium uptake in the sarcoplasmic reticulum, and by probing its dynamical activation upon phosphorylation. Our results underline the importance of using an ensemble approach to characterise the conformational transitions that are often responsible for the biological function of oligomeric membrane protein states. PMID:26975211
Direct computation of parameters for accurate polarizable force fields
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.
Accurate ab initio energy gradients in chemical compound space.
Anatole von Lilienfeld, O
2009-10-28
Analytical potential energy derivatives, based on the Hellmann-Feynman theorem, are presented for any pair of isoelectronic compounds. Since energies are not necessarily monotonic functions between compounds, these derivatives can fail to predict the right trends of the effect of alchemical mutation. However, quantitative estimates without additional self-consistency calculations can be made when the Hellmann-Feynman derivative is multiplied with a linearization coefficient that is obtained from a reference pair of compounds. These results suggest that accurate predictions can be made regarding any molecule's energetic properties as long as energies and gradients of three other molecules have been provided. The linearization coefficent can be interpreted as a quantitative measure of chemical similarity. Presented numerical evidence includes predictions of electronic eigenvalues of saturated and aromatic molecular hydrocarbons. PMID:19894922
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
Pause Point Spectra in DNA Constant-Force Unzipping
Weeks, J. D.; Lucks, J. B.; Kafri, Y.; Danilowicz, C.; Nelson, D. R.; Prentiss, M.
2005-01-01
Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the locations of pause points can be extracted in the form of a pause point spectrum. A simple theoretical model of DNA constant-force unzipping is presented, which generates theoretical pause point spectra through Monte Carlo simulation of the unzipping process. The locations of peaks in the experimental and theoretical pause point spectra are found to be nearly coincident below 6000 basepairs for unzipping the bacteriophage λ-genome. The model only requires the sequence, temperature, and a set of empirical basepair binding and stacking energy parameters, and the good agreement with experiment suggests that pause point locations are primarily determined by the DNA sequence. The model is also used to predict pause point spectra for the bacteriophage φX174 genome. The algorithm for extracting the pause point spectrum might also be useful for studying related systems which exhibit pausing behavior such as molecular motors. PMID:15695634
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.
FAST TRACK COMMUNICATION Accurate estimate of α variation and isotope shift parameters in Na and Mg+
NASA Astrophysics Data System (ADS)
Sahoo, B. K.
2010-12-01
We present accurate calculations of fine-structure constant variation coefficients and isotope shifts in Na and Mg+ using the relativistic coupled-cluster method. In our approach, we are able to discover the roles of various correlation effects explicitly to all orders in these calculations. Most of the results, especially for the excited states, are reported for the first time. It is possible to ascertain suitable anchor and probe lines for the studies of possible variation in the fine-structure constant by using the above results in the considered systems.
Quantitative structure-activity relationships (QSARs) are developed relating biotic and abiotic pseudo-first-order disappearance rate constants of halogenated hydrocarbons in anoxic sediments to a number of readily available molecular descriptors. ased upon knowledge of the under...
Phototransformation Rate Constants of PAHs Associated with Soot Particles
Kim, Daekyun; Young, Thomas M.; Anastasio, Cort
2013-01-01
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 (k0p), the effective diffusion coefficients (Deff), and the light penetration depths (z0.5) 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 z0.5 is more sensitive to the soot layer thickness than the k0p value. As the thickness of the soot layer increases, the z0.5 values increase, but the k0p 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 k0p and z0.5 in thinner layers, Deff 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. PMID:23247292
A simple, sensitive, and accurate alcohol electrode
Verduyn, C.; Scheffers, W.A.; Van Dijken, J.P.
1983-04-01
The construction and performance of an enzyme electrode is described which specifically detects lower primary aliphatic alcohols in aqueous solutions. The electrode consists of a commercial Clark-type oxygen electrode on which alcohol oxidase (E.C. 1.1.3.13) and catalase were immobilized. The decrease in electrode current is linearly proportional to ethanol concentrations betwee 1 and 25 ppm. The response of the electrode remains constant during 400 assays over a period of two weeks. The response time is between 1 and 2 min. Assembly of the electrode takes less than 1 h.
Accurately Mapping M31's Microlensing Population
NASA Astrophysics Data System (ADS)
Crotts, Arlin
2004-07-01
We propose to augment an existing microlensing survey of M31 with source identifications provided by a modest amount of ACS {and WFPC2 parallel} observations to yield an accurate measurement of the masses responsible for microlensing in M31, and presumably much of its dark matter. The main benefit of these data is the determination of the physical {or "einstein"} timescale of each microlensing event, rather than an effective {"FWHM"} timescale, allowing masses to be determined more than twice as accurately as without HST data. The einstein timescale is the ratio of the lensing cross-sectional radius and relative velocities. Velocities are known from kinematics, and the cross-section is directly proportional to the {unknown} lensing mass. We cannot easily measure these quantities without knowing the amplification, hence the baseline magnitude, which requires the resolution of HST to find the source star. This makes a crucial difference because M31 lens m ass determinations can be more accurate than those towards the Magellanic Clouds through our Galaxy's halo {for the same number of microlensing events} due to the better constrained geometry in the M31 microlensing situation. Furthermore, our larger survey, just completed, should yield at least 100 M31 microlensing events, more than any Magellanic survey. A small amount of ACS+WFPC2 imaging will deliver the potential of this large database {about 350 nights}. For the whole survey {and a delta-function mass distribution} the mass error should approach only about 15%, or about 6% error in slope for a power-law distribution. These results will better allow us to pinpoint the lens halo fraction, and the shape of the halo lens spatial distribution, and allow generalization/comparison of the nature of halo dark matter in spiral galaxies. In addition, we will be able to establish the baseline magnitude for about 50, 000 variable stars, as well as measure an unprecedentedly deta iled color-magnitude diagram and luminosity
Accurate measurement of unsteady state fluid temperature
NASA Astrophysics Data System (ADS)
Jaremkiewicz, Magdalena
2016-07-01
In this paper, two accurate methods for determining the transient fluid temperature were presented. Measurements were conducted for boiling water since its temperature is known. At the beginning the thermometers are at the ambient temperature and next they are immediately immersed into saturated water. The measurements were carried out with two thermometers of different construction but with the same housing outer diameter equal to 15 mm. One of them is a K-type industrial thermometer widely available commercially. The temperature indicated by the thermometer was corrected considering the thermometers as the first or second order inertia devices. The new design of a thermometer was proposed and also used to measure the temperature of boiling water. Its characteristic feature is a cylinder-shaped housing with the sheath thermocouple located in its center. The temperature of the fluid was determined based on measurements taken in the axis of the solid cylindrical element (housing) using the inverse space marching method. Measurements of the transient temperature of the air flowing through the wind tunnel using the same thermometers were also carried out. The proposed measurement technique provides more accurate results compared with measurements using industrial thermometers in conjunction with simple temperature correction using the inertial thermometer model of the first or second order. By comparing the results, it was demonstrated that the new thermometer allows obtaining the fluid temperature much faster and with higher accuracy in comparison to the industrial thermometer. Accurate measurements of the fast changing fluid temperature are possible due to the low inertia thermometer and fast space marching method applied for solving the inverse heat conduction problem.
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.
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.
Accurate density functional thermochemistry for larger molecules.
Raghavachari, K.; Stefanov, B. B.; Curtiss, L. A.; Lucent Tech.
1997-06-20
Density functional methods are combined with isodesmic bond separation reaction energies to yield accurate thermochemistry for larger molecules. Seven different density functionals are assessed for the evaluation of heats of formation, Delta H 0 (298 K), for a test set of 40 molecules composed of H, C, O and N. The use of bond separation energies results in a dramatic improvement in the accuracy of all the density functionals. The B3-LYP functional has the smallest mean absolute deviation from experiment (1.5 kcal mol/f).
New law requires 'medically accurate' lesson plans.
1999-09-17
The California Legislature has passed a bill requiring all textbooks and materials used to teach about AIDS be medically accurate and objective. Statements made within the curriculum must be supported by research conducted in compliance with scientific methods, and published in peer-reviewed journals. Some of the current lesson plans were found to contain scientifically unsupported and biased information. In addition, the bill requires material to be "free of racial, ethnic, or gender biases." The legislation is supported by a wide range of interests, but opposed by the California Right to Life Education Fund, because they believe it discredits abstinence-only material. PMID:11366835
(In)validity of the constant field and constant currents assumptions in theories of ion transport.
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
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).
Constant crunch coordinates for black hole simulations
NASA Astrophysics Data System (ADS)
Gentle, Adrian P.; Holz, Daniel E.; Kheyfets, Arkady; Laguna, Pablo; Miller, Warner A.; Shoemaker, Deirdre M.
2001-03-01
We reinvestigate the utility of time-independent constant mean curvature foliations for the numerical simulation of a single spherically symmetric black hole. Each spacelike hypersurface of such a foliation is endowed with the same constant value of the trace of the extrinsic curvature tensor K. Of the three families of K-constant surfaces possible (classified according to their asymptotic behaviors), we single out a subfamily of singularity-avoiding surfaces that may be particularly useful, and provide an analytic expression for the closest approach such surfaces make to the singularity. We then utilize a nonzero shift to yield families of K-constant surfaces which (1) avoid the black hole singularity, and thus the need to excise the singularity, (2) are asymptotically null, aiding in gravity wave extraction, (3) cover the physically relevant part of the spacetime, (4) are well behaved (regular) across the horizon, and (5) are static under evolution, and therefore have no ``grid stretching/ sucking'' pathologies. Preliminary numerical runs demonstrate that we can stably evolve a single spherically symmetric static black hole using this foliation. We wish to emphasize that this coordinatization produces K-constant surfaces for a single black hole spacetime that are regular, static, and stable throughout their evolution.
Athermal nonlinear elastic constants of amorphous solids.
Karmakar, Smarajit; Lerner, Edan; Procaccia, Itamar
2010-08-01
We derive expressions for the lowest nonlinear elastic constants of amorphous solids in athermal conditions (up to third order), in terms of the interaction potential between the constituent particles. The effect of these constants cannot be disregarded when amorphous solids undergo instabilities such as plastic flow or fracture in the athermal limit; in such situations the elastic response increases enormously, bringing the system much beyond the linear regime. We demonstrate that the existing theory of thermal nonlinear elastic constants converges to our expressions in the limit of zero temperature. We motivate the calculation by discussing two examples in which these nonlinear elastic constants play a crucial role in the context of elastoplasticity of amorphous solids. The first example is the plasticity-induced memory that is typical to amorphous solids (giving rise to the Bauschinger effect). The second example is how to predict the next plastic event from knowledge of the nonlinear elastic constants. Using the results of our calculations we derive a simple differential equation for the lowest eigenvalue of the Hessian matrix in the external strain near mechanical instabilities; this equation predicts how the eigenvalue vanishes at the mechanical instability and the value of the strain where the mechanical instability takes place. PMID:20866874
Athermal nonlinear elastic constants of amorphous solids
NASA Astrophysics Data System (ADS)
Karmakar, Smarajit; Lerner, Edan; Procaccia, Itamar
2010-08-01
We derive expressions for the lowest nonlinear elastic constants of amorphous solids in athermal conditions (up to third order), in terms of the interaction potential between the constituent particles. The effect of these constants cannot be disregarded when amorphous solids undergo instabilities such as plastic flow or fracture in the athermal limit; in such situations the elastic response increases enormously, bringing the system much beyond the linear regime. We demonstrate that the existing theory of thermal nonlinear elastic constants converges to our expressions in the limit of zero temperature. We motivate the calculation by discussing two examples in which these nonlinear elastic constants play a crucial role in the context of elastoplasticity of amorphous solids. The first example is the plasticity-induced memory that is typical to amorphous solids (giving rise to the Bauschinger effect). The second example is how to predict the next plastic event from knowledge of the nonlinear elastic constants. Using the results of our calculations we derive a simple differential equation for the lowest eigenvalue of the Hessian matrix in the external strain near mechanical instabilities; this equation predicts how the eigenvalue vanishes at the mechanical instability and the value of the strain where the mechanical instability takes place.
NASA Astrophysics Data System (ADS)
Skone, Jonathan; Govoni, Marco; Galli, Giulia
Dielectric-dependent hybrid [DDH] functionals have recently been shown to yield highly accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than standard GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. In the present talk we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using material dependent, non-empirical parameters. Comparing with state of the art GW calculations and experiment, we show that such RS hybrids yield accurate electronic properties of both molecules and solids, including energy gaps, photoelectron spectra and absolute ionization potentials. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and DOE-BES.
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.
Accurate radiative transfer calculations for layered media.
Selden, Adrian C
2016-07-01
Simple yet accurate results for radiative transfer in layered media with discontinuous refractive index are obtained by the method of K-integrals. These are certain weighted integrals applied to the angular intensity distribution at the refracting boundaries. The radiative intensity is expressed as the sum of the asymptotic angular intensity distribution valid in the depth of the scattering medium and a transient term valid near the boundary. Integrated boundary equations are obtained, yielding simple linear equations for the intensity coefficients, enabling the angular emission intensity and the diffuse reflectance (albedo) and transmittance of the scattering layer to be calculated without solving the radiative transfer equation directly. Examples are given of half-space, slab, interface, and double-layer calculations, and extensions to multilayer systems are indicated. The K-integral method is orders of magnitude more accurate than diffusion theory and can be applied to layered scattering media with a wide range of scattering albedos, with potential applications to biomedical and ocean optics. PMID:27409700
Fast and accurate propagation of coherent light
Lewis, R. D.; Beylkin, G.; Monzón, L.
2013-01-01
We describe a fast algorithm to propagate, for any user-specified accuracy, a time-harmonic electromagnetic field between two parallel planes separated by a linear, isotropic and homogeneous medium. The analytical formulation of this problem (ca 1897) requires the evaluation of the so-called Rayleigh–Sommerfeld integral. If the distance between the planes is small, this integral can be accurately evaluated in the Fourier domain; if the distance is very large, it can be accurately approximated by asymptotic methods. In the large intermediate region of practical interest, where the oscillatory Rayleigh–Sommerfeld kernel must be applied directly, current numerical methods can be highly inaccurate without indicating this fact to the user. In our approach, for any user-specified accuracy ϵ>0, we approximate the kernel by a short sum of Gaussians with complex-valued exponents, and then efficiently apply the result to the input data using the unequally spaced fast Fourier transform. The resulting algorithm has computational complexity , where we evaluate the solution on an N×N grid of output points given an M×M grid of input samples. Our algorithm maintains its accuracy throughout the computational domain. PMID:24204184
How Accurately can we Calculate Thermal Systems?
Cullen, D; Blomquist, R N; Dean, C; Heinrichs, D; Kalugin, M A; Lee, M; Lee, Y; MacFarlan, R; Nagaya, Y; Trkov, A
2004-04-20
I would like to determine how accurately a variety of neutron transport code packages (code and cross section libraries) can calculate simple integral parameters, such as K{sub eff}, for systems that are sensitive to thermal neutron scattering. Since we will only consider theoretical systems, we cannot really determine absolute accuracy compared to any real system. Therefore rather than accuracy, it would be more precise to say that I would like to determine the spread in answers that we obtain from a variety of code packages. This spread should serve as an excellent indicator of how accurately we can really model and calculate such systems today. Hopefully, eventually this will lead to improvements in both our codes and the thermal scattering models that they use in the future. In order to accomplish this I propose a number of extremely simple systems that involve thermal neutron scattering that can be easily modeled and calculated by a variety of neutron transport codes. These are theoretical systems designed to emphasize the effects of thermal scattering, since that is what we are interested in studying. I have attempted to keep these systems very simple, and yet at the same time they include most, if not all, of the important thermal scattering effects encountered in a large, water-moderated, uranium fueled thermal system, i.e., our typical thermal reactors.
Accurate shear measurement with faint sources
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.
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.
Accurate determination of characteristic relative permeability curves
NASA Astrophysics Data System (ADS)
Krause, Michael H.; Benson, Sally M.
2015-09-01
A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.
Clusters of Galaxies and the Hubble Constant
NASA Astrophysics Data System (ADS)
Falcon, N.
2008-09-01
The expansion rate, at height scale, of the Universe, is given for the value of the Hubble constant (H0). Several methods have used by determinations of the Hubble constant: CMB anisotropy's, Supernovae observation and AGN at height red-shift. In this work, we used the Grainge et al (3) method by estimated of the Hubble constant thought of the Sunyaev-Zel'dovich effect and the result of the VSA interferometer (Teide Observatory) and the X-ray data by ROSAT. We obtain, h ? 0,78, in accord with other report by cluster of galaxies (Mason et al, 2001) as higher than of the standard value h =0,71 obtain by other method. We discussed the systematic fount of error and possible discrepant by assumptions of the spheroid and isothermal in cluster and the Sunyaev- Zel'dovich Kinetic effect.
Binary Solid Propellants for Constant Momentum Missions
Pakhomov, Andrew V.; Mahaffy, Kevin E.
2008-04-28
A constant momentum mission is achieved when the speed of the vehicle in the inertial frame of reference is equal to the speed of exhaust relative to the vehicle. Due to 100% propulsive efficiency such missions are superior to traditional constant specific impulse missions. A new class of solid binary propellants for constant momentum missions is under development. A typical propellant column is prepared as a solid solution of two components, with composition gradually changing from 100% of a propellant of high coupling coefficient (C{sub m}) to one which has high specific impulse (I{sub sp}). The high coupling component is ablated first, gradually giving way to the high I{sub sp} component, as the vehicle accelerates. This study opens new opportunities for further design of complex propellants for laser propulsion, providing variable C{sub m} and I{sub sp} during missions.
Optimizing constant wavelength neutron powder diffractometers
NASA Astrophysics Data System (ADS)
Cussen, Leo D.
2016-06-01
This article describes an analytic method to optimize constant wavelength neutron powder diffractometers. It recasts the accepted mathematical description of resolution and intensity in terms of new variables and includes terms for vertical divergence, wavelength and some sample scattering effects. An undetermined multiplier method is applied to the revised equations to minimize the RMS value of resolution width at constant intensity and fixed wavelength. A new understanding of primary spectrometer transmission (presented elsewhere) can then be applied to choose beam elements to deliver an optimum instrument. Numerical methods can then be applied to choose the best wavelength.
Environmental dependence of masses and coupling constants
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.
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.
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.
Coulomb field in a constant electromagnetic background
NASA Astrophysics Data System (ADS)
Adorno, T. C.; Gitman, D. M.; Shabad, A. E.
2016-06-01
Nonlinear Maxwell equations are written up to the third-power deviations from a constant-field background, valid within any local nonlinear electrodynamics including QED with a Euler-Heisenberg (EH) effective Lagrangian. The linear electric response to an imposed static finite-sized charge is found in the vacuum filled by an arbitrary combination of constant and homogeneous electric and magnetic fields. The modified Coulomb field and corrections to the total charge and to the charge density are given in terms of derivatives of the effective Lagrangian with respect to the field invariants. These are specialized for the EH Lagrangian.
Image segmentation via piecewise constant regression
NASA Astrophysics Data System (ADS)
Acton, Scott T.; Bovik, Alan C.
1994-09-01
We introduce a novel unsupervised image segmentation technique that is based on piecewise constant (PICO) regression. Given an input image, a PICO output image for a specified feature size (scale) is computed via nonlinear regression. The regression effectively provides the constant region segmentation of the input image that has a minimum deviation from the input image. PICO regression-based segmentation avoids the problems of region merging, poor localization, region boundary ambiguity, and region fragmentation. Additionally, our segmentation method is particularly well-suited for corrupted (noisy) input data. An application to segmentation and classification of remotely sensed imagery is provided.
Black hole constraints on varying fundamental constants.
MacGibbon, Jane H
2007-08-10
We apply the generalized second law of thermodynamics and derive upper limits on the variation in the fundamental constants. The maximum variation in the electronic charge permitted for black holes accreting and emitting in the present cosmic microwave background corresponds to a variation in the fine-structure constant of Deltaalpha/alpha approximately 2 x 10(-23) per second. This value matches the variation measured by Webb et al. [Phys. Rev. Lett. 82, 884 (1999); Phys. Rev. Lett. 87, 091301 (2001)] using absorption lines in the spectra of distant quasars and suggests the variation mechanism may be a coupling between the electron and the cosmic photon background. PMID:17930813
Atomic weights: no longer constants of nature
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
Atomic Weights No Longer Constants of Nature
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.
Microfabricated microengine with constant rotation rate
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.
Cosmological constant in scale-invariant theories
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.
Our Universe from the cosmological constant
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.
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.
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.
Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory
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 K_{1 }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 UO_{2}^{2+} complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K_{1} values are significantly overestimated. Accurate predictions of the absolute log K_{1} values (root mean square deviation from experiment < 1.0 for log K_{1} 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.
Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory
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
Predicting stability constants for uranyl complexes using density functional theory.
Vukovic, Sinisa; Hay, Benjamin P; Bryantsev, Vyacheslav S
2015-04-20
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 use density functional theory (B3LYP) and the integral equation formalism polarizable continuum model (IEF-PCM) to compute aqueous stability constants for UO2(2+) 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 chelating capability to uranyl. PMID:25835578
Prediction of turbulent coaxial streams of constant and variable density
NASA Astrophysics Data System (ADS)
Johnson, Richard W.
1993-08-01
The present study investigates the accuracy of well-known turbulence models in simulating the mean velocity, turbulence, and concentration fields for the cases of constant and variable density, turbulent, low Mach number, isothermal, confined coaxial streams of different bulk mean velocities, or axisymmetric mixing layers. The standard k-epsilon eddy viscosity model and an anisotropic thin shear algebraic stress model (ASM) are employed for the constant density case. Results for the k-epsilon model are determined to be qualitatively satisfactory and superior to those for the thin shear ASM, though both show excessive radial diffusion of axial momentum. Based on these conclusions, the k-epsilon model, extended for variable density, is used for numerical simulations of a similar flow where the inner stream gas has a density four times that of the outer stream gas. Simulations for the velocity using the k-epsilon model are again found to be qualitatively accurate. Predictions for the concentration field, however, are in good agreement with the data. The flow fields studied are idealizations of a particular configuration once proposed for a gas core reactor (GCR) nuclear propulsion engine. Nuclear propulsion for space travel, once considered in the 1960s and early 1970s, is being reconsidered, especially for manned interplanetary travel.
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.