Sample records for accurate molecular constants

  1. Molecular Model of a Quantum Dot Beyond the Constant Interaction Approximation

    NASA Astrophysics Data System (ADS)

    Temirov, Ruslan; Green, Matthew F. B.; Friedrich, Niklas; Leinen, Philipp; Esat, Taner; Chmielniak, Pawel; Sarwar, Sidra; Rawson, Jeff; Kögerler, Paul; Wagner, Christian; Rohlfing, Michael; Tautz, F. Stefan

    2018-05-01

    We present a physically intuitive model of molecular quantum dots beyond the constant interaction approximation. It accurately describes their charging behavior and allows the extraction of important molecular properties that are otherwise experimentally inaccessible. The model is applied to data recorded with a noncontact atomic force microscope on three different molecules that act as a quantum dot when attached to the microscope tip. The results are in excellent agreement with first-principles simulations.

  2. Reliable and accurate extraction of Hamaker constants from surface force measurements.

    PubMed

    Miklavcic, S J

    2018-08-15

    A simple and accurate closed-form expression for the Hamaker constant that best represents experimental surface force data is presented. Numerical comparisons are made with the current standard least squares approach, which falsely assumes error-free separation measurements, and a nonlinear version assuming independent measurements of force and separation are subject to error. The comparisons demonstrate that not only is the proposed formula easily implemented it is also considerably more accurate. This option is appropriate for any value of Hamaker constant, high or low, and certainly for any interacting system exhibiting an inverse square distance dependent van der Waals force. Copyright © 2018 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2015-10-29

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

  4. Method for accurate determination of dissociation constants of optical ratiometric systems: chemical probes, genetically encoded sensors, and interacting molecules.

    PubMed

    Pomorski, Adam; Kochańczyk, Tomasz; Miłoch, Anna; Krężel, Artur

    2013-12-03

    Ratiometric chemical probes and genetically encoded sensors are of high interest for both analytical chemists and molecular biologists. Their high sensitivity toward the target ligand and ability to obtain quantitative results without a known sensor concentration have made them a very useful tool in both in vitro and in vivo assays. Although ratiometric sensors are widely used in many applications, their successful and accurate usage depends on how they are characterized in terms of sensing target molecules. The most important feature of probes and sensors besides their optical parameters is an affinity constant toward analyzed molecules. The literature shows that different analytical approaches are used to determine the stability constants, with the ratio approach being most popular. However, oversimplification and lack of attention to detail results in inaccurate determination of stability constants, which in turn affects the results obtained using these sensors. Here, we present a new method where ratio signal is calibrated for borderline values of intensities of both wavelengths, instead of borderline ratio values that generate errors in many studies. At the same time, the equation takes into account the cooperativity factor or fluorescence artifacts and therefore can be used to characterize systems with various stoichiometries and experimental conditions. Accurate determination of stability constants is demonstrated utilizing four known optical ratiometric probes and sensors, together with a discussion regarding other, currently used methods.

  5. Mobility-based correction for accurate determination of binding constants by capillary electrophoresis-frontal analysis.

    PubMed

    Qian, Cheng; Kovalchik, Kevin A; MacLennan, Matthew S; Huang, Xiaohua; Chen, David D Y

    2017-06-01

    Capillary electrophoresis frontal analysis (CE-FA) can be used to determine binding affinity of molecular interactions. However, its current data processing method mandate specific requirement on the mobilities of the binding pair in order to obtain accurate binding constants. This work shows that significant errors are resulted when the mobilities of the interacting species do not meet these requirements. Therefore, the applicability of CE-FA in many real word applications becomes questionable. An electrophoretic mobility-based correction method is developed in this work based on the flux of each species. A simulation program and a pair of model compounds are used to verify the new equations and evaluate the effectiveness of this method. Ibuprofen and hydroxypropyl-β-cyclodextrinare used to demonstrate the differences in the obtained binding constant by CE-FA when different calculation methods are used, and the results are compared with those obtained by affinity capillary electrophoresis (ACE). The results suggest that CE-FA, with the mobility-based correction method, can be a generally applicable method for a much wider range of applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed

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

    2016-03-08

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

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

    NASA Technical Reports Server (NTRS)

    Kendall, J. M., Sr.

    1981-01-01

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

  8. 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.

  9. Accurate Measurement of the Optical Constants for Organic and Organophosphorous Liquid Layers and Drops

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Myers, Tanya L.; Tonkyn, Russell G.; Danby, Tyler O.

    We present accurate measurements for the determination of the optical constants for a series of organic liquids, including organophosphorous compounds. Bulk liquids are rarely encountered in the environment, but more commonly are present as droplets of liquids or thin layers on various substrates. Providing reference spectra to account for the plethora of morphological conditions that may be encountered under different scenarios is a challenge. An alternative approach is to provide the complex optical constants, n and k, which can be used to model the optical phenomena in media and at interfaces, minimizing the need for a vast number of laboratorymore » measurements. In this work, we present improved protocols for measuring the optical constants for a series of liquids that span the range from 7800 to 400 cm-1. The broad spectral range means that one needs to account for both the strong and weak spectral features that are encountered, all of which can be useful for detection, depending on the scenario. To span this dynamic range, both long and short cells are required for accurate measurements. The protocols are presented along with experimental and modeling results for thin layers of silicone oil on aluminum.« less

  10. Constant-pH molecular dynamics using stochastic titration

    NASA Astrophysics Data System (ADS)

    Baptista, António M.; Teixeira, Vitor H.; Soares, Cláudio M.

    2002-09-01

    A new method is proposed for performing constant-pH molecular dynamics (MD) simulations, that is, MD simulations where pH is one of the external thermodynamic parameters, like the temperature or the pressure. The protonation state of each titrable site in the solute is allowed to change during a molecular mechanics (MM) MD simulation, the new states being obtained from a combination of continuum electrostatics (CE) calculations and Monte Carlo (MC) simulation of protonation equilibrium. The coupling between the MM/MD and CE/MC algorithms is done in a way that ensures a proper Markov chain, sampling from the intended semigrand canonical distribution. This stochastic titration method is applied to succinic acid, aimed at illustrating the method and examining the choice of its adjustable parameters. The complete titration of succinic acid, using constant-pH MD simulations at different pH values, gives a clear picture of the coupling between the trans/gauche isomerization and the protonation process, making it possible to reconcile some apparently contradictory results of previous studies. The present constant-pH MD method is shown to require a moderate increase of computational cost when compared to the usual MD method.

  11. Constant size descriptors for accurate machine learning models of molecular properties

    NASA Astrophysics Data System (ADS)

    Collins, Christopher R.; Gordon, Geoffrey J.; von Lilienfeld, O. Anatole; Yaron, David J.

    2018-06-01

    Two different classes of molecular representations for use in machine learning of thermodynamic and electronic properties are studied. The representations are evaluated by monitoring the performance of linear and kernel ridge regression models on well-studied data sets of small organic molecules. One class of representations studied here counts the occurrence of bonding patterns in the molecule. These require only the connectivity of atoms in the molecule as may be obtained from a line diagram or a SMILES string. The second class utilizes the three-dimensional structure of the molecule. These include the Coulomb matrix and Bag of Bonds, which list the inter-atomic distances present in the molecule, and Encoded Bonds, which encode such lists into a feature vector whose length is independent of molecular size. Encoded Bonds' features introduced here have the advantage of leading to models that may be trained on smaller molecules and then used successfully on larger molecules. A wide range of feature sets are constructed by selecting, at each rank, either a graph or geometry-based feature. Here, rank refers to the number of atoms involved in the feature, e.g., atom counts are rank 1, while Encoded Bonds are rank 2. For atomization energies in the QM7 data set, the best graph-based feature set gives a mean absolute error of 3.4 kcal/mol. Inclusion of 3D geometry substantially enhances the performance, with Encoded Bonds giving 2.4 kcal/mol, when used alone, and 1.19 kcal/mol, when combined with graph features.

  12. 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%.

  13. 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…

  14. Accurate Determination of the Values of Fundamental Physical Constants: The Basis of the New "Quantum" SI Units

    NASA Astrophysics Data System (ADS)

    Karshenboim, S. G.

    2018-03-01

    The metric system appeared as the system of units designed for macroscopic (laboratory scale) measurements. The progress in accurate determination of the values of quantum constants (such as the Planck constant) in SI units shows that the capabilities in high-precision measurement of microscopic and macroscopic quantities in terms of the same units have increased substantially recently. At the same time, relative microscopic measurements (for example, the comparison of atomic transition frequencies or atomic masses) are often much more accurate than relative measurements of macroscopic quantities. This is the basis for the strategy to define units in microscopic phenomena and then use them on the laboratory scale, which plays a crucial role in practical methodological applications determined by everyday life and technologies. The international CODATA task group on fundamental constants regularly performs an overall analysis of the precision world data (the so-called Adjustment of the Fundamental Constants) and publishes their recommended values. The most recent evaluation was based on the data published by the end of 2014; here, we review the corresponding data and results. The accuracy in determination of the Boltzmann constant has increased, the consistency of the data on determination of the Planck constant has improved; it is these two dimensional constants that will be used in near future as the basis for the new definition of the kelvin and kilogram, respectively. The contradictions in determination of the Rydberg constant and the proton charge radius remain. The accuracy of determination of the fine structure constant and relative atomic weight of the electron has improved. Overall, we give a detailed review of the state of the art in precision determination of the values of fundamental constants. The mathematical procedure of the Adjustment, the new data and results are considered in detail. The limitations due to macroscopic properties of material

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

    PubMed

    Arthur, Evan J; Brooks, Charles L

    2016-09-15

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

  16. 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

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

    PubMed

    Steiner, Richard

    2013-01-01

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

  18. 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.

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

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  20. Constant pH Molecular Dynamics of Proteins in Explicit Solvent with Proton Tautomerism

    PubMed Central

    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

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

    PubMed

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

    2014-07-01

    pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.

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

    PubMed Central

    Yogurtcu, Osman N.; Johnson, Margaret E.

    2015-01-01

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

  3. Accurate approximation of in-ecliptic trajectories for E-sail with constant pitch angle

    NASA Astrophysics Data System (ADS)

    Huo, Mingying; Mengali, Giovanni; Quarta, Alessandro A.

    2018-05-01

    Propellantless continuous-thrust propulsion systems, such as electric solar wind sails, may be successfully used for new space missions, especially those requiring high-energy orbit transfers. When the mass-to-thrust ratio is sufficiently large, the spacecraft trajectory is characterized by long flight times with a number of revolutions around the Sun. The corresponding mission analysis, especially when addressed within an optimal context, requires a significant amount of simulation effort. Analytical trajectories are therefore useful aids in a preliminary phase of mission design, even though exact solution are very difficult to obtain. The aim of this paper is to present an accurate, analytical, approximation of the spacecraft trajectory generated by an electric solar wind sail with a constant pitch angle, using the latest mathematical model of the thrust vector. Assuming a heliocentric circular parking orbit and a two-dimensional scenario, the simulation results show that the proposed equations are able to accurately describe the actual spacecraft trajectory for a long time interval when the propulsive acceleration magnitude is sufficiently small.

  4. Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

    DOE PAGES

    Radak, Brian K.; Chipot, Christophe; Suh, Donghyuk; ...

    2017-11-07

    We report that an increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementationmore » of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Finally, illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.« less

  5. Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Radak, Brian K.; Chipot, Christophe; Suh, Donghyuk

    We report that an increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementationmore » of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Finally, illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.« less

  6. Machine Learning of Accurate Energy-Conserving Molecular Force Fields

    NASA Astrophysics Data System (ADS)

    Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

    Efficient and accurate access to the Born-Oppenheimer potential energy surface (PES) is essential for long time scale molecular dynamics (MD) simulations. Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio MD trajectories (AIMD). The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/Å for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, malonaldehyde, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative MD simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

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

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-05

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

  8. 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.

  9. Precisely and Accurately Inferring Single-Molecule Rate Constants

    PubMed Central

    Kinz-Thompson, Colin D.; Bailey, Nevette A.; Gonzalez, Ruben L.

    2017-01-01

    The kinetics of biomolecular systems can be quantified by calculating the stochastic rate constants that govern the biomolecular state versus time trajectories (i.e., state trajectories) of individual biomolecules. To do so, the experimental signal versus time trajectories (i.e., signal trajectories) obtained from observing individual biomolecules are often idealized to generate state trajectories by methods such as thresholding or hidden Markov modeling. Here, we discuss approaches for idealizing signal trajectories and calculating stochastic rate constants from the resulting state trajectories. Importantly, we provide an analysis of how the finite length of signal trajectories restrict the precision of these approaches, and demonstrate how Bayesian inference-based versions of these approaches allow rigorous determination of this precision. Similarly, we provide an analysis of how the finite lengths and limited time resolutions of signal trajectories restrict the accuracy of these approaches, and describe methods that, by accounting for the effects of the finite length and limited time resolution of signal trajectories, substantially improve this accuracy. Collectively, therefore, the methods we consider here enable a rigorous assessment of the precision, and a significant enhancement of the accuracy, with which stochastic rate constants can be calculated from single-molecule signal trajectories. PMID:27793280

  10. Oscillating PDF in termini of circadian pacemaker neurons and synchronous molecular clocks in downstream neurons are not sufficient for sustenance of activity rhythms in constant darkness.

    PubMed

    Prakash, Pavitra; Nambiar, Aishwarya; Sheeba, Vasu

    2017-01-01

    In Drosophila, neuropeptide Pigment Dispersing Factor (PDF) is expressed in small and large ventral Lateral Neurons (sLNv and lLNv), among which sLNv are critical for activity rhythms in constant darkness. Studies show that this is mediated by rhythmic accumulation and likely secretion of PDF from sLNv dorsal projections, which in turn synchronises molecular oscillations in downstream circadian neurons. Using targeted expression of a neurodegenerative protein Huntingtin in LNv, we evoke a selective loss of neuropeptide PDF and clock protein PERIOD from sLNv soma. However, PDF is not lost from sLNv dorsal projections and lLNv. These flies are behaviourally arrhythmic in constant darkness despite persistence of PDF oscillations in sLNv dorsal projections and synchronous PERIOD oscillations in downstream circadian neurons. We find that PDF oscillations in sLNv dorsal projections are not sufficient for sustenance of activity rhythms in constant darkness and this is suggestive of an additional component that is possibly dependent on sLNv molecular clock and PDF in sLNv soma. Additionally, despite loss of PERIOD in sLNv, their activity rhythms entrain to light/dark cycles indicating that sLNv molecular clocks are not necessary for entrainment. Under constant light, these flies lack PDF from both soma and dorsal projections of sLNv, and when subjected to light/dark cycles, show morning and evening anticipation and accurately phased morning and evening peaks. Thus, under light/dark cycles, PDF in sLNv is not necessary for morning anticipation.

  11. Oscillating PDF in termini of circadian pacemaker neurons and synchronous molecular clocks in downstream neurons are not sufficient for sustenance of activity rhythms in constant darkness

    PubMed Central

    Prakash, Pavitra; Nambiar, Aishwarya; Sheeba, Vasu

    2017-01-01

    In Drosophila, neuropeptide Pigment Dispersing Factor (PDF) is expressed in small and large ventral Lateral Neurons (sLNv and lLNv), among which sLNv are critical for activity rhythms in constant darkness. Studies show that this is mediated by rhythmic accumulation and likely secretion of PDF from sLNv dorsal projections, which in turn synchronises molecular oscillations in downstream circadian neurons. Using targeted expression of a neurodegenerative protein Huntingtin in LNv, we evoke a selective loss of neuropeptide PDF and clock protein PERIOD from sLNv soma. However, PDF is not lost from sLNv dorsal projections and lLNv. These flies are behaviourally arrhythmic in constant darkness despite persistence of PDF oscillations in sLNv dorsal projections and synchronous PERIOD oscillations in downstream circadian neurons. We find that PDF oscillations in sLNv dorsal projections are not sufficient for sustenance of activity rhythms in constant darkness and this is suggestive of an additional component that is possibly dependent on sLNv molecular clock and PDF in sLNv soma. Additionally, despite loss of PERIOD in sLNv, their activity rhythms entrain to light/dark cycles indicating that sLNv molecular clocks are not necessary for entrainment. Under constant light, these flies lack PDF from both soma and dorsal projections of sLNv, and when subjected to light/dark cycles, show morning and evening anticipation and accurately phased morning and evening peaks. Thus, under light/dark cycles, PDF in sLNv is not necessary for morning anticipation. PMID:28558035

  12. 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.

  13. Machine learning of accurate energy-conserving molecular force fields.

    PubMed

    Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof T; Müller, Klaus-Robert

    2017-05-01

    Using conservation of energy-a fundamental property of closed classical and quantum mechanical systems-we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol -1 for energies and 1 kcal mol -1 Å̊ -1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

  14. Machine learning of accurate energy-conserving molecular force fields

    PubMed Central

    Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

    2017-01-01

    Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

    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.

  16. Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles.

    PubMed

    Petrini, Paula A; Silva, Ricardo M L; de Oliveira, Rafael F; Merces, Leandro; Bof Bufon, Carlos C

    2018-06-29

    Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscopy. The incorporation of molecular materials in devices is not a trivial task as the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (k CuPc ) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al 2 O 3 layers, and the CuPc molecular ensembles have been fabricated and evaluated. The Al 2 O 3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (<30 nm). From the electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (k CuPc  = 4.5 ± 0.5). These values suggest a mild contribution of the molecular orientation on the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology.

  17. Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles

    NASA Astrophysics Data System (ADS)

    Petrini, Paula A.; Silva, Ricardo M. L.; de Oliveira, Rafael F.; Merces, Leandro; Bof Bufon, Carlos C.

    2018-06-01

    Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscopy. The incorporation of molecular materials in devices is not a trivial task as the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (k CuPc) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al2O3 layers, and the CuPc molecular ensembles have been fabricated and evaluated. The Al2O3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (<30 nm). From the electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (k CuPc = 4.5 ± 0.5). These values suggest a mild contribution of the molecular orientation on the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology.

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

    PubMed

    Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

    2016-06-21

    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.

  19. Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free Energies

    PubMed Central

    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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chen, Wen-Hwa, E-mail: whchen@pme.nthu.edu.tw; National Applied Research Laboratories, Taipei 10622, Taiwan, ROC; Wu, Chun-Hung

    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. Inmore » 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.« less

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

    2016-06-21

    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 aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} 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{sup •} 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.« less

  2. Elastic constants from microscopic strain fluctuations

    PubMed

    Sengupta; Nielaba; Rao; Binder

    2000-02-01

    Fluctuations of the instantaneous local Lagrangian strain epsilon(ij)(r,t), measured with respect to a static "reference" lattice, are used to obtain accurate estimates of the elastic constants of model solids from atomistic computer simulations. The measured strains are systematically coarse-grained by averaging them within subsystems (of size L(b)) of a system (of total size L) in the canonical ensemble. Using a simple finite size scaling theory we predict the behavior of the fluctuations as a function of L(b)/L and extract elastic constants of the system in the thermodynamic limit at nonzero temperature. Our method is simple to implement, efficient, and general enough to be able to handle a wide class of model systems, including those with singular potentials without any essential modification. We illustrate the technique by computing isothermal elastic constants of "hard" and "soft" disk triangular solids in two dimensions from Monte Carlo and molecular dynamics simulations. We compare our results with those from earlier simulations and theory.

  3. Finite-Temperature Behavior of PdH x Elastic Constants Computed by Direct Molecular Dynamics

    DOE PAGES

    Zhou, X. W.; Heo, T. W.; Wood, B. C.; ...

    2017-05-30

    In this paper, robust time-averaged molecular dynamics has been developed to calculate finite-temperature elastic constants of a single crystal. We find that when the averaging time exceeds a certain threshold, the statistical errors in the calculated elastic constants become very small. We applied this method to compare the elastic constants of Pd and PdH 0.6 at representative low (10 K) and high (500 K) temperatures. The values predicted for Pd match reasonably well with ultrasonic experimental data at both temperatures. In contrast, the predicted elastic constants for PdH 0.6 only match well with ultrasonic data at 10 K; whereas, atmore » 500 K, the predicted values are significantly lower. We hypothesize that at 500 K, the facile hydrogen diffusion in PdH 0.6 alters the speed of sound, resulting in significantly reduced values of predicted elastic constants as compared to the ultrasonic experimental data. Finally, literature mechanical testing experiments seem to support this hypothesis.« less

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

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

  5. Molecular acidity: An accurate description with information-theoretic approach in density functional reactivity theory.

    PubMed

    Cao, Xiaofang; Rong, Chunying; Zhong, Aiguo; Lu, Tian; Liu, Shubin

    2018-01-15

    Molecular acidity is one of the important physiochemical properties of a molecular system, yet its accurate calculation and prediction are still an unresolved problem in the literature. In this work, we propose to make use of the quantities from the information-theoretic (IT) approach in density functional reactivity theory and provide an accurate description of molecular acidity from a completely new perspective. To illustrate our point, five different categories of acidic series, singly and doubly substituted benzoic acids, singly substituted benzenesulfinic acids, benzeneseleninic acids, phenols, and alkyl carboxylic acids, have been thoroughly examined. We show that using IT quantities such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, information gain, Onicescu information energy, and relative Rényi entropy, one is able to simultaneously predict experimental pKa values of these different categories of compounds. Because of the universality of the quantities employed in this work, which are all density dependent, our approach should be general and be applicable to other systems as well. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  6. Molecular dynamics simulation of low dielectric constant polymer electrolytes

    NASA Astrophysics Data System (ADS)

    Wheatle, Bill; Lynd, Nathaniel; Ganesan, Venkat

    Recent experimental studies measured the ionic conductivities of a series of poly(glycidyl ether)s with varying neat dielectric constants (ɛ), viscosities (η), and glass transition temperatures (Tg), as hosts for lithium bistrifluoromethanesulfonimide (LiTFSI) salt. In such a context, it was demonstrated that the ionic conductivity of these polymer electrolytes was a function of ɛ rather than Tg or η, suggesting that there may exist regimes in which ionic conductivity is not limited by slow segmental dynamics but rather by low ionic dissociation. Motivated by such results, we used atomistic molecular dynamics to study the structure and transport characteristics of the same set of host polymers. We found that the coordination number of TFSI- about Li+ in the first solvation shell and the total fraction of free ions increased as a function of ɛ, implying the polymer hosts enhanced ion dissociation. In addition, we found that increasing the dielectric constant of the host polymer enhanced self-correlated ion transport, as evidenced by an increase in the diffusion coefficients of each ion species. Overall, we confirmed that limited ion dissociation in low- ɛ polymer electrolyte hosts hampers ionic conductivity. We would like to thank the National Science Foundation Graduate Research Fellowship Program for funding this research endeavor.

  7. Conversion of calibration curves for accurate estimation of molecular weight averages and distributions of polyether polyols by conventional size exclusion chromatography.

    PubMed

    Xu, Xiuqing; Yang, Xiuhan; Martin, Steven J; Mes, Edwin; Chen, Junlan; Meunier, David M

    2018-08-17

    Accurate measurement of molecular weight averages (M¯ n, M¯ w, M¯ z ) and molecular weight distributions (MWD) of polyether polyols by conventional SEC (size exclusion chromatography) is not as straightforward as it would appear. Conventional calibration with polystyrene (PS) standards can only provide PS apparent molecular weights which do not provide accurate estimates of polyol molecular weights. Using polyethylene oxide/polyethylene glycol (PEO/PEG) for molecular weight calibration could improve the accuracy, but the retention behavior of PEO/PEG is not stable in THF-based (tetrahydrofuran) SEC systems. In this work, two approaches for calibration curve conversion with narrow PS and polyol molecular weight standards were developed. Equations to convert PS-apparent molecular weight to polyol-apparent molecular weight were developed using both a rigorous mathematical analysis and graphical plot regression method. The conversion equations obtained by the two approaches were in good agreement. Factors influencing the conversion equation were investigated. It was concluded that the separation conditions such as column batch and operating temperature did not have significant impact on the conversion coefficients and a universal conversion equation could be obtained. With this conversion equation, more accurate estimates of molecular weight averages and MWDs for polyether polyols can be achieved from conventional PS-THF SEC calibration. Moreover, no additional experimentation is required to convert historical PS equivalent data to reasonably accurate molecular weight results. Copyright © 2018. Published by Elsevier B.V.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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 resultsmore » 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.« less

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Costandy, Joseph; Michalis, Vasileios K.; Economou, Ioannis G., E-mail: i.tsimpanogiannis@qatar.tamu.edu, E-mail: ioannis.economou@qatar.tamu.edu

    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.

  12. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

    PubMed Central

    Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

    2017-01-01

    Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding. PMID:28729875

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

    PubMed Central

    2016-01-01

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

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

    DOE PAGES

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

    2015-06-04

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

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

    PubMed Central

    2015-01-01

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

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

    PubMed

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

    2015-04-01

    Molecular dynamics simulations studies are carried out on hydroxyl terminated polyethers that are useful in energetic polymeric binder applications. Energetic polymers derived from oxetanes with heterocyclic side chains with different energetic substituents are designed and simulated under the ensembles of constant particle number, pressure, temperature (NPT) and constant particle number, volume, temperature (NVT). Specific volume of different amorphous polymeric models is predicted using NPT-MD simulations as a function of temperature. Plots of specific volume versus temperature exhibited a characteristic change in slope when amorphous systems change from glassy to rubbery state. Several material properties such as Young's, shear, and bulk modulus, Poisson's ratio, etc. are predicted from equilibrated structures and established the structure-property relations among designed polymers. Energetic performance parameters of these polymers are calculated and results reveal that the performance of the designed polymers is comparable to the benchmark energetic polymers like polyNIMMO, polyAMMO and polyBAMO. Overall, it is worthy remark that this molecular simulations study on novel energetic polyethers provides a good guidance on mastering the design principles and allows us to design novel polymers of tailored properties. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Coarse gaining of molecular crystals: limitations imposed by molecular flexibility

    NASA Astrophysics Data System (ADS)

    Picu, Catalin; Pal, Anirban

    Molecular crystals include molecular electronics, energetic materials, pharmaceuticals and some food components. In many of these applications the small scale mechanical behavior of the crystal is important such as for example in energetic materials where detonation is induced by the formation of hot spots which are induced thermomechanically, and in pharmaceuticals where phase stability is critical for the biochemical activity of the drug. Accurate modeling of these processes requires resolving the atomistic scale details of the material. However, the cost of these models is very large due to the complexity of the molecules forming the crystal, and some form of coarse graning is necessary. In this study we identify the limitations imposed by the need to accurately capture molecular flexibility on the development of coarse grained models for the energetic molecular crystal RDX. We define guidelines for the definition of coarse grained models that target elastic and plastic crystal scale properties such as elastic constants, thermal expansion, compressibility, the critical stress for the motion of dislocations (Peierls stress) and the stacking fault energy This work was supported by the ARO through Grant W911NF-09-1-0330 and AFRL through Grant FA8651-16-1-0004.

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

    PubMed

    Chen, Wei; Shen, Jana K

    2014-10-15

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma. Copyright © 2014 Wiley Periodicals, Inc.

  19. Modeling crystal growth from solution with molecular dynamics simulations: approaches to transition rate constants.

    PubMed

    Reilly, Anthony M; Briesen, Heiko

    2012-01-21

    The feasibility of using the molecular dynamics (MD) simulation technique to study crystal growth from solution quantitatively, as well as to obtain transition rate constants, has been studied. The dynamics of an interface between a solution of Lennard-Jones particles and the (100) face of an fcc lattice comprised of solute particles have been studied using MD simulations, showing that MD is, in principle, capable of following growth behavior over large supersaturation and temperature ranges. Using transition state theory, and a nearest-neighbor approximation growth and dissolution rate constants have been extracted from equilibrium MD simulations at a variety of temperatures. The temperature dependence of the rates agrees well with the expected transition state theory behavior. © 2012 American Institute of Physics

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

    NASA Astrophysics Data System (ADS)

    Sellers, Michael; Lisal, Martin; Brennan, John

    2015-06-01

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

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

    PubMed

    Buryak, Ilya; Vigasin, Andrey A

    2015-12-21

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

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

    PubMed Central

    Chen, Wei; Shen, Jana K.

    2014-01-01

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma. PMID:25142416

  3. Accurate L-Band Measurements of the Dielectric Constant of Seawater

    NASA Technical Reports Server (NTRS)

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

    2007-01-01

    A new temperature controlled microwave cavity system to measure the complex dielectric constant of seawater at 1.413 GHz is discussed. The system is being developed to measure seawater for temperatures from O C to 30 C and salinities from 10 to 40 psu, The paper discusses the construction of the measurement system and initial stability tests.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Buryak, Ilya; Vigasin, Andrey A., E-mail: vigasin@ifaran.ru

    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 basedmore » on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.« less

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

    PubMed Central

    Mountain, Raymond D.; Harvey, Allan H.

    2015-01-01

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

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

    PubMed

    Mountain, Raymond D; Harvey, Allan H

    2015-10-01

    Modeling of mineral reaction equilibria and aqueous-phase speciation of C-O-H fluids requires the dielectric constant of the fluid mixture, which is not known from experiment and is typically estimated by some rule for mixing pure-component values. In order to evaluate different proposed mixing rules, we use molecular dynamics simulation to calculate the dielectric constant of a model H 2 O-CO 2 mixture at temperatures of 700 K and 1000 K at pressures up to 3 GPa. We find that theoretically based mixing rules that depend on combining the molar polarizations of the pure fluids systematically overestimate the dielectric constant of the mixture, as would be expected for mixtures of nonpolar and strongly polar components. The commonly used semiempirical mixing rule due to Looyenga works well for this system at the lower pressures studied, but somewhat underestimates the dielectric constant at higher pressures and densities, especially at the water-rich end of the composition range.

  7. Accurate calibration of a molecular beam time-of-flight mass spectrometer for on-line analysis of high molecular weight species.

    PubMed

    Apicella, B; Wang, X; Passaro, M; Ciajolo, A; Russo, C

    2016-10-15

    Time-of-Flight (TOF) Mass Spectrometry is a powerful analytical technique, provided that an accurate calibration by standard molecules in the same m/z range of the analytes is performed. Calibration in a very large m/z range is a difficult task, particularly in studies focusing on the detection of high molecular weight clusters of different molecules or high molecular weight species. External calibration is the most common procedure used for TOF mass spectrometric analysis in the gas phase and, generally, the only available standards are made up of mixtures of noble gases, covering a small mass range for calibration, up to m/z 136 (higher mass isotope of xenon). In this work, an accurate calibration of a Molecular Beam Time-of Flight Mass Spectrometer (MB-TOFMS) is presented, based on the use of water clusters up to m/z 3000. The advantages of calibrating a MB-TOFMS with water clusters for the detection of analytes with masses above those of the traditional calibrants such as noble gases were quantitatively shown by statistical calculations. A comparison of the water cluster and noble gases calibration procedures in attributing the masses to a test mixture extending up to m/z 800 is also reported. In the case of the analysis of combustion products, another important feature of water cluster calibration was shown, that is the possibility of using them as "internal standard" directly formed from the combustion water, under suitable experimental conditions. The water clusters calibration of a MB-TOFMS gives rise to a ten-fold reduction in error compared to the traditional calibration with noble gases. The consequent improvement in mass accuracy in the calibration of a MB-TOFMS has important implications in various fields where detection of high molecular mass species is required. In combustion products analysis, it is also possible to obtain a new calibration spectrum before the acquisition of each spectrum, only modifying some operative conditions. Copyright © 2016

  8. 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).

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

    PubMed

    Alecu, I M; Truhlar, Donald G

    2011-12-29

    Multistructural canonical variational-transition-state theory with multidimensional tunneling (MS-CVT/MT) is employed to calculate thermal rate constants for the abstraction of hydrogen atoms from both positions of methanol by the hydroperoxyl and methyl radicals over the temperature range 100-3000 K. The M08-HX hybrid meta-generalized gradient approximation density functional and M08-HX with specific reaction parameters, both with the maug-cc-pVTZ basis set, were validated in part 1 of this study (Alecu, I. M.; Truhlar, D. G. J. Phys. Chem. A2011, 115, 2811) against highly accurate CCSDT(2)(Q)/CBS calculations for the energetics of these reactions, and they are used here to compute the properties of all stationary points and the energies, gradients, and Hessians of nonstationary points along each considered reaction path. The internal rotations in some of the transition states are found to be highly anharmonic and strongly coupled to each other, and they generate multiple structures (conformations) whose contributions are included in the partition function. It is shown that the previous estimates for these rate constants used to build kinetic models for the combustion of methanol, some of which were based on transition state theory calculations with one-dimensional tunneling corrections and harmonic-oscillator approximations or separable one-dimensional hindered rotor treatments of torsions, are appreciably different than the ones presently calculated using MS-CVT/MT. The rate constants obtained from the best MS-CVT/MT calculations carried out in this study, in which the important effects of corner cutting due to small and large reaction path curvature are captured via a microcanonical optimized multidimensional tunneling (μOMT) treatment, are recommended for future refinement of the kinetic model for methanol combustion. © 2011 American Chemical Society

  10. Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

    NASA Astrophysics Data System (ADS)

    Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

    2018-06-01

    We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

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

    NASA Astrophysics Data System (ADS)

    Grønbech-Jensen, Niels; Farago, Oded

    2014-11-01

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

  12. 40 CFR 86.519-90 - Constant volume sampler calibration.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 19 2013-07-01 2013-07-01 false Constant volume sampler calibration... Regulations for 1978 and Later New Motorcycles; Test Procedures § 86.519-90 Constant volume sampler calibration. (a) The CVS (Constant Volume Sampler) is calibrated using an accurate flowmeter and restrictor...

  13. 40 CFR 86.519-90 - Constant volume sampler calibration.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 19 2012-07-01 2012-07-01 false Constant volume sampler calibration... Regulations for 1978 and Later New Motorcycles; Test Procedures § 86.519-90 Constant volume sampler calibration. (a) The CVS (Constant Volume Sampler) is calibrated using an accurate flowmeter and restrictor...

  14. 40 CFR 86.519-90 - Constant volume sampler calibration.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 18 2011-07-01 2011-07-01 false Constant volume sampler calibration... Regulations for 1978 and Later New Motorcycles; Test Procedures § 86.519-90 Constant volume sampler calibration. (a) The CVS (Constant Volume Sampler) is calibrated using an accurate flowmeter and restrictor...

  15. 40 CFR 86.519-90 - Constant volume sampler calibration.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 19 2014-07-01 2014-07-01 false Constant volume sampler calibration... Regulations for 1978 and Later New Motorcycles; Test Procedures § 86.519-90 Constant volume sampler calibration. (a) The CVS (Constant Volume Sampler) is calibrated using an accurate flowmeter and restrictor...

  16. 40 CFR 86.519-90 - Constant volume sampler calibration.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 18 2010-07-01 2010-07-01 false Constant volume sampler calibration... Regulations for 1978 and Later New Motorcycles; Test Procedures § 86.519-90 Constant volume sampler calibration. (a) The CVS (Constant Volume Sampler) is calibrated using an accurate flowmeter and restrictor...

  17. Prediction of Rate Constant for Supramolecular Systems with Multiconfigurations.

    PubMed

    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 (k(off)/k(on)) 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 k(off) 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 k(off)/k(on) 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.

  18. 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.

  19. dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments.

    PubMed

    Petukhov, Viktor; Guo, Jimin; Baryawno, Ninib; Severe, Nicolas; Scadden, David T; Samsonova, Maria G; Kharchenko, Peter V

    2018-06-19

    Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing and troubleshooting of these experiments, with few software options currently available. Here, we describe a flexible pipeline for processing droplet-based transcriptome data that implements barcode corrections, classification of cell quality, and diagnostic information about the droplet libraries. We introduce advanced methods for correcting composition bias and sequencing errors affecting cellular and molecular barcodes to provide more accurate estimates of molecular counts in individual cells.

  20. Photochemical parameters of atmospheric source gases: accurate determination of OH reaction rate constants over atmospheric temperatures, UV and IR absorption spectra

    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

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

    PubMed Central

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

    2014-01-01

    Recent interest in the development of surfactant-based nano delivery systems targeting tumor sites has sparked our curiosity to understand the detailed mechanism of the self-assembly and phase transitions of pH-sensitive surfactants. Towards this goal we applied a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with the hybrid-solvent scheme and pH-based replica-exchange protocol, to study de novo self-assembly of 30 and 40 lauric acids, a simple model titratable surfactant. We observed the formation of a gel-state bilayer at low and intermediate pH and a spherical micelle at high pH, with the phase transition starting at 20–30% ionization and completing at 50%. The degree of cooperativity for the transition increases from the 30-mer to the 40-mer. The calculated apparent or bulk pKa value is 7.0 for the 30-mer and 7.5 for the 40-mer. Congruent with experiment, these data demonstrate that CpHMD is capable of accurately modeling large conformational transitions of surfactant systems while allowing simultaneous proton titration of constituent molecules. We suggest that CpHMD simulations may become a useful tool to aid in the design and development of pH-sensitive nanocarriers for a variety of biomedical and technological applications. PMID:24215478

  2. Molecular continua for polymeric liquids in large-amplitude oscillatory shear flow

    NASA Astrophysics Data System (ADS)

    Giacomin, A. Jeffrey; Saengow, Chaimongkol

    2018-05-01

    In this paper, we connect a molecular description of the rheology of a polymeric liquid to a continuum description, and then test this connection for large-amplitude oscillatory shear (LAOS) flow. Specifically, for the continuum description, we use the 6-constant Oldroyd framework, and for the molecular, we use the simplest relevant molecular model, the suspension of rigid dumbbells. By relevant, we mean predicting at least higher harmonics in the shear stress response in LAOS. We call this connection a molecular continuum, and we examine two ways of arriving at this connection. The first goes through the retarded motion expansion, and the second expands each of a set of specific material functions (complex, steady shear, and steady uniaxial extensional viscosities). Both ways involve in comparing the coefficients of expansions and then solve for the six constants of the continuum framework in terms of the two constants of the rigid dumbbell suspension. The purpose of a molecular continuum is that many well-known results for rigid dumbbell suspensions in other flow fields can also be easily obtained, without having to firstly find the orientation distribution function. In this paper, we focus on the recent result for the rigid dumbbell suspension in LAOS. We compare the accuracies of the retarded motion molecular continuum (RMMC) with the material function molecular continuum (MFMC). We find the RMMC to be the most accurate for LAOS.

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

    EPA Science Inventory

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

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

    PubMed

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

    2016-08-01

    The active site of HIV protease (HIV-PR) is covered by two flaps. These flaps are known to be essential for the catalytic activity of the HIV-PR, but their exact conformations at the different stages of the enzymatic pathway remain subject to debate. Understanding the correct functional dynamics of the flaps might aid the development of new HIV-PR inhibitors. It is known that, the HIV-PR catalytic efficiency is pH-dependent, likely due to the influence of processes such as charge transfer and protonation/deprotonation of ionizable residues. Several Molecular Dynamics (MD) simulations have reported information about the HIV-PR flaps. However, in MD simulations the protonation of a residue is fixed and thus it is not possible to study the correlation between conformation and protonation state. To address this shortcoming, this work attempts to capture, through Constant pH Molecular Dynamics (CpHMD), the conformations of the apo, substrate-bound and inhibitor-bound HIV-PR, which differ drastically in their flap arrangements. The results show that the HIV-PR flaps conformations are defined by the protonation of the catalytic residues Asp25/Asp25' and that these residues are sensitive to pH changes. This study suggests that the catalytic aspartates can modulate the opening of the active site and substrate binding. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    DOE PAGES

    Sjostrom, Travis; Daligault, Jerome

    2014-10-10

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

  6. Accurate Calibration and Uncertainty Estimation of the Normal Spring Constant of Various AFM Cantilevers

    PubMed Central

    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

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

    PubMed

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

    2015-03-10

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

  8. Note: Spring constant calibration of nanosurface-engineered atomic force microscopy cantilevers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ergincan, O., E-mail: orcunergincan@gmail.com; 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.

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

    PubMed

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

    2014-01-07

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

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

    PubMed

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

    2014-09-15

    The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

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

    PubMed

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

    2016-07-01

    In advanced oxidation processes (AOPs), the aqueous hydroxyl radical (HO) acts as a strong oxidant to react with organic contaminants. The hydroxyl radical rate constant (kHO) is important for evaluating and modelling of the AOPs. In this study, quantitative structure-property relationship (QSPR) method is applied to model the hydroxyl radical rate constant for a diverse dataset of 457 water contaminants from 27 various chemical classes. The constricted binary particle swarm optimization and multiple-linear regression (BPSO-MLR) are used to obtain the best model with eight theoretical descriptors. An optimized feed forward neural network (FFNN) is developed to investigate the complex performance of the selected molecular parameters with kHO. Although the FFNN prediction results are more accurate than those obtained using BPSO-MLR, the application of the latter is much more convenient. Various internal and external validation techniques indicate that the obtained models could predict the logarithmic hydroxyl radical rate constants of a large number of water contaminants with less than 4% absolute relative error. Finally, the above-mentioned proposed models are compared to those reported earlier and the structural factors contributing to the AOP degradation efficiency are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. 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.

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

    PubMed

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

    2016-11-08

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

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

    NASA Astrophysics Data System (ADS)

    Pontoppidan, Klaus

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

    The A\\ ^1B_1 \\leftarrow \\tilde{X}\\ ^1A^{\\prime } excitation into the dipole-bound state of the cyanomethyl anion (CH2CN-) 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 \\tilde{X}\\ ^1A^{\\prime } CH2CN- in order to assist in laboratory studies and astronomical observations.

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

    PubMed

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

    2017-02-14

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

  17. Quantitative LC-MS of polymers: determining accurate molecular weight distributions by combined size exclusion chromatography and electrospray mass spectrometry with maximum entropy data processing.

    PubMed

    Gruendling, Till; Guilhaus, Michael; Barner-Kowollik, Christopher

    2008-09-15

    We report on the successful application of size exclusion chromatography (SEC) combined with electrospray ionization mass spectrometry (ESI-MS) and refractive index (RI) detection for the determination of accurate molecular weight distributions of synthetic polymers, corrected for chromatographic band broadening. The presented method makes use of the ability of ESI-MS to accurately depict the peak profiles and retention volumes of individual oligomers eluting from the SEC column, whereas quantitative information on the absolute concentration of oligomers is obtained from the RI-detector only. A sophisticated computational algorithm based on the maximum entropy principle is used to process the data gained by both detectors, yielding an accurate molecular weight distribution, corrected for chromatographic band broadening. Poly(methyl methacrylate) standards with molecular weights up to 10 kDa serve as model compounds. Molecular weight distributions (MWDs) obtained by the maximum entropy procedure are compared to MWDs, which were calculated by a conventional calibration of the SEC-retention time axis with peak retention data obtained from the mass spectrometer. Comparison showed that for the employed chromatographic system, distributions below 7 kDa were only weakly influenced by chromatographic band broadening. However, the maximum entropy algorithm could successfully correct the MWD of a 10 kDa standard for band broadening effects. Molecular weight averages were between 5 and 14% lower than the manufacturer stated data obtained by classical means of calibration. The presented method demonstrates a consistent approach for analyzing data obtained by coupling mass spectrometric detectors and concentration sensitive detectors to polymer liquid chromatography.

  18. 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.

  19. Connecting Fundamental Constants

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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 willmore » 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.« less

  20. Elastic constants and dynamics in nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Humpert, Anja; Allen, Michael P.

    2015-09-01

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

  1. Constant pH Accelerated Molecular Dynamics Investigation of the pH Regulation Mechanism of Dinoflagellate Luciferase.

    PubMed

    Donnan, Patrick H; Ngo, Phong D; Mansoorabadi, Steven O

    2018-01-23

    The bioluminescence reaction in dinoflagellates involves the oxidation of an open-chain tetrapyrrole by the enzyme dinoflagellate luciferase (LCF). The activity of LCF is tightly regulated by pH, where the enzyme is essentially inactive at pH ∼8 and optimally active at pH ∼6. Little is known about the mechanism of LCF or the structure of the active form of the enzyme, although it has been proposed that several intramolecularly conserved histidine residues in the N-terminal region are important for the pH regulation mechanism. Here, constant pH accelerated molecular dynamics was employed to gain insight into the conformational activation of LCF induced by acidification.

  2. Accurate acceleration of kinetic Monte Carlo simulations through the modification of rate constants.

    PubMed

    Chatterjee, Abhijit; Voter, Arthur F

    2010-05-21

    We present a novel computational algorithm called the accelerated superbasin kinetic Monte Carlo (AS-KMC) method that enables a more efficient study of rare-event dynamics than the standard KMC method while maintaining control over the error. In AS-KMC, the rate constants for processes that are observed many times are lowered during the course of a simulation. As a result, rare processes are observed more frequently than in KMC and the time progresses faster. We first derive error estimates for AS-KMC when the rate constants are modified. These error estimates are next employed to develop a procedure for lowering process rates with control over the maximum error. Finally, numerical calculations are performed to demonstrate that the AS-KMC method captures the correct dynamics, while providing significant CPU savings over KMC in most cases. We show that the AS-KMC method can be employed with any KMC model, even when no time scale separation is present (although in such cases no computational speed-up is observed), without requiring the knowledge of various time scales present in the system.

  3. 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.

  4. Resonant vibrational-excitation cross sections and rate constants for low-energy electron scattering by molecular oxygen

    NASA Astrophysics Data System (ADS)

    Laporta, V.; Celiberto, R.; Tennyson, J.

    2013-04-01

    Resonant vibrational-excitation cross sections and rate constants for electron scattering by molecular oxygen are presented. Transitions between all 42 vibrational levels of O_2({X}\\, ^3\\Sigma_g^{-}) are considered. Molecular rotations are parametrized by the rotational quantum number J, which is considered in the range 1-151. The lowest four resonant states of O_2^- , 2Πg, 2Πu, ^4\\Sigma_u^- and ^2\\Sigma_u^- are taken into account. The calculations are performed using the fixed-nuclei R-matrix approach to determine the resonance positions and widths, and the boomerang model to characterize the nuclei motion. Two energy regions below and above 4 eV are investigated: the first one is characterized by sharp structures in the cross section and the second by a broad resonance peaked at 10 eV. The computed cross sections are compared with theoretical and experimental results available in the literature for both energy regions, and are made available for use by modelers. The effect of including rotational motion is found to be non-negligible.

  5. Simple liquid models with corrected dielectric constants

    PubMed Central

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

    2012-01-01

    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 parameterized 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 parameterizations also happen to give better values for other properties, such as the self-diffusion coefficient. We believe that parameterizing fixed-charge solvent models to fit experimental dielectric constants may provide better and more efficient ways to treat solvents in computer simulations. PMID:22397577

  6. Static dielectric constant of water within a bilayer using recent water models: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Meneses-Juárez, Efrain; Rivas-Silva, Juan Francisco; González-Melchor, Minerva

    2018-05-01

    The water confined within a surfactant bilayer is studied using different water models via molecular dynamics simulations. We considered four representative rigid models of water: the SPC/E and the TIP4P/2005, which are commonly used in numerical calculations and the more recent TIP4Q and SPC/ε models, developed to reproduce the dielectric behaviour of pure water. The static dielectric constant of the confined water was analyzed as a function of the temperature for the four models. In all cases it decreases as the temperature increases. Additionally, the static dielectric constant of the bilayer-water system was estimated through its expression in terms of the fluctuations in the total dipole moment, usually applied for isotropic systems. The estimated dielectric was compared with the available experimental data. We found that the TIP4Q and the SPC/ε produce closer values to the experimental data than the other models, particularly at room temperature. It was found that the probability of finding the sodium ion close to the head of the surfactant decreases as the temperature increases, thus the head of the surfactant is more exposed to the interaction with water when the temperature is higher.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zarycz, M. Natalia C., E-mail: mnzarycz@gmail.com; Provasi, Patricio F., E-mail: patricio@unne.edu.ar; Sauer, Stephan P. A., E-mail: sauer@kiku.dk

    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 themore » 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.« less

  8. 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.

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

    PubMed

    Jia, Lijuan; Shen, Zhemin; Su, Pingru

    2016-05-01

    Fenton oxidation is a promising water treatment method to degrade organic pollutants. In this study, 30 different organic compounds were selected and their reaction rate constants (k) were determined for the Fenton oxidation process. Gaussian09 and Material Studio software sets were used to carry out calculations and obtain values of 10 different molecular descriptors for each studied compound. Ferric-oxyhydroxide coagulation experiments were conducted to determine the coagulation percentage. Based upon the adsorption capacity, all of the investigated organic compounds were divided into two groups (Group A and Group B). The percentage adsorption of organic compounds in Group A was less than 15% (wt./wt.) and that in the Group B was higher than 15% (wt./wt.). For Group A, removal of the compounds by oxidation was the dominant process while for Group B, removal by both oxidation and coagulation (as a synergistic process) took place. Results showed that the relationship between the rate constants (k values) and the molecular descriptors of Group A was more pronounced than for Group B compounds. For the oxidation-dominated process, EHOMO and Fukui indices (f(0)x, f(-)x, f(+)x) were the most significant factors. The influence of bond order was more significant for the synergistic process of oxidation and coagulation than for the oxidation-dominated process. The influences of all other molecular descriptors on the synergistic process were weaker than on the oxidation-dominated process. Copyright © 2015. Published by Elsevier B.V.

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

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

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

  11. Solvent fluctuations and nuclear quantum effects modulate the molecular hyperpolarizability of water

    NASA Astrophysics Data System (ADS)

    Liang, Chungwen; Tocci, Gabriele; Wilkins, David M.; Grisafi, Andrea; Roke, Sylvie; Ceriotti, Michele

    2017-07-01

    Second-harmonic scattering (SHS) experiments provide a unique approach to probe noncentrosymmetric environments in aqueous media, from bulk solutions to interfaces, living cells, and tissue. A central assumption made in analyzing SHS experiments is that each molecule scatters light according to a constant molecular hyperpolarizability tensor β(2 ). Here, we investigate the dependence of the molecular hyperpolarizability of water on its environment and internal geometric distortions, in order to test the hypothesis of constant β(2 ). We use quantum chemistry calculations of the hyperpolarizability of a molecule embedded in point-charge environments obtained from simulations of bulk water. We demonstrate that both the heterogeneity of the solvent configurations and the quantum mechanical fluctuations of the molecular geometry introduce large variations in the nonlinear optical response of water. This finding has the potential to change the way SHS experiments are interpreted: In particular, isotopic differences between H2O and D2O could explain recent SHS observations. Finally, we show that a machine-learning framework can predict accurately the fluctuations of the molecular hyperpolarizability. This model accounts for the microscopic inhomogeneity of the solvent and represents a step towards quantitative modeling of SHS experiments.

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

    PubMed

    Wallace, Jason A; Shen, Jana K

    2012-11-14

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

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

    PubMed Central

    Wallace, Jason A.; Shen, Jana K.

    2012-01-01

    Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pKa values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future. PMID:23163362

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

    NASA Astrophysics Data System (ADS)

    Chen, Yongzhi; Chen, Xin; Deng, Yuefan

    2007-07-01

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

  15. Accurate structural and spectroscopic characterization of prebiotic molecules: The neutral and cationic acetyl cyanide and their related species.

    PubMed

    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.

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

    PubMed

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

    2015-10-01

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

  17. Strip dielectric wave guide antenna-for the measurement of dielectric constant of low-loss materials

    NASA Astrophysics Data System (ADS)

    Rastogi, Alok Kumar; Tiwari, A. K.; Shrivastava, R. P.

    1993-07-01

    The value of dielectric constant are the most important parameters in material science technology. In micro-wave and millimeter wave circuits using dielectric materials the values of this parameters should be known accurately. It is observed that the number of methods are reported in litrature, however these methods impose difficulties in experimentation and are not very accurate. In this paper a novel approach to the measurement of the dielectric constant of low loss materials at micro-wave and millimeter wave frequencies has been discussed. In this method by using antenna theory, a metallic strip dielectric guide is taken in to constideration and band reject phenomenon of dielectric antenna is used. Frequency response of an antenna in band reject mode is a function of the dimensional parameters, such as the metallic strip period, the profile of the metallic strip and the dielectric constant of the material used. Hence if one measure the frequency responce of the antenna in band reject mode, the dielectric constant of the material is determined provided all other parameters are known. This method gives a direct measure of dielectric constant and is quite accurate as computer techniques are used for evaluating the dielectric constant. This method verified experimentally also.

  18. A CONSTANT MOLECULAR GAS DEPLETION TIME IN NEARBY DISK GALAXIES

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bigiel, F.; Leroy, A. K.; Walter, F.

    2011-04-01

    We combine new sensitive, wide-field CO data from the HERACLES survey with ultraviolet and infrared data from GALEX and Spitzer to compare the surface densities of H{sub 2}, {Sigma}{sub H2}, and the recent star formation rate, {Sigma}{sub SFR}, over many thousands of positions in 30 nearby disk galaxies. We more than quadruple the size of the galaxy sample compared to previous work and include targets with a wide range of galaxy properties. Even though the disk galaxies in this study span a wide range of properties, we find a strong, and approximately linear correlation between {Sigma}{sub SFR} and {Sigma}{sub H2}more » at our common resolution of 1 kpc. This implies a roughly constant median H{sub 2} consumption time, {tau}{sup H2}{sub Dep} = {Sigma}{sub H2}/{Sigma}{sub SFR}, of {approx}2.35 Gyr (including heavy elements) across our sample. At 1 kpc resolution, there is only a weak correlation between {Sigma}{sub H2} and {tau}{sup H2}{sub Dep} over the range {Sigma}{sub H2} {approx} 5-100 M{sub sun} pc{sup -2}, which is probed by our data. We compile a broad set of literature measurements that have been obtained using a variety of star formation tracers, sampling schemes, and physical scales and show that overall, these data yield almost exactly the same results, although with more scatter. We interpret these results as strong, albeit indirect evidence that star formation proceeds in a uniform way in giant molecular clouds in the disks of spiral galaxies.« less

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  20. Developments toward more accurate molecular modeling of liquids

    NASA Astrophysics Data System (ADS)

    Evans, Tom J.

    2000-12-01

    The general goal of this research has been to improve upon existing combined quantum mechanics/molecular mechanics (QM/MM) methodologies. Error weighting functions have been introduced into the perturbative Monte Carlo (PMC) method for use with QM/MM. The PMC approach, introduced earlier, provides a means to reduce the number of full self-consistent field (SCF) calculations in simulations using the QM/MM potential by evoking perturbation theory to calculate energy changes due to displacements of a MM molecule. This will allow the ab initio QM/MM approach to be applied to systems that require more advanced, computationally demanding treatments of the QM and/or MM regions. Efforts have also been made to improve the accuracy of the representation of the solvent molecules usually represented by MM force fields. Results from an investigation of the applicability of the embedded density functional theory (EDFT) for studying physical properties of solutions will be presented. In this approach, the solute wavefunction is solved self- consistently in the field of individually frozen electron-density solvent molecules. To test its accuracy, the potential curves for interactions between Li+, Cl- and H2O with a single frozen-density H 2O molecule in different orientations have been calculated. With the development of the more sophisticated effective fragment potential (EFP) representation of solvent molecules, a QM/EFP technique was created. This hybrid QM/EFP approach was used to investigate the solvation of Li + by small clusters of water, as a test case for larger ionic dusters. The EFP appears to provide an accurate representation of the strong interactions that exist between Li+ and H2O. With the QM/EFP methodology comes an increased computational expense, resulting in an even greater need to rely on the PMC approach. However, while including the PMC into the hybrid QM/EFP technique, it was discovered that the previous implementation of the PMC was done incorrectly

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu

    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.more » 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.« less

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

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2014-05-16

    Accurate values for the Henry's law constants are essential to describe the environmental dynamics of a solute, but substantial errors are recognized in many reported data due to practical difficulties in measuring solubility and/or vapor pressure. Despite such awareness, validation of experimental approaches has scarcely been made. An experimental approach based on thermal desorption-gas chromatography-mass spectrometery (TD-GC-MS) method was developed to concurrently allow the accurate determination of target compounds from the headspace and aqueous samples in closed equilibrated system. The analysis of six aromatics and eight non-aromatic oxygenates was then carried out in a static headspace mode. An estimation of the potential bias and mass balance (i.e., sum of mass measured individually from gas and liquid phases vs. the mass initially added to the system) demonstrates compound-specific phase dependency so that the best results are obtained by aqueous (less soluble aromatics) and headspace analysis (more soluble non-aromatics). Accordingly, we were able to point to the possible sources of biases in previous studies and provide the best estimates for the Henry's constants (Matm(-1)): benzene (0.17), toluene (0.15), p-xylene (0.13), m-xylene (0.13), o-xylene (0.19), styrene (0.27); propionaldehyde (9.26), butyraldehyde (6.19), isovaleraldehyde (2.14), n-valeraldehyde (3.98), methyl ethyl ketone (10.5), methyl isobutyl ketone (3.93), n-butyl acetate (2.41), and isobutyl alcohol (22.2). Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Accurate description of charged excitations in molecular solids from embedded many-body perturbation theory

    NASA Astrophysics Data System (ADS)

    Li, Jing; D'Avino, Gabriele; Duchemin, Ivan; Beljonne, David; Blase, Xavier

    2018-01-01

    We present a novel hybrid quantum/classical approach to the calculation of charged excitations in molecular solids based on the many-body Green's function G W formalism. Molecules described at the G W level are embedded into the crystalline environment modeled with an accurate classical polarizable scheme. This allows the calculation of electron addition and removal energies in the bulk and at crystal surfaces where charged excitations are probed in photoelectron experiments. By considering the paradigmatic case of pentacene and perfluoropentacene crystals, we discuss the different contributions from intermolecular interactions to electronic energy levels, distinguishing between polarization, which is accounted for combining quantum and classical polarizabilities, and crystal field effects, that can impact energy levels by up to ±0.6 eV. After introducing band dispersion, we achieve quantitative agreement (within 0.2 eV) on the ionization potential and electron affinity measured at pentacene and perfluoropentacene crystal surfaces characterized by standing molecules.

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

    PubMed Central

    2015-01-01

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

  5. Virtual screening using molecular simulations.

    PubMed

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

    2011-06-01

    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 of 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 whereas 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. Copyright © 2011 Wiley-Liss, Inc.

  6. High-Accuracy Quartic Force Field Calculations for the Spectroscopic Constants and Vibrational Frequencies of 1(exp 1)A' l-C3H(-): A Possible Link to Lines Observed in the Horsehead Nebula PDR

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

    It has been shown that rotational lines observed in the Horsehead nebula photon-dominated-region (PDR) are probably not caused by l-C3H+, as was originally suggested. In the search for viable alternative candidate carriers, quartic force fields are employed here to provide highly accurate rotational constants, as well as fundamental vibrational frequencies, for another candidate carrier: 1 (sup 1)A' C3H(-). The ab initio computed spectroscopic constants provided in this work are, compared to those necessary to define the observed lines, as accurate as the computed spectroscopic constants for many of the known interstellar anions. Additionally, the computed D-eff for C3H(-) is three times closer to the D deduced from the observed Horsehead nebula lines relative to l-C3H(+). As a result, 1 (sup 1)A' C3H(-). is a more viable candidate for these observed rotational transitions and would be the seventh confirmed interstellar anion detected within the past decade and the first C(sub n)H(-) molecular anion with an odd n.

  7. Strong resetting of the mammalian clock by constant light followed by constant darkness

    PubMed Central

    Chen, Rongmin; Seo, Dong-oh; Bell, Elijah; von Gall, Charlotte; Lee, Choogon

    2008-01-01

    The mammalian molecular circadian clock in the suprachiasmatic nuclei (SCN) regulates locomotor activity rhythms as well as clocks in peripheral tissues (Reppert and Weaver, 2002; Ko and Takahashi, 2006). Constant light (LL) can induce behavioral and physiological arrhythmicity, by desynchronizing clock cells in the SCN (Ohta et al., 2005). We examined how the disordered clock cells resynchronize by probing the molecular clock and measuring behavior in mice transferred from LL to constant darkness (DD). The circadian locomotor activity rhythms disrupted in LL become robustly rhythmic again from the beginning of DD, and the starting phase of the rhythm in DD is specific, not random, suggesting that the desynchronized clock cells are quickly reset in an unconventional manner by the L:D transition. By measuring mPERIOD protein rhythms, we showed that the SCN and peripheral tissue clocks quickly become rhythmic again in phase with the behavioral rhythms. We propose that this resetting mechanism may be different from conventional phase shifting, which involves light-induction of Period genes (Albrecht et al., 1997; Shearman et al., 1997; Shigeyoshi et al., 1997). Using our functional insights, we could shift the circadian phase of locomotor activity rhythms by 12 hours using a 15-hour LL treatment: essentially producing phase reversal by a single light pulse, a feat that has not been reported previously in wild-type mice and that has potential clinical utility. PMID:19005049

  8. Molecular processes in a high temperature shock layer

    NASA Technical Reports Server (NTRS)

    Guberman, S. L.

    1984-01-01

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

  9. Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging.

    PubMed

    Dracínský, Martin; Kaminský, Jakub; Bour, Petr

    2009-03-07

    Relative importance of anharmonic corrections to molecular vibrational energies, nuclear magnetic resonance (NMR) chemical shifts, and J-coupling constants was assessed for a model set of methane derivatives, differently charged alanine forms, and sugar models. Molecular quartic force fields and NMR parameter derivatives were obtained quantum mechanically by a numerical differentiation. In most cases the harmonic vibrational function combined with the property second derivatives provided the largest correction of the equilibrium values, while anharmonic corrections (third and fourth energy derivatives) were found less important. The most computationally expensive off-diagonal quartic energy derivatives involving four different coordinates provided a negligible contribution. The vibrational corrections of NMR shifts were small and yielded a convincing improvement only for very accurate wave function calculations. For the indirect spin-spin coupling constants the averaging significantly improved already the equilibrium values obtained at the density functional theory level. Both first and complete second shielding derivatives were found important for the shift corrections, while for the J-coupling constants the vibrational parts were dominated by the diagonal second derivatives. The vibrational corrections were also applied to some isotopic effects, where the corrected values reasonably well reproduced the experiment, but only if a full second-order expansion of the NMR parameters was included. Contributions of individual vibrational modes for the averaging are discussed. Similar behavior was found for the methane derivatives, and for the larger and polar molecules. The vibrational averaging thus facilitates interpretation of previous experimental results and suggests that it can make future molecular structural studies more reliable. Because of the lengthy numerical differentiation required to compute the NMR parameter derivatives their analytical implementation in

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  11. An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

    1995-01-01

    A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

  12. ESTIMATION OF CARBOXYLIC ACID ESTER HYDROLYSIS RATE CONSTANTS

    EPA Science Inventory

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

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

    PubMed Central

    Füsti-Molnár, László; Merz, Kenneth M.

    2008-01-01

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

  14. Accurate sub-millimetre rest frequencies for HOCO+ and DOCO+ ions

    NASA Astrophysics Data System (ADS)

    Bizzocchi, L.; Lattanzi, V.; Laas, J.; Spezzano, S.; Giuliano, B. M.; Prudenzano, D.; Endres, C.; Sipilä, O.; Caselli, P.

    2017-06-01

    Context. HOCO+ is a polar molecule that represents a useful proxy for its parent molecule CO2, which is not directly observable in the cold interstellar medium. This cation has been detected towards several lines of sight, including massive star forming regions, protostars, and cold cores. Despite the obvious astrochemical relevance, protonated CO2 and its deuterated variant, DOCO+, still lack an accurate spectroscopic characterisation. Aims: The aim of this work is to extend the study of the ground-state pure rotational spectra of HOCO+ and DOCO+ well into the sub-millimetre region. Methods: Ground-state transitions have been recorded in the laboratory using a frequency-modulation absorption spectrometer equipped with a free-space glow-discharge cell. The ions were produced in a low-density, magnetically confined plasma generated in a suitable gas mixture. The ground-state spectra of HOCO+ and DOCO+ have been investigated in the 213-967 GHz frequency range; 94 new rotational transitions have been detected. Additionally, 46 line positions taken from the literature have been accurately remeasured. Results: The newly measured lines have significantly enlarged the available data sets for HOCO+ and DOCO+, thus enabling the determination of highly accurate rotational and centrifugal distortion parameters. Our analysis shows that all HOCO+ lines with Ka ≥ 3 are perturbed by a ro-vibrational interaction that couples the ground state with the v5 = 1 vibrationally excited state. This resonance has been explicitly treated in the analysis in order to obtain molecular constants with clear physical meaning. Conclusions: The improved sets of spectroscopic parameters provide enhanced lists of very accurate sub-millimetre rest frequencies of HOCO+ and DOCO+ for astrophysical applications. These new data challenge a recent tentative identification of DOCO+ towards a pre-stellar core. Supplementary tables are only available at the CDS via anonymous ftp to http

  15. Tolman lengths and rigidity constants of multicomponent fluids: Fundamental theory and numerical examples

    NASA Astrophysics Data System (ADS)

    Aasen, Ailo; Blokhuis, Edgar M.; Wilhelmsen, Øivind

    2018-05-01

    The curvature dependence of the surface tension can be described by the Tolman length (first-order correction) and the rigidity constants (second-order corrections) through the Helfrich expansion. We present and explain the general theory for this dependence for multicomponent fluids and calculate the Tolman length and rigidity constants for a hexane-heptane mixture by use of square gradient theory. We show that the Tolman length of multicomponent fluids is independent of the choice of dividing surface and present simple formulae that capture the change in the rigidity constants for different choices of dividing surface. For multicomponent fluids, the Tolman length, the rigidity constants, and the accuracy of the Helfrich expansion depend on the choice of path in composition and pressure space along which droplets and bubbles are considered. For the hexane-heptane mixture, we find that the most accurate choice of path is the direction of constant liquid-phase composition. For this path, the Tolman length and rigidity constants are nearly linear in the mole fraction of the liquid phase, and the Helfrich expansion represents the surface tension of hexane-heptane droplets and bubbles within 0.1% down to radii of 3 nm. The presented framework is applicable to a wide range of fluid mixtures and can be used to accurately represent the surface tension of nanoscopic bubbles and droplets.

  16. Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteases.

    PubMed

    Sadiq, S Kashif; Wright, David W; Kenway, Owain A; Coveney, Peter V

    2010-05-24

    Accurate calculation of important thermodynamic properties, such as macromolecular binding free energies, is one of the principal goals of molecular dynamics simulations. However, single long simulation frequently produces incorrectly converged quantitative results due to inadequate sampling of conformational space in a feasible wall-clock time. Multiple short (ensemble) simulations have been shown to explore conformational space more effectively than single long simulations, but the two methods have not yet been thermodynamically compared. Here we show that, for end-state binding free energy determination methods, ensemble simulations exhibit significantly enhanced thermodynamic sampling over single long simulations and result in accurate and converged relative binding free energies that are reproducible to within 0.5 kcal/mol. Completely correct ranking is obtained for six HIV-1 protease variants bound to lopinavir with a correlation coefficient of 0.89 and a mean relative deviation from experiment of 0.9 kcal/mol. Multidrug resistance to lopinavir is enthalpically driven and increases through a decrease in the protein-ligand van der Waals interaction, principally due to the V82A/I84V mutation, and an increase in net electrostatic repulsion due to water-mediated disruption of protein-ligand interactions in the catalytic region. Furthermore, we correctly rank, to within 1 kcal/mol of experiment, the substantially increased chemical potency of lopinavir binding to the wild-type protease compared to saquinavir and show that lopinavir takes advantage of a decreased net electrostatic repulsion to confer enhanced binding. Our approach is dependent on the combined use of petascale computing resources and on an automated simulation workflow to attain the required level of sampling and turn around time to obtain the results, which can be as little as three days. This level of performance promotes integration of such methodology with clinical decision support systems for

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

    PubMed

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

    2006-01-28

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

  18. Elasticity of crystalline molecular explosives

    DOE PAGES

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

    2015-04-14

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

  19. Proton dissociation properties of arylphosphonates: Determination of accurate Hammett equation parameters.

    PubMed

    Dargó, Gergő; Bölcskei, Adrienn; Grün, Alajos; Béni, Szabolcs; Szántó, Zoltán; Lopata, Antal; Keglevich, György; Balogh, György T

    2017-09-05

    Determination of the proton dissociation constants of several arylphosphonic acid derivatives was carried out to investigate the accuracy of the Hammett equations available for this family of compounds. For the measurement of the pK a values modern, accurate methods, such as the differential potentiometric titration and NMR-pH titration were used. We found our results significantly different from the pK a values reported before (pK a1 : MAE = 0.16 pK a2 : MAE=0.59). Based on our recently measured pK a values, refined Hammett equations were determined that might be used for predicting highly accurate ionization constants of newly synthesized compounds (pK a1 =1.70-0.894σ, pK a2 =6.92-0.934σ). Copyright © 2017 Elsevier B.V. All rights reserved.

  20. 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.

  1. Toward more accurate loss tangent measurements in reentrant cavities

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Moyer, R. D.

    1980-05-01

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

  2. Accurate Solution of Multi-Region Continuum Biomolecule Electrostatic Problems Using the Linearized Poisson-Boltzmann Equation with Curved Boundary Elements

    PubMed Central

    Altman, Michael D.; Bardhan, Jaydeep P.; White, Jacob K.; Tidor, Bruce

    2009-01-01

    We present a boundary-element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson–Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion-exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix-vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near-singular integrals over the curved boundary elements. Finally, we present a general boundary-integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite-difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid-binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved-element BEM is important when more sophisticated techniques, such as non-rigid-binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry

  3. Interaction potential for indium phosphide: a molecular dynamics and first-principles study of the elastic constants, generalized stacking fault and surface energies.

    PubMed

    Branicio, Paulo Sergio; Rino, José Pedro; Gan, Chee Kwan; Tsuzuki, Hélio

    2009-03-04

    Indium phosphide is investigated using molecular dynamics (MD) simulations and density-functional theory calculations. MD simulations use a proposed effective interaction potential for InP fitted to a selected experimental dataset of properties. The potential consists of two- and three-body terms that represent atomic-size effects, charge-charge, charge-dipole and dipole-dipole interactions as well as covalent bond bending and stretching. Predictions are made for the elastic constants as a function of density and temperature, the generalized stacking fault energy and the low-index surface energies.

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

    PubMed

    Schneider, André; Nguyen, Christophe

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  6. Flux Renormalization in Constant Power Burnup Calculations

    DOE PAGES

    Isotalo, Aarno E.; Aalto Univ., Otaniemi; Davidson, Gregory G.; ...

    2016-06-15

    To more accurately represent the desired power in a constant power burnup calculation, the depletion steps of the calculation can be divided into substeps and the neutron flux renormalized on each substep to match the desired power. Here, this paper explores how such renormalization should be performed, how large a difference it makes, and whether using renormalization affects results regarding the relative performance of different neutronics–depletion coupling schemes. When used with older coupling schemes, renormalization can provide a considerable improvement in overall accuracy. With previously published higher order coupling schemes, which are more accurate to begin with, renormalization has amore » much smaller effect. Finally, while renormalization narrows the differences in the accuracies of different coupling schemes, their order of accuracy is not affected.« less

  7. Precision Timing of PSR J0437-4715: An Accurate Pulsar Distance, a High Pulsar Mass, and a Limit on the Variation of Newton's Gravitational Constant

    NASA Astrophysics Data System (ADS)

    Verbiest, J. P. W.; Bailes, M.; van Straten, W.; Hobbs, G. B.; Edwards, R. T.; Manchester, R. N.; Bhat, N. D. R.; Sarkissian, J. M.; Jacoby, B. A.; Kulkarni, S. R.

    2008-05-01

    Analysis of 10 years of high-precision timing data on the millisecond pulsar PSR J0437-4715 has resulted in a model-independent kinematic distance based on an apparent orbital period derivative, dot Pb , determined at the 1.5% level of precision (Dk = 157.0 +/- 2.4 pc), making it one of the most accurate stellar distance estimates published to date. The discrepancy between this measurement and a previously published parallax distance estimate is attributed to errors in the DE200 solar system ephemerides. The precise measurement of dot Pb allows a limit on the variation of Newton's gravitational constant, |Ġ/G| <= 23 × 10-12 yr-1. We also constrain any anomalous acceleration along the line of sight to the pulsar to |a⊙/c| <= 1.5 × 10-18 s-1 at 95% confidence, and derive a pulsar mass, mpsr = 1.76 +/- 0.20 M⊙, one of the highest estimates so far obtained.

  8. Instanton rate constant calculations close to and above the crossover temperature.

    PubMed

    McConnell, Sean; Kästner, Johannes

    2017-11-15

    Canonical instanton theory is known to overestimate the rate constant close to a system-dependent crossover temperature and is inapplicable above that temperature. We compare the accuracy of the reaction rate constants calculated using recent semi-classical rate expressions to those from canonical instanton theory. We show that rate constants calculated purely from solving the stability matrix for the action in degrees of freedom orthogonal to the instanton path is not applicable at arbitrarily low temperatures and use two methods to overcome this. Furthermore, as a by-product of the developed methods, we derive a simple correction to canonical instanton theory that can alleviate this known overestimation of rate constants close to the crossover temperature. The combined methods accurately reproduce the rate constants of the canonical theory along the whole temperature range without the spurious overestimation near the crossover temperature. We calculate and compare rate constants on three different reactions: H in the Müller-Brown potential, methylhydroxycarbene → acetaldehyde and H 2  + OH → H + H 2 O. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  9. Integrating a Smartphone and Molecular Modeling for Determining the Binding Constant and Stoichiometry Ratio of the Iron(II)-Phenanthroline Complex: An Activity for Analytical and Physical Chemistry Laboratories

    ERIC Educational Resources Information Center

    de Morais, Camilo de L. M.; Silva, Se´rgio R. B.; Vieira, Davi S.; Lima, Ka´ssio M. G.

    2016-01-01

    The binding constant and stoichiometry ratio for the formation of iron(II)-(1,10-phenanthroline) or iron(II)-o-phenanthroline complexes has been determined by a combination of a low-cost analytical method using a smartphone and a molecular modeling method as a laboratory experiment designed for analytical and physical chemistry courses. Intensity…

  10. 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%.

  11. Advances in the analysis and design of constant-torque springs

    NASA Technical Reports Server (NTRS)

    McGuire, John R.; Yura, Joseph A.

    1996-01-01

    In order to improve the design procedure of constant-torque springs used in aerospace applications, several new analysis techniques have been developed. These techniques make it possible to accurately construct a torque-rotation curve for any general constant-torque spring configuration. These new techniques allow for friction in the system to be included in the analysis, an area of analysis that has heretofore been unexplored. The new analysis techniques also include solutions for the deflected shape of the spring as well as solutions for drum and roller support reaction forces. A design procedure incorporating these new capabilities is presented.

  12. Examination of Effective Dielectric Constants Derived from Non-Spherical Melting Hydrometeor

    NASA Astrophysics Data System (ADS)

    Liao, L.; Meneghini, R.

    2009-04-01

    The bright band, a layer of enhanced radar echo associated with melting hydrometeors, is often observed in stratiform rain. Understanding the microphysical properties of melting hydrometeors and their scattering and propagation effects is of great importance in accurately estimating parameters of the precipitation from spaceborne radar and radiometers. However, one of the impediments in the study of the radar signature of the melting layer is the determination of effective dielectric constants of melting hydrometeors. Although a number of mixing formulas are available to compute the effective dielectric constants, their results vary to a great extent when water is a component of the mixture, such as in the case of melting snow. It is also physically unclear as to how to select among these various formulas. Furthermore, the question remains as to whether these mixing formulas can be applied to computations of radar polarimetric parameters from non-spherical melting particles. Recently, several approaches using numerical methods have been developed to derive the effective dielectric constants of melting hydrometeors, i.e., mixtures consisting of air, ice and water, based on more realistic melting models of particles, in which the composition of the melting hydrometeor is divided into a number of identical cells. Each of these cells is then assigned in a probabilistic way to be water, ice or air according to the distribution of fractional water contents for a particular particle. While the derived effective dielectric constants have been extensively tested at various wavelengths over a range of particle sizes, these numerical experiments have been restricted to the co-polarized scattering parameters from spherical particles. As polarimetric radar has been increasingly used in the study of microphysical properties of hydrometeors, an extension of the theory to polarimetric variables should provide additional information on melting processes. To account for polarimetric

  13. Theoretical rate constants of super-exchange hole transfer and thermally induced hopping in DNA.

    PubMed

    Shimazaki, Tomomi; Asai, Yoshihiro; Yamashita, Koichi

    2005-01-27

    Recently, the electronic properties of DNA have been extensively studied, because its conductivity is important not only to the study of fundamental biological problems, but also in the development of molecular-sized electronics and biosensors. We have studied theoretically the reorganization energies, the activation energies, the electronic coupling matrix elements, and the rate constants of hole transfer in B-form double-helix DNA in water. To accommodate the effects of DNA nuclear motions, a subset of reaction coordinates for hole transfer was extracted from classical molecular dynamics (MD) trajectories of DNA in water and then used for ab initio quantum chemical calculations of electron coupling constants based on the generalized Mulliken-Hush model. A molecular mechanics (MM) method was used to determine the nuclear Franck-Condon factor. The rate constants for two types of mechanisms of hole transfer-the thermally induced hopping (TIH) and the super-exchange mechanisms-were determined based on Marcus theory. We found that the calculated matrix elements are strongly dependent on the conformations of the nucleobase pairs of hole-transferable DNA and extend over a wide range of values for the "rise" base-step parameter but cluster around a particular value for the "twist" parameter. The calculated activation energies are in good agreement with experimental results. Whereas the rate constant for the TIH mechanism is not dependent on the number of A-T nucleobase pairs that act as a bridge, the rate constant for the super-exchange process rapidly decreases when the length of the bridge increases. These characteristic trends in the calculated rate constants effectively reproduce those in the experimental data of Giese et al. [Nature 2001, 412, 318]. The calculated rate constants were also compared with the experimental results of Lewis et al. [Nature 2000, 406, 51].

  14. Elongational flow of polymer melts at constant strain rate, constant stress and constant force

    NASA Astrophysics Data System (ADS)

    Wagner, Manfred H.; Rolón-Garrido, Víctor H.

    2013-04-01

    Characterization of polymer melts in elongational flow is typically performed at constant elongational rate or rarely at constant tensile stress conditions. One of the disadvantages of these deformation modes is that they are hampered by the onset of "necking" instabilities according to the Considère criterion. Experiments at constant tensile force have been performed even more rarely, in spite of the fact that this deformation mode is free from necking instabilities and is of considerable industrial relevance as it is the correct analogue of steady fiber spinning. It is the objective of the present contribution to present for the first time a full experimental characterization of a long-chain branched polyethylene melt in elongational flow. Experiments were performed at constant elongation rate, constant tensile stress and constant tensile force by use of a Sentmanat Extensional Rheometer (SER) in combination with an Anton Paar MCR301 rotational rheometer. The accessible experimental window and experimental limitations are discussed. The experimental data are modelled by using the Wagner I model. Predictions of the steady-start elongational viscosity in constant strain rate and creep experiments are found to be identical, albeit only by extrapolation of the experimental data to Hencky strains of the order of 6. For constant stress experiments, a minimum in the strain rate and a corresponding maximum in the elongational viscosity is found at a Hencky strain of the order of 3, which, although larger than the steady-state value, follows roughly the general trend of the steady-state elongational viscosity. The constitutive analysis also reveals that constant tensile force experiments indicate a larger strain hardening potential than seen in constant elongation rate or constant tensile stress experiments. This may be indicative of the effect of necking under constant elongation rate or constant tensile stress conditions according to the Considère criterion.

  15. Steady-State Computation of Constant Rotational Rate Dynamic Stability Derivatives

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Green, Lawrence L.

    2000-01-01

    Dynamic stability derivatives are essential to predicting the open and closed loop performance, stability, and controllability of aircraft. Computational determination of constant-rate dynamic stability derivatives (derivatives of aircraft forces and moments with respect to constant rotational rates) is currently performed indirectly with finite differencing of multiple time-accurate computational fluid dynamics solutions. Typical time-accurate solutions require excessive amounts of computational time to complete. Formulating Navier-Stokes (N-S) equations in a rotating noninertial reference frame and applying an automatic differentiation tool to the modified code has the potential for directly computing these derivatives with a single, much faster steady-state calculation. The ability to rapidly determine static and dynamic stability derivatives by computational methods can benefit multidisciplinary design methodologies and reduce dependency on wind tunnel measurements. The CFL3D thin-layer N-S computational fluid dynamics code was modified for this study to allow calculations on complex three-dimensional configurations with constant rotation rate components in all three axes. These CFL3D modifications also have direct application to rotorcraft and turbomachinery analyses. The modified CFL3D steady-state calculation is a new capability that showed excellent agreement with results calculated by a similar formulation. The application of automatic differentiation to CFL3D allows the static stability and body-axis rate derivatives to be calculated quickly and exactly.

  16. 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.

  17. Molecular beam electric resonance study of KCN, K 13CN and KC 15N

    NASA Astrophysics Data System (ADS)

    van Vaals, J. J.; Leo Meerts, W.; Dymanus, A.

    1984-08-01

    The microwave spectra of the isotopic species K 13CN and KC 15N have been investigated by molecular beam electric resonance spectroscopy, using the seeded beam technique. For both isotopic species about 20 rotational transitions originating in the ground vibrational state were observed in the frequency range 9-38 GHz. The observed transitions were fitted to an asymmetric rotor model to determine the three rotational, as well as the five quartic and three sextic centrifugal distortion constants. The hyperfine spectrum of KCN has been unravelled with the help of microwave-microwave double-resonance techniques. One hundred and forty hyperfine transitions in 11 rotational transitions have been assigned. The hyperfine structures of K 13CN and KC 15N were also studied. For all three isotopic species the quadrupole coupling constants and some spin-rotation coupling constants could be deduced. The rotational constants of the 13C and 15N isotopically substituted species of potassium cyanide, combined with those of the normal isotopic species (determined more accurately in this work), allowed an accurate and unambiguous evaluation of the structure, which was confirmed to be T shaped. Both the effective structure of the ground vibrational state and the substitution structure were evaluated. The results for the effective structural parameters are r CN = 1.169(3) Å, r KC = 2.716(9) Å, and r KN = 2.549(9) Å. The values obtained for the principal hyperfine coupling constant eQqz(N), the angle between the CN axis and zN, and the bond length rCN indicate that in gaseous potassium cyanide the CN group can be considered as an almost unperturbed CN - ion.

  18. Accurate density functional prediction of molecular electron affinity with the scaling corrected Kohn–Sham frontier orbital energies

    NASA Astrophysics Data System (ADS)

    Zhang, DaDi; Yang, Xiaolong; Zheng, Xiao; Yang, Weitao

    2018-04-01

    Electron affinity (EA) is the energy released when an additional electron is attached to an atom or a molecule. EA is a fundamental thermochemical property, and it is closely pertinent to other important properties such as electronegativity and hardness. However, accurate prediction of EA is difficult with density functional theory methods. The somewhat large error of the calculated EAs originates mainly from the intrinsic delocalisation error associated with the approximate exchange-correlation functional. In this work, we employ a previously developed non-empirical global scaling correction approach, which explicitly imposes the Perdew-Parr-Levy-Balduz condition to the approximate functional, and achieve a substantially improved accuracy for the calculated EAs. In our approach, the EA is given by the scaling corrected Kohn-Sham lowest unoccupied molecular orbital energy of the neutral molecule, without the need to carry out the self-consistent-field calculation for the anion.

  19. Combining Graphical and Analytical Methods with Molecular Simulations To Analyze Time-Resolved FRET Measurements of Labeled Macromolecules Accurately

    PubMed Central

    2017-01-01

    Förster resonance energy transfer (FRET) measurements from a donor, D, to an acceptor, A, fluorophore are frequently used in vitro and in live cells to reveal information on the structure and dynamics of DA labeled macromolecules. Accurate descriptions of FRET measurements by molecular models are complicated because the fluorophores are usually coupled to the macromolecule via flexible long linkers allowing for diffusional exchange between multiple states with different fluorescence properties caused by distinct environmental quenching, dye mobilities, and variable DA distances. It is often assumed for the analysis of fluorescence intensity decays that DA distances and D quenching are uncorrelated (homogeneous quenching by FRET) and that the exchange between distinct fluorophore states is slow (quasistatic). This allows us to introduce the FRET-induced donor decay, εD(t), a function solely depending on the species fraction distribution of the rate constants of energy transfer by FRET, for a convenient joint analysis of fluorescence decays of FRET and reference samples by integrated graphical and analytical procedures. Additionally, we developed a simulation toolkit to model dye diffusion, fluorescence quenching by the protein surface, and FRET. A benchmark study with simulated fluorescence decays of 500 protein structures demonstrates that the quasistatic homogeneous model works very well and recovers for single conformations the average DA distances with an accuracy of < 2%. For more complex cases, where proteins adopt multiple conformations with significantly different dye environments (heterogeneous case), we introduce a general analysis framework and evaluate its power in resolving heterogeneities in DA distances. The developed fast simulation methods, relying on Brownian dynamics of a coarse-grained dye in its sterically accessible volume, allow us to incorporate structural information in the decay analysis for heterogeneous cases by relating dye states

  20. High-level theoretical study of the reaction between hydroxyl and ammonia: Accurate rate constants from 200 to 2500 K

    NASA Astrophysics Data System (ADS)

    Nguyen, Thanh Lam; Stanton, John F.

    2017-10-01

    Hydrogen abstraction from NH3 by OH to produce H2O and NH2—an important reaction in combustion of NH3 fuel—was studied with a theoretical approach that combines high level quantum chemistry and advanced chemical kinetics methods. Thermal rate constants calculated from first principles agree well (within 5%-20%) with available experimental data over a temperature range that extends from 200 to 2500 K. Quantum mechanical tunneling effects were found to be important; they lead to a decided curvature and non-Arrhenius behavior for the rate constant.

  1. High-level theoretical study of the reaction between hydroxyl and ammonia: Accurate rate constants from 200 to 2500 K.

    PubMed

    Nguyen, Thanh Lam; Stanton, John F

    2017-10-21

    Hydrogen abstraction from NH 3 by OH to produce H 2 O and NH 2 -an important reaction in combustion of NH 3 fuel-was studied with a theoretical approach that combines high level quantum chemistry and advanced chemical kinetics methods. Thermal rate constants calculated from first principles agree well (within 5%-20%) with available experimental data over a temperature range that extends from 200 to 2500 K. Quantum mechanical tunneling effects were found to be important; they lead to a decided curvature and non-Arrhenius behavior for the rate constant.

  2. High-level theoretical study of the reaction between hydroxyl and ammonia: Accurate rate constants from 200 to 2500 K

    DOE PAGES

    Nguyen, Thanh Lam; Stanton, John F.

    2017-06-02

    Hydrogen abstraction from NH 3 by OH to produce H 2O and NH 2 — an important reaction in combustion of NH 3 fuel — was studied with a theoretical approach that combines high level quantum chemistry and advanced chemical kinetics methods. Thermal rate constants calculated from first principles agree well (within 5 to 20%) with available experimental data over a temperature range that extends from 200 to 2500 K. Here, quantum mechanical tunneling effects were found to be important; they lead to a decided curvature and non-Arrhenius behavior for the rate constant.

  3. FOREWORD: International determination of the Avogadro constant International determination of the Avogadro constant

    NASA Astrophysics Data System (ADS)

    Massa, Enrico; Nicolaus, Arnold

    2011-04-01

    This issue of Metrologia collects papers about the results of an international research project aimed at the determination of the Avogadro constant, NA, by counting the atoms in a silicon crystal highly enriched with the isotope 28Si. Fifty years ago, Egidi [1] thought about realizing an atomic mass standard. In 1965, Bonse and Hart [2] operated the first x-ray interferometer, thus paving the way to the achievement of Egidi's dream, and soon Deslattes et al [3] completed the first counting of the atoms in a natural silicon crystal. The present project, outlined by Zosi [4] in 1983, began in 2004 by combining the experiences and capabilities of the BIPM, INRIM, IRMM, NIST, NPL, NMIA, NMIJ and PTB. The start signal, ratified by a memorandum of understanding, was a contract for the production of a silicon crystal highly enriched with 28Si. The enrichment process was undertaken by the Central Design Bureau of Machine Building in St Petersburg. Subsequently, a polycrystal was grown in the Institute of Chemistry of High-Purity Substances of the Russian Academy of Sciences in Nizhny Novgorod and a 28Si boule was grown and purified by the Leibniz-Institut für Kristallzüchtung in Berlin. Isotope enrichment made it possible to apply isotope dilution mass spectroscopy, to determine the Avogadro constant with unprecedented accuracy, and to fulfil Egidi's dream. To convey Egidi's 'fantasy' into practice, two 28Si kilogram prototypes shaped as quasi-perfect spheres were manufactured by the Australian Centre for Precision Optics; their isotopic composition, molar mass, mass, volume, density and lattice parameter were accurately determined and their surfaces were chemically and physically characterized at the atomic scale. The paper by Andreas et al reviews the work carried out; it collates all the findings and illustrates how Avogadro's constant was obtained. Impurity concentration and gradients in the enriched crystal were measured by infrared spectroscopy and taken into

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Oba, Yuki; Kawatsu, Tsutomu; Tachikawa, Masanori, E-mail: tachi@yokohama-cu.ac.jp

    2016-08-14

    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 twomore » 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.« less

  5. Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

    DOE PAGES

    Radak, Brian K.; Roux, Benoît

    2016-10-07

    Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance.more » An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.« less

  6. 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.

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

    PubMed

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

    2017-04-24

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

  8. Defect-induced change of temperature-dependent elastic constants in BCC iron

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gao, N.; Setyawan, W.; Zhang, S. H.

    2017-07-01

    The effects of radiation-induced defects (randomly distributed vacancies, voids, and interstitial dislocation loops) on temperature-dependent elastic constants, C11, C12, and C44 in BCC iron, are studied with molecular dynamics method. The elastic constants are found to decrease with increasing temperatures for all cases containing different defects. The presence of vacancies, voids, or interstitial loops further decreases the elastic constants. For a given number of point defects, the randomly distributed vacancies show the strongest effect compared to voids or interstitial loops. All these results are expected to provide useful information to combine with experimental results for further understanding of radiation damage.

  9. Estimation of thermodynamic acidity constants of some penicillinase-resistant penicillins.

    PubMed

    Demiralay, Ebru Çubuk; Üstün, Zehra; Daldal, Y Doğan

    2014-03-01

    In this work, thermodynamic acidity constants (pssKa) of methicillin, oxacillin, nafcillin, cloxacilin, dicloxacillin were determined with reverse phase liquid chromatographic method (RPLC) by taking into account the effect of the activity coefficients in hydro-organic water-acetonitrile binary mixtures. From these values, thermodynamic aqueous acidity constants of these drugs were calculated by different approaches. The linear relationships established between retention factors of the species and the polarity parameter of the mobile phase (ET(N)) was proved to predict accurately retention in LC as a function of the acetonitrile content (38%, 40% and 42%, v/v). Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Shock-induced transformations in crystalline RDX: a uniaxial constant-stress Hugoniostat molecular dynamics simulation study.

    PubMed

    Bedrov, Dmitry; Hooper, Justin B; Smith, Grant D; Sewell, Thomas D

    2009-07-21

    Molecular dynamics (MD) simulations of uniaxial shock compression along the [100] and [001] directions in the alpha polymorph of hexahydro-1,3,5-trinitro-1,3,5-triazine (alpha-RDX) have been conducted over a wide range of shock pressures using the uniaxial constant stress Hugoniostat method [Ravelo et al., Phys. Rev. B 70, 014103 (2004)]. We demonstrate that the Hugoniostat method is suitable for studying shock compression in atomic-scale models of energetic materials without the necessity to consider the extremely large simulation cells required for an explicit shock wave simulation. Specifically, direct comparison of results obtained using the Hugoniostat approach to those reported by Thompson and co-workers [Phys. Rev. B 78, 014107 (2008)] based on large-scale MD simulations of shocks using the shock front absorbing boundary condition (SFABC) approach indicates that Hugoniostat simulations of systems containing several thousand molecules reproduced the salient features observed in the SFABC simulations involving roughly a quarter-million molecules, namely, nucleation and growth of nanoscale shear bands for shocks propagating along the [100] direction and the polymorphic alpha-gamma phase transition for shocks directed along the [001] direction. The Hugoniostat simulations yielded predictions of the Hugoniot elastic limit for the [100] shock direction consistent with SFABC simulation results.

  11. The Effect of Membrane Environment on Surfactant Protein C Stability Studied by Constant-pH Molecular Dynamics.

    PubMed

    Carvalheda, Catarina A; Campos, Sara R R; Baptista, António M

    2015-10-26

    Pulmonary surfactant protein C (SP-C) is a small peptide with two covalently linked fatty acyl chains that plays a crucial role in the formation and stabilization of the pulmonary surfactant reservoirs during the compression and expansion steps of the respiratory cycle. Although its function is known to be tightly related to its highly hydrophobic character and key interactions maintained with specific lipid components, much is left to understand about its molecular mechanism of action. Also, although it adopts a mainly helical structure while associated with the membrane, factors as pH variation and deacylation have been shown to affect its stability and function. In this work, the conformational behavior of both the acylated and deacylated SP-C isoforms was studied in a DPPC bilayer under different pH conditions using constant-pH molecular dynamics simulations. Our findings show that both protein isoforms are remarkably stable over the studied pH range, even though the acylated isoform exhibits a labile helix-turn-helix motif rarely observed in the other isoform. We estimate similar tilt angles for the two isoforms over the studied pH range, with a generally higher degree of internalization of the basic N-terminal residues in the deacylated case, and observe and discuss some protonation-conformation coupling effects. Both isoforms establish contacts with the surrounding lipid molecules (preferentially with the sn-2 ester bonds) and have a local effect on the conformational behavior of the surrounding lipid molecules, the latter being more pronounced for acylated SP-C.

  12. Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rastogi, Monisha; Vaish, Rahul, E-mail: rahul@iitmandi.ac.in; Materials Research Centre, Indian Institute of Science, Bangalore 560 012

    2015-05-15

    The present work aims to investigate the phase transition, dispersion and diffusion behavior of nanocomposites of carbon nanotube (CNT) and straight chain alkanes. These materials are potential candidates for organic phase change materials(PCMs) and have attracted flurry of research recently. Accurate experimental evaluation of the mass, thermal and transport properties of such composites is both difficult as well as economically taxing. Additionally it is crucial to understand the factors that results in modification or enhancement of their characteristic at atomic or molecular level. Classical molecular dynamics approach has been extended to elucidate the same. Bulk atomistic models have been generatedmore » and subjected to rigorous multistage equilibration. To reaffirm the approach, both canonical and constant-temperature, constant- pressure ensembles were employed to simulate the models under consideration. Explicit determination of kinetic, potential, non-bond and total energy assisted in understanding the enhanced thermal and transport property of the nanocomposites from molecular point of view. Crucial parameters including mean square displacement and simulated self diffusion coefficient precisely define the balance of the thermodynamic and hydrodynamic interactions. Radial distribution function also reflected the density variation, strength and mobility of the nanocomposites. It is expected that CNT functionalization could improve the dispersion within n-alkane matrix. This would further ameliorate the mass and thermal properties of the composite. Additionally, the determined density was in good agreement with experimental data. Thus, molecular dynamics can be utilized as a high throughput technique for theoretical investigation of nanocomposites PCMs.« less

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

    PubMed

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

    2012-09-28

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

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

    PubMed Central

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

    2012-01-01

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

  15. Spectroscopic Constants of the Known Electronic States of Lead Monofluoride

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McRaven, C.P.; Sivakumar, P.; Shafer-Ray, N.E.

    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} = 3/2more » state.« less

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

    PubMed

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

    2011-12-01

    Proton uptake or release controls many important biological processes, such as energy transduction, virus replication, and catalysis. Accurate pK(a) prediction informs about proton pathways, thereby revealing detailed acid-base mechanisms. Physics-based methods in the framework of molecular dynamics simulations not only offer pK(a) predictions but also inform about the physical origins of pK(a) shifts and provide details of ionization-induced conformational relaxation and large-scale transitions. One such method is the recently developed continuous constant pH molecular dynamics (CPHMD) method, which has been shown to be an accurate and robust pK(a) prediction tool for naturally occurring titratable residues. To further examine the accuracy and limitations of CPHMD, we blindly predicted the pK(a) values for 87 titratable residues introduced in various hydrophobic regions of staphylococcal nuclease and variants. The predictions gave a root-mean-square deviation of 1.69 pK units from experiment, and there were only two pK(a)'s with errors greater than 3.5 pK units. Analysis of the conformational fluctuation of titrating side-chains in the context of the errors of calculated pK(a) values indicate that explicit treatment of conformational flexibility and the associated dielectric relaxation gives CPHMD a distinct advantage. Analysis of the sources of errors suggests that more accurate pK(a) predictions can be obtained for the most deeply buried residues by improving the accuracy in calculating desolvation energies. Furthermore, it is found that the generalized Born implicit-solvent model underlying the current CPHMD implementation slightly distorts the local conformational environment such that the inclusion of an explicit-solvent representation may offer improvement of accuracy. Copyright © 2011 Wiley-Liss, Inc.

  17. Predicting heterocyclic ring coupling constants through a conformational search of tetra-O-methyl-(+)-catechin

    Treesearch

    Fred L. Tobiason; Richard W. Hemingway

    1994-01-01

    A GMMX conformational search routine gives a family of conformations that reflects the Boltzmann-averaged heterocyclic ring conformation as evidenced by accurate prediction of all three coupling constants observed for tetra-O-methyl-(+)-catechin.

  18. Predicting heterocyclic ring coupling constants through a conformational search of tetra-o-methyl-(+)-catechin

    Treesearch

    Fred L. Tobiason; Richard w. Hemingway

    1994-01-01

    A GMMXe conformational search routine gives a family a conformations that reflects the boltzmann-averaged heterocyclic ring conformation as evidence by accurate prediction of all three coupling constants observed for tetra-O-methyl-(+)-catechin.

  19. Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.

    PubMed

    Moal, Iain H; Bates, Paul A

    2012-01-01

    The prediction of protein-protein kinetic rate constants provides a fundamental test of our understanding of molecular recognition, and will play an important role in the modeling of complex biological systems. In this paper, a feature selection and regression algorithm is applied to mine a large set of molecular descriptors and construct simple models for association and dissociation rate constants using empirical data. Using separate test data for validation, the predicted rate constants can be combined to calculate binding affinity with accuracy matching that of state of the art empirical free energy functions. The models show that the rate of association is linearly related to the proportion of unbound proteins in the bound conformational ensemble relative to the unbound conformational ensemble, indicating that the binding partners must adopt a geometry near to that of the bound prior to binding. Mirroring the conformational selection and population shift mechanism of protein binding, the models provide a strong separate line of evidence for the preponderance of this mechanism in protein-protein binding, complementing structural and theoretical studies.

  20. Computation of Dielectric Response in Molecular Solids for High Capacitance Organic Dielectrics.

    PubMed

    Heitzer, Henry M; Marks, Tobin J; Ratner, Mark A

    2016-09-20

    The dielectric response of a material is central to numerous processes spanning the fields of chemistry, materials science, biology, and physics. Despite this broad importance across these disciplines, describing the dielectric environment of a molecular system at the level of first-principles theory and computation remains a great challenge and is of importance to understand the behavior of existing systems as well as to guide the design and synthetic realization of new ones. Furthermore, with recent advances in molecular electronics, nanotechnology, and molecular biology, it has become necessary to predict the dielectric properties of molecular systems that are often difficult or impossible to measure experimentally. In these scenarios, it is would be highly desirable to be able to determine dielectric response through efficient, accurate, and chemically informative calculations. A good example of where theoretical modeling of dielectric response would be valuable is in the development of high-capacitance organic gate dielectrics for unconventional electronics such as those that could be fabricated by high-throughput printing techniques. Gate dielectrics are fundamental components of all transistor-based logic circuitry, and the combination high dielectric constant and nanoscopic thickness (i.e., high capacitance) is essential to achieving high switching speeds and low power consumption. Molecule-based dielectrics offer the promise of cheap, flexible, and mass producible electronics when used in conjunction with unconventional organic or inorganic semiconducting materials to fabricate organic field effect transistors (OFETs). The molecular dielectrics developed to date typically have limited dielectric response, which results in low capacitances, translating into poor performance of the resulting OFETs. Furthermore, the development of better performing dielectric materials has been hindered by the current highly empirical and labor-intensive pace of synthetic

  1. Folding molecular dynamics simulations accurately predict the effect of mutations on the stability and structure of a vammin-derived peptide.

    PubMed

    Koukos, Panagiotis I; Glykos, Nicholas M

    2014-08-28

    Folding molecular dynamics simulations amounting to a grand total of 4 μs of simulation time were performed on two peptides (with native and mutated sequences) derived from loop 3 of the vammin protein and the results compared with the experimentally known peptide stabilities and structures. The simulations faithfully and accurately reproduce the major experimental findings and show that (a) the native peptide is mostly disordered in solution, (b) the mutant peptide has a well-defined and stable structure, and (c) the structure of the mutant is an irregular β-hairpin with a non-glycine β-bulge, in excellent agreement with the peptide's known NMR structure. Additionally, the simulations also predict the presence of a very small β-hairpin-like population for the native peptide but surprisingly indicate that this population is structurally more similar to the structure of the native peptide as observed in the vammin protein than to the NMR structure of the isolated mutant peptide. We conclude that, at least for the given system, force field, and simulation protocol, folding molecular dynamics simulations appear to be successful in reproducing the experimentally accessible physical reality to a satisfactory level of detail and accuracy.

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

    PubMed

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

    2013-01-17

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    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.

  5. Simulation of electric double-layer capacitors: evaluation of constant potential method

    NASA Astrophysics Data System (ADS)

    Wang, Zhenxing; Laird, Brian; Yang, Yang; Olmsted, David; Asta, Mark

    2014-03-01

    Atomistic simulations can play an important role in understanding electric double-layer capacitors (EDLCs) at a molecular level. In such simulations, typically the electrode surface is modeled using fixed surface charges, which ignores the charge fluctuation induced by local fluctuations in the electrolyte solution. In this work we evaluate an explicit treatment of charges, namely constant potential method (CPM)[1], in which the electrode charges are dynamically updated to maintain constant electrode potential. We employ a model system with a graphite electrode and a LiClO4/acetonitrile electrolyte, examined as a function of electrode potential differences. Using various molecular and macroscopic properties as metrics, we compare CPM simulations on this system to results using fixed surface charges. Specifically, results for predicted capacity, electric potential gradient and solvent density profile are identical between the two methods; However, ion density profiles and solvation structure yield significantly different results.

  6. 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).

  7. Molecular docking and molecular dynamics simulation analyses of urea with ammoniated and ammoxidized lignin.

    PubMed

    Li, Wenzhuo; Zhang, Song; Zhao, Yingying; Huang, Shuaiyu; Zhao, Jiangshan

    2017-01-01

    Ammoniated lignin, prepared through the Mannich reaction of lignin, has more advantages as a slow-release carrier of urea molecules than ammoxidized lignin and lignin. The advantages of the ammoniated lignin include its amine groups added and its high molecular mass kept as similar as that of lignin. Three organic molecules including guaiacyl, 2-hydroxybenzylamine and 5-carbamoylpentanoic acid are monomers respectively in lignin, ammoniated lignin and ammoxidized lignin. We studied the difference between the interactions of lignin, ammoniated lignin and ammoxidized lignin with respect to urea, based on radial distribution functions (RDFs) results from molecular dynamics (MD) simulations. Glass transition temperature (T g ) and solubility parameter (δ) of ammoniated and ammoxidized lignin have been calculated by MD simulations in the constant-temperature and constant-pressure ensemble (NPT). Molecular docking results showed the interaction sites of the urea onto the ammoniated and ammoxidized lignin and three different interaction modes were identified. Root mean square deviation (RMSD) values could indicate the mobilities of the urea molecule affected by the three different interaction modes. A series of MD simulations in the constant-temperature and constant-volume ensemble (NVT) helped us to calculate the diffusivity of urea which was affected by the content of urea in ammoniated and ammoxidized lignin. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    PubMed

    Pathak, Arup K

    2015-03-01

    Constant pH molecular dynamics (CpHMD) is a commonly used sampling method, which incorporates the coupling of conformational flexibility and protonation state of a protein during the simulation by using pH as an external parameter. The effects on the structure and stability of a hyperstable variant of staphylococcal nuclease (Δ+PHS) protein of an artificial charge pair buried in its hydrophobic core are investigated by applying both CpHMD and accelerated molecular dynamics coupled with constant pH (CpHaMD) methods. Generalized Born electrostatics is used to model the solvent water. Two sets of starting coordinates of V23E/L36K variant of Δ+PHS, namely, Maestro generated coordinates from Δ+PHS and crystal structure coordinates of the same are considered for detail investigations. On the basis of root mean square displacement (RMSD) and root mean square fluctuations (RMSF) calculations, it is observed that this variant is stable over a wide range of pH. The calculated pKa values for aspartate and glutamate residues based on both CpHMD and CpHaMD simulations are consistent with the reported experimental values (within ± 0.5 to ± 1.5 pH unit), which clearly indicates that the local chemical environment of the carboxylic acids in V23E/L36K variant are comparable to the parent form. The strong salt bridge interaction between the mutated pair, E23/K36 and additional hydrogen bonds formed in the V23E/L36K variant, may help to compensate for the unfavorable self-energy experienced by the burial of these residues in the hydrophobic core. However, from RMSD, RMSF, and pKa analysis, no significant change in the global conformation of V23E/L36K variant with respect to the parent form, Δ+PHS is noticed. © 2014 Wiley Periodicals, Inc.

  9. Radiomics biomarkers for accurate tumor progression prediction of oropharyngeal cancer

    NASA Astrophysics Data System (ADS)

    Hadjiiski, Lubomir; Chan, Heang-Ping; Cha, Kenny H.; Srinivasan, Ashok; Wei, Jun; Zhou, Chuan; Prince, Mark; Papagerakis, Silvana

    2017-03-01

    Accurate tumor progression prediction for oropharyngeal cancers is crucial for identifying patients who would best be treated with optimized treatment and therefore minimize the risk of under- or over-treatment. An objective decision support system that can merge the available radiomics, histopathologic and molecular biomarkers in a predictive model based on statistical outcomes of previous cases and machine learning may assist clinicians in making more accurate assessment of oropharyngeal tumor progression. In this study, we evaluated the feasibility of developing individual and combined predictive models based on quantitative image analysis from radiomics, histopathology and molecular biomarkers for oropharyngeal tumor progression prediction. With IRB approval, 31, 84, and 127 patients with head and neck CT (CT-HN), tumor tissue microarrays (TMAs) and molecular biomarker expressions, respectively, were collected. For 8 of the patients all 3 types of biomarkers were available and they were sequestered in a test set. The CT-HN lesions were automatically segmented using our level sets based method. Morphological, texture and molecular based features were extracted from CT-HN and TMA images, and selected features were merged by a neural network. The classification accuracy was quantified using the area under the ROC curve (AUC). Test AUCs of 0.87, 0.74, and 0.71 were obtained with the individual predictive models based on radiomics, histopathologic, and molecular features, respectively. Combining the radiomics and molecular models increased the test AUC to 0.90. Combining all 3 models increased the test AUC further to 0.94. This preliminary study demonstrates that the individual domains of biomarkers are useful and the integrated multi-domain approach is most promising for tumor progression prediction.

  10. Molecular Thermometry

    PubMed Central

    McCabe, Kevin M.; Hernandez, Mark

    2010-01-01

    Conventional temperature measurements rely on material responses to heat, which can be detected visually. When Galileo developed an air expansion based device to detect temperature changes, Santorio, a contemporary physician, added a scale to create the first thermometer. With this instrument, patients’ temperatures could be measured, recorded and related to changing health conditions. Today, advances in materials science and bioengineering provide new ways to report temperature at the molecular level in real time. In this review the scientific foundations and history of thermometry underpin a discussion of the discoveries emerging from the field of molecular thermometry. Intracellular nanogels and heat sensing biomolecules have been shown to accurately report temperature changes at the nano-scale. Various systems will soon provide the ability to accurately measure temperature changes at the tissue, cellular, and even sub-cellular level, allowing for detection and monitoring of very small changes in local temperature. In the clinic this will lead to enhanced detection of tumors and localized infection, and accurate and precise monitoring of hyperthermia based therapies. Some nanomaterial systems have even demonstrated a theranostic capacity for heat-sensitive, local delivery of chemotherapeutics. Just as early thermometry moved into the clinic, so too will these molecular thermometers. PMID:20139796

  11. Rotationally resolved fluorescence spectroscopy of molecular iodine

    NASA Astrophysics Data System (ADS)

    Lemon, Christopher; Canagaratna, Sebastian; Gray, Jeffrey

    2008-03-01

    Vibration-electronic spectroscopy of I2 vapor is a common, important experiment in physical chemistry lab courses. We use narrow bandwidth diode-pumped solid state (DPSS) lasers to excite specific rotational levels; these lasers are surprisingly stable and are now available at low cost. We also use efficient miniature fiber-optic spectrometers to resolve rotational fluorescence patterns in a vibrational progression. The resolution enables thorough and accurate analysis of spectroscopic constants for the ground electronic state. The high signal-to-noise ratio, which is easily achieved, also enables students to precisely measure fluorescence band intensities, providing further insight into vibrational wavefunctions and the molecular potential function. We will provide a detailed list of parts for the apparatus as well as modeling algorithms with statistical evaluation to facilitate widespread adoption of these experimental improvements by instructors of intermediate and advanced lab courses.

  12. Accurate ab initio Quartic Force Fields of Cyclic and Bent HC2N Isomers

    NASA Technical Reports Server (NTRS)

    Inostroza, Natalia; Huang, Xinchuan; Lee, Timothy J.

    2012-01-01

    Highly correlated ab initio quartic force field (QFFs) are used to calculate the equilibrium structures and predict the spectroscopic parameters of three HC2N isomers. Specifically, the ground state quasilinear triplet and the lowest cyclic and bent singlet isomers are included in the present study. Extensive treatment of correlation effects were included using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T). Dunning s correlation-consistent basis sets cc-pVXZ, X=3,4,5, were used, and a three-point formula for extrapolation to the one-particle basis set limit was used. Core-correlation and scalar relativistic corrections were also included to yield highly accurate QFFs. The QFFs were used together with second-order perturbation theory (with proper treatment of Fermi resonances) and variational methods to solve the nuclear Schr dinger equation. The quasilinear nature of the triplet isomer is problematic, and it is concluded that a QFF is not adequate to describe properly all of the fundamental vibrational frequencies and spectroscopic constants (though some constants not dependent on the bending motion are well reproduced by perturbation theory). On the other hand, this procedure (a QFF together with either perturbation theory or variational methods) leads to highly accurate fundamental vibrational frequencies and spectroscopic constants for the cyclic and bent singlet isomers of HC2N. All three isomers possess significant dipole moments, 3.05D, 3.06D, and 1.71D, for the quasilinear triplet, the cyclic singlet, and the bent singlet isomers, respectively. It is concluded that the spectroscopic constants determined for the cyclic and bent singlet isomers are the most accurate available, and it is hoped that these will be useful in the interpretation of high-resolution astronomical observations or laboratory experiments.

  13. A new estimate of the Hubble constant using the Virgo cluster distance

    NASA Astrophysics Data System (ADS)

    Visvanathan, N.

    The Hubble constant, which defines the size and age of the universe, remains substantially uncertain. Attention is presently given to an improved distance to the Virgo Cluster obtained by means of the 1.05-micron luminosity-H I width relation of spirals. In order to improve the absolute calibration of the relation, accurate distances to the nearby SMC, LMC, N6822, SEX A and N300 galaxies have also been obtained, on the basis of the near-IR P-L relation of the Cepheids. A value for the global Hubble constant of 67 + or 4 km/sec per Mpc is obtained.

  14. Constants and pseudo-constants of the Kadomtsev-Petviashvili equation.

    PubMed

    Case, K M

    1985-08-01

    Elucidating earlier work, it is shown that the Kadomtsev-Petviashvili equation has n + 2 constants for all n >/= 0. It also has a pseudo-constant from which the constants can be obtained by differentiation with respect to time. The pseudo-constant can be obtained from a basis functional J(n) ((n+2)) = -1/18 [unk] y(n+2)q by taking repeated Poisson brackets with the Hamiltonian.

  15. Transient times in linear metabolic pathways under constant affinity constraints.

    PubMed

    Lloréns, M; Nuño, J C; Montero, F

    1997-10-15

    In the early seventies, Easterby began the analytical study of transition times for linear reaction schemes [Easterby (1973) Biochim. Biophys. Acta 293, 552-558]. In this pioneer work and in subsequent papers, a state function (the transient time) was used to measure the period before the stationary state, for systems constrained to work under both constant and variable input flux, was reached. Despite the undoubted usefulness of this quantity to describe the time-dependent features of these kinds of systems, its application to the study of chemical reactions under other constraints is questionable. In the present work, a generalization of these magnitudes to linear metabolic pathways functioning under a constant-affinity constraint is carried out. It is proved that classical definitions of transient times do not reflect the actual properties of the transition to the steady state in systems evolving under this restriction. Alternatively, a more adequate framework for interpretation of the transient times for systems with both constant and variable input flux is suggested. Within this context, new definitions that reflect more accurately the transient characteristics of constant affinity systems are stated. Finally, the meaning of these transient times is discussed.

  16. The effects of rigid motions on elastic network model force constants

    PubMed Central

    Lezon, Timothy R.

    2012-01-01

    Elastic network models provide an efficient way to quickly calculate protein global dynamics from experimentally determined structures. The model’s single parameter, its force constant, determines the physical extent of equilibrium fluctuations. The values of force constants can be calculated by fitting to experimental data, but the results depend on the type of experimental data used. Here we investigate the differences between calculated values of force constants _t to data from NMR and X-ray structures. We find that X-ray B factors carry the signature of rigid-body motions, to the extent that B factors can be almost entirely accounted for by rigid motions alone. When fitting to more refined anisotropic temperature factors, the contributions of rigid motions are significantly reduced, indicating that the large contribution of rigid motions to B factors is a result of over-fitting. No correlation is found between force constants fit to NMR data and those fit to X-ray data, possibly due to the inability of NMR data to accurately capture protein dynamics. PMID:22228562

  17. The effects of rigid motions on elastic network model force constants.

    PubMed

    Lezon, Timothy R

    2012-04-01

    Elastic network models provide an efficient way to quickly calculate protein global dynamics from experimentally determined structures. The model's single parameter, its force constant, determines the physical extent of equilibrium fluctuations. The values of force constants can be calculated by fitting to experimental data, but the results depend on the type of experimental data used. Here, we investigate the differences between calculated values of force constants and data from NMR and X-ray structures. We find that X-ray B factors carry the signature of rigid-body motions, to the extent that B factors can be almost entirely accounted for by rigid motions alone. When fitting to more refined anisotropic temperature factors, the contributions of rigid motions are significantly reduced, indicating that the large contribution of rigid motions to B factors is a result of over-fitting. No correlation is found between force constants fit to NMR data and those fit to X-ray data, possibly due to the inability of NMR data to accurately capture protein dynamics. Copyright © 2011 Wiley Periodicals, Inc.

  18. Constants and pseudo-constants of the Kadomtsev-Petviashvili equation

    PubMed Central

    Case, K. M.

    1985-01-01

    Elucidating earlier work, it is shown that the Kadomtsev-Petviashvili equation has n + 2 constants for all n ≥ 0. It also has a pseudo-constant from which the constants can be obtained by differentiation with respect to time. The pseudo-constant can be obtained from a basis functional Jn(n+2) = -1/18 [unk] yn+2q by taking repeated Poisson brackets with the Hamiltonian. PMID:16593588

  19. Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Simulations of the Molecular Crystal alphaRDX

    DTIC Science & Technology

    2013-08-01

    potential for HMX / RDX (3, 9). ...................................................................................8 1 1. Purpose This work...6 dispersion and electrostatic interactions. Constants for the SB potential are given in table 1. 8 Table 1. SB potential for HMX / RDX (3, 9...modeling dislocations in the energetic molecular crystal RDX using the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Misra, Mayank; Kumar, Sanat K., E-mail: sk2794@columbia.edu; Mannodi-Kanakkithodi, Arun

    2016-06-21

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

  1. Constants and pseudo-constants of the Kadomtsev-Petviashvili equation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Case, K.M.

    1985-08-01

    Elucidating earlier work, it is shown that the Kadomtsev-Petviashvili equation has n + 2 constants for all n greater than or equal to 0. It also has a pseudo-constant from which the constants can be obtained by differentiation with respect to time. The pseudo-constant can be obtained from a basis functional J/sub n/sup (n+2)/ = -1/18 integral y/sup n+2/ q by taking repeated Poisson brackets with the Hamiltonian.

  2. Increased Accuracy in the Measurement of the Dielectric Constant of Seawater at 1.413 GHz

    NASA Technical Reports Server (NTRS)

    Zhou, Y.; Lang R.; Drego, C.; Utku, C.; LeVine, D.

    2012-01-01

    This paper describes the latest results for the measurements of the dielectric constant at 1.413 GHz by using a resonant cavity technique. The purpose of these measurements is to develop an accurate relationship for the dependence of the dielectric constant of sea water on temperature and salinity which is needed by the Aquarius inversion algorithm to retrieve salinity. Aquarius is the major instrument on the Aquarius/SAC-D observatory, a NASA/CONAE satellite mission launched in June of20ll with the primary mission of measuring global sea surface salinity to an accuracy of 0.2 psu. Aquarius measures salinity with a 1.413 GHz radiometer and uses a scatterometer to compensate for the effects of surface roughness. The core part of the seawater dielectric constant measurement system is a brass microwave cavity that is resonant at 1.413 GHz. The seawater is introduced into the cavity through a capillary glass tube having an inner diameter of 0.1 mm. The change of resonance frequency and the cavity Q value are used to determine the real and imaginary parts of the dielectric constant of seawater introduced into the thin tube. Measurements are automated with the help of software developed at the George Washington University. In this talk, new results from measurements made since September 2010 will be presented for salinities 30, 35 and 38 psu with a temperature range of O C to 350 C in intervals of 5 C. These measurements are more accurate than earlier measurements made in 2008 because of a new method for measuring the calibration constant using methanol. In addition, the variance of repeated seawater measurements has been reduced by letting the system stabilize overnight between temperature changes. The new results are compared to the Kline Swift and Meissner Wentz model functions. The importance of an accurate model function will be illustrated by using these model functions to invert the Aquarius brightness temperature to get the salinity values. The salinity values

  3. Concise NMR approach for molecular dynamics characterizations in organic solids.

    PubMed

    Aliev, Abil E; Courtier-Murias, Denis

    2013-08-22

    Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the α and γ polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics.

  4. Equations for description of nonlinear standing waves in constant-cross-sectioned resonators.

    PubMed

    Bednarik, Michal; Cervenka, Milan

    2014-03-01

    This work is focused on investigation of applicability of two widely used model equations for description of nonlinear standing waves in constant-cross-sectioned resonators. The investigation is based on the comparison of numerical solutions of these model equations with solutions of more accurate model equations whose validity has been verified experimentally in a number of published papers.

  5. Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.

    PubMed

    Huang, Yu-Ming M; McCammon, J Andrew; Miao, Yinglong

    2018-04-10

    Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recover biomolecular free energy profiles.

  6. Determination of ionization constants by paper electrophoresis.

    PubMed Central

    Tate, M E

    1981-01-01

    Dimensionless apparent ionization constants of charged low-molecular-weight species may be obtained from paper-electrophoretic data at 20-25 degrees C with buffers (I0.1-0.5) of measured pH (1.5-12.5) containing oxalate ions. Relative mobilities rather than absolute mobilities were measured by using glycerol and m-nitrobenzenesulphonate respectively as standards of zero and unit mobility. Application of the procedure to ionizations of adenine, adenosine, 2'-deoxyadenosine, 3'-deoxyadenosine, 3':5'-cyclic AMP, ADP, ADP-glucose-agrocin 84 and ATP is described. PMID:6976169

  7. Estimation of Hammett sigma constants of substituted benzenes through accurate density-functional calculation of core-electron binding energy shifts

    NASA Astrophysics Data System (ADS)

    Takahata, Yuji; Chong, Delano P.

    For substituted benzenes such as (p-F-C6H4-Z), Linderberg et al. 1 demonstrated the validity of an equation similar to: ΔCEBE ≈ κσ, where ΔCEBE is the difference in core-electron binding energies (CEBEs) of the fluorinated carbon in p-F-C6H4-Z and that in FC6H5, the parameter κ is a function of the type of reaction, and σ is the Hammett substituent (σ) constant. In this work, CEBEs of ring carbon atoms for a series of para disubstituted molecules p-F-C6H4-Z were first calculated using Density Functional Theory (DFT) with the scheme ΔEKS (PW86-PW91)/TZP+Crel//HF/6-31G*. An average absolute deviation of 0.13 eV from experiment was obtained for the CEBEs. Then we performed a linear regression analysis in the form of Y = A+B*X for a plot of Hammett σp constants against calculated shifts ΔCEBEs (in eV) for the fluorinated carbon. The results were: A = -0.08 and B = 1.01, with correlation coefficient R = 0.973, standard deviation = 0.12, and P < 0.0001. The intercept A of the fitted line, close to zero, shows that the Hammett σp constant is proportional to the calculated ΔCEBEs. On the other hand, the slope B of the straight line gives an estimate of the parameter κ. Similar statistical correlations were obtained for the carbon atoms ortho and meta to the substituent Z.

  8. Quantitative Prediction of Rate Constants for Aqueous Racemization To Avoid Pointless Stereoselective Syntheses

    PubMed Central

    Ballard, Andrew; Ahmad, Hiwa O.; Narduolo, Stefania; Rosa, Lucy; Chand, Nikki; Cosgrove, David A.; Varkonyi, Peter; Asaad, Nabil; Tomasi, Simone

    2017-01-01

    Abstract Racemization has a large impact upon the biological properties of molecules but the chemical scope of compounds with known rate constants for racemization in aqueous conditions was hitherto limited. To address this remarkable blind spot, we have measured the kinetics for racemization of 28 compounds using circular dichroism and 1H NMR spectroscopy. We show that rate constants for racemization (measured by ourselves and others) correlate well with deprotonation energies from quantum mechanical (QM) and group contribution calculations. Such calculations thus provide predictions of the second‐order rate constants for general‐base‐catalyzed racemization that are usefully accurate. When applied to recent publications describing the stereoselective synthesis of compounds of purported biological value, the calculations reveal that racemization would be sufficiently fast to render these expensive syntheses pointless. PMID:29072355

  9. Correct implementation of polarization constants in wurtzite materials and impact on III-nitrides

    DOE PAGES

    Dreyer, Cyrus E.; Janotti, Anderson; Van de Walle, Chris G.; ...

    2016-06-20

    Here, accurate values for polarization discontinuities between pyroelectric materials are critical for understanding and designing the electronic properties of heterostructures. For wurtzite materials, the zincblende structure has been used in the literature as a reference to determine the effective spontaneous polarization constants. We show that, because the zincblende structure has a nonzero formal polarization, this method results in a spurious contribution to the spontaneous polarization differences between materials. In addition, we address the correct choice of "improper" versus "proper" piezoelectric constants. For the technologically important III-nitride materials GaN, AlN, and InN, we determine polarization discontinuities using a consistent reference basedmore » on the layered hexagonal structure and the correct choice of piezoelectric constants, and discuss the results in light of available experimental data.« less

  10. Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

    NASA Astrophysics Data System (ADS)

    Tiwary, Pratyush

    This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well

  11. Invited Review Article: Measurements of the Newtonian constant of gravitation, G

    NASA Astrophysics Data System (ADS)

    Rothleitner, C.; Schlamminger, S.

    2017-11-01

    By many accounts, the Newtonian constant of gravitation G is the fundamental constant that is most difficult to measure accurately. Over the past three decades, more than a dozen precision measurements of this constant have been performed. However, the scatter of the data points is much larger than the uncertainties assigned to each individual measurement, yielding a Birge ratio of about five. Today, G is known with a relative standard uncertainty of 4.7 × 10-5, which is several orders of magnitudes greater than the relative uncertainties of other fundamental constants. In this article, various methods to measure G are discussed. A large array of different instruments ranging from the simple torsion balance to the sophisticated atom interferometer can be used to determine G. Some instruments, such as the torsion balance can be used in several different ways. In this article, the advantages and disadvantages of different instruments as well as different methods are discussed. A narrative arc from the historical beginnings of the different methods to their modern implementation is given. Finally, the article ends with a brief overview of the current state of the art and an outlook.

  12. Invited Review Article: Measurements of the Newtonian constant of gravitation, G.

    PubMed

    Rothleitner, C; Schlamminger, S

    2017-11-01

    By many accounts, the Newtonian constant of gravitation G is the fundamental constant that is most difficult to measure accurately. Over the past three decades, more than a dozen precision measurements of this constant have been performed. However, the scatter of the data points is much larger than the uncertainties assigned to each individual measurement, yielding a Birge ratio of about five. Today, G is known with a relative standard uncertainty of 4.7 × 10 -5 , which is several orders of magnitudes greater than the relative uncertainties of other fundamental constants. In this article, various methods to measure G are discussed. A large array of different instruments ranging from the simple torsion balance to the sophisticated atom interferometer can be used to determine G. Some instruments, such as the torsion balance can be used in several different ways. In this article, the advantages and disadvantages of different instruments as well as different methods are discussed. A narrative arc from the historical beginnings of the different methods to their modern implementation is given. Finally, the article ends with a brief overview of the current state of the art and an outlook.

  13. 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.

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

    PubMed

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

    2013-01-15

    Photodegradation is a key process governing the residence time and fate of polycyclic aromatic hydrocarbons (PAHs) in particles, both in the atmosphere and after deposition. We have measured photodegradation rate constants of PAHs in bulk deposits of soot particles illuminated with simulated sunlight. The photodegradation rate constants at the surface (k(p)(0)), the effective diffusion coefficients (D(eff)), and the light penetration depths (z(0.5)) for PAHs on soot layers of variable thickness were determined by fitting experimental data with a model of coupled photolysis and diffusion. The overall disappearance rates of irradiated low molecular weight PAHs (with 2-3 rings) on soot particles were influenced by fast photodegradation and fast diffusion kinetics, while those of high molecular weight PAHs (with 4 or more rings) were apparently controlled by either the combination of slow photodegradation and slow diffusion kinetics or by very slow diffusion kinetics alone. The value of z(0.5) is more sensitive to the soot layer thickness than the k(p)(0) value. As the thickness of the soot layer increases, the z(0.5) values increase, but the k(p)(0) values are almost constant. The effective diffusion coefficients calculated from dark experiments are generally higher than those from the model fitting method for illumination experiments. Due to the correlation between k(p)(0) and z(0.5) in thinner layers, D(eff) should be estimated by an independent method for better accuracy. Despite some limitations of the model used in this study, the fitted parameters were useful for describing empirical results of photodegradation of soot-associated PAHs. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Phototransformation Rate Constants of PAHs Associated with Soot Particles

    PubMed Central

    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

  16. Accurate pressure gradient calculations in hydrostatic atmospheric models

    NASA Technical Reports Server (NTRS)

    Carroll, John J.; Mendez-Nunez, Luis R.; Tanrikulu, Saffet

    1987-01-01

    A method for the accurate calculation of the horizontal pressure gradient acceleration in hydrostatic atmospheric models is presented which is especially useful in situations where the isothermal surfaces are not parallel to the vertical coordinate surfaces. The present method is shown to be exact if the potential temperature lapse rate is constant between the vertical pressure integration limits. The technique is applied to both the integration of the hydrostatic equation and the computation of the slope correction term in the horizontal pressure gradient. A fixed vertical grid and a dynamic grid defined by the significant levels in the vertical temperature distribution are employed.

  17. Infrared Spectra and Optical Constants of Astronomical Ices: II. Ethane and Ethylene

    NASA Technical Reports Server (NTRS)

    Hudson, Reggie L.; Gerakines, Perry A.; Moore, M. H.

    2014-01-01

    Infrared spectroscopic observations have established the presence of hydrocarbon ices on Pluto and other TNOs, but the abundances of such molecules cannot be deduced without accurate optical constants (n, k) and reference spectra. In this paper we present our recent measurements of near- and mid-infrared optical constants for ethane (C2H6) and ethylene (C2H4) in multiple ice phases and at multiple temperatures. As in our recent work on acetylene (C2H2), we also report new measurements of the index of refraction of each ice at 670 nm. Comparisons are made to earlier work where possible, and electronic versions of our new results are made available.

  18. Binding constants of membrane-anchored receptors and ligands depend strongly on the nanoscale roughness of membranes.

    PubMed

    Hu, Jinglei; Lipowsky, Reinhard; Weikl, Thomas R

    2013-09-17

    Cell adhesion and the adhesion of vesicles to the membranes of cells or organelles are pivotal for immune responses, tissue formation, and cell signaling. The adhesion processes depend sensitively on the binding constant of the membrane-anchored receptor and ligand proteins that mediate adhesion, but this constant is difficult to measure in experiments. We have investigated the binding of membrane-anchored receptor and ligand proteins with molecular dynamics simulations. We find that the binding constant of the anchored proteins strongly decreases with the membrane roughness caused by thermally excited membrane shape fluctuations on nanoscales. We present a theory that explains the roughness dependence of the binding constant for the anchored proteins from membrane confinement and that relates this constant to the binding constant of soluble proteins without membrane anchors. Because the binding constant of soluble proteins is readily accessible in experiments, our results provide a useful route to compute the binding constant of membrane-anchored receptor and ligand proteins.

  19. Molecular Building Block-Based Electronic Charges for High-Throughput Screening of Metal-Organic Frameworks for Adsorption Applications.

    PubMed

    Argueta, Edwin; Shaji, Jeena; Gopalan, Arun; Liao, Peilin; Snurr, Randall Q; Gómez-Gualdrón, Diego A

    2018-01-09

    Metal-organic frameworks (MOFs) are porous crystalline materials with attractive properties for gas separation and storage. Their remarkable tunability makes it possible to create millions of MOF variations but creates the need for fast material screening to identify promising structures. Computational high-throughput screening (HTS) is a possible solution, but its usefulness is tied to accurate predictions of MOF adsorption properties. Accurate adsorption simulations often require an accurate description of electrostatic interactions, which depend on the electronic charges of the MOF atoms. HTS-compatible methods to assign charges to MOF atoms need to accurately reproduce electrostatic potentials (ESPs) and be computationally affordable, but current methods present an unsatisfactory trade-off between computational cost and accuracy. We illustrate a method to assign charges to MOF atoms based on ab initio calculations on MOF molecular building blocks. A library of building blocks with built-in charges is thus created and used by an automated MOF construction code to create hundreds of MOFs with charges "inherited" from the constituent building blocks. The molecular building block-based (MBBB) charges are similar to REPEAT charges-which are charges that reproduce ESPs obtained from ab initio calculations on crystallographic unit cells of nanoporous crystals-and thus similar predictions of adsorption loadings, heats of adsorption, and Henry's constants are obtained with either method. The presented results indicate that the MBBB method to assign charges to MOF atoms is suitable for use in computational high-throughput screening of MOFs for applications that involve adsorption of molecules such as carbon dioxide.

  20. Comparing Vibrationally Averaged Nuclear Shielding Constants by Quantum Diffusion Monte Carlo and Second-Order Perturbation Theory.

    PubMed

    Ng, Yee-Hong; Bettens, Ryan P A

    2016-03-03

    Using the method of modified Shepard's interpolation to construct potential energy surfaces of the H2O, O3, and HCOOH molecules, we compute vibrationally averaged isotropic nuclear shielding constants ⟨σ⟩ of the three molecules via quantum diffusion Monte Carlo (QDMC). The QDMC results are compared to that of second-order perturbation theory (PT), to see if second-order PT is adequate for obtaining accurate values of nuclear shielding constants of molecules with large amplitude motions. ⟨σ⟩ computed by the two approaches differ for the hydrogens and carbonyl oxygen of HCOOH, suggesting that for certain molecules such as HCOOH where big displacements away from equilibrium happen (internal OH rotation), ⟨σ⟩ of experimental quality may only be obtainable with the use of more sophisticated and accurate methods, such as quantum diffusion Monte Carlo. The approach of modified Shepard's interpolation is also extended to construct shielding constants σ surfaces of the three molecules. By using a σ surface with the equilibrium geometry as a single data point to compute isotropic nuclear shielding constants for each descendant in the QDMC ensemble representing the ground state wave function, we reproduce the results obtained through ab initio computed σ to within statistical noise. Development of such an approach could thereby alleviate the need for any future costly ab initio σ calculations.

  1. Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.

    PubMed Central

    Guenot, J.; Kollman, P. A.

    1992-01-01

    Although aqueous simulations with periodic boundary conditions more accurately describe protein dynamics than in vacuo simulations, these are computationally intensive for most proteins. Trp repressor dynamic simulations with a small water shell surrounding the starting model yield protein trajectories that are markedly improved over gas phase, yet computationally efficient. Explicit water in molecular dynamics simulations maintains surface exposure of protein hydrophilic atoms and burial of hydrophobic atoms by opposing the otherwise asymmetric protein-protein forces. This properly orients protein surface side chains, reduces protein fluctuations, and lowers the overall root mean square deviation from the crystal structure. For simulations with crystallographic waters only, a linear or sigmoidal distance-dependent dielectric yields a much better trajectory than does a constant dielectric model. As more water is added to the starting model, the differences between using distance-dependent and constant dielectric models becomes smaller, although the linear distance-dependent dielectric yields an average structure closer to the crystal structure than does a constant dielectric model. Multiplicative constants greater than one, for the linear distance-dependent dielectric simulations, produced trajectories that are progressively worse in describing trp repressor dynamics. Simulations of bovine pancreatic trypsin were used to ensure that the trp repressor results were not protein dependent and to explore the effect of the nonbonded cutoff on the distance-dependent and constant dielectric simulation models. The nonbonded cutoff markedly affected the constant but not distance-dependent dielectric bovine pancreatic trypsin inhibitor simulations. As with trp repressor, the distance-dependent dielectric model with a shell of water surrounding the protein produced a trajectory in better agreement with the crystal structure than a constant dielectric model, and the physical

  2. Non-polarizable force field of water based on the dielectric constant: TIP4P/ε.

    PubMed

    Fuentes-Azcatl, Raúl; Alejandre, José

    2014-02-06

    The static dielectric constant at room temperature and the temperature of maximum density are used as target properties to develop, by molecular dynamics simulations, the TIP4P/ε force field of water. The TIP4P parameters are used as a starting point. The key step, to determine simultaneously both properties, is to perform simulations at 240 K where a molecular dipole moment of minimum density is found. The minimum is shifted to larger values of μ as the distance between the oxygen atom and site M, lOM, decreases. First, the parameters that define the dipole moment are adjusted to reproduce the experimental dielectric constant and then the Lennard-Jones parameters are varied to match the temperature of maximum density. The minimum on density at 240 K allows understanding why reported TIP4P models fail to reproduce the temperature of maximum density, the dielectric constant, or both properties. The new model reproduces some of the thermodynamic and transport anomalies of water. Additionally, the dielectric constant, thermodynamics, and dynamical and structural properties at different temperatures and pressures are in excellent agreement with experimental data. The computational cost of the new model is the same as that of the TIP4P.

  3. Accurate determinations of alpha(s) from realistic lattice QCD.

    PubMed

    Mason, Q; Trottier, H D; Davies, C T H; Foley, K; Gray, A; Lepage, G P; Nobes, M; Shigemitsu, J

    2005-07-29

    We obtain a new value for the QCD coupling constant by combining lattice QCD simulations with experimental data for hadron masses. Our lattice analysis is the first to (1) include vacuum polarization effects from all three light-quark flavors (using MILC configurations), (2) include third-order terms in perturbation theory, (3) systematically estimate fourth and higher-order terms, (4) use an unambiguous lattice spacing, and (5) use an [symbol: see text](a2)-accurate QCD action. We use 28 different (but related) short-distance quantities to obtain alpha((5)/(MS))(M(Z)) = 0.1170(12).

  4. Tritiated Water on Molecular Sieve without Hydrogen Production

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Walters, R.T.

    2001-09-10

    Several molecular sieve beds loaded with tritiated water failed to generate hydrogen gas from tritium self-radiolysis at the expected rate. Preliminary gamma-ray irradiation experiments of 4A molecular sieve with varying amounts of oxygen in the over-gas evoke a quenching mechanism. The data suggest that the gas phase rate constant for the production of hydrogen gas is several orders of magnitude smaller than the third order rate constant for scavenging of radical fragments by oxygen.

  5. Molecular dynamics test of the Brownian description of Na(+) motion in water

    NASA Technical Reports Server (NTRS)

    Wilson, M. A.; Pohorille, A.; Pratt, L. R.

    1985-01-01

    The present paper provides the results of molecular dynamics calculations on a Na(+) ion in aqueous solution. Attention is given to the sodium-oxygen and sodium-hydrogen radial distribution functions, the velocity autocorrelation function for the Na(+) ion, the autocorrelation function of the force on the stationary ion, and the accuracy of Brownian motion assumptions which are basic to hydrodynamic models of ion dyanmics in solution. It is pointed out that the presented calculations provide accurate data for testing theories of ion dynamics in solution. The conducted tests show that it is feasible to calculate Brownian friction constants for ions in aqueous solutions. It is found that for Na(+) under the considered conditions the Brownian mobility is in error by only 60 percent.

  6. A New Contribution for WYP 2005: The Golden Ratio, Bohr Radius, Planck's Constant, Fine-Structure Constant and g-Factors

    NASA Astrophysics Data System (ADS)

    Heyrovska, R.; Narayan, S.

    2005-10-01

    Recently, the ground state Bohr radius (aB) of hydrogen was shown to be divided into two Golden sections, aB,p = aB/ø2 and aB,e = aB/ø at the point of electrical neutrality, where ø = 1.618 is the Golden ratio (R. Heyrovska, Molecular Physics 103: 877-882, and the literature cited therein). The origin of the difference of two energy terms in the Rydberg equation was thus shown to be in the ground state energy itself, as shown below: EH = (1/2)e2/(κaB) = (1/2)(e2/κ) [(1/aB,p - (1/aB,e)] (1). This work brings some new results that 1) a unit charge in vacuum has a magnetic moment, 2) (e2/2κ) in eq. (1) is an electromagnetic condenser constant, 3) the de Broglie wavelengths of the proton and electron correspond to the Golden arcs of a circle with the Bohr radius, 4) the fine structure constant (α) is the ratio of the Planck's constants without and with the interaction of light with matter, 5) the g-factors of the electron and proton, ge/2 and gp/2 divide the Bohr radius at the magnetic center and 6) the ``mysterious'' value (137.036) of α -1 = (360/ø2) - (2/ø3), where (2/ø3) arises from the difference, (gp - ge).

  7. Accurate Measurement of the Optical Constants n and k for a Series of 57 Inorganic and Organic Liquids for Optical Modeling and Detection.

    PubMed

    Myers, Tanya L; Tonkyn, Russell G; Danby, Tyler O; Taubman, Matthew S; Bernacki, Bruce E; Birnbaum, Jerome C; Sharpe, Steven W; Johnson, Timothy J

    2018-04-01

    For optical modeling and other purposes, we have created a library of 57 liquids for which we have measured the complex optical constants n and k. These liquids vary in their nature, ranging in properties that include chemical structure, optical band strength, volatility, and viscosity. By obtaining the optical constants, one can model most optical phenomena in media and at interfaces including reflection, refraction, and dispersion. Based on the works of others, we have developed improved protocols using multiple path lengths to determine the optical constants n/k for dozens of liquids, including inorganic, organic, and organophosphorus compounds. Detailed descriptions of the measurement and data reduction protocols are discussed; agreement of the derived optical constant n and k values with literature values are presented. We also present results using the n/k values as applied to an optical modeling scenario whereby the derived data are presented and tested for models of 1 µm and 100 µm layers for dimethyl methylphosphonate (DMMP) on both metal (aluminum) and dielectric (soda lime glass) substrates to show substantial differences between the reflected signal from highly reflective substrates and less-reflective substrates.

  8. Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

    PubMed Central

    Xue, Yi; Skrynnikov, Nikolai R

    2014-01-01

    Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

  9. Dose equivalent rate constants and barrier transmission data for nuclear medicine facility dose calculations and shielding design.

    PubMed

    Kusano, Maggie; Caldwell, Curtis B

    2014-07-01

    A primary goal of nuclear medicine facility design is to keep public and worker radiation doses As Low As Reasonably Achievable (ALARA). To estimate dose and shielding requirements, one needs to know both the dose equivalent rate constants for soft tissue and barrier transmission factors (TFs) for all radionuclides of interest. Dose equivalent rate constants are most commonly calculated using published air kerma or exposure rate constants, while transmission factors are most commonly calculated using published tenth-value layers (TVLs). Values can be calculated more accurately using the radionuclide's photon emission spectrum and the physical properties of lead, concrete, and/or tissue at these energies. These calculations may be non-trivial due to the polyenergetic nature of the radionuclides used in nuclear medicine. In this paper, the effects of dose equivalent rate constant and transmission factor on nuclear medicine dose and shielding calculations are investigated, and new values based on up-to-date nuclear data and thresholds specific to nuclear medicine are proposed. To facilitate practical use, transmission curves were fitted to the three-parameter Archer equation. Finally, the results of this work were applied to the design of a sample nuclear medicine facility and compared to doses calculated using common methods to investigate the effects of these values on dose estimates and shielding decisions. Dose equivalent rate constants generally agreed well with those derived from the literature with the exception of those from NCRP 124. Depending on the situation, Archer fit TFs could be significantly more accurate than TVL-based TFs. These results were reflected in the sample shielding problem, with unshielded dose estimates agreeing well, with the exception of those based on NCRP 124, and Archer fit TFs providing a more accurate alternative to TVL TFs and a simpler alternative to full spectral-based calculations. The data provided by this paper should assist

  10. Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

    NASA Astrophysics Data System (ADS)

    van Eijck, L.; Merzel, F.; Rols, S.; Ollivier, J.; Forsyth, V. T.; Johnson, M. R.

    2011-08-01

    Quantifying the molecular elasticity of DNA is fundamental to our understanding of its biological functions. Recently different groups, through experiments on tailored DNA samples and numerical models, have reported a range of stretching force constants (0.3 to 3N/m). However, the most direct, microscopic measurement of DNA stiffness is obtained from the dispersion of its vibrations. A new neutron scattering spectrometer and aligned, wet spun samples have enabled such measurements, which provide the first data of collective excitations of DNA and yield a force constant of 83N/m. Structural and dynamic order persists unchanged to within 15 K of the melting point of the sample, precluding the formation of bubbles. These findings are supported by large scale phonon and molecular dynamics calculations, which reconcile hard and soft force constants.

  11. Improved Accuracy of Low Affinity Protein-Ligand Equilibrium Dissociation Constants Directly Determined by Electrospray Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Jaquillard, Lucie; Saab, Fabienne; Schoentgen, Françoise; Cadene, Martine

    2012-05-01

    There is continued interest in the determination by ESI-MS of equilibrium dissociation constants (KD) that accurately reflect the affinity of a protein-ligand complex in solution. Issues in the measurement of KD are compounded in the case of low affinity complexes. Here we present a KD measurement method and corresponding mathematical model dealing with both gas-phase dissociation (GPD) and aggregation. To this end, a rational mathematical correction of GPD (fsat) is combined with the development of an experimental protocol to deal with gas-phase aggregation. A guide to apply the method to noncovalent protein-ligand systems according to their kinetic behavior is provided. The approach is validated by comparing the KD values determined by this method with in-solution KD literature values. The influence of the type of molecular interactions and instrumental setup on fsat is examined as a first step towards a fine dissection of factors affecting GPD. The method can be reliably applied to a wide array of low affinity systems without the need for a reference ligand or protein.

  12. Accurate Structural Correlations from Maximum Likelihood Superpositions

    PubMed Central

    Theobald, Douglas L; Wuttke, Deborah S

    2008-01-01

    The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. PMID:18282091

  13. Multi-target QSPR modeling for simultaneous prediction of multiple gas-phase kinetic rate constants of diverse chemicals

    NASA Astrophysics Data System (ADS)

    Basant, Nikita; Gupta, Shikha

    2018-03-01

    The reactions of molecular ozone (O3), hydroxyl (•OH) and nitrate (NO3) radicals are among the major pathways of removal of volatile organic compounds (VOCs) in the atmospheric environment. The gas-phase kinetic rate constants (kO3, kOH, kNO3) are thus, important in assessing the ultimate fate and exposure risk of atmospheric VOCs. Experimental data for rate constants are not available for many emerging VOCs and the computational methods reported so far address a single target modeling only. In this study, we have developed a multi-target (mt) QSPR model for simultaneous prediction of multiple kinetic rate constants (kO3, kOH, kNO3) of diverse organic chemicals considering an experimental data set of VOCs for which values of all the three rate constants are available. The mt-QSPR model identified and used five descriptors related to the molecular size, degree of saturation and electron density in a molecule, which were mechanistically interpretable. These descriptors successfully predicted three rate constants simultaneously. The model yielded high correlations (R2 = 0.874-0.924) between the experimental and simultaneously predicted endpoint rate constant (kO3, kOH, kNO3) values in test arrays for all the three systems. The model also passed all the stringent statistical validation tests for external predictivity. The proposed multi-target QSPR model can be successfully used for predicting reactivity of new VOCs simultaneously for their exposure risk assessment.

  14. A Modified ELISA Accurately Measures Secretion of High Molecular Weight Hyaluronan (HA) by Graves' Disease Orbital Cells

    PubMed Central

    Krieger, Christine C.

    2014-01-01

    Excess production of hyaluronan (hyaluronic acid [HA]) in the retro-orbital space is a major component of Graves' ophthalmopathy, and regulation of HA production by orbital cells is a major research area. In most previous studies, HA was measured by ELISAs that used HA-binding proteins for detection and rooster comb HA as standards. We show that the binding efficiency of HA-binding protein in the ELISA is a function of HA polymer size. Using gel electrophoresis, we show that HA secreted from orbital cells is primarily comprised of polymers more than 500 000. We modified a commercially available ELISA by using 1 million molecular weight HA as standard to accurately measure HA of this size. We demonstrated that IL-1β-stimulated HA secretion is at least 2-fold greater than previously reported, and activation of the TSH receptor by an activating antibody M22 from a patient with Graves' disease led to more than 3-fold increase in HA production in both fibroblasts/preadipocytes and adipocytes. These effects were not consistently detected with the commercial ELISA using rooster comb HA as standard and suggest that fibroblasts/preadipocytes may play a more prominent role in HA remodeling in Graves' ophthalmopathy than previously appreciated. PMID:24302624

  15. Effect of pH on the hinge region of influenza viral protein: a combined constant pH and well-tempered molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Pathak, Arup Kumar

    2018-05-01

    Despite the knowledge that the influenza protein, hemagglutinin, undergoes a large conformational change at low pH during the process of fusion with the host cell, its molecular mechanism remains elusive. The present constant pH molecular dynamics (CpHMD) study identifies the residues responsible for large conformational change in acidic condition. Based on the pKa calculations, it is predicted that His-106 is much more responsible for the large conformational change than any other residues in the hinge region of hemagglutinin protein. Potential of mean force profile from well-tempered meta-dynamics (WT-MtD) simulation is also generated along the folding pathway by considering radius of gyration (R gyr) as a collective variable (CV). It is very clear from the present WT-MtD study, that the initial bending starts at that hinge region, which may trigger other conformational changes. Both the protein–protein and protein–water HB time correlation functions are monitored along the folding pathway. The protein–protein (full or hinge region) HB time correlation functions are always found to be stronger than those of the protein–water time correlation functions. The dynamical balance between protein–protein and protein–water HB interactions favors the stabilization of the folded state.

  16. An eclipsing-binary distance to the Large Magellanic Cloud accurate to two per cent.

    PubMed

    Pietrzyński, G; Graczyk, D; Gieren, W; Thompson, I B; Pilecki, B; Udalski, A; Soszyński, I; Kozłowski, S; Konorski, P; Suchomska, K; Bono, G; Moroni, P G Prada; Villanova, S; Nardetto, N; Bresolin, F; Kudritzki, R P; Storm, J; Gallenne, A; Smolec, R; Minniti, D; Kubiak, M; Szymański, M K; Poleski, R; Wyrzykowski, L; Ulaczyk, K; Pietrukowicz, P; Górski, M; Karczmarek, P

    2013-03-07

    In the era of precision cosmology, it is essential to determine the Hubble constant to an accuracy of three per cent or better. At present, its uncertainty is dominated by the uncertainty in the distance to the Large Magellanic Cloud (LMC), which, being our second-closest galaxy, serves as the best anchor point for the cosmic distance scale. Observations of eclipsing binaries offer a unique opportunity to measure stellar parameters and distances precisely and accurately. The eclipsing-binary method was previously applied to the LMC, but the accuracy of the distance results was lessened by the need to model the bright, early-type systems used in those studies. Here we report determinations of the distances to eight long-period, late-type eclipsing systems in the LMC, composed of cool, giant stars. For these systems, we can accurately measure both the linear and the angular sizes of their components and avoid the most important problems related to the hot, early-type systems. The LMC distance that we derive from these systems (49.97 ± 0.19 (statistical) ± 1.11 (systematic) kiloparsecs) is accurate to 2.2 per cent and provides a firm base for a 3-per-cent determination of the Hubble constant, with prospects for improvement to 2 per cent in the future.

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

    PubMed Central

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

    1992-01-01

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

  18. Accelerating Sequential Gaussian Simulation with a constant path

    NASA Astrophysics Data System (ADS)

    Nussbaumer, Raphaël; Mariethoz, Grégoire; Gravey, Mathieu; Gloaguen, Erwan; Holliger, Klaus

    2018-03-01

    Sequential Gaussian Simulation (SGS) is a stochastic simulation technique commonly employed for generating realizations of Gaussian random fields. Arguably, the main limitation of this technique is the high computational cost associated with determining the kriging weights. This problem is compounded by the fact that often many realizations are required to allow for an adequate uncertainty assessment. A seemingly simple way to address this problem is to keep the same simulation path for all realizations. This results in identical neighbourhood configurations and hence the kriging weights only need to be determined once and can then be re-used in all subsequent realizations. This approach is generally not recommended because it is expected to result in correlation between the realizations. Here, we challenge this common preconception and make the case for the use of a constant path approach in SGS by systematically evaluating the associated benefits and limitations. We present a detailed implementation, particularly regarding parallelization and memory requirements. Extensive numerical tests demonstrate that using a constant path allows for substantial computational gains with very limited loss of simulation accuracy. This is especially the case for a constant multi-grid path. The computational savings can be used to increase the neighbourhood size, thus allowing for a better reproduction of the spatial statistics. The outcome of this study is a recommendation for an optimal implementation of SGS that maximizes accurate reproduction of the covariance structure as well as computational efficiency.

  19. Simulation of weak polyelectrolytes: a comparison between the constant pH and the reaction ensemble method

    NASA Astrophysics Data System (ADS)

    Landsgesell, Jonas; Holm, Christian; Smiatek, Jens

    2017-03-01

    The reaction ensemble and the constant pH method are well-known chemical equilibrium approaches to simulate protonation and deprotonation reactions in classical molecular dynamics and Monte Carlo simulations. In this article, we demonstrate the similarity between both methods under certain conditions. We perform molecular dynamics simulations of a weak polyelectrolyte in order to compare the titration curves obtained by both approaches. Our findings reveal a good agreement between the methods when the reaction ensemble is used to sweep the reaction constant. Pronounced differences between the reaction ensemble and the constant pH method can be observed for stronger acids and bases in terms of adaptive pH values. These deviations are due to the presence of explicit protons in the reaction ensemble method which induce a screening of electrostatic interactions between the charged titrable groups of the polyelectrolyte. The outcomes of our simulation hint to a better applicability of the reaction ensemble method for systems in confined geometries and titrable groups in polyelectrolytes with different pKa values.

  20. Comment on "Comment on 'Constant temperature molecular dynamics simulations by means of a stochastic collision model. II. The harmonic oscillator' [J. Chem. Phys. 104, 3732 (1996)]" [J. Chem. Phys. 106, 1646 (1997)].

    PubMed

    Kast, Stefan M

    2004-03-08

    An argument brought forward by Sholl and Fichthorn against the stochastic collision-based constant temperature algorithm for molecular dynamics simulations developed by Kast et al. is refuted. It is demonstrated that the large temperature fluctuations noted by Sholl and Fichthorn are due to improperly chosen initial conditions within their formulation of the algorithm. With the original form or by suitable initialization of their variant no deficient behavior is observed.

  1. 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.

  2. An exact closed form solution for constant area compressible flow with friction and heat transfer

    NASA Technical Reports Server (NTRS)

    Sturas, J. I.

    1971-01-01

    The well-known differential equation for the one-dimensional flow of a compressible fluid with heat transfer and wall friction has no known solution in closed form for the general case. This report presents a closed form solution for the special case of constant heat flux per unit length and constant specific heat. The solution was obtained by choosing the square of a dimensionless flow parameter as one of the independent variables to describe the flow. From this exact solution, an approximate simplified form is derived that is applicable for predicting subsonic flow performance characteristics for many types of constant area passages in internal flow. The data included in this report are considered sufficiently accurate for use as a guide in analyzing and designing internal gas flow systems.

  3. In-situ GPR test for three-dimensional mapping of the dielectric constant in a rock mass

    NASA Astrophysics Data System (ADS)

    Elkarmoty, Mohamed; Colla, Camilla; Gabrielli, Elena; Papeschi, Paolo; Bonduà, Stefano; Bruno, Roberto

    2017-11-01

    The Ground Penetrating Radar (GPR) is used to detect subsurface anomalies in several applications. The more the velocity of propagation or the dielectric constant is estimated accurately, the more the detection of anomalies at true subsurface depth can be accurately obtained. Since many GPR applications are performed in rock mass with non-homogeneous discontinuous nature, errors in estimating a bulk velocity of propagation or dielectric constant are possible. This paper presents a new in-situ GPR test for mapping the dielectric constant variability in a rock mass. The main aim is to investigate to what extent the dielectric constant is variable in the micro and macro scale of a typical rock mass and to give attention to GPR users in rock mass mediums. The methodology of this research is based on the insertion of steel rods in a rock mass, thus acting as reflectors. The velocity of propagation can be then modeled, from hyperbolic reflections, in the form of velocity pathways from antenna positions to a buried rod. Each pathway is characterized by discrete points which are assumed in three dimensions as centers of micro cubic rock mass. This allows converting the velocity of propagation into a dielectric constant for mapping and modeling the dielectric constant in a volumetric rock mass using a volumetric data visualization software program (Voxler). In a case study, 6 steel drilling rods were diagonally inserted in a vertical face of a bench in a sandstone quarry. Five equally spaced parallel lines, almost perpendicular to the orientations of the rods, were surveyed by a dual frequency GPR antenna of 200 and 600 MHz. The results show that the dielectric constant is randomly varied within the micro and macro scale either in single radargrams or in the volumetric rock mass. The proposed method can be useful if considered in signal processing software programs, particularly in presence of subsurface utilities with known geometry and dimension, allowing converting

  4. Inflation with a smooth constant-roll to constant-roll era transition

    NASA Astrophysics Data System (ADS)

    Odintsov, S. D.; Oikonomou, V. K.

    2017-07-01

    In this paper, we study canonical scalar field models, with a varying second slow-roll parameter, that allow transitions between constant-roll eras. In the models with two constant-roll eras, it is possible to avoid fine-tunings in the initial conditions of the scalar field. We mainly focus on the stability of the resulting solutions, and we also investigate if these solutions are attractors of the cosmological system. We shall calculate the resulting scalar potential and, by using a numerical approach, we examine the stability and attractor properties of the solutions. As we show, the first constant-roll era is dynamically unstable towards linear perturbations, and the cosmological system is driven by the attractor solution to the final constant-roll era. As we demonstrate, it is possible to have a nearly scale-invariant power spectrum of primordial curvature perturbations in some cases; however, this is strongly model dependent and depends on the rate of the final constant-roll era. Finally, we present, in brief, the essential features of a model that allows oscillations between constant-roll eras.

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

    USGS Publications Warehouse

    Lee, M.W.; Meuwly, M.

    2013-01-01

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

  6. Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

    DOE PAGES

    Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2015-04-02

    The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log 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 logmore » 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.« less

  7. The hubble constant.

    PubMed

    Huchra, J P

    1992-04-17

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

  8. 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.

  9. 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.

  10. Influence of Analyte Concentration on Stability Constant Values Determined by Capillary Electrophoresis.

    PubMed

    Sursyakova, Viktoria V; Burmakina, Galina V; Rubaylo, Anatoly I

    2016-08-01

    The influence of analyte concentration when compared with the concentration of a charged ligand in background electrolyte (BGE) on the measured values of electrophoretic mobilities and stability constants (association, binding or formation constants) is studied using capillary electrophoresis (CE) and a dynamic mathematical simulator of CE. The study is performed using labile complexes (with fast kinetics) of iron (III) and 5-sulfosalicylate ions (ISC) as an example. It is shown that because the ligand concentration in the analyte zone is not equal to that in BGE, considerable changes in the migration times and electrophoretic mobilities are observed, resulting in systematic errors in the stability constant values. Of crucial significance is the slope of the dependence of the electrophoretic mobility decrease on the ligand equilibrium concentration. Without prior information on this dependence to accurately evaluate the stability constants for similar systems, the total ligand concentration must be at least >50-100 times higher than the total concentration of analyte. Experimental ISC peak fronting and the difference between the direction of the experimental pH dependence of the electrophoretic mobility decrease and the mathematical simulation allow assuming the presence of capillary wall interaction. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

    PubMed

    Ovchinnikov, Victor; Nam, Kwangho; Karplus, Martin

    2016-08-25

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

  12. Si Lattice, Avogadro Constant, and X- and Gamma-Ray Measurements: Contributions by R.D. Deslattes

    NASA Astrophysics Data System (ADS)

    Kessler, Jr.

    2002-04-01

    The achievement of x-ray interferometry in 1965 opened the possibility of more accurately measuring the lattice spacing of a diffraction crystal on a scale directly tied to the SI system of units. The road from the possible to reality required moving objects and measuring translations with sub-atomic accuracy. The improved crystal lattice spacing determinations had a significant impact on two fundamental measurement areas: 1) the amount of substance (the mole and the associated Avogadro Constant), and 2) short wavelengths (the x- and gamma-ray regions). Progress in both areas required additional metrological advances: density and isotopic abundance measurements are needed for the Avogadro constant and small angle measurements are required for the determination of short wavelengths. The x- and gamma-ray measurements have led to more accurate wavelength standards and neutron binding energy measurements that connect gamma-ray measurements to precision atomic mass measurements, particularly the neutron mass. Richard D. Deslattes devoted much of his scientific career to this measurement program. His outstanding contributions and insights will be reviewed.

  13. Direct measurement of electron transfer distance decay constants of single redox proteins by electrochemical tunneling spectroscopy.

    PubMed

    Artés, Juan M; Díez-Pérez, Ismael; Sanz, Fausto; Gorostiza, Pau

    2011-03-22

    We present a method to measure directly and at the single-molecule level the distance decay constant that characterizes the rate of electron transfer (ET) in redox proteins. Using an electrochemical tunneling microscope under bipotentiostatic control, we obtained current−distance spectroscopic recordings of individual redox proteins confined within a nanometric tunneling gap at a well-defined molecular orientation. The tunneling current decays exponentially, and the corresponding decay constant (β) strongly supports a two-step tunneling ET mechanism. Statistical analysis of decay constant measurements reveals differences between the reduced and oxidized states that may be relevant to the control of ET rates in enzymes and biological electron transport chains.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    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 H2O, N2H+, NO2+, and C2H2 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 N2H+ where it is concluded that basis set extrapolation is still preferred. The differences for H2O and NO2+ are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C2H2, 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 N2H+ and NO2+ were computed, including basis set extrapolation, core-correlation, scalar relativity, and higher

  15. The statistical analysis of circadian phase and amplitude in constant-routine core-temperature data

    NASA Technical Reports Server (NTRS)

    Brown, E. N.; Czeisler, C. A.

    1992-01-01

    Accurate estimation of the phases and amplitude of the endogenous circadian pacemaker from constant-routine core-temperature series is crucial for making inferences about the properties of the human biological clock from data collected under this protocol. This paper presents a set of statistical methods based on a harmonic-regression-plus-correlated-noise model for estimating the phases and the amplitude of the endogenous circadian pacemaker from constant-routine core-temperature data. The methods include a Bayesian Monte Carlo procedure for computing the uncertainty in these circadian functions. We illustrate the techniques with a detailed study of a single subject's core-temperature series and describe their relationship to other statistical methods for circadian data analysis. In our laboratory, these methods have been successfully used to analyze more than 300 constant routines and provide a highly reliable means of extracting phase and amplitude information from core-temperature data.

  16. Molecular Approaches to Thyroid Cancer Diagnosis

    PubMed Central

    Hsiao, Susan J.; Nikiforov, Yuri E.

    2014-01-01

    Thyroid nodules are common, and the accurate diagnosis of cancer or benign disease is important for the effective clinical management of these patients. Molecular markers are a helpful diagnostic tool, particularly for cytologically indeterminate thyroid nodules. In the past few years, significant progress has been made in developing molecular markers for clinical use in fine needle aspiration (FNA) specimens, including gene mutation panels and gene expression classifiers. With the availability of next generation sequencing technology, gene mutation panels can be expanded to interrogate multiple genes simultaneously and to provide yet more accurate diagnostic information. In addition, recently several new molecular markers in thyroid cancer have been identified that offer diagnostic, prognostic, and therapeutic information that could potentially be of value in guiding individualized management of patients with thyroid nodules. PMID:24829266

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

    PubMed

    Velazquez, Hector A; Hamelberg, Donald

    2015-02-21

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

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

    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.

  19. Kinetics of molecular transitions with dynamic disorder in single-molecule pulling experiments

    NASA Astrophysics Data System (ADS)

    Zheng, Yue; Li, Ping; Zhao, Nanrong; Hou, Zhonghuai

    2013-05-01

    Macromolecular transitions are subject to large fluctuations of rate constant, termed as dynamic disorder. The individual or intrinsic transition rates and activation free energies can be extracted from single-molecule pulling experiments. Here we present a theoretical framework based on a generalized Langevin equation with fractional Gaussian noise and power-law memory kernel to study the kinetics of macromolecular transitions to address the effects of dynamic disorder on barrier-crossing kinetics under external pulling force. By using the Kramers' rate theory, we have calculated the fluctuating rate constant of molecular transition, as well as the experimentally accessible quantities such as the force-dependent mean lifetime, the rupture force distribution, and the speed-dependent mean rupture force. Particular attention is paid to the discrepancies between the kinetics with and without dynamic disorder. We demonstrate that these discrepancies show strong and nontrivial dependence on the external force or the pulling speed, as well as the barrier height of the potential of mean force. Our results suggest that dynamic disorder is an important factor that should be taken into account properly in accurate interpretations of single-molecule pulling experiments.

  20. Constant pH simulations of pH responsive polymers

    NASA Astrophysics Data System (ADS)

    Sharma, Arjun; Smith, J. D.; Walters, Keisha B.; Rick, Steven W.

    2016-12-01

    Polyacidic polymers can change structure over a narrow range of pH in a competition between the hydrophobic effect, which favors a compact state, and electrostatic repulsion, which favors an extended state. Constant pH molecular dynamics computer simulations of poly(methacrylic acid) reveal that there are two types of structural changes, one local and one global, which make up the overall response. The local structural response depends on the tacticity of the polymer and leads to different cooperative effects for polymers with different stereochemistries, demonstrating both positive and negative cooperativities.

  1. Molecular Weight Effects on the Viscoelastic Response of a Polyimide

    NASA Technical Reports Server (NTRS)

    Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.

    2000-01-01

    The effect of molecular weight on the viscoelastic performance of an advanced polymer (LaRC -SI) was investigated through the use of creep compliance tests. Testing consisted of short-term isothermal creep and recovery with the creep segments performed under constant load. The tests were conducted at three temperatures below the glass transition temperature of each material with different molecular weight. Through the use of time-aging-time superposition procedures, the material constants, material master curves and aging-related parameters were evaluated at each temperature for a given molecular weight. The time-temperature superposition technique helped to describe the effect of temperature on the timescale of the viscoelastic response of each molecular weight. It was shown that the low molecular weight materials have increased creep compliance and creep compliance rate, and are more sensitive to temperature than the high molecular weight materials. Furthermore, a critical molecular weight transition was observed to occur at a weight-average molecular weight of approximately 25000 g/mol below which, the temperature sensitivity of the time-temperature superposition shift factor increases rapidly.

  2. Measurement of the Dielectric Constant of Seawater at L-Band: Techniques and Measurements

    NASA Technical Reports Server (NTRS)

    Lang, R.; Utku, C.; Tarkocin, Y.; LeVine, D.

    2009-01-01

    Satellite instruments, that will monitor salinity from space in the near future, require an accurate relationship between salinity/temperature and seawater dielectric constant. This paper will review measurements that were made of the dielectric constant of seawater during the past several years. The objective of the measurements is to determine the dependence of the dielectric constant of seawater on salinity and on temperature, more accurately than in the past. by taking advantage of modem instrumentation. The measurements of seawater permittivity have been performed as a function of salinity and temperature using a transmission resonant cavity technique. The measurements have been made in the salinity range of 10 to 38 psu and in the temperature range of IOU C to 35 C. These results will be useful in algorithm development for sensor systems such as SMOS and Aquarius. The measurement system consists of a brass microwave cavity that is resonant at 1.413 GHz. The seawater is introduced into the cavity through a capillary glass tube having an inner diameter of 0.1 mm. The diameter of the tube has been made very small so that the amount of seawater introduced in the cavity is small - thus maintaining the sensitivity of the measurements and allowing the use of perturbation theory predicting the seawater permittivity. The change in resonant frequency and the change in cavity Q can be used to determine the real and imaginary pare of the dielectric constant of seawater introduced into the slender tube. The microwave measurements are made by an HPS722D network analyzer. The cavity has been immersed in a uateriethylene-glycol bath which is connected to a Lauda circulator. The circulator keeps the brass cavity at a temperature constant to within 0.01 degrees. The system is automated using a Visual Basic program to control the analyzer and to collect the data. The results of the dielectric constant measurements of seawater will be presented. The measurement results will be

  3. EXPRESS: Accurate Measurement of the Optical Constants n and k for a Series of 57 Inorganic and Organic Liquids for Optical Modeling and Detection

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Myers, Tanya L.; Tonkyn, Russell G.; Danby, Tyler O.

    For optical modeling and other purposes, we have created a library of 57 liquids for which we have measured the complex optical constants n and k. These liquids vary in their nature, ranging in properties including chemical structure, optical band strength, volatility and viscosity. By obtaining the optical constants one can in principle model most optical phenomena in media and at interfaces including reflection, refraction and dispersion. Based on the original methods of J.E. Bertie et al.1 [1Bert1], we have developed improved protocols using multiple path lengths to determine the optical constants n/k for dozens of liquids, including inorganic, organicmore » and organophosphorus compounds. Detailed descriptions of the measurement and data reduction protocols are discussed; agreement of the derived optical constant n and k values with literature values are presented. We also present results using the n/k values as applied to an optical modeling scenario whereby the derived data are presented and tested for models of 1 µm and 100 µm layers for DMMP (dimethyl methyl phosphonate) on both metal (aluminum) and dielectric (soda lime glass) substrates to show substantial differences between the reflected signal from highly reflective substrates and less-reflective substrates.« less

  4. Constant frequency pulsed phase-locked-loop instrument for measurement of ultrasonic velocity

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    A new instrument based on a constant-frequency pulsed phase-locked-loop (CFPPLL) concept has been developed to accurately measure the ultrasonic wave velocity in liquids and changes in ultrasonic wave velocity in solids and liquids. An analysis of the system shows that it is immune to many of the frequency-dependent effects that plague other techniques. Measurements of the sound velocity in ultrapure water are used to confirm the analysis. The results are in excellent agreement with values from the literature, and establish that the CFPPLL provides a reliable, accurate way to measure velocities, as well as for monitoring small changes in velocity without the sensitivity to frequency-dependent phase shifts common to other measurement systems. The estimated sensitivity to phase changes is better than a few parts in 10 to the 7th.

  5. Compensation of Verdet Constant Temperature Dependence by Crystal Core Temperature Measurement

    PubMed Central

    Petricevic, Slobodan J.; Mihailovic, Pedja M.

    2016-01-01

    Compensation of the temperature dependence of the Verdet constant in a polarimetric extrinsic Faraday sensor is of major importance for applying the magneto-optical effect to AC current measurements and magnetic field sensing. This paper presents a method for compensating the temperature effect on the Faraday rotation in a Bi12GeO20 crystal by sensing its optical activity effect on the polarization of a light beam. The method measures the temperature of the same volume of crystal that effects the beam polarization in a magnetic field or current sensing process. This eliminates the effect of temperature difference found in other indirect temperature compensation methods, thus allowing more accurate temperature compensation for the temperature dependence of the Verdet constant. The method does not require additional changes to an existing Δ/Σ configuration and is thus applicable for improving the performance of existing sensing devices. PMID:27706043

  6. Determination of temperature dependence of full matrix material constants of PZT-8 piezoceramics using only one sample.

    PubMed

    Zhang, Yang; Tang, Liguo; Tian, Hua; Wang, Jiyang; Cao, Wenwu; Zhang, Zhongwu

    2017-08-15

    Resonant ultrasound spectroscopy (RUS) was used to determine the temperature dependence of full matrix material constants of PZT-8 piezoceramics from room temperature to 100 °C. Property variations from sample to samples can be eliminated by using only one sample, so that data self-consistency can be guaranteed. The RUS measurement system error was estimated to be lower than 2.35%. The obtained full matrix material constants at different temperatures all have excellent self-consistency, which can help accurately predict device performance at high temperatures using finite element simulations.

  7. Development of a Novel Leak-Free Constant-Pressure Cylinder for Certified Reference Materials of Liquid Hydrocarbon Mixtures.

    PubMed

    Kim, Yong Doo; Kang, Ji Hwan; Bae, Hyun Kil; Kang, Namgoo; Oh, Sang Hyub; Lee, Jin-Hong; Woo, Jin Chun; Lee, Sangil

    2017-11-21

    Liquid hydrocarbon mixtures such as liquefied petroleum gas and liquefied natural gas are becoming integral parts of the world's energy system. Certified reference materials (CRMs) of liquid hydrocarbon mixtures are necessary to allow assessment of the accuracy and traceability of the compositions of such materials. A piston-type constant-pressure cylinder (PCPC) comprising chambers for a pressurizing gas (helium) and liquid (hydrocarbons) separated by a piston can be used to develop accurate and traceable liquid hydrocarbon mixture CRMs. The development of accurate CRMs relies on the maintenance of their composition. However, a PCPC might allow hydrocarbons to leak owing to the imperfect seal of the piston. In this study, a novel leak-free bellows-type constant-pressure cylinder (BCPC) is designed and evaluated by comparison with PCPCs. Liquid hydrocarbon mixtures consisting of ethane, propane, propene, isobutane, n-butane, 1-butene, and isopentane were prepared in both types of constant pressure cylinders and then monitored to check leakages between the gas and liquid chambers. Overall, notable leakage occurred from and into both chambers in the PCPCs, whereas no leakage occurred in the BCPCs in the three months after their gravimetric preparation. The BCPCs maintained no leakage even 10 months after their preparation, whereas the PCPCs showed significantly increasing leakage during the same period.

  8. Optical constants of neat liquid-chemical warfare agents and related materials measured by infrared spectroscopic ellipsometry

    NASA Astrophysics Data System (ADS)

    Yang, C. S.-C.; Williams, B. R.; Hulet, M. S.; Tiwald, T. E.; Miles, R. W., Jr.; Samuels, A. C.

    2011-05-01

    We studied various liquids using a vertical attenuated total reflection (ATR) liquid sampling assembly in conjunction with Infrared Variable Angle Spectroscopic Ellipsometry (IR-VASE), to determine the infrared optical constants of several bulk liquids related to chemical warfare. The index of refraction, n, and the extinction coefficient, k, of isopropyl methylphosphonofluoridate (Sarin or GB), isopropyl alcohol (IPA) (a precursor of GB), and dimethyl methylphosphonate (DMMP)-a commonly employed simulant for GB, measured by our vertical ATR IR-VASE setup are closely matched to those found in other studies. We also report the optical constants of cyclohexyl methylphosphonofluoridate (GF), 2-(diisopropylamino)ethyl methylphosphonothioate (VX), bis-(2-chloroethyl) sulfide (HD), and 2-chlorovinyl dichloroarsine (L, Lewisite). The ATR IR-VASE technique affords an accurate measurement of the optical constants of these hazardous compounds.

  9. Determining accurate distances to nearby galaxies

    NASA Astrophysics Data System (ADS)

    Bonanos, Alceste Zoe

    2005-11-01

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

  10. Determination of the Temperature Dependence of Heat Capacity for Some Molecular Crystals of Nitro Compounds

    NASA Astrophysics Data System (ADS)

    Kovalev, Yu. M.; Kuropatenko, V. F.

    2018-05-01

    An analysis of the existing approximations used for describing the dependence of heat capacity at a constant volume on the temperature of a molecular crystal has been carried out. It is shown that the considered Debye and Einstein approximations do not enable one to adequately describe the dependence of heat capacity at a constant volume on the temperature of the molecular crystals of nitro compounds. This inference requires the development of special approximations that would describe both low-frequency and high-frequency parts of the vibrational spectra of molecular crystals. This work presents a universal dependence allowing one to describe the dependence of heat capacity at a constant volume on temperature for a number of molecular crystals of nitro compounds.

  11. Economic Load Dispatch Using Adaptive Social Acceleration Constant Based Particle Swarm Optimization

    NASA Astrophysics Data System (ADS)

    Jain, N. K.; Nangia, Uma; Jain, Jyoti

    2018-04-01

    In this paper, an Adaptive Social Acceleration Constant based Particle Swarm Optimization (ASACPSO) has been developed which uses the best value of social acceleration constant (Csg). Three formulations of Csg have been used to search for the best value of Csg. These three formulations led to the development of three algorithms-ALDPSO, AELDPSO-I and AELDPSO-II which were implemented for Economic Load Dispatch of IEEE 5 bus, 14 bus and 30 bus systems. The best value of Csg was selected based on the minimum number of Kounts i.e. number of function evaluations required to minimize the function. This value of Csg was directly used in basic PSO algorithm which led to the development of ASACPSO algorithm. ASACPSO was found to converge faster and give more accurate results compared to BPSO for IEEE 5, 14 and 30 bus systems.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    2015-05-12

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  13. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    DOE PAGES

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

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C 7H 10O 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.« less

  14. Construction of exact constants of motion and effective models for many-body localized systems

    NASA Astrophysics Data System (ADS)

    Goihl, M.; Gluza, M.; Krumnow, C.; Eisert, J.

    2018-04-01

    One of the defining features of many-body localization is the presence of many quasilocal conserved quantities. These constants of motion constitute a cornerstone to an intuitive understanding of much of the phenomenology of many-body localized systems arising from effective Hamiltonians. They may be seen as local magnetization operators smeared out by a quasilocal unitary. However, accurately identifying such constants of motion remains a challenging problem. Current numerical constructions often capture the conserved operators only approximately, thus restricting a conclusive understanding of many-body localization. In this work, we use methods from the theory of quantum many-body systems out of equilibrium to establish an alternative approach for finding a complete set of exact constants of motion which are in addition guaranteed to represent Pauli-z operators. By this we are able to construct and investigate the proposed effective Hamiltonian using exact diagonalization. Hence, our work provides an important tool expected to further boost inquiries into the breakdown of transport due to quenched disorder.

  15. A two force-constant model for complexes B⋯M-X (B is a Lewis base and MX is any diatomic molecule): Intermolecular stretching force constants from centrifugal distortion constants D(J) or Δ(J).

    PubMed

    Bittner, Dror M; Walker, Nicholas R; Legon, Anthony C

    2016-02-21

    A two force-constant model is proposed for complexes of the type B⋯MX, in which B is a simple Lewis base of at least C2v symmetry and MX is any diatomic molecule lying along a Cn axis (n ≥ 2) of B. The model assumes a rigid subunit B and that force constants beyond quadratic are negligible. It leads to expressions that allow, in principle, the determination of three quadratic force constants F11, F12, and F22 associated with the r(B⋯M) = r2 and r(M-X) = r1 internal coordinates from the equilibrium centrifugal distortion constants DJ (e) or ΔJ (e), the equilibrium principal axis coordinates a1 and a2, and equilibrium principal moments of inertia. The model can be applied generally to complexes containing different types of intermolecular bond. For example, the intermolecular bond of B⋯MX can be a hydrogen bond if MX is a hydrogen halide, a halogen-bond if MX is a dihalogen molecule, or a stronger, coinage-metal bond if MX is a coinage metal halide. The equations were tested for BrCN, for which accurate equilibrium spectroscopic constants and a complete force field are available. In practice, equilibrium values of DJ (e) or ΔJ (e) for B⋯MX are not available and zero-point quantities must be used instead. The effect of doing so has been tested for BrCN. The zero-point centrifugal distortion constants DJ (0) or ΔJ (0) for all B⋯MX investigated so far are of insufficient accuracy to allow F11 and F22 to be determined simultaneously, even under the assumption F12 = 0 which is shown to be reasonable for BrCN. The calculation of F22 at a series of fixed values of F11 reveals, however, that in cases for which F11 is sufficiently larger than F22, a good approximation to F22 is obtained. Plots of F22 versus F11 have been provided for Kr⋯CuCl, Xe⋯CuCl, OC⋯CuCl, and C2H2⋯AgCl as examples. Even in cases where F22 ∼ F11 (e.g., OC⋯CuCl), such plots will yield either F22 or F11 if the other becomes available.

  16. A two force-constant model for complexes B⋯M-X (B is a Lewis base and MX is any diatomic molecule): Intermolecular stretching force constants from centrifugal distortion constants DJ or ΔJ

    NASA Astrophysics Data System (ADS)

    Bittner, Dror M.; Walker, Nicholas R.; Legon, Anthony C.

    2016-02-01

    A two force-constant model is proposed for complexes of the type B⋯MX, in which B is a simple Lewis base of at least C2v symmetry and MX is any diatomic molecule lying along a Cn axis (n ≥ 2) of B. The model assumes a rigid subunit B and that force constants beyond quadratic are negligible. It leads to expressions that allow, in principle, the determination of three quadratic force constants F11, F12, and F22 associated with the r(B⋯M) = r2 and r(M-X) = r1 internal coordinates from the equilibrium centrifugal distortion constants DJ e or ΔJ e , the equilibrium principal axis coordinates a1 and a2, and equilibrium principal moments of inertia. The model can be applied generally to complexes containing different types of intermolecular bond. For example, the intermolecular bond of B⋯MX can be a hydrogen bond if MX is a hydrogen halide, a halogen-bond if MX is a dihalogen molecule, or a stronger, coinage-metal bond if MX is a coinage metal halide. The equations were tested for BrCN, for which accurate equilibrium spectroscopic constants and a complete force field are available. In practice, equilibrium values of DJ e or ΔJ e for B⋯MX are not available and zero-point quantities must be used instead. The effect of doing so has been tested for BrCN. The zero-point centrifugal distortion constants DJ 0 or ΔJ 0 for all B⋯MX investigated so far are of insufficient accuracy to allow F11 and F22 to be determined simultaneously, even under the assumption F12 = 0 which is shown to be reasonable for BrCN. The calculation of F22 at a series of fixed values of F11 reveals, however, that in cases for which F11 is sufficiently larger than F22, a good approximation to F22 is obtained. Plots of F22 versus F11 have been provided for Kr⋯CuCl, Xe⋯CuCl, OC⋯CuCl, and C2H2⋯AgCl as examples. Even in cases where F22 ˜ F11 (e.g., OC⋯CuCl), such plots will yield either F22 or F11 if the other becomes available.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

  18. Effect of elastic constants of liquid crystals in their electro-optical properties

    NASA Astrophysics Data System (ADS)

    Parang, Z.; Ghaffary, T.; Gharahbeigi, M. M.

    Recently following the success of the density functional theory (DFT) in obtaining the structure and thermodynamics of homogeneous and inhomogeneous classical systems such as simple fluids, dipolar fluid and binary hard spheres, this theory was also applied to obtain the density profile of a molecular fluid in between hard planar walls by Kalpaxis and Rickayzen. In the theory of molecular fluids, the direct correlation function (DCF) can be used to calculate the equation of state, free energy, phase transition, elastic constants, etc. It is well known that the hard core molecular models play an important role in understanding complex liquids such as liquid crystals. In this paper, a classical fluid of nonspherical molecules is studied. The required homogeneous (DCF) is obtained by solving Orenstein-Zernike (OZ) integral equation numerically. Some of the molecules in the liquid crystals have a sphere shape and this kind of molecular fluid is considered here. The DCF sphere of the molecular fluid is calculated and it will be shown that the results are in good agreement with the pervious works and the results of computer simulation. Finally the electro-optical properties of ellipsoid liquid crystal using DCF of these molecules are calculated.

  19. Molecular methods for pathogen detection and quantification

    USDA-ARS?s Scientific Manuscript database

    Ongoing interest in convenient, inexpensive, fast, sensitive and accurate techniques for detecting and/or quantifying the presence of soybean pathogens has resulted in increased usage of molecular tools. The method of extracting a molecular target (usually DNA or RNA) for detection depends wholly up...

  20. Extracting Diffusion Constants from Echo-Time-Dependent PFG NMR Data Using Relaxation-Time Information

    NASA Astrophysics Data System (ADS)

    Vandusschoten, D.; Dejager, P. A.; Vanas, H.

    Heterogeneous (bio)systems are often characterized by several water-containing compartments that differ in relaxation time values and diffusion constants. Because of the relatively small differences among these diffusion constants, nonoptimal measuring conditions easily lead to the conclusion that a single diffusion constant suffices to describe the water mobility in a heterogeneous (bio)system. This paper demonstrates that the combination of a T2 measurement and diffusion measurements at various echo times (TE), based on the PFG MSE sequence, enables the accurate determination of diffusion constants which are less than a factor of 2 apart. This new method gives errors of the diffusion constant below 10% when two fractions are present, while the standard approach of a biexponential fit to the diffusion data in identical circumstances gives larger (>25%) errors. On application of this approach to water in apple parenchyma tissue, the diffusion constant of water in the vacuole of the cells ( D = 1.7 × 10 -9 m 2/s) can be distinguished from that of the cytoplasm ( D = 1.0 × 10 -9 m 2/s). Also, for mung bean seedlings, the cell size determined by PFG MSE measurements increased from 65 to 100 μm when the echo time increased from 150 to 900 ms, demonstrating that the interpretation of PFG SE data used to investigate cell sizes is strongly dependent on the T2 values of the fractions within the sample. Because relaxation times are used to discriminate the diffusion constants, we propose to name this approach diffusion analysis by relaxation- time- separated (DARTS) PFG NMR.

  1. Microwave Spectrum, Structure, and Nuclear Quadrupole Coupling Constants of 1-Bromo-1-fluoroethane.

    PubMed

    Tatamitani; Kuwano; Fuchigami; Oe; Ogata

    1999-08-01

    The microwave spectrum of 1-bromo-1-fluoroethane, CHBrF-CH(3) and CHBrF-CH(2)D ((79/81)Br), has been studied for the first time from 8 to 41 GHz. A least-squares analysis of the observed a- and b-type transition frequencies gave rotational and centrifugal distortion constants and components of the bromine nuclear quadrupole coupling constant tensor in the principal axes system as follows: A = 8979.428(5) MHz, B = 2883.898(3) MHz, C = 2310.535(3) MHz, Delta(J) = 0.74(2) kHz, Delta(JK) = 2.49(3) kHz, Delta(K) = 5.3(5) kHz, delta(J) = 0.146(1) kHz, delta(K) = 2.75(4) kHz, chi(aa) = 493.49(29) MHz, chi(bb) - chi(cc) = -38.89(11) MHz, and ||chi(ab) || = 161.8(28) MHz for the CH(79)BrF-CH(3) species; A = 8979.257(5) MHz, B = 2859.072(3) MHz, C = 2294.572(3), Delta(J) = 0.76(2) kHz, Delta(JK) = 2.51(3) kHz, Delta(K) = 4.5(4) kHz, delta(J) = 0.145(1) kHz, delta(K) = 2.70(4) kHz, chi(aa) = 412.42(27) MHz, chi(bb) - chi(cc) = -32.56 (11) MHz, and ||chi(ab) || = 133.3(3) MHz for the CH(81)BrF-CH(3) species. The structural parameters are calculated from the 24 observed rotational constants, and electronic properties of the carbon-bromine bond in 1-bromo-1-fluoroethane are evaluated from the observed nuclear quadrupole coupling constants. These molecular properties are compared with those of other related molecules. The molecular structure of 1-bromo-1-fluoroethane is found to be very close to that of 1,1-difluoroethane except for the C-Br bond. Copyright 1999 Academic Press.

  2. Microwave Spectrum, Structure, and Nuclear Quadrupole Coupling Constants of 1-Bromo-1-fluoroethane

    NASA Astrophysics Data System (ADS)

    Tatamitani, Yoshio; Kuwano, Susumu; Fuchigami, Kiyokatu; Oe, Sumio; Ogata, Teruhiko

    1999-08-01

    The microwave spectrum of 1-bromo-1-fluoroethane, CHBrF-CH3 and CHBrF-CH2D (79/81Br), has been studied for the first time from 8 to 41 GHz. A least-squares analysis of the observed a- and b-type transition frequencies gave rotational and centrifugal distortion constants and components of the bromine nuclear quadrupole coupling constant tensor in the principal axes system as follows: A = 8979.428(5) MHz, B = 2883.898(3) MHz, C = 2310.535(3) MHz, ΔJ = 0.74(2) kHz, ΔJK = 2.49(3) kHz, ΔK = 5.3(5) kHz, δJ = 0.146(1) kHz, δK = 2.75(4) kHz, χaa = 493.49(29) MHz, χbb - χcc = -38.89(11) MHz, and ‖χab‖ = 161.8(28) MHz for the CH79BrF-CH3 species; A = 8979.257(5) MHz, B = 2859.072(3) MHz, C = 2294.572(3), ΔJ = 0.76(2) kHz, ΔJK = 2.51(3) kHz, ΔK = 4.5(4) kHz, δJ = 0.145(1) kHz, δK = 2.70(4) kHz, χaa = 412.42(27) MHz, χbb - χcc = -32.56 (11) MHz, and ‖χab‖ = 133.3(3) MHz for the CH81BrF-CH3 species. The structural parameters are calculated from the 24 observed rotational constants, and electronic properties of the carbon-bromine bond in 1-bromo-1-fluoroethane are evaluated from the observed nuclear quadrupole coupling constants. These molecular properties are compared with those of other related molecules. The molecular structure of 1-bromo-1-fluoroethane is found to be very close to that of 1,1-difluoroethane except for the C-Br bond.

  3. pyQms enables universal and accurate quantification of mass spectrometry data.

    PubMed

    Leufken, Johannes; Niehues, Anna; Sarin, L Peter; Wessel, Florian; Hippler, Michael; Leidel, Sebastian A; Fufezan, Christian

    2017-10-01

    Quantitative mass spectrometry (MS) is a key technique in many research areas (1), including proteomics, metabolomics, glycomics, and lipidomics. Because all of the corresponding molecules can be described by chemical formulas, universal quantification tools are highly desirable. Here, we present pyQms, an open-source software for accurate quantification of all types of molecules measurable by MS. pyQms uses isotope pattern matching that offers an accurate quality assessment of all quantifications and the ability to directly incorporate mass spectrometer accuracy. pyQms is, due to its universal design, applicable to every research field, labeling strategy, and acquisition technique. This opens ultimate flexibility for researchers to design experiments employing innovative and hitherto unexplored labeling strategies. Importantly, pyQms performs very well to accurately quantify partially labeled proteomes in large scale and high throughput, the most challenging task for a quantification algorithm. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Diffusion Monte Carlo method for evaluating Hamaker constants

    NASA Astrophysics Data System (ADS)

    Maezono, Ryo; Hongo, Kenta

    We evaluated Hamaker's constants for Si6H12 (CHS) to investigate its wettability, which is industrially useful but no references available. The constant is fundamental for wettability, but not directly accessible by experiments. Ab initio estimations are therefore in demand, and surely give an impact for broader fields such as tribology where the wettability plays an important role. The evaluation of binding curves itself could be a big challenge if it is applied to a practical molecule such as CHS, because highly accurate descriptions of electron correlations in vdW bindings get tough for such larger sizes with anisotropy. We applied DMC to overcome this difficulty, showing a new direction for wettability issues. Since ab intio estimations rely on simple assumptions such as additivity (and hence we denote it as Aadd), it would include biases. Taking a benzene as a benchmark, we compared Aadd evaluated from several available binding curves with other reported AL (estimations based on Lifshitz theory). By the comparison, we get trends of biases in Aa dd due to non-additivity and anisotropy because AL is expected to capture these effects to some extent in macroscopic manner. The expected trends here surprisingly well explain the series of results for CHS.

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

    EPA Science Inventory

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

  6. Computation of Nonretarded London Dispersion Coefficients and Hamaker Constants of Copper Phthalocyanine.

    PubMed

    Zhao, Yan; Ng, Hou T; Hanson, Eric; Dong, Jiannan; Corti, David S; Franses, Elias I

    2010-02-09

    A time-dependent density functional theory (TDDFT) scheme has been validated for predictions of the dispersion coefficients of five molecules (H2O, NH3, CO2, C6H6, and pentane) and for predictions of the static dipole polarizabilities of three organometallic compounds (TiCl4, OsO4, and Ge(CH3)4). The convergence of grid spacing has been examined, and two types of pseudopotentials and 13 density functionals have been tested. The nonretarded Hamaker constants A11 are calculated by employing a semiempirical parameter a along with the standard Hamaker constant equation. The parameter a is optimized against six accurate Hamaker constants obtained from the full Lifshitz theory. The dispersion coefficients of copper phthalocyanine CuPc and CuPc-SO3H are then computed. Using the theoretical densities of ρ1 = 1.63 and 1.62 g/cm(3), the Hamaker constants A11 of crystalline α-CuPc and β-CuPc are found to be 14.73 × 10(-20) and 14.66 × 10(-20) J, respectively. Using the experimentally derived density of ρ1 = 1.56 g/cm(3) for a commercially available β-CuPc (nanoparticles of ∼90 nm hydrodynamic diameter), A11 = 13.52 × 10(-20) J is found. Its corresponding effective Hamaker constant in water (A121) is calculated to be 3.07 × 10(-20) J. All computed A11 values for CuPc are noted to be higher than those reported previously.

  7. Precise Measurements of the Masses of Cs, Rb and Na A New Route to the Fine Structure Constant

    NASA Astrophysics Data System (ADS)

    Rainville, Simon; Bradley, Michael P.; Porto, James V.; Thompson, James K.; Pritchard, David E.

    2001-01-01

    We report new values for the atomic masses of the alkali 133Cs, 87Rb, 85Rb, and 23Na with uncertainties ≤ 0.2 ppb. These results, obtained using Penning trap single ion mass spectrometry, are typically two orders of magnitude more accurate than previously measured values. Combined with values of h/m atom from atom interferometry measurements and accurate wavelength measurements for different atoms, these values will lead to new ppb-level determinations of the molar Planck constant N A h and the fine structure constant α. This route to α is based on simple physics. It can potentially achieve the several ppb level of accuracy needed to test the QED determination of α extracted from measurements of the electron g factor. We also demonstrate an electronic cooling technique that cools our detector and ion below the 4 K ambient temperature. This technique improves by about a factor of three our ability to measure the ion's axial motion.

  8. Gastric Cancer Cells in Peritoneal Lavage Fluid: A Systematic Review Comparing Cytological with Molecular Detection for Diagnosis of Peritoneal Metastases and Prediction of Peritoneal Recurrences.

    PubMed

    Virgilio, Edoardo; Giarnieri, Enrico; Giovagnoli, Maria Rosaria; Montagnini, Monica; Proietti, Antonella; D'Urso, Rosaria; Mercantini, Paolo; Valabrega, Stefano; Balducci, Genoveffa; Cavallini, Marco

    2018-03-01

    Detecting free tumor cells in the peritoneal lavage fluid of gastric cancer patients permits to assess a more accurate prognosis, predict peritoneal recurrence and select cases for a more aggressive treatment. Currently, cytology and molecular biology comprise the two most popular methods of detection that are under constant study by researchers. We burrowed into the available literature comparing cytological with molecular detection of free intraperitoneal gastric cancer cells. PubMed, Science Direct, Scopus and Google Scholar were the search engines investigated. As of 2017, 51 dedicated studies have been published. Messenger RNA of carcinoembryonic antigen was the genetic target most frequently described. The genetic technique is usually superior to cytology in sensitivity (38-100% vs. 12.3-67% respectively), whereas cytological examination tends to show a slight pre-eminence in specificity (approximately 100%). So far, given the imperfection of each method, employment of both cytology and molecular examination seem to be mandatory. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  9. Discovering interesting molecular substructures for molecular classification.

    PubMed

    Lam, Winnie W M; Chan, Keith C C

    2010-06-01

    Given a set of molecular structure data preclassified into a number of classes, the molecular classification problem is concerned with the discovering of interesting structural patterns in the data so that "unseen" molecules not originally in the dataset can be accurately classified. To tackle the problem, interesting molecular substructures have to be discovered and this is done typically by first representing molecular structures in molecular graphs, and then, using graph-mining algorithms to discover frequently occurring subgraphs in them. These subgraphs are then used to characterize different classes for molecular classification. While such an approach can be very effective, it should be noted that a substructure that occurs frequently in one class may also does occur in another. The discovering of frequent subgraphs for molecular classification may, therefore, not always be the most effective. In this paper, we propose a novel technique called mining interesting substructures in molecular data for classification (MISMOC) that can discover interesting frequent subgraphs not just for the characterization of a molecular class but also for the distinguishing of it from the others. Using a test statistic, MISMOC screens each frequent subgraph to determine if they are interesting. For those that are interesting, their degrees of interestingness are determined using an information-theoretic measure. When classifying an unseen molecule, its structure is then matched against the interesting subgraphs in each class and a total interestingness measure for the unseen molecule to be classified into a particular class is determined, which is based on the interestingness of each matched subgraphs. The performance of MISMOC is evaluated using both artificial and real datasets, and the results show that it can be an effective approach for molecular classification.

  10. L-band Dielectric Constant Measurements of Seawater (Oral presentation and SMOS Poster)

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

    This paper describes a resonant cavity technique for the measurement of the dielectric constant of seawater as a function of its salinity. Accurate relationships between salinity and dielectric constant (which determines emissivity) are needed for sensor systems such as SMOS and Aquarius that will monitor salinity from space in the near future. The purpose of the new measurements is to establish the dependence of the dielectric constant of seawater on salinity in contemporary units (e.g. psu) and to take advantage of modern instrumentation to increase the accuracy of these measurements. The measurement device is a brass cylindrical cavity 16cm in diameter and 7cm in height. The seawater is introduced into the cavity through a slender glass tube having an inner diameter of 0.1 mm. By assuming that this small amount of seawater slightly perturbs the internal fields in the cavity, perturbation theory can be employed. A simple formula results relating the real part of the dielectric constant to the change in resonant frequency of the cavity. In a similar manner, the imaginary part of the dielectric constant is related to the change in the cavity s Q. The expected accuracy of the cavity technique is better than 1% for the real part and 1 to 2% for the imaginary part. Presently, measurements of methanol have been made and agree with precision measurements in the literature to within 1% in both real and imaginary parts. Measurements have been made of the dielectric constant of seawater samples from Ocean Scientific in the United Kingdom with salinities of 10, 30, 35 and 38 psu. All measurements were made at room temperature. Plans to make measurements at a range of temperatures and salinities will be discussed.

  11. Spectral parameters and Hamaker constants of silicon hydride compounds and organic solvents.

    PubMed

    Masuda, Takashi; Matsuki, Yasuo; Shimoda, Tatsuya

    2009-12-15

    Cyclopentasilane (CPS) and polydihydrosilane, which consist of hydrogen and silicon only, are unique materials that can be used to produce intrinsic silicon film in a liquid process, such as spin coating or an ink-jet method. Wettability and solubility of general organic solvents including the above can be estimated by Hamaker constants, which are calculated according to the Lifshitz theory. In order to calculate a Hamaker constant by the simple spectral method (SSM), it is necessary to obtain absorption frequency and function of oscillator strength in the ultraviolet region. In this report, these physical quantities were obtained by means of an optical method. As a result of examination of the relation between molecular structures and ultraviolet absorption frequencies, which were obtained from various liquid materials, it was concluded that ultraviolet absorption frequencies became smaller as electrons were delocalized. In particular, the absorption frequencies were found to be very small for CPS and polydihydrosilane due to sigma-conjugate of their electrons. The Hamaker constants of CPS and polydihydrosilane were successfully calculated based on the obtained absorption frequency and function of oscillator strength.

  12. Prediction of glass transition temperature of freeze-dried formulations by molecular dynamics simulation.

    PubMed

    Yoshioka, Sumie; Aso, Yukio; Kojima, Shigeo

    2003-06-01

    To examine whether the glass transition temperature (Tg) of freeze-dried formulations containing polymer excipients can be accurately predicted by molecular dynamics simulation using software currently available on the market. Molecular dynamics simulations were carried out for isomaltodecaose, a fragment of dextran, and alpha-glucose, the repeated unit of dextran. in the presence or absence of water molecules. Estimated values of Tg were compared with experimental values obtained by differential scanning calorimetry (DSC). Isothermal-isobaric molecular dynamics simulations (NPTMD) and isothermal molecular dynamics simulations at a constant volume (NVTMD) were carried out using the software package DISCOVER (Material Studio) with the Polymer Consortium Force Field. Mean-squared displacement and radial distribution function were calculated. NVTMD using the values of density obtained by NPTMD provided the diffusivity of glucose-ring oxygen and water oxygen in amorphous alpha-glucose and isomaltodecaose, which exhibited a discontinuity in temperature dependence due to glass transition. Tg was estimated to be approximately 400K and 500K for pure amorphous a-glucose and isomaltodecaose, respectively, and in the presence of one water molecule per glucose unit, Tg was 340K and 360K, respectively. Estimated Tg values were higher than experimentally determined values because of the very fast cooling rates in the simulations. However, decreases in Tg on hydration and increases in Tg associated with larger fragment size could be demonstrated. The results indicate that molecular dynamics simulation is a useful method for investigating the effects of hydration and molecular weight on the Tg of lyophilized formulations containing polymer excipients. although the relationship between cooling rates and Tg must first be elucidated to predict Tg vales observed by DSC measurement. January 16.

  13. Fast high-throughput method for the determination of acidity constants by capillary electrophoresis: I. Monoprotic weak acids and bases.

    PubMed

    Fuguet, Elisabet; Ràfols, Clara; Bosch, Elisabeth; Rosés, Martí

    2009-04-24

    A new and fast method to determine acidity constants of monoprotic weak acids and bases by capillary zone electrophoresis based on the use of an internal standard (compound of similar nature and acidity constant as the analyte) has been developed. This method requires only two electrophoretic runs for the determination of an acidity constant: a first one at a pH where both analyte and internal standard are totally ionized, and a second one at another pH where both are partially ionized. Furthermore, the method is not pH dependent, so an accurate measure of the pH of the buffer solutions is not needed. The acidity constants of several phenols and amines have been measured using internal standards of known pK(a), obtaining a mean deviation of 0.05 pH units compared to the literature values.

  14. A Comprehensive Strategy for Accurate Mutation Detection of the Highly Homologous PMS2.

    PubMed

    Li, Jianli; Dai, Hongzheng; Feng, Yanming; Tang, Jia; Chen, Stella; Tian, Xia; Gorman, Elizabeth; Schmitt, Eric S; Hansen, Terah A A; Wang, Jing; Plon, Sharon E; Zhang, Victor Wei; Wong, Lee-Jun C

    2015-09-01

    Germline mutations in the DNA mismatch repair gene PMS2 underlie the cancer susceptibility syndrome, Lynch syndrome. However, accurate molecular testing of PMS2 is complicated by a large number of highly homologous sequences. To establish a comprehensive approach for mutation detection of PMS2, we have designed a strategy combining targeted capture next-generation sequencing (NGS), multiplex ligation-dependent probe amplification, and long-range PCR followed by NGS to simultaneously detect point mutations and copy number changes of PMS2. Exonic deletions (E2 to E9, E5 to E9, E8, E10, E14, and E1 to E15), duplications (E11 to E12), and a nonsense mutation, p.S22*, were identified. Traditional multiplex ligation-dependent probe amplification and Sanger sequencing approaches cannot differentiate the origin of the exonic deletions in the 3' region when PMS2 and PMS2CL share identical sequences as a result of gene conversion. Our approach allows unambiguous identification of mutations in the active gene with a straightforward long-range-PCR/NGS method. Breakpoint analysis of multiple samples revealed that recurrent exon 14 deletions are mediated by homologous Alu sequences. Our comprehensive approach provides a reliable tool for accurate molecular analysis of genes containing multiple copies of highly homologous sequences and should improve PMS2 molecular analysis for patients with Lynch syndrome. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  15. Evaluation of molecular dynamics simulation methods for ionic liquid electric double layers.

    PubMed

    Haskins, Justin B; Lawson, John W

    2016-05-14

    We investigate how systematically increasing the accuracy of various molecular dynamics modeling techniques influences the structure and capacitance of ionic liquid electric double layers (EDLs). The techniques probed concern long-range electrostatic interactions, electrode charging (constant charge versus constant potential conditions), and electrolyte polarizability. Our simulations are performed on a quasi-two-dimensional, or slab-like, model capacitor, which is composed of a polarizable ionic liquid electrolyte, [EMIM][BF4], interfaced between two graphite electrodes. To ensure an accurate representation of EDL differential capacitance, we derive new fluctuation formulas that resolve the differential capacitance as a function of electrode charge or electrode potential. The magnitude of differential capacitance shows sensitivity to different long-range electrostatic summation techniques, while the shape of differential capacitance is affected by charging technique and the polarizability of the electrolyte. For long-range summation techniques, errors in magnitude can be mitigated by employing two-dimensional or corrected three dimensional electrostatic summations, which led to electric fields that conform to those of a classical electrostatic parallel plate capacitor. With respect to charging, the changes in shape are a result of ions in the Stern layer (i.e., ions at the electrode surface) having a higher electrostatic affinity to constant potential electrodes than to constant charge electrodes. For electrolyte polarizability, shape changes originate from induced dipoles that soften the interaction of Stern layer ions with the electrode. The softening is traced to ion correlations vertical to the electrode surface that induce dipoles that oppose double layer formation. In general, our analysis indicates an accuracy dependent differential capacitance profile that transitions from the characteristic camel shape with coarser representations to a more diffuse

  16. Kinetics of the reaction of the heaviest hydrogen atom with H2, the 4Heμ + H2 → 4HeμH + H reaction: Experiments, accurate quantal calculations, and variational transition state theory, including kinetic isotope effects for a factor of 36.1 in isotopic mass

    NASA Astrophysics Data System (ADS)

    Fleming, Donald G.; Arseneau, Donald J.; Sukhorukov, Oleksandr; Brewer, Jess H.; Mielke, Steven L.; Truhlar, Donald G.; Schatz, George C.; Garrett, Bruce C.; Peterson, Kirk A.

    2011-11-01

    The neutral muonic helium atom 4Heμ, in which one of the electrons of He is replaced by a negative muon, may be effectively regarded as the heaviest isotope of the hydrogen atom, with a mass of 4.115 amu. We report details of the first muon spin rotation (μSR) measurements of the chemical reaction rate constant of 4Heμ with molecular hydrogen, 4Heμ + H2 → 4HeμH + H, at temperatures of 295.5, 405, and 500 K, as well as a μSR measurement of the hyperfine coupling constant of muonic He at high pressures. The experimental rate constants, kHeμ, are compared with the predictions of accurate quantum mechanical (QM) dynamics calculations carried out on a well converged Born-Huang (BH) potential energy surface, based on complete configuration interaction calculations and including a Born-Oppenheimer diagonal correction. At the two highest measured temperatures the agreement between the quantum theory and experiment is good to excellent, well within experimental uncertainties that include an estimate of possible systematic error, but at 295.5 K the quantum calculations for kHeμ are below the experimental value by 2.1 times the experimental uncertainty estimates. Possible reasons for this discrepancy are discussed. Variational transition state theory calculations with multidimensional tunneling have also been carried out for kHeμ on the BH surface, and they agree with the accurate QM rate constants to within 30% over a wider temperature range of 200-1000 K. Comparisons between theory and experiment are also presented for the rate constants for both the D + H2 and Mu + H2 reactions in a novel study of kinetic isotope effects for the H + H2 reactions over a factor of 36.1 in isotopic mass of the atomic reactant.

  17. A Molecular Iodine Spectral Data Set for Rovibronic Analysis

    ERIC Educational Resources Information Center

    Williamson, J. Charles; Kuntzleman, Thomas S.; Kafader, Rachael A.

    2013-01-01

    A data set of 7,381 molecular iodine vapor rovibronic transitions between the X and B electronic states has been prepared for an advanced undergraduate spectroscopic analysis project. Students apply standard theoretical techniques to these data and determine the values of three X-state constants (image omitted) and four B-state constants (image…

  18. Constant load and constant volume response of municipal solid waste in simple shear.

    PubMed

    Zekkos, Dimitrios; Fei, Xunchang

    2017-05-01

    Constant load and constant volume simple shear testing was conducted on relatively fresh municipal solid waste (MSW) from two landfills in the United States, one in Michigan and a second in Texas, at respective natural moisture content below field capacity. The results were assessed in terms of two failure strain criteria, at 10% and 30% shear strain, and two interpretations of effective friction angle. Overall, friction angle obtained assuming that the failure plane is horizontal and at 10% shear strain resulted in a conservative estimation of shear strength of MSW. Comparisons between constant volume and constant load simple shear testing results indicated significant differences in the shear response of MSW with the shear resistance in constant volume being lower than the shear resistance in constant load. The majority of specimens were nearly uncompacted during specimen preparation to reproduce the state of MSW in bioreactor landfills or in uncontrolled waste dumps. The specimens had identical percentage of <20mm material but the type of <20mm material was different. The <20mm fraction from Texas was finer and of high plasticity. MSW from Texas was overall weaker in both constant load and constant volume conditions compared to Michigan waste. The results of these tests suggest the possibility of significantly lower shear strength of MSW in bioreactor landfills where waste is placed with low compaction effort and constant volume, i.e., "undrained", conditions may occur. Compacted MSW specimens resulted in shear strength parameters that are higher than uncompacted specimens and closer to values reported in the literature. However, the normalized undrained shear strength in simple shear for uncompacted and compacted MSW was still higher than the normalized undrained shear strength reported in the literature for clayey and silty soils. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. A relativistic coupled-cluster interaction potential and rovibrational constants for the xenon dimer

    NASA Astrophysics Data System (ADS)

    Jerabek, Paul; Smits, Odile; Pahl, Elke; Schwerdtfeger, Peter

    2018-01-01

    An accurate potential energy curve has been derived for the xenon dimer using state-of-the-art relativistic coupled-cluster theory up to quadruple excitations accounting for both basis set superposition and incompleteness errors. The data obtained is fitted to a computationally efficient extended Lennard-Jones potential form and to a modified Tang-Toennies potential function treating the short- and long-range part separately. The vibrational spectrum of Xe2 obtained from a numerical solution of the rovibrational Schrödinger equation and subsequently derived spectroscopic constants are in excellent agreement with experimental values. We further present solid-state calculations for xenon using a static many-body expansion up to fourth-order in the xenon interaction potential including dynamic effects within the Einstein approximation. Again we find very good agreement with the experimental (face-centred cubic) lattice constant and cohesive energy.

  20. Accurate diblock copolymer phase boundaries at strong segregations

    NASA Astrophysics Data System (ADS)

    Matsen, M. W.; Whitmore, M. D.

    1996-12-01

    We examine the lamellar/cylinder and cylinder/sphere phase boundaries for strongly segregated diblock copolymer melts using self-consistent-field theory (SCFT) and the standard Gaussian chain model. Calculations are performed with and without the conventional unit-cell approximation (UCA). We find that for strongly segregated melts, the UCA simply produces a small constant shift in each of the phase boundaries. Furthermore, the boundaries are found to be linear at strong segregations when plotted versus (χN)-1, which allows for accurate extrapolations to χN=∞. Our calculations using the UCA allow direct comparisons to strong-segregation theory (SST), which is accepted as the χN=∞ limit of SCFT. A significant discrepancy between the SST and SCFT results indicate otherwise, suggesting that the present formulation of SST is incomplete.

  1. Identification of Weak Acids and Bases by Titration with Primary Standards. A Modern Version of an Old Analytical Chemistry Experiment.

    ERIC Educational Resources Information Center

    Thompson, Robert Q.

    1988-01-01

    Describes a laboratory exercise in which acid dissociation constants and molecular weights are extracted from sample data and the sample is identified. Emphasizes accurate volumetric work while bringing to practice the concepts of acid-base equilibria, activity coefficients, and thermodynamic constants. (CW)

  2. Accurate van der Waals coefficients from density functional theory

    PubMed Central

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

    2012-01-01

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

  3. The Multicenter Aerobic Iron Respiratory Chain of Acidithiobacillus ferrooxidans Functions as an Ensemble with a Single Macroscopic Rate Constant

    DOE PAGES

    Li, Ting-Feng; Painter, Richard G.; Ban, Bhupal; ...

    2015-06-03

    Electron transfer reactions among three prominent colored proteins in intact cells of Acidithiobacillus ferrooxidans were monitored using an integrating cavity absorption meter that permitted the acquisition of accurate absorbance data in suspensions of cells that scattered light. The concentrations of proteins in the periplasmic space were estimated to be 350 and 25 mg/ml for rusticyanin and cytochrome c, respectively; cytochrome a was present as one molecule for every 91 nm2 in the cytoplasmic membrane. All three proteins were rapidly reduced to the same relative extent when suspensions of live bacteria were mixed with different concentrations of ferrous ions at pHmore » 1.5. The subsequent molecular oxygen-dependent oxidation of the multicenter respiratory chain occurred with a single macroscopic rate constant, regardless of the proteins' in vitro redox potentials or their putative positions in the aerobic iron respiratory chain. The crowded electron transport proteins in the periplasm of the organism constituted an electron conductive medium where the network of protein interactions functioned in a concerted fashion as a single ensemble with a standard reduction potential of 650 mV. The appearance of product ferric ions was correlated with the reduction levels of the periplasmic electron transfer proteins; the limiting first-order catalytic rate constant for aerobic respiration on iron was 7,400 s -1. The ability to conduct direct spectrophotometric studies under noninvasive physiological conditions represents a new and powerful approach to examine the extent and rates of biological events in situ without disrupting the complexity of the live cellular environment.« less

  4. Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

    NASA Astrophysics Data System (ADS)

    Chen, Chen; Arntsen, Christopher; Voth, Gregory A.

    2017-10-01

    Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

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

    PubMed Central

    Syganow, A; von Kitzing, E

    1999-01-01

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

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

    PubMed Central

    Kind, Tobias; Fiehn, Oliver

    2007-01-01

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

  7. The Hubble Constant from Supernovae

    NASA Astrophysics Data System (ADS)

    Saha, Abhijit; Macri, Lucas M.

    The decades-long quest to obtain a precise and accurate measurement of the local expansion rate of the universe (the Hubble Constant or H0) has greatly benefited from the use of supernovae (SNe). Starting from humble beginnings (dispersions of ˜ 0.5 mag in the Hubble flow in the late 1960s/early 1970s), the increasingly more sophisticated understanding, classification, and analysis of these events turned type Ia SNe into the premiere choice for a secondary distance indicator by the early 1990s. While some systematic uncertainties specific to SNe and to Cepheid-based distances to the calibrating host galaxies still contribute to the H0 error budget, the major emphasis over the past two decades has been on reducing the statistical uncertainty by obtaining ever-larger samples of distances to SN hosts. Building on early efforts with the first-generation instruments on the Hubble Space Telescope, recent observations with the latest instruments on this facility have reduced the estimated total uncertainty on H0 to 2.4 % and shown a path to reach a 1 % measurement by the end of the decade, aided by Gaia and the James Webb Space Telescope.

  8. Accurate high-speed liquid handling of very small biological samples.

    PubMed

    Schober, A; Günther, R; Schwienhorst, A; Döring, M; Lindemann, B F

    1993-08-01

    Molecular biology techniques require the accurate pipetting of buffers and solutions with volumes in the microliter range. Traditionally, hand-held pipetting devices are used to fulfill these requirements, but many laboratories have also introduced robotic workstations for the handling of liquids. Piston-operated pumps are commonly used in manually as well as automatically operated pipettors. These devices cannot meet the demands for extremely accurate pipetting of very small volumes at the high speed that would be necessary for certain applications (e.g., in sequencing projects with high throughput). In this paper we describe a technique for the accurate microdispensation of biochemically relevant solutions and suspensions with the aid of a piezoelectric transducer. It is suitable for liquids of a viscosity between 0.5 and 500 milliPascals. The obtainable drop sizes range from 5 picoliters to a few nanoliters with up to 10,000 drops per second. Liquids can be dispensed in single or accumulated drops to handle a wide volume range. The system proved to be excellently suitable for the handling of biological samples. It did not show any detectable negative impact on the biological function of dissolved or suspended molecules or particles.

  9. Effect of Phenol Molecular Structure on Bacterial Transformation Rate Constants in Pond and River Samples

    PubMed Central

    Paris, Doris F.; Wolfe, N. Lee; Steen, William C.; Baughman, George L.

    1983-01-01

    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 catechols, with the exception of p-hydroxybenzoic acid, the product of p-acetylphenol. A different product suggested a different pathway; p-acetylphenol, therefore, was deleted from the data base. PMID:16346236

  10. Cosmological constant and quantum gravitational corrections to the running fine structure constant.

    PubMed

    Toms, David J

    2008-09-26

    The quantum gravitational contribution to the renormalization group behavior of the electric charge in Einstein-Maxwell theory with a cosmological constant is considered. Quantum gravity is shown to lead to a contribution to the running charge not present when the cosmological constant vanishes. This reopens the possibility, suggested by Robinson and Wilczek, of altering the scaling behavior of gauge theories at high energies although our result differs. We show the possibility of an ultraviolet fixed point that is linked directly to the cosmological constant.

  11. Soluble Molecularly Imprinted Nanorods for Homogeneous Molecular Recognition

    NASA Astrophysics Data System (ADS)

    Liang, Rongning; Wang, Tiantian; Zhang, Huan; Yao, Ruiqing; Qin, Wei

    2018-03-01

    Nowadays, it is still difficult for molecularly imprinted polymer (MIPs) to achieve homogeneous recognition since they cannot be easily dissolved in organic or aqueous phase. To address this issue, soluble molecularly imprinted nanorods have been synthesized by using soluble polyaniline doped with a functionalized organic protonic acid as the polymer matrix. By employing 1-naphthoic acid as a model, the proposed imprinted nanorods exhibit an excellent solubility and good homogeneous recognition ability. The imprinting factor for the soluble imprinted nanoroads is 6.8. The equilibrium dissociation constant and the apparent maximum number of the proposed imprinted nanorods are 248.5 μM and 22.1 μmol/g, respectively. We believe that such imprinted nanorods may provide an appealing substitute for natural receptors in homogeneous recognition related fields.

  12. Nonlinear vibrational excitations in molecular crystals molecular mechanics calculations

    NASA Astrophysics Data System (ADS)

    Pumilia, P.; Abbate, S.; Baldini, G.; Ferro, D. R.; Tubino, R.

    1992-03-01

    The coupling constant for vibrational solitons χ has been examined in a molecular mechanics model for acetanilide (ACN) molecular crystal. According to A.C. Scott, solitons can form and propagate in solid acetanilide over a threshold energy value. This can be regarded as a structural model for the spines of hydrogen bond chains stabilizing the α helical structure of proteins. A one dimensional hydrogen bond chain of ACN has been built, for which we have found that, even though experimental parameters are correctly predicted, the excessive rigidity of the isolated chain prevents the formation of a localized distortion around the excitation. Yet, C=O coupling value with softer lattice modes could be rather high, allowing self-trapping to take place.

  13. 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).

  14. Ab initio molecular dynamics in a finite homogeneous electric field.

    PubMed

    Umari, P; Pasquarello, Alfredo

    2002-10-07

    We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

  15. B-meson decay constant from unquenched lattice QCD.

    PubMed

    Gray, Alan; Wingate, Matthew; Davies, Christine T H; Gulez, Emel; Lepage, G Peter; Mason, Quentin; Nobes, Matthew; Shigemitsu, Junko

    2005-11-18

    We present determinations of the -meson decay constant f(B) and f(B)(s)/f(B) using the MILC Collaboration unquenched gauge configurations, which include three flavors of light sea quarks. The mass of one of the sea quarks is kept around the strange quark mass, and we explore a range in masses for the two lighter sea quarks down to m(s)/8. The heavy quark is simulated using nonrelativistic QCD, and both the valence and sea light quarks are represented by the highly improved (AsqTad) staggered quark action. The good chiral properties of the latter action allow for a more accurate chiral extrapolation to physical up and down quarks than has been possible in the past. We find f(B)=216(9)(19)(4)(6) MeV and f(B)(s)/f(B)=1.20(3)(1).

  16. Multi-wavelength spectrophotometric determination of acidity constant of some newly synthesized Schiff bases and their QSPR study

    NASA Astrophysics Data System (ADS)

    Hemmateenejad, Bahram; Emami, Leila; Sharghi, Hashem

    2010-01-01

    The acidity constants of some newly synthesized Schiff base derivatives were determined by hard-model based multivariate data analysis of the spectrophotometric data in the course of pH-metric titration in 50% (v/v) methanol-water binary solvent. The employed data analysis method was also able to extract the pure spectra and pH-dependent concentration profiles of the acid-base species. The molecules that possess different substituents (both electron donating and withdrawing) on the ortho-, meta- and para-positions of one of the phenyl ring showed variable acidity constants ranging from 8.77 to 11.07 whereas the parent molecule had an acidity constant of 10.25. To investigate the quantitative effects of changing of substitution pattern on the acidity constant, a quantitative structure-property relation analysis was conducted using substituent constants and molecular descriptor. Some models with high statistical quality (measured by cross-validation Q2) were obtained. It was found that the acidity constant of the studied molecules in the methanol-water mixed solvent not only is affected by electronic features of the solutes but also by the lipophilic interaction between methanol part of solvent and the deprotonated solutes.

  17. Experimental determination of micromachined discrete and continuous device spring constants using nanoindentation method

    NASA Astrophysics Data System (ADS)

    Chan, M. L.; Tay, Francis E.; Logeeswaran, V. J.; Zeng, Kaiyang; Shen, Lu; Chau, Fook S.

    2002-04-01

    A rapid and accurate static and quasi-static method for determining the out-of-plane spring constraints of cantilevers and a micromachined vibratory sensor is presented. In the past, much of the effort in nanoindentation application was to investigate the thin-film mechanical properties. In this paper, we have utilized the nanoindentation method to measure directly some micromachined device (e.g. microgyroscope) spring constants. The cantilevers and devices tested were fabricated using the MUMPS process and an SOI process (patent pending). Spring constants are determined using a commercial nanoindentation apparatus UMIS-2000 configured with both Berkovich and spherical indenter tip that can be placed onto the device with high accuracy. Typical load resolution is 20micrometers N to 0.5N and a displacement resolution of 0.05nm. Information was deduced from the penetration depth versus load curves during both loading and unloading.

  18. Constant symplectic 2-groupoids

    NASA Astrophysics Data System (ADS)

    Mehta, Rajan Amit; Tang, Xiang

    2018-05-01

    We propose a definition of symplectic 2-groupoid which includes integrations of Courant algebroids that have been recently constructed. We study in detail the simple but illustrative case of constant symplectic 2-groupoids. We show that the constant symplectic 2-groupoids are, up to equivalence, in one-to-one correspondence with a simple class of Courant algebroids that we call constant Courant algebroids. Furthermore, we find a correspondence between certain Dirac structures and Lagrangian sub-2-groupoids.

  19. Studies on chalcone derivatives: complex formation, thermal behavior, stability constant and antioxidant activity.

    PubMed

    El-Sayed, Yusif S; Gaber, M

    2015-02-25

    The chalcone 3-[4'-dimethylaminophenyl]-1-(2-pyridyl) prop-2-en-1-one (DMAPP) and 3-(4'-diethylaminophenyl)-1-(2-pyridinyl) prop-2-en-1-one abbreviated as DEAPP have been synthesized and characterized with IR, (1)H NMR, (13)C NMR spectroscopic techniques as described previously (El-Daly et al., 2008; Gaber et al., 2009; El-Sayed, 2013). By using UV visible spectroscopy method the mole fraction ratio for copper with DMAPP and DEAPP complexes were determined and it was found to be 1:1. The stability constants of this complex have been determined by Job's method. The stability constant (Kf) of copper with DMAPP and DEAPP complexes in universal buffer pH=3.2 was determined to be 9.9×10(4) and 5.2×10(4) respectively. The effect of Cu(II) ion on the emission spectrum of the free chalcone is also assigned. Adherence to Beer's law and Ringbom optimum concentration ranges are determined. The thermal decomposition of the metal complexes is studied by TGA technique. The kinetic parameters like activation energy, pre-exponential factor and entropy of activation are estimated. The structure of complexes was energetically optimized through molecular mechanics applying MM(+) force field coupled with molecular dynamics simulation. The bond lengths and bond angles have been calculated to confirm the geometry of the ligands and their Cu(II) complexes. The mode of interaction of the chalcone to copper nanoparticles was studied. The apparent association constants of the colloidal copper nanoparticles:chalcone complexes in solution were evaluated using the spectral method and compared with the formation constant of the Cu(II) chalcone complexes. Antioxidant activity of these chalcones was evaluated by using 1,1'-diphenyl-2-picrylhydrazyl (DPPH) radicals scavenging method, which showed that the antioxidant activity of DMAPP has higher value than the DEAPP. Semi-empirical study results showed that DMAPP have higher dipole moment than DEAPP. Copyright © 2014 Elsevier B.V. All rights

  20. Studies on chalcone derivatives: Complex formation, thermal behavior, stability constant and antioxidant activity

    NASA Astrophysics Data System (ADS)

    El-Sayed, Yusif S.; Gaber, M.

    2015-02-01

    The chalcone 3-[4‧-dimethylaminophenyl]-1-(2-pyridyl) prop-2-en-1-one (DMAPP) and 3-(4‧-diethylaminophenyl)-1-(2-pyridinyl) prop-2-en-1-one abbreviated as DEAPP have been synthesized and characterized with IR, 1H NMR, 13C NMR spectroscopic techniques as described previously (El-Daly et al., 2008; Gaber et al., 2009; El-Sayed, 2013). By using UV visible spectroscopy method the mole fraction ratio for copper with DMAPP and DEAPP complexes were determined and it was found to be 1:1. The stability constants of this complex have been determined by Job's method. The stability constant (Kf) of copper with DMAPP and DEAPP complexes in universal buffer pH = 3.2 was determined to be 9.9 × 104 and 5.2 × 104 respectively. The effect of Cu(II) ion on the emission spectrum of the free chalcone is also assigned. Adherence to Beer's law and Ringbom optimum concentration ranges are determined. The thermal decomposition of the metal complexes is studied by TGA technique. The kinetic parameters like activation energy, pre-exponential factor and entropy of activation are estimated. The structure of complexes was energetically optimized through molecular mechanics applying MM+ force field coupled with molecular dynamics simulation. The bond lengths and bond angles have been calculated to confirm the geometry of the ligands and their Cu(II) complexes. The mode of interaction of the chalcone to copper nanoparticles was studied. The apparent association constants of the colloidal copper nanoparticles:chalcone complexes in solution were evaluated using the spectral method and compared with the formation constant of the Cu(II) chalcone complexes. Antioxidant activity of these chalcones was evaluated by using 1,1‧-diphenyl-2-picrylhydrazyl (DPPHrad) radicals scavenging method, which showed that the antioxidant activity of DMAPP has higher value than the DEAPP. Semi-empirical study results showed that DMAPP have higher dipole moment than DEAPP [1].

  1. Nonlinear elastic response of strong solids: First-principles calculations of the third-order elastic constants of diamond

    DOE PAGES

    Hmiel, A.; Winey, J. M.; Gupta, Y. M.; ...

    2016-05-23

    Accurate theoretical calculations of the nonlinear elastic response of strong solids (e.g., diamond) constitute a fundamental and important scientific need for understanding the response of such materials and for exploring the potential synthesis and design of novel solids. However, without corresponding experimental data, it is difficult to select between predictions from different theoretical methods. Recently the complete set of third-order elastic constants (TOECs) for diamond was determined experimentally, and the validity of various theoretical approaches to calculate the same may now be assessed. We report on the use of density functional theory (DFT) methods to calculate the six third-order elasticmore » constants of diamond. Two different approaches based on homogeneous deformations were used: (1) an energy-strain fitting approach using a prescribed set of deformations, and (2) a longitudinal stress-strain fitting approach using uniaxial compressive strains along the [100], [110], and [111] directions, together with calculated pressure derivatives of the second-order elastic constants. The latter approach provides a direct comparison to the experimental results. The TOECs calculated using the energy-strain approach differ significantly from the measured TOECs. In contrast, calculations using the longitudinal stress-uniaxial strain approach show good agreement with the measured TOECs and match the experimental values significantly better than the TOECs reported in previous theoretical studies. Lastly, our results on diamond have demonstrated that, with proper analysis procedures, first-principles calculations can indeed be used to accurately calculate the TOECs of strong solids.« less

  2. Instrumentation in molecular imaging.

    PubMed

    Wells, R Glenn

    2016-12-01

    In vivo molecular imaging is a challenging task and no single type of imaging system provides an ideal solution. Nuclear medicine techniques like SPECT and PET provide excellent sensitivity but have poor spatial resolution. Optical imaging has excellent sensitivity and spatial resolution, but light photons interact strongly with tissues and so only small animals and targets near the surface can be accurately visualized. CT and MRI have exquisite spatial resolution, but greatly reduced sensitivity. To overcome the limitations of individual modalities, molecular imaging systems often combine individual cameras together, for example, merging nuclear medicine cameras with CT or MRI to allow the visualization of molecular processes with both high sensitivity and high spatial resolution.

  3. The measurement system of birefringence and Verdet constant of optical fiber

    NASA Astrophysics Data System (ADS)

    Huang, Yi; Chen, Li; Guo, Qiang; Pang, Fufei; Wen, Jianxiang; Shang, Yana; Wang, Tingyun

    2013-12-01

    The Faraday magneto-optical effect of optical fiber has many applications in monitoring magnetic field and electric current. When a linearly polarized light propagates in the direction of a magnetic field, the plane of polarization will rotate linearly proportional to the strength of the applied magnetic field, which following the relationship of θF =VBl. θF is the Faraday rotation angle, which is proportional to the magnetic flux density B and the Verdet constant V . However, when the optical fiber contains the effect of linear birefringence, the detection of Faraday rotation angle will depend on the line birefringence. In order to determine the Verdet constant of an optical fiber under a linear birefringence, the fiber birefringence needs to be accurately measured. In this work, a model is applied to analyze the polarization properties of an optical fiber by using the Jones matrix method. A measurement system based on the lock-in amplifier technology is designed to test the Verdet constant and the birefringence of optical fiber. The magnetic field is produced by a solenoid with a DC current. A tunable laser is intensity modulated with a motorized rotating chopper. The actuator supplies a signal as the phase-locked synchronization reference to the signal of the lock-in amplifier. The measurement accuracy is analyzed and the sensitivity of the system is optimized. In this measurement system, the Verdet constant of the SMF-28 fiber was measured to be 0.56±0.02 rad/T·m at 1550nm. This setup is well suitable for measuring the high signal-to-noise ratio (SNR) sensitivity for lock-in amplifier at a low magnetic field strength.

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

    PubMed

    Sheehy, Philip M; Ramstad, Tore

    2005-10-04

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

  5. Evaluation and comparison of diffusion MR methods for measuring apparent transcytolemmal water exchange rate constant

    NASA Astrophysics Data System (ADS)

    Tian, Xin; Li, Hua; Jiang, Xiaoyu; Xie, Jingping; Gore, John C.; Xu, Junzhong

    2017-02-01

    Two diffusion-based approaches, CG (constant gradient) and FEXI (filtered exchange imaging) methods, have been previously proposed for measuring transcytolemmal water exchange rate constant kin, but their accuracy and feasibility have not been comprehensively evaluated and compared. In this work, both computer simulations and cell experiments in vitro were performed to evaluate these two methods. Simulations were done with different cell diameters (5, 10, 20 μm), a broad range of kin values (0.02-30 s-1) and different SNR's, and simulated kin's were directly compared with the ground truth values. Human leukemia K562 cells were cultured and treated with saponin to selectively change cell transmembrane permeability. The agreement between measured kin's of both methods was also evaluated. The results suggest that, without noise, the CG method provides reasonably accurate estimation of kin especially when it is smaller than 10 s-1, which is in the typical physiological range of many biological tissues. However, although the FEXI method overestimates kin even with corrections for the effects of extracellular water fraction, it provides reasonable estimates with practical SNR's and more importantly, the fitted apparent exchange rate AXR showed approximately linear dependence on the ground truth kin. In conclusion, either CG or FEXI method provides a sensitive means to characterize the variations in transcytolemmal water exchange rate constant kin, although the accuracy and specificity is usually compromised. The non-imaging CG method provides more accurate estimation of kin, but limited to large volume-of-interest. Although the accuracy of FEXI is compromised with extracellular volume fraction, it is capable of spatially mapping kin in practice.

  6. New constraints on time-dependent variations of fundamental constants using Planck data

    NASA Astrophysics Data System (ADS)

    Hart, Luke; Chluba, Jens

    2018-02-01

    Observations of the cosmic microwave background (CMB) today allow us to answer detailed questions about the properties of our Universe, targeting both standard and non-standard physics. In this paper, we study the effects of varying fundamental constants (i.e. the fine-structure constant, αEM, and electron rest mass, me) around last scattering using the recombination codes COSMOREC and RECFAST++. We approach the problem in a pedagogical manner, illustrating the importance of various effects on the free electron fraction, Thomson visibility function and CMB power spectra, highlighting various degeneracies. We demonstrate that the simpler RECFAST++ treatment (based on a three-level atom approach) can be used to accurately represent the full computation of COSMOREC. We also include explicit time-dependent variations using a phenomenological power-law description. We reproduce previous Planck 2013 results in our analysis. Assuming constant variations relative to the standard values, we find the improved constraints αEM/αEM, 0 = 0.9993 ± 0.0025 (CMB only) and me/me, 0 = 1.0039 ± 0.0074 (including BAO) using Planck 2015 data. For a redshift-dependent variation, αEM(z) = αEM(z0) [(1 + z)/1100]p with αEM(z0) ≡ αEM, 0 at z0 = 1100, we obtain p = 0.0008 ± 0.0025. Allowing simultaneous variations of αEM(z0) and p yields αEM(z0)/αEM, 0 = 0.9998 ± 0.0036 and p = 0.0006 ± 0.0036. We also discuss combined limits on αEM and me. Our analysis shows that existing data are not only sensitive to the value of the fundamental constants around recombination but also its first time derivative. This suggests that a wider class of varying fundamental constant models can be probed using the CMB.

  7. A first-passage scheme for determination of overall rate constants for non-diffusion-limited suspensions

    NASA Astrophysics Data System (ADS)

    Lu, Shih-Yuan; Yen, Yi-Ming

    2002-02-01

    A first-passage scheme is devised to determine the overall rate constant of suspensions under the non-diffusion-limited condition. The original first-passage scheme developed for diffusion-limited processes is modified to account for the finite incorporation rate at the inclusion surface by using a concept of the nonzero survival probability of the diffusing entity at entity-inclusion encounters. This nonzero survival probability is obtained from solving a relevant boundary value problem. The new first-passage scheme is validated by an excellent agreement between overall rate constant results from the present development and from an accurate boundary collocation calculation for the three common spherical arrays [J. Chem. Phys. 109, 4985 (1998)], namely simple cubic, body-centered cubic, and face-centered cubic arrays, for a wide range of P and f. Here, P is a dimensionless quantity characterizing the relative rate of diffusion versus surface incorporation, and f is the volume fraction of the inclusion. The scheme is further applied to random spherical suspensions and to investigate the effect of inclusion coagulation on overall rate constants. It is found that randomness in inclusion arrangement tends to lower the overall rate constant for f up to the near close-packing value of the regular arrays because of the inclusion screening effect. This screening effect turns stronger for regular arrays when f is near and above the close-packing value of the regular arrays, and consequently the overall rate constant of the random array exceeds that of the regular array. Inclusion coagulation too induces the inclusion screening effect, and leads to lower overall rate constants.

  8. Modifying scoping codes to accurately calculate TMI-cores with lifetimes greater than 500 effective full-power days

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bai, D.; Levine, S.L.; Luoma, J.

    1992-01-01

    The Three Mile Island unit 1 core reloads have been designed using fast but accurate scoping codes, PSUI-LEOPARD and ADMARC. PSUI-LEOPARD has been normalized to EPRI-CPM2 results and used to calculate the two-group constants, whereas ADMARC is a modern two-dimensional, two-group diffusion theory nodal code. Problems in accuracy were encountered for cycles 8 and higher as the core lifetime was increased beyond 500 effective full-power days. This is because the heavier loaded cores in both {sup 235}U and {sup 10}B have harder neutron spectra, which produces a change in the transport effect in the baffle reflector region, and the burnablemore » poison (BP) simulations were not accurate enough for the cores containing the increased amount of {sup 10}B required in the BP rods. In the authors study, a technique has been developed to take into account the change in the transport effect in the baffle region by modifying the fast neutron diffusion coefficient as a function of cycle length and core exposure or burnup. A more accurate BP simulation method is also developed, using integral transport theory and CPM2 data, to calculate the BP contribution to the equivalent fuel assembly (supercell) two-group constants. The net result is that the accuracy of the scoping codes is as good as that produced by CASMO/SIMULATE or CPM2/SIMULATE when comparing with measured data.« less

  9. Three-body interactions and the elastic constants of hcp solid 4He

    NASA Astrophysics Data System (ADS)

    Barnes, Ashleigh L.; Hinde, Robert J.

    2017-09-01

    The effect of three-body interactions on the elastic properties of hexagonal close packed solid 4He is investigated using variational path integral (VPI) Monte Carlo simulations. The solid's nonzero elastic constants are calculated, at T = 0 K and for a range of molar volumes from 7.88 cm3/mol to 20.78 cm3/mol, from the bulk modulus and the three pure shear constants C0, C66, and C44. Three-body interactions are accounted for using our recently reported perturbative treatment based on the nonadditive three-body potential of Cencek et al. Previous studies have attempted to account for the effect of three-body interactions on the elastic properties of solid 4He; however, these calculations have treated zero point motions using either the Einstein or Debye approximations, which are insufficient in the molar volume range where solid 4He is characterized as a quantum solid. Our VPI calculations allow for a more accurate treatment of the zero point motions which include atomic correlation. From these calculations, we find that agreement with the experimental bulk modulus is significantly improved when three-body interactions are considered. In addition, three-body interactions result in non-negligible differences in the calculated pure shear constants and nonzero elastic constants, particularly at higher densities, where differences of up to 26.5% are observed when three-body interactions are included. We compare to the available experimental data and find that our results are generally in as good or better agreement with experiment as previous theoretical investigations.

  10. Estimation of Nutation Time Constant Model Parameters for On-Axis Spinning Spacecraft

    NASA Technical Reports Server (NTRS)

    Schlee, Keith; Sudermann, James

    2008-01-01

    Calculating an accurate nutation time constant for a spinning spacecraft is an important step for ensuring mission success. Spacecraft nutation is caused by energy dissipation about the spin axis. Propellant slosh in the spacecraft fuel tanks is the primary source for this dissipation and can be simulated using a forced motion spin table. Mechanical analogs, such as pendulums and rotors, are typically used to simulate propellant slosh. A strong desire exists for an automated method to determine these analog parameters. The method presented accomplishes this task by using a MATLAB Simulink/SimMechanics based simulation that utilizes the Parameter Estimation Tool.

  11. Reflection mass spectrometry technique for monitoring and controlling composition during molecular beam epitaxy

    DOEpatents

    Brennan, T.M.; Hammons, B.E.; Tsao, J.Y.

    1992-12-15

    A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a substrate by accurately measuring the molecular fluxes reflected from the substrate. The reflected flux is extremely sensitive to the state of the growing surface and the measurements obtained enable control of newly forming surfaces that are dynamically changing as a result of growth. 3 figs.

  12. Reflection mass spectrometry technique for monitoring and controlling composition during molecular beam epitaxy

    DOEpatents

    Brennan, Thomas M.; Hammons, B. Eugene; Tsao, Jeffrey Y.

    1992-01-01

    A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a substrate by accurately measuring the molecular fluxes reflected from the substrate. The reflected flux is extremely sensitive to the state of the growing surface and the measurements obtained enable control of newly forming surfaces that are dynamically changing as a result of growth.

  13. Frequency Domain Fluorescent Molecular Tomography and Molecular Probes for Small Animal Imaging

    NASA Astrophysics Data System (ADS)

    Kujala, Naresh Gandhi

    Fluorescent molecular tomography (FMT) is a noninvasive biomedical optical imaging that enables 3-dimensional quantitative determination of fluorochromes distributed in biological tissues. There are three methods for imaging large volume tissues based on different light sources: (a) using a light source of constant intensity, through a continuous or constant wave, (b) using a light source that is intensity modulated with a radio frequency (RF), and (c) using ultrafast pulses in the femtosecond range. In this study, we have developed a frequency domain fluorescent molecular tomographic system based on the heterodyne technique, using a single source and detector pair that can be used for small animal imaging. In our system, the intensity of the laser source is modulated with a RF frequency to produce a diffuse photon density wave in the tissue. The phase of the diffuse photon density wave is measured by comparing the reference signal with the signal from the tissue using a phasemeter. The data acquisition was performed by using a Labview program. The results suggest that we can measure the phase change from the heterogeneous inside tissue. Combined with fiber optics and filter sets, the system can be used to sensitively image the targeted fluorescent molecular probes, allowing the detection of cancer at an early stage. We used the system to detect the tumor-targeting molecular probe Alexa Fluor 680 and Alexa Fluor 750 bombesin peptide conjugates in phantoms as well as mouse tissues. We also developed and evaluated fluorescent Bombesin (BBN) probes to target gastrin-releasing peptide (GRP) receptors for optical molecular imaging. GRP receptors are over-expressed in several types of human cancer cells, including breast, prostate, small cell lung, and pancreatic cancers. BBN is a 14 amino acid peptide that is an analogue to human gastrin-releasing peptide that binds specifically to GRPr receptors. BBN conjugates are significant in cancer detection and therapy. The

  14. Pauling's electronegativity equation and a new corollary accurately predict bond dissociation enthalpies and enhance current understanding of the nature of the chemical bond.

    PubMed

    Matsunaga, Nikita; Rogers, Donald W; Zavitsas, Andreas A

    2003-04-18

    Contrary to other recent reports, Pauling's original electronegativity equation, applied as Pauling specified, describes quite accurately homolytic bond dissociation enthalpies of common covalent bonds, including highly polar ones, with an average deviation of +/-1.5 kcal mol(-1) from literature values for 117 such bonds. Dissociation enthalpies are presented for more than 250 bonds, including 79 for which experimental values are not available. Some previous evaluations of accuracy gave misleadingly poor results by applying the equation to cases for which it was not derived and for which it should not reproduce experimental values. Properly interpreted, the results of the equation provide new and quantitative insights into many facets of chemistry such as radical stabilities, factors influencing reactivity in electrophilic aromatic substitutions, the magnitude of steric effects, conjugative stabilization in unsaturated systems, rotational barriers, molecular and electronic structure, and aspects of autoxidation. A new corollary of the original equation expands its applicability and provides a rationale for previously observed empirical correlations. The equation raises doubts about a new bonding theory. Hydrogen is unique in that its electronegativity is not constant.

  15. 1,2-Difluoroethane: the angular dependance on 1J(CF) coupling constants is independent of hyperconjugation.

    PubMed

    Freitas, Matheus P; Bühl, Michael; O'Hagan, David

    2012-02-28

    1,2-Difluoroethane is widely recognised to adopt a lower energy gauche rather than anti conformation; this gauche effect has its origin in hyperconjugation; however, surprisingly the (1)J(CF) coupling constant is not influenced by hyperconjugation; instead, its magnitude changes with the overall molecular dipole. This journal is © The Royal Society of Chemistry 2012

  16. Theoretical study on the dimerization of Si(OH) 4 in aqueous solution and its dependence on temperature and dielectric constant

    NASA Astrophysics Data System (ADS)

    Tossell, J. A.

    2005-01-01

    Energetics for the condensation dimerization reaction of monosilicic acid: 2Si(⇒SiOH+HO have been calculated quantum mechanically, in gas-phase and aqueous solution, over a range of temperatures and dielectric constants. The calculated gas phase energy, E g, for this reaction is -6.6 kcal/mol at the very accurate composite G2 level, but the vibrational, rotational and translational contributions to the free energy in the gas-phase, ΔG VRT, sum to + 2.5 kcal/mol and the hydration free energy contribution calculated with a polarizable continuum model, ΔΔG COSMO, for a dielectric constant of 78.5, is about + 6.2 kcal/mol. Thus, the free energy change for the reaction in aqueous solution at ambient conditions is about + 2.1 kcal/mol and the equilibrium constant is ˜10 -1.5, in reasonable agreement with experiment. As T increases, ΔG VRT increases slowly. As the dielectric constant decreases (for example, under high T and P conditions in the supercritical region), ΔΔG COSMO decreases substantially. Thus, at elevated T and P, if the effective dielectric constant of the aqueous fluid is 10 or less, the reaction becomes much more favorable, consistent with recent experimental observations. The PΔV contribution to the enthalpy is also considered, but cannot be accurately determined. We have also calculated 29Si-NMR shieldings and Raman frequencies for Si(OH) 4, Si 2O 7H 6 and some other oligomeric silicates. We correctly reproduce the separation of monomer and dimer peaks observed in the 29Si-NMR spectrra at ambient T and P. The Raman spectral data are somewhat ambiguous, and the new peaks seen at high T and P could arise either from the dimer or from a 3-ring trimer, which is calculated to be highly stabilized entropically at high T.

  17. Fundamental constants and high-resolution spectroscopy

    NASA Astrophysics Data System (ADS)

    Bonifacio, P.; Rahmani, H.; Whitmore, J. B.; Wendt, M.; Centurion, M.; Molaro, P.; Srianand, R.; Murphy, M. T.; Petitjean, P.; Agafonova, I. I.; D'Odorico, S.; Evans, T. M.; Levshakov, S. A.; Lopez, S.; Martins, C. J. A. P.; Reimers, D.; Vladilo, G.

    2014-01-01

    Absorption-line systems detected in high resolution quasar spectra can be used to compare the value of dimensionless fundamental constants such as the fine-structure constant, α, and the proton-to-electron mass ratio, μ = m_p/m_e, as measured in remote regions of the Universe to their value today on Earth. In recent years, some evidence has emerged of small temporal and also spatial variations in α on cosmological scales which may reach a fractional level of ≈ 10 ppm (parts per million). We are conducting a Large Programme of observations with the Very Large Telescope's Ultraviolet and Visual Echelle Spectrograph (UVES), and are obtaining high-resolution ({R ≈ 60 000}) and high signal-to-noise ratio (S/N ≈ 100) spectra calibrated specifically to study the variations of the fundamental constants. We here provide a general overview of the Large Programme and report on the first results for these two constants, discussed in detail in Molaro et al. (2013) and Rahmani et al. (2013). A stringent bound for Δα/α is obtained for the absorber at z_abs = 1.6919 towards HE 2217-2818. The absorption profile is complex with several very narrow features, and is modeled with 32 velocity components. The relative variation in α in this system is +1.3± 2.4_stat ± 1.0_sys ppm if Al II λ 1670 Å and three Fe II transitions are used, and +1.1 ± 2.6_stat ppm in a slightly different analysis with only Fe II transitions used. This is one of the tightest bounds on α-variation from an individual absorber and reveals no evidence for variation in α at the 3-ppm precision level (1σ confidence). The expectation at this sky position of the recently-reported dipolar variation of α is (3.2-5.4)±1.7 ppm depending on dipole model used and this constraint of Δα/α at face value is not supporting this expectation but not inconsistent with it at the 3σ level. For the proton-to-electron mass ratio the analysis of the H_2 absorption lines of the z_abs ≈ 2.4018 damped Lyα system

  18. CODATA Fundamental Physical Constants

    National Institute of Standards and Technology Data Gateway

    SRD 121 NIST 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.

  19. Elastic constants of stressed and unstressed materials in the phase-field crystal model

    NASA Astrophysics Data System (ADS)

    Wang, Zi-Le; Huang, Zhi-Feng; Liu, Zhirong

    2018-04-01

    A general procedure is developed to investigate the elastic response and calculate the elastic constants of stressed and unstressed materials through continuum field modeling, particularly the phase-field crystal (PFC) models. It is found that for a complete description of system response to elastic deformation, the variations of all the quantities of lattice wave vectors, their density amplitudes (including the corresponding anisotropic variation and degeneracy breaking), the average atomic density, and system volume should be incorporated. The quantitative and qualitative results of elastic constant calculations highly depend on the physical interpretation of the density field used in the model, and also importantly, on the intrinsic pressure that usually pre-exists in the model system. A formulation based on thermodynamics is constructed to account for the effects caused by constant pre-existing stress during the homogeneous elastic deformation, through the introducing of a generalized Gibbs free energy and an effective finite strain tensor used for determining the elastic constants. The elastic properties of both solid and liquid states can be well produced by this unified approach, as demonstrated by an analysis for the liquid state and numerical evaluations for the bcc solid phase. The numerical calculations of bcc elastic constants and Poisson's ratio through this method generate results that are consistent with experimental conditions, and better match the data of bcc Fe given by molecular dynamics simulations as compared to previous work. The general theory developed here is applicable to the study of different types of stressed or unstressed material systems under elastic deformation.

  20. Pseudo-extravasation rate constant of dynamic susceptibility contrast-MRI determined from pharmacokinetic first principles.

    PubMed

    Li, Xin; Varallyay, Csanad G; Gahramanov, Seymur; Fu, Rongwei; Rooney, William D; Neuwelt, Edward A

    2017-11-01

    Dynamic susceptibility contrast-magnetic resonance imaging (DSC-MRI) is widely used to obtain informative perfusion imaging biomarkers, such as the relative cerebral blood volume (rCBV). The related post-processing software packages for DSC-MRI are available from major MRI instrument manufacturers and third-party vendors. One unique aspect of DSC-MRI with low-molecular-weight gadolinium (Gd)-based contrast reagent (CR) is that CR molecules leak into the interstitium space and therefore confound the DSC signal detected. Several approaches to correct this leakage effect have been proposed throughout the years. Amongst the most popular is the Boxerman-Schmainda-Weisskoff (BSW) K 2 leakage correction approach, in which the K 2 pseudo-first-order rate constant quantifies the leakage. In this work, we propose a new method for the BSW leakage correction approach. Based on the pharmacokinetic interpretation of the data, the commonly adopted R 2 * expression accounting for contributions from both intravascular and extravasating CR components is transformed using a method mathematically similar to Gjedde-Patlak linearization. Then, the leakage rate constant (K L ) can be determined as the slope of the linear portion of a plot of the transformed data. Using the DSC data of high-molecular-weight (~750 kDa), iron-based, intravascular Ferumoxytol (FeO), the pharmacokinetic interpretation of the new paradigm is empirically validated. The primary objective of this work is to empirically demonstrate that a linear portion often exists in the graph of the transformed data. This linear portion provides a clear definition of the Gd CR pseudo-leakage rate constant, which equals the slope derived from the linear segment. A secondary objective is to demonstrate that transformed points from the initial transient period during the CR wash-in often deviate from the linear trend of the linearized graph. The inclusion of these points will have a negative impact on the accuracy of the leakage

  1. 2JHH-resolved HSQC: Exclusive determination of geminal proton-proton coupling constants

    NASA Astrophysics Data System (ADS)

    Marcó, Núria; Nolis, Pau; Gil, Roberto R.; Parella, Teodor

    2017-09-01

    The measurement of two-bond proton-proton coupling constants (2JHH) in prochiral CH2 groups from the F2 dimension of 2D spectra is not easy due to the usual presence of complex multiplet J patterns, line broadening effects and strong coupling artifacts. These drawbacks are particularly pronounced and frequent in AB spin systems, as those normally exhibited by the pair of diastereotopic CH2 protons. Here, a novel 2JHH-resolved HSQC experiment for the exclusive and accurate determination of the magnitude of 2JHH from the doublet displayed along the highly-resolved indirect F1 dimension is described. A pragmatic 2JHH NMR profile affords a fast overview of the full range of existing 2JHH values. In addition, a 2JHH/δ(13C)-scaled version proves to be an efficient solution when severe signal overlapping complicate a rigorous analysis. The performance of the method is compared with other current techniques and illustrated by the determination of challenging residual dipolar 2DHH coupling constants of small molecules dissolved in weakly orienting media.

  2. Multiaxial Fatigue Damage Parameter and Life Prediction without Any Additional Material Constants

    PubMed Central

    Yu, Zheng-Yong; Liu, Qiang; Liu, Yunhan

    2017-01-01

    Based on the critical plane approach, a simple and efficient multiaxial fatigue damage parameter with no additional material constants is proposed for life prediction under uniaxial/multiaxial proportional and/or non-proportional loadings for titanium alloy TC4 and nickel-based superalloy GH4169. Moreover, two modified Ince-Glinka fatigue damage parameters are put forward and evaluated under different load paths. Results show that the generalized strain amplitude model provides less accurate life predictions in the high cycle life regime and is better for life prediction in the low cycle life regime; however, the generalized strain energy model is relatively better for high cycle life prediction and is conservative for low cycle life prediction under multiaxial loadings. In addition, the Fatemi–Socie model is introduced for model comparison and its additional material parameter k is found to not be a constant and its usage is discussed. Finally, model comparison and prediction error analysis are used to illustrate the superiority of the proposed damage parameter in multiaxial fatigue life prediction of the two aviation alloys under various loadings. PMID:28792487

  3. Multiaxial Fatigue Damage Parameter and Life Prediction without Any Additional Material Constants.

    PubMed

    Yu, Zheng-Yong; Zhu, Shun-Peng; Liu, Qiang; Liu, Yunhan

    2017-08-09

    Based on the critical plane approach, a simple and efficient multiaxial fatigue damage parameter with no additional material constants is proposed for life prediction under uniaxial/multiaxial proportional and/or non-proportional loadings for titanium alloy TC4 and nickel-based superalloy GH4169. Moreover, two modified Ince-Glinka fatigue damage parameters are put forward and evaluated under different load paths. Results show that the generalized strain amplitude model provides less accurate life predictions in the high cycle life regime and is better for life prediction in the low cycle life regime; however, the generalized strain energy model is relatively better for high cycle life prediction and is conservative for low cycle life prediction under multiaxial loadings. In addition, the Fatemi-Socie model is introduced for model comparison and its additional material parameter k is found to not be a constant and its usage is discussed. Finally, model comparison and prediction error analysis are used to illustrate the superiority of the proposed damage parameter in multiaxial fatigue life prediction of the two aviation alloys under various loadings.

  4. The CC/DFT Route towards Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as Case Study

    PubMed Central

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2018-01-01

    The structures, relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of Pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semi-experimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg. for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt- and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol−1. Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm−1 are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  5. Ab Initio Molecular Dynamics and Lattice Dynamics-Based Force Field for Modeling Hexagonal Boron Nitride in Mechanical and Interfacial Applications.

    PubMed

    Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel

    2018-04-05

    Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.

  6. Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.

    PubMed

    Roe, Daniel R; Bergonzo, Christina; Cheatham, Thomas E

    2014-04-03

    Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency.

  7. Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

    PubMed Central

    2015-01-01

    Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency. PMID:24625009

  8. Touchless attitude correction for satellite with constant magnetic moment

    NASA Astrophysics Data System (ADS)

    Ao, Hou-jun; Yang, Le-ping; Zhu, Yan-wei; Zhang, Yuan-wen; Huang, Huan

    2017-09-01

    Rescue of satellite with attitude fault is of great value. Satellite with improper injection attitude may lose contact with ground as the antenna points to the wrong direction, or encounter energy problems as solar arrays are not facing the sun. Improper uploaded command may set the attitude out of control, exemplified by Japanese Hitomi spacecraft. In engineering practice, traditional physical contact approaches have been applied, yet with a potential risk of collision and a lack of versatility since the mechanical systems are mission-specific. This paper puts forward a touchless attitude correction approach, in which three satellites are considered, one having constant dipole and two having magnetic coils to control attitude of the first. Particular correction configurations are designed and analyzed to maintain the target's orbit during the attitude correction process. A reference coordinate system is introduced to simplify the control process and avoid the singular value problem of Euler angles. Based on the spherical triangle basic relations, the accurate varying geomagnetic field is considered in the attitude dynamic mode. Sliding mode control method is utilized to design the correction law. Finally, numerical simulation is conducted to verify the theoretical derivation. It can be safely concluded that the no-contact attitude correction approach for the satellite with uniaxial constant magnetic moment is feasible and potentially applicable to on-orbit operations.

  9. Gravity–capillary waves in finite depth on flows of constant vorticity

    PubMed Central

    Hsu, Hung-Chu; Francius, Marc; Kharif, Christian

    2016-01-01

    This paper considers two-dimensional periodic gravity–capillary waves propagating steadily in finite depth on a linear shear current (constant vorticity). A perturbation series solution for steady periodic waves, accurate up to the third order, is derived using a classical Stokes expansion procedure, which allows us to include surface tension effects in the analysis of wave–current interactions in the presence of constant vorticity. The analytical results are then compared with numerical computations with the full equations. The main results are (i) the phase velocity is strongly dependent on the value of the vorticity; (ii) the singularities (Wilton singularities) in the Stokes expansion in powers of wave amplitude that correspond to a Bond number of 1/2 and 1/3, which are the consequences of the non-uniformity in the ordering of the Fourier coefficients, are found to be influenced by vorticity; (iii) different surface profiles of capillary–gravity waves are computed and the effect of vorticity on those profiles is shown to be important, in particular that the solutions exhibit type-2-like wave features, characterized by a secondary maximum on the surface profile with a trough between the two maxima. PMID:27956873

  10. Kinetic determinations of accurate relative oxidation potentials of amines with reactive radical cations.

    PubMed

    Gould, Ian R; Wosinska, Zofia M; Farid, Samir

    2006-01-01

    Accurate oxidation potentials for organic compounds are critical for the evaluation of thermodynamic and kinetic properties of their radical cations. Except when using a specialized apparatus, electrochemical oxidation of molecules with reactive radical cations is usually an irreversible process, providing peak potentials, E(p), rather than thermodynamically meaningful oxidation potentials, E(ox). In a previous study on amines with radical cations that underwent rapid decarboxylation, we estimated E(ox) by correcting the E(p) from cyclic voltammetry with rate constants for decarboxylation obtained using laser flash photolysis. Here we use redox equilibration experiments to determine accurate relative oxidation potentials for the same amines. We also describe an extension of these experiments to show how relative oxidation potentials can be obtained in the absence of equilibrium, from a complete kinetic analysis of the reversible redox kinetics. The results provide support for the previous cyclic voltammetry/laser flash photolysis method for determining oxidation potentials.

  11. 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.

  12. Transcriptome analysis of the Bombyx mori fat body after constant high temperature treatment shows differences between the sexes.

    PubMed

    Wang, Hua; Fang, Yan; Wang, Lipeng; Zhu, Wenjuan; Ji, Haipeng; Wang, Haiying; Xu, Shiqing; Sima, Yanghu

    2014-09-01

    Ambient temperature plays a large role in insect growth, development and even their distribution. The elucidation of the associated molecular mechanism that underlies the effect of constant high temperature will enables us to further understand the stress responses. We constructed four digital gene expression libraries from the fat body of female and male Bombyx mori. Differential gene expression was analyzed after constant high temperature treatment. The results showed that there were significant changes to the gene expression in the fat body after heat treatment, especially in binding, catalytic, cellular and metabolic processes. Constant high temperature may induce more traditional cryoprotectants, such as glycerol, glycogen, sorbitol and lipids, to protect cells from damage, and induce heat oxidative stress in conjunction with the heat shock proteins. The data also indicated a difference between males and females. The heat shock protein-related genes were up-regulated in both sexes but the expression of Hsp25.4 and DnaJ5 were down-regulated in the male fat body of B. mori. This is the first report of such a result. Constant high temperature also affected the expression of other functional genes and differences were observed between male and female fat bodies in the expression of RPS2, RPL37A and MREL. These findings provide abundant data on the effect of high temperature on insects at the molecular level. The data will also be beneficial to the study of differences between the sexes, manifested in variations in gene expression under high temperature.

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

    PubMed

    Fohlmeister, Jürgen F

    2015-06-01

    The structural similarity between the primary molecules of voltage-gated Na and K channels (alpha subunits) and activation gating in the Hodgkin-Huxley model is brought into full agreement by increasing the model's sodium kinetics to fourth order (m(3) → m(4)). Both structures then virtually imply activation gating by four independent subprocesses acting in parallel. The kinetics coalesce in four-dimensional (4D) cubic diagrams (16 states, 32 reversible transitions) that show the structure to be highly failure resistant against significant partial loss of gating function. Rate constants, as fitted in phase plot data of retinal ganglion cell excitation, reflect the molecular nature of the gating transitions. Additional dimensions (6D cubic diagrams) accommodate kinetically coupled sodium inactivation and gating processes associated with beta subunits. The gating transitions of coupled sodium inactivation appear to be thermodynamically irreversible; response to dielectric surface charges (capacitive displacement) provides a potential energy source for those transitions and yields highly energy-efficient excitation. A comparison of temperature responses of the squid giant axon (apparently Arrhenius) and mammalian channel gating yields kinetic Q10 = 2.2 for alpha unit gating, whose transitions are rate-limiting at mammalian temperatures; beta unit kinetic Q10 = 14 reproduces the observed non-Arrhenius deviation of mammalian gating at low temperatures; the Q10 of sodium inactivation gating matches the rate-limiting component of activation gating at all temperatures. The model kinetics reproduce the physiologically large frequency range for repetitive firing in ganglion cells and the physiologically observed strong temperature dependence of recovery from inactivation. Copyright © 2015 the American Physiological Society.

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

    PubMed Central

    2015-01-01

    The structural similarity between the primary molecules of voltage-gated Na and K channels (alpha subunits) and activation gating in the Hodgkin-Huxley model is brought into full agreement by increasing the model's sodium kinetics to fourth order (m3 → m4). Both structures then virtually imply activation gating by four independent subprocesses acting in parallel. The kinetics coalesce in four-dimensional (4D) cubic diagrams (16 states, 32 reversible transitions) that show the structure to be highly failure resistant against significant partial loss of gating function. Rate constants, as fitted in phase plot data of retinal ganglion cell excitation, reflect the molecular nature of the gating transitions. Additional dimensions (6D cubic diagrams) accommodate kinetically coupled sodium inactivation and gating processes associated with beta subunits. The gating transitions of coupled sodium inactivation appear to be thermodynamically irreversible; response to dielectric surface charges (capacitive displacement) provides a potential energy source for those transitions and yields highly energy-efficient excitation. A comparison of temperature responses of the squid giant axon (apparently Arrhenius) and mammalian channel gating yields kinetic Q10 = 2.2 for alpha unit gating, whose transitions are rate-limiting at mammalian temperatures; beta unit kinetic Q10 = 14 reproduces the observed non-Arrhenius deviation of mammalian gating at low temperatures; the Q10 of sodium inactivation gating matches the rate-limiting component of activation gating at all temperatures. The model kinetics reproduce the physiologically large frequency range for repetitive firing in ganglion cells and the physiologically observed strong temperature dependence of recovery from inactivation. PMID:25867741

  15. Molecular origin of limiting shear stress of elastohydrodynamic lubrication oil film studied by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Washizu, Hitoshi; Ohmori, Toshihide; Suzuki, Atsushi

    2017-06-01

    All-atom molecular dynamics simulations of an elastohydrodynamic lubrication oil film are performed to study the effect of pressure. Fluid molecules of n-hexane are confined between two solid plates under a constant normal force of 0.1-8.0 GPa. Traction simulations are performed by applying relative sliding motion to the solid plates. A transition in the traction behavior is observed around 0.5-2.0 GPa, which corresponds to the viscoelastic region to the plastic-elastic region, which are experimentally observed. This phase transition is related to the suppression of the fluctuation in molecular motion.

  16. 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).

  17. Toward an understanding of the turbidity measurement of heterocoagulation rate constants of dispersions containing particles of different sizes.

    PubMed

    Liu, Jie; Xu, Shenghua; Sun, Zhiwei

    2007-11-06

    Our previous studies have shown that the determination of coagulation rate constants by turbidity measurement becomes impossible for a certain operating wavelength (that is, its blind point) because at this wavelength the change in the turbidity of a dispersion completely loses its response to the coagulation process. Therefore, performing the turbidity measurement in the wavelength range near the blind point should be avoided. In this article, we demonstrate that the turbidity measurement of the rate constant for coagulation of a binary dispersion containing particles of two different sizes (heterocoagulation) presents special difficulties because the blind point shifts with not only particle size but also with the component fraction. Some important aspects of the turbidity measurement for the heterocoagulation rate constant are discussed and experimentally tested. It is emphasized that the T-matrix method can be used to correctly evaluate extinction cross sections of doublets formed during the heterocoagulation process, which is the key data determining the rate constant from the turbidity measurement, and choosing the appropriate operating wavelength and component fraction are important to achieving a more accurate rate constant. Finally, a simple scheme in experimentally determining the sensitivity of the turbidity changes with coagulation over a wavelength range is proposed.

  18. Transient diffraction grating measurements of molecular diffusion in the undergraduate laboratory

    NASA Astrophysics Data System (ADS)

    Spiegel, Daniel R.; Tuli, Santona

    2011-07-01

    Diffusion is a central process in many biological, chemical, and physical systems. We describe an experiment that employs the interference of laser beams to allow the measurement of molecular diffusion on submillimeter length scales. The interference fringes of two intersecting pump beams within a dye solution create a sinusoidal distribution of long-lived molecular excited states. A third probe beam is incident at a wavelength at which the indices of refraction of the ground and excited states are different, so the probe beam diffracts from the spatially periodic excited-state pattern. After the pump beams are switched off, the excited-state periodicity washes out as the system diffuses back to equilibrium. The molecular diffusion constant is obtained from the rate constant of the exponential decay of the diffracted beam. It is also possible to measure the excited-state lifetime.

  19. Molecular-Level Simulations of the Turbulent Taylor-Green Flow

    NASA Astrophysics Data System (ADS)

    Gallis, M. A.; Bitter, N. P.; Koehler, T. P.; Plimpton, S. J.; Torczynski, J. R.; Papadakis, G.

    2017-11-01

    The Direct Simulation Monte Carlo (DSMC) method, a statistical, molecular-level technique that provides accurate solutions to the Boltzmann equation, is applied to the turbulent Taylor-Green vortex flow. The goal of this work is to investigate whether DSMC can accurately simulate energy decay in a turbulent flow. If so, then simulating turbulent flows at the molecular level can provide new insights because the energy decay can be examined in detail from molecular to macroscopic length scales, thereby directly linking molecular relaxation processes to macroscopic transport processes. The DSMC simulations are performed on half a million cores of Sequoia, the 17 Pflop platform at Lawrence Livermore National Laboratory, and the kinetic-energy dissipation rate and the energy spectrum are computed directly from the molecular velocities. The DSMC simulations are found to reproduce the Kolmogorov -5/3 law and to agree with corresponding Navier-Stokes simulations obtained using a spectral method. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

  20. Electronic excitations in molecular solids: bridging theory and experiment.

    PubMed

    Skelton, Jonathan M; da Silva, E Lora; Crespo-Otero, Rachel; Hatcher, Lauren E; Raithby, Paul R; Parker, Stephen C; Walsh, Aron

    2015-01-01

    As the spatial and temporal resolution accessible to experiment and theory converge, computational chemistry is an increasingly powerful tool for modelling and interpreting spectroscopic data. However, the study of molecular processes, in particular those related to electronic excitations (e.g. photochemistry), frequently pushes quantum-chemical techniques to their limit. The disparity in the level of theory accessible to periodic and molecular calculations presents a significant challenge when modelling molecular crystals, since accurate calculations require a high level of theory to describe the molecular species, but must also take into account the influence of the crystalline environment on their properties. In this article, we briefly review the different classes of quantum-chemical techniques, and present an overview of methods that account for environmental influences with varying levels of approximation. Using a combination of solid-state and molecular calculations, we quantitatively evaluate the performance of implicit-solvent models for the [Ni(Et4dien)(η2-O,ON)(η1-NO2)] linkage-isomer system as a test case. We focus particularly on the accurate reproduction of the energetics of the isomerisation, and on predicting spectroscopic properties to compare with experimental results. This work illustrates how the synergy between periodic and molecular calculations can be exploited for the study of molecular crystals, and forms a basis for the investigation of more challenging phenomena, such as excited-state dynamics, and for further methodological developments.

  1. Uniform function constants of motion and their first-order perturbation

    NASA Astrophysics Data System (ADS)

    Prato, Domingo; Hamity, Victor H.

    2005-05-01

    The main purpose of this work is to present some uniform function constants of motion rather than the well-known quantities arising from spacetime symmetries. These constants are usually associated with the intrinsic characteristics of the trajectories of a particle in a central potential field. We treat two cases. The first is the Lenz vector which sometimes is found in the literature [1, 2]; the other is associated with the isotropic harmonic oscillator, of relative importance in some simple models of the classical molecular interaction. The first example is applied to describe the perturbation of the trajectories in the Rutherford scattering and the precession of the Keplerian orbit of a planet. In the other case the conserved quantity is a symmetric tensor. We find the eigenvectors and eigenvalues of that tensor while at the same time we obtain the solution to the problem of calculating the rotation rate of the orbits in first order of a perturbation parameter in the potential energy, by performing a simple coordinate transformation in the Cartesian plane. We think that the present work addresses many aspects of mechanics with a didactical interest in other physics or mathematics courses.

  2. Tachyon constant-roll inflation

    NASA Astrophysics Data System (ADS)

    Mohammadi, A.; Saaidi, Kh.; Golanbari, T.

    2018-04-01

    The constant-roll inflation is studied where the inflaton is taken as a tachyon field. Based on this approach, the second slow-roll parameter is taken as a constant which leads to a differential equation for the Hubble parameter. Finding an exact solution for the Hubble parameter is difficult and leads us to a numerical solution for the Hubble parameter. On the other hand, since in this formalism the slow-roll parameter η is constant and could not be assumed to be necessarily small, the perturbation parameters should be reconsidered again which, in turn, results in new terms appearing in the amplitude of scalar perturbations and the scalar spectral index. Utilizing the numerical solution for the Hubble parameter, we estimate the perturbation parameter at the horizon exit time and compare it with observational data. The results show that, for specific values of the constant parameter η , we could have an almost scale-invariant amplitude of scalar perturbations. Finally, the attractor behavior for the solution of the model is presented, and we determine that the feature could be properly satisfied.

  3. Accurate high-throughput structure mapping and prediction with transition metal ion FRET

    PubMed Central

    Yu, Xiaozhen; Wu, Xiongwu; Bermejo, Guillermo A.; Brooks, Bernard R.; Taraska, Justin W.

    2013-01-01

    Mapping the landscape of a protein’s conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein Maltose Binding Protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells. PMID:23273426

  4. RE-EXAMINING LARSON'S SCALING RELATIONSHIPS IN GALACTIC MOLECULAR CLOUDS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Heyer, Mark; Krawczyk, Coleman; Duval, Julia

    The properties of Galactic molecular clouds tabulated by Solomon et al. (SRBY) are re-examined using the Boston University-FCRAO Galactic Ring Survey of {sup 13}CO J = 1-0 emission. These new data provide a lower opacity tracer of molecular clouds and improved angular and spectral resolution compared with previous surveys of molecular line emission along the Galactic Plane. We calculate giant molecular cloud (GMC) masses within the SRBY cloud boundaries assuming local thermodynamic equilibrium (LTE) conditions throughout the cloud and a constant H{sub 2} to {sup 13}CO abundance, while accounting for the variation of the {sup 12}C/{sup 13}C with galactocentric radius.more » The LTE-derived masses are typically five times smaller than the SRBY virial masses. The corresponding median mass surface density of molecular hydrogen for this sample is 42 M{sub sun} pc{sup -2}, which is significantly lower than the value derived by SRBY (median 206 M{sub sun} pc{sup -2}) that has been widely adopted by most models of cloud evolution and star formation. This discrepancy arises from both the extrapolation by SRBY of velocity dispersion, size, and CO luminosity to the 1 K antenna temperature isophote that likely overestimates the GMC masses and our assumption of constant {sup 13}CO abundance over the projected area of each cloud. Owing to the uncertainty of molecular abundances in the envelopes of clouds, the mass surface density of GMCs could be larger than the values derived from our {sup 13}CO measurements. From velocity dispersions derived from the {sup 13}CO data, we find that the coefficient of the cloud structure functions, v{sup 0} = {sigma}{sub v}/R {sup 1/2}, is not constant, as required to satisfy Larson's scaling relationships, but rather systematically varies with the surface density of the cloud as {approx}{sigma}{sup 0.5} as expected for clouds in self-gravitational equilibrium.« less

  5. Diffusion in liquid Germanium using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.

    1996-03-01

    We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.

  6. Watt balance experiments for the determination of the Planck constant and the redefinition of the kilogram

    NASA Astrophysics Data System (ADS)

    Stock, M.

    2013-02-01

    Since 1889 the international prototype of the kilogram has served as the definition of the unit of mass in the International System of Units (SI). It is the last material artefact to define a base unit of the SI, and it influences several other base units. This situation is no longer acceptable in a time of ever increasing measurement precision. It is therefore planned to redefine the unit of mass by fixing the numerical value of the Planck constant. At the same time three other base units, the ampere, the kelvin and the mole, will be redefined. As a first step, the kilogram redefinition requires a highly accurate determination of the Planck constant in the present SI system, with a relative uncertainty of the order of 1 part in 108. The most promising experiment for this purpose, and for the future realization of the kilogram, is the watt balance. It compares mechanical and electrical power and makes use of two macroscopic quantum effects, thus creating a relationship between a macroscopic mass and the Planck constant. In this paper the background for the choice of the Planck constant for the kilogram redefinition is discussed and the role of the Planck constant in physics is briefly reviewed. The operating principle of watt balance experiments is explained and the existing experiments are reviewed. An overview is given of all presently available experimental determinations of the Planck constant, and it is shown that further investigation is needed before the redefinition of the kilogram can take place. This article is based on a lecture given at the International School of Physics ‘Enrico Fermi’, Course CLXXXV: Metrology and Physical Constants, held in Varenna on 17-27 July 2012. It will also be published in the proceedings of the school, edited by E Bava, M Kühne and A M Rossi (IOS Press, Amsterdam and SIF, Bologna).

  7. Numerical results on the transcendence of constants involving pi, e, and Euler's constant

    NASA Technical Reports Server (NTRS)

    Bailey, David H.

    1988-01-01

    The existence of simple polynomial equations (integer relations) for the constants e/pi, e + pi, log pi, gamma (Euler's constant), e exp gamma, gamma/e, gamma/pi, and log gamma is investigated by means of numerical computations. The recursive form of the Ferguson-Fourcade algorithm (Ferguson and Fourcade, 1979; Ferguson, 1986 and 1987) is implemented on the Cray-2 supercomputer at NASA Ames, applying multiprecision techniques similar to those described by Bailey (1988) except that FFTs are used instead of dual-prime-modulus transforms for multiplication. It is shown that none of the constants has an integer relation of degree eight or less with coefficients of Euclidean norm 10 to the 9th or less.

  8. Accurate atomistic potentials and training sets for boron-nitride nanostructures

    NASA Astrophysics Data System (ADS)

    Tamblyn, Isaac

    Boron nitride nanotubes exhibit exceptional structural, mechanical, and thermal properties. They are optically transparent and have high thermal stability, suggesting a wide range of opportunities for structural reinforcement of materials. Modeling can play an important role in determining the optimal approach to integrating nanotubes into a supporting matrix. Developing accurate, atomistic scale models of such nanoscale interfaces embedded within composites is challenging, however, due to the mismatch of length scales involved. Typical nanotube diameters range from 5-50 nm, with a length as large as a micron (i.e. a relevant length-scale for structural reinforcement). Unlike their carbon-based counterparts, well tested and transferable interatomic force fields are not common for BNNT. In light of this, we have developed an extensive training database of BN rich materials, under conditions relevant for BNNT synthesis and composites based on extensive first principles molecular dynamics simulations. Using this data, we have produced an artificial neural network potential capable of reproducing the accuracy of first principles data at significantly reduced computational cost, allowing for accurate simulation at the much larger length scales needed for composite design.

  9. Constant-Pressure Hydraulic Pump

    NASA Technical Reports Server (NTRS)

    Galloway, C. W.

    1982-01-01

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

  10. Piezoelectric ceramics with high dielectric constants for ultrasonic medical transducers.

    PubMed

    Hosono, Yasuharu; Yamashita, Yohachi

    2005-10-01

    Complex system ceramics Pb(Sc(1/2)Nb(1/2))O3-Pb(Mg(1/3)Nb(2/3))O3-Pb(Ni(1/2)Nb(1/2))O3-(Pb0.965,Sr0.035) (Zr,Ti)O3 (PSN-PMN-PNN-PSZT abbreviated PSMNZT) have been synthesized by the conventional technique, and dielectric and piezoelectric properties of the ceramics have been investigated for ultrasonic medical transducers. High capacitances of the transducers are desired in order to match the electrical impedance between the transducers and the coaxial cable in array probes. Although piezoelectric ceramics that have high dielectric constants (epsilon33t/epsilon0 > 5000, k'33 < 70%) are produced in many foundries, the dielectric constants are insufficient. However, we have reported that low molecular mass B-site ions in the lead-perovskite structures are important in realizing better dielectric and piezoelectric properties. We focused on the complex system ceramics PSMNZT that consists of light B-site elements. The maximum dielectric constant, epsilon33T/epsilon0 = 7, 200, was confirmed in the ceramics, where k'33 = 69%, d33 = 940 pC/N, and T(c) = 135 degrees C were obtained. Moreover, pulse-echo characteristics were simulated using the Mason model. The PSMNZT ceramic probe showed echo amplitude about 5.5 dB higher than that of the conventional PZT ceramic probe (PZT-5H type). In this paper, the electrical properties of the PSMNZT ceramics and the simulation results for pulse-echo characteristics of the phased-array probes are introduced.

  11. Molecular clock of HIV-1 envelope genes under early immune selection

    DOE PAGES

    Park, Sung Yong; Love, Tanzy M. T.; Perelson, Alan S.; ...

    2016-06-01

    Here, the molecular clock hypothesis that genes or proteins evolve at a constant rate is a key tool to reveal phylogenetic relationships among species. Using the molecular clock, we can trace an infection back to transmission using HIV-1 sequences from a single time point. Whether or not a strict molecular clock applies to HIV-1’s early evolution in the presence of immune selection has not yet been fully examined.

  12. Molecular clock of HIV-1 envelope genes under early immune selection

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Park, Sung Yong; Love, Tanzy M. T.; Perelson, Alan S.

    Here, the molecular clock hypothesis that genes or proteins evolve at a constant rate is a key tool to reveal phylogenetic relationships among species. Using the molecular clock, we can trace an infection back to transmission using HIV-1 sequences from a single time point. Whether or not a strict molecular clock applies to HIV-1’s early evolution in the presence of immune selection has not yet been fully examined.

  13. Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

  14. Physicochemical properties of polycyclic aromatic hydrocarbons: Aqueous solubilities, n-octanol/water partition coefficients, and Henry`s law constants

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Maagd, P.G.J. de; Opperhuizen, A.; Sijm, D.T.H.M.

    Aqueous solubilities, n-octanol/water partition coefficients (K{sub ow}S), and Henry`s law constants were determined for a range of polycyclic aromatic hydrocarbons (PAHs) using a generator-column, slow-stirring, and gas-purge method, respectively. The currently obtained data were compared to available literature data. For seven of the PAHs no K{sub ow}S previously were determined with the slow-stirring method. For four of the PAHs the present study reports the first experimental Henry`s law constants. Relationships between subcooled liquid solubilities, K{sub ow}S, and Henry`s law constants as a function of molar volume are discussed. A consistent data set was obtained, for which an excellent correlation wasmore » found between subcooled liquid solubility and molar volume. A linear fit did not accurately describe the relationship between log K{sub ow} and molar volume. This is probably due to a decreasing solubility in n-octanol with increasing molar volume. Finally, a high correlation was found between Henry`s law constant and molar volume. The presently obtained dataset can be used to predict the fate and behavior of unsubstituted homocyclic PAHs.« less

  15. Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments.

    PubMed

    Karaboga, Arnaud S; Petronin, Florent; Marchetti, Gino; Souchet, Michel; Maigret, Bernard

    2013-04-01

    Since 3D molecular shape is an important determinant of biological activity, designing accurate 3D molecular representations is still of high interest. Several chemoinformatic approaches have been developed to try to describe accurate molecular shapes. Here, we present a novel 3D molecular description, namely harmonic pharma chemistry coefficient (HPCC), combining a ligand-centric pharmacophoric description projected onto a spherical harmonic based shape of a ligand. The performance of HPCC was evaluated by comparison to the standard ROCS software in a ligand-based virtual screening (VS) approach using the publicly available directory of useful decoys (DUD) data set comprising over 100,000 compounds distributed across 40 protein targets. Our results were analyzed using commonly reported statistics such as the area under the curve (AUC) and normalized sum of logarithms of ranks (NSLR) metrics. Overall, our HPCC 3D method is globally as efficient as the state-of-the-art ROCS software in terms of enrichment and slightly better for more than half of the DUD targets. Since it is largely admitted that VS results depend strongly on the nature of the protein families, we believe that the present HPCC solution is of interest over the current ligand-based VS methods. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Estimation of Hamaker constants of ceramic materials from optical data using Lifshitz theory

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bergstroem, L.; Meurk, A.; Rowcliffe, D.J.

    1996-02-01

    The Hamaker constants of eight different ceramic materials, 6H-SiC, tetragonal, partially stabilized ZrO{sub 2} (3% Y{sub 2}O{sub 3}), {beta}-Si{sub 3}N{sub 4}, {alpha}-Al{sub 2}O{sub 3}, Y{sub 2}O{sub 3}, sapphire (single-crystal {alpha}-Al{sub 2}O{sub 3}), MgO, MgAl{sub 2}O{sub 4}, and fused silica, across air, water, and n-dodecane at room temperature and across silica at 2,000 K have been calculated from optical data using the Lifshitz theory. Spectroscopic ellipsometry was used to measure the photon energy dependence of the refractive index, n, and the extinction coefficient, k, in the visible and near-UV range on several important ceramic materials. This relatively simple, nondestructive technique hasmore » proved to yield reliable optical data on sintered, polycrystalline materials such as Si{sub 3}N{sub 4}, SiC, ZrO{sub 2}, Al{sub 2}O{sub 3}, and ZnO. For the other materials, Y{sub 2}O{sub 3}, sapphire, MgO, MgAl{sub 2}O{sub 4}, and fused silica, optical data from the literature were used to calculate the Hamaker constants. The calculated Hamaker constants were estimated to be accurate within {+-} 10%.« less

  17. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

    PubMed

    Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

    2013-02-19

    Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

  18. Photoconductivity of Low-Bandgap Polymer and Polymer: Fullerene Bulk Heterojunction Studied by Constant Photocurrent Method

    NASA Astrophysics Data System (ADS)

    Malov, V. V.; Tameev, A. R.; Novikov, S. V.; Khenkin, M. V.; Kazanskii, A. G.; Vannikov, A. V.

    2015-08-01

    Optical and photoelectric properties of modern photosensitive polymers are of great interest due to their prospects for photovoltaic applications. In particular, an investigation of absorption and photoconductivity edge of these materials could provide valuable information. For these purpose we applied the constant photocurrent method which has proved its efficiency for inorganic materials. PCDTBT and PTB7 polymers were used as objects for the study as well as their blends with a fullerene derivative PC71BM. The measurements by constant photocurrent method (CPM) show that formation of bulk heterojunction (BHJ) in the blends increases photoconductivity and results in a redshift of the photocurrent edge in the doped polymers compared with that in the neat polymers. Obtained from CPM data, spectral dependences of absorption coefficient were approximated using Gaussian distribution of density-of-states within HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) bands. The approximation procedure allowed us to evaluate rather optical than electrical bandgaps for the studied materials. Moreover, spectra of polymer:PC71BM blends were fitted well by the sum of two Gaussian peaks which reveal both the transitions within the polymer and the transitions involving charge transfer states at the donor-acceptor interface in the BHJ.

  19. Persimmon breeding in Japan for pollination-constant non-astringent (PCNA) type with marker-assisted selection.

    PubMed

    Sato, Akihiko; Yamada, Masahiko

    2016-01-01

    Oriental persimmon (Diospyros kaki) originated in Eastern Asia, and many indigenous cultivars have been developed in China, Japan, and Korea. These cultivars are classified into four groups based on their natural astringency loss on the tree and seed formation: pollination-constant non-astringent (PCNA), pollination-variant non-astringent (PVNA), pollination-constant astringent (PCA), and pollination-variant astringent (PVA). PCNA is the most desirable type because the fruit can be eaten without any postharvest treatment; therefore, one of the goals of our persimmon breeding programs is to release superior PCNA cultivars. The PCNA genotype is recessive to the other three non-PCNA genotypes, and PCNA-type F1 offspring are obtained exclusively from crosses among PCNA genotypes. Moreover, the number of superior PCNA cross-parents have been limited. In the late 1980s, inbreeding depression became obvious, especially in terms of fruit size, tree vigor, and productivity. To mitigate the inbreeding, a backcross program using PCNA [(non-PCNA × PCNA) × PCNA] was started in 1990. This process, however, was inefficient because only 15% of the offspring were PCNA, and all offspring had to be grown to the fruiting stage. Therefore, molecular markers linked to the PCNA locus were developed for discriminating PCNA offspring. A molecular marker linked to Chinese PCNA has also been developed.

  20. Recent development of nanoparticles for molecular imaging

    NASA Astrophysics Data System (ADS)

    Kim, Jonghoon; Lee, Nohyun; Hyeon, Taeghwan

    2017-10-01

    Molecular imaging enables us to non-invasively visualize cellular functions and biological processes in living subjects, allowing accurate diagnosis of diseases at early stages. For successful molecular imaging, a suitable contrast agent with high sensitivity is required. To date, various nanoparticles have been developed as contrast agents for medical imaging modalities. In comparison with conventional probes, nanoparticles offer several advantages, including controllable physical properties, facile surface modification and long circulation time. In addition, they can be integrated with various combinations for multimodal imaging and therapy. In this opinion piece, we highlight recent advances and future perspectives of nanomaterials for molecular imaging. This article is part of the themed issue 'Challenges for chemistry in molecular imaging'.

  1. Statistical errors in molecular dynamics averages

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Schiferl, S.K.; Wallace, D.C.

    1985-11-15

    A molecular dynamics calculation produces a time-dependent fluctuating signal whose average is a thermodynamic quantity of interest. The average of the kinetic energy, for example, is proportional to the temperature. A procedure is described for determining when the molecular dynamics system is in equilibrium with respect to a given variable, according to the condition that the mean and the bandwidth of the signal should be sensibly constant in time. Confidence limits for the mean are obtained from an analysis of a finite length of the equilibrium signal. The role of serial correlation in this analysis is discussed. The occurence ofmore » unstable behavior in molecular dynamics data is noted, and a statistical test for a level shift is described.« less

  2. Construction of Lines of Constant Density and Constant Refractive Index for Ternary Liquid Mixtures.

    ERIC Educational Resources Information Center

    Tasic, Aleksandar Z.; Djordjevic, Bojan D.

    1983-01-01

    Demonstrates construction of density constant and refractive index constant lines in triangular coordinate system on basis of systematic experimental determinations of density and refractive index for both homogeneous (single-phase) ternary liquid mixtures (of known composition) and the corresponding binary compositions. Background information,…

  3. Measuring Solar Radiation Incident on Earth: Solar Constant-3 (SOLCON-3)

    NASA Technical Reports Server (NTRS)

    Crommelynck, Dominique; Joukoff, Alexandre; Dewitte, Steven

    2002-01-01

    Life on Earth is possible because the climate conditions on Earth are relatively mild. One element of the climate on Earth, the temperature, is determined by the heat exchanges between the Earth and its surroundings, outer space. The heat exchanges take place in the form of electromagnetic radiation. The Earth gains energy because it absorbs solar radiation, and it loses energy because it emits thermal infrared radiation to cold space. The heat exchanges are in balance: the heat gained by the Earth through solar radiation equals the heat lost through thermal radiation. When the balance is perturbed, a temperature change and hence a climate change of the Earth will occur. One possible perturbation of the balance is the CO2 greenhouse effect: when the amount of CO2 in the atmosphere increases, this will reduce the loss of thermal infrared radiation to cold space. Earth will gain more heat and hence the temperature will rise. Another perturbation of the balance can occur through variation of the amount of energy emitted by the sun. When the sun emits more energy, this will directly cause a rise of temperature on Earth. For a long time scientists believed that the energy emitted by the sun was constant. The 'solar constant' is defined as the amount of solar energy received per unit surface at a distance of one astronomical unit (the average distance of Earth's orbit) from the sun. Accurate measurements of the variations of the solar constant have been made since 1978. From these we know that the solar constant varies approximately with the 11-year solar cycle observed in other solar phenomena, such as the occurrence of sunspots, dark spots that are sometimes visible on the solar surface. When a sunspot occurs on the sun, since the spot is dark, the radiation (light) emitted by the sun drops instantaneously. Oddly, periods of high solar activity, when a lot of sunspot numbers increase, correspond to periods when the average solar constant is high. This indicates that

  4. Measurement of the fine-structure constant as a test of the Standard Model

    NASA Astrophysics Data System (ADS)

    Parker, Richard H.; Yu, Chenghui; Zhong, Weicheng; Estey, Brian; Müller, Holger

    2018-04-01

    Measurements of the fine-structure constant α require methods from across subfields and are thus powerful tests of the consistency of theory and experiment in physics. Using the recoil frequency of cesium-133 atoms in a matter-wave interferometer, we recorded the most accurate measurement of the fine-structure constant to date: α = 1/137.035999046(27) at 2.0 × 10‑10 accuracy. Using multiphoton interactions (Bragg diffraction and Bloch oscillations), we demonstrate the largest phase (12 million radians) of any Ramsey-Bordé interferometer and control systematic effects at a level of 0.12 part per billion. Comparison with Penning trap measurements of the electron gyromagnetic anomaly ge ‑ 2 via the Standard Model of particle physics is now limited by the uncertainty in ge ‑ 2; a 2.5σ tension rejects dark photons as the reason for the unexplained part of the muon’s magnetic moment at a 99% confidence level. Implications for dark-sector candidates and electron substructure may be a sign of physics beyond the Standard Model that warrants further investigation.

  5. On the Universality of the Kolmogorov Constant in Numerical Simulations of Turbulence

    NASA Technical Reports Server (NTRS)

    Yeung, P. K.; Zhou, Ye

    1997-01-01

    Motivated by a recent survey of experimental data, we examine data on the Kolmogorov spectrum constant in numerical simulations of isotropic turbulence, using results both from previous studies and from new direct numerical simulations over a range of Reynolds numbers (up to 240 on the Taylor scale) at grid resolutions up to 512(exp 3). It is noted that in addition to k(exp -5/3) scaling, identification of a true inertial range requires spectral isotropy in the same wavenumber range. We found that a plateau in the compensated three-dimensional energy spectrum at k(eta) approx. = 0.1 - -0.2, commonly used to infer the Kolmogorov constant from the compensated three-dimensional energy spectrum, actually does not represent proper inertial range behavior. Rather, a proper, if still approximate, inertial range emerges at k(eta) approx. = 0.02 - 0.05 when R(sub lambda) increases beyond 140. The new simulations indicate proportionality constants C(sub 1) and C in the one- and three-dimensional energy spectra respectively about 0.60 and 1.62. If the turbulence were perfectly isotropic then use of isotropy relations in wavenumber space (C(sub 1) = 18/55 C) would imply that C(sub 1) approx. = 0.53 for C = 1.62, in excellent agreement with experiments. However the one- and three-dimensional estimates are not fully consistent, because of departures (due to numerical and statistical limitations) from isotropy of the computed spectra at low wavenumbers. The inertial scaling of structure functions in physical space is briefly addressed. Since DNS is still restricted to moderate Reynolds numbers, an accurate evaluation of the Kolmogorov constant is very difficult. We focus on providing new insights on the interpretation of Kolmogorov 1941 similarity in the DNS literature and do not consider issues pertaining to the refined similarity hypotheses of Kolmogorov (K62).

  6. An improved electronic determination of the Boltzmann constant by Johnson noise thermometry.

    PubMed

    Qu, Jifeng; Benz, Samuel P; Coakley, Kevin; Rogalla, Horst; Tew, Weston L; White, Rod; Zhou, Kunli; Zhou, Zhenyu

    2017-08-01

    Recent measurements using acoustic gas thermometry have determined the value of the Boltzmann constant, k , with a relative uncertainty less than 1 × 10 -6 . These results have been supported by a measurement with a relative uncertainty of 1.9 × 10 -6 made with dielectric-constant gas thermometry. Together, the measurements meet the requirements of the International Committee for Weights and Measures and enable them to proceed with the redefinition of the kelvin in 2018. In further support, we provide a new determination of k using a purely electronic approach, Johnson noise thermometry, in which the thermal noise power generated by a sensing resistor immersed in a triple-point-of-water cell is compared to the noise power of a quantum-accurate pseudo-random noise waveform of nominally equal noise power. The experimental setup differs from that of the 2015 determination in several respects: a 100 Ω resistor is used as the thermal noise source, identical thin coaxial cables made of solid beryllium-copper conductors and foam dielectrics are used to connect the thermal and quantum-accurate noise sources to the correlator so as to minimize the temperature and frequency sensitivity of the impedances in the connecting leads, and no trimming capacitors or inductors are inserted into the connecting leads. The combination of reduced uncertainty due to spectral mismatches in the connecting leads and reduced statistical uncertainty due to a longer integration period of 100 d results in an improved determination of k = 1.380 649 7(37) × 10 -23 J K -1 with a relative standard uncertainty of 2.7 × 10 -6 and a relative offset of 0.89 × 10 -6 from the CODATA 2014 recommended value. The most significant terms in the uncertainty budget, the statistical uncertainty and the spectral-mismatch uncertainty, are uncorrelated with the corresponding uncertainties in the 2015 measurements.

  7. Finite element approximation of the radiative transport equation in a medium with piece-wise constant refractive index

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lehtikangas, O., E-mail: Ossi.Lehtikangas@uef.fi; Tarvainen, T.; Department of Computer Science, University College London, Gower Street, London WC1E 6BT

    2015-02-01

    The radiative transport equation can be used as a light transport model in a medium with scattering particles, such as biological tissues. In the radiative transport equation, the refractive index is assumed to be constant within the medium. However, in biomedical media, changes in the refractive index can occur between different tissue types. In this work, light propagation in a medium with piece-wise constant refractive index is considered. Light propagation in each sub-domain with a constant refractive index is modeled using the radiative transport equation and the equations are coupled using boundary conditions describing Fresnel reflection and refraction phenomena onmore » the interfaces between the sub-domains. The resulting coupled system of radiative transport equations is numerically solved using a finite element method. The approach is tested with simulations. The results show that this coupled system describes light propagation accurately through comparison with the Monte Carlo method. It is also shown that neglecting the internal changes of the refractive index can lead to erroneous boundary measurements of scattered light.« less

  8. The observational constraint on constant-roll inflation

    NASA Astrophysics Data System (ADS)

    Gao, Qing

    2018-07-01

    We discuss the constant-roll inflation with constant ɛ2 and constant \\bar η . By using the method of Bessel function approximation, the analytical expressions for the scalar and tensor power spectra, the scalar and tensor spectral tilts, and the tensor to scalar ratio are derived up to the first order of ɛ1. The model with constant ɛ2 is ruled out by the observations at the 3σ confidence level, and the model with constant \\bar η is consistent with the observations at the 1σ confidence level. The potential for the model with constant \\bar η is also obtained from the Hamilton-Jacobi equation. Although the observations constrain the constant-roll inflation to be the slow-roll inflation, the n s- r results from the constant-roll inflation are not the same as those from the slow-roll inflation even when \\bar η 0.01.

  9. Elastic constants of calcite

    USGS Publications Warehouse

    Peselnick, L.; Robie, R.A.

    1962-01-01

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

  10. Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

    PubMed

    Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

    2015-04-21

    Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

  11. 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.

  12. Mean excitation energies for molecular ions

    NASA Astrophysics Data System (ADS)

    Jensen, Phillip W. K.; Sauer, Stephan P. A.; Oddershede, Jens; Sabin, John R.

    2017-03-01

    The essential material constant that determines the bulk of the stopping power of high energy projectiles, the mean excitation energy, is calculated for a range of smaller molecular ions using the RPA method. It is demonstrated that the mean excitation energy of both molecules and atoms increase with ionic charge. However, while the mean excitation energies of atoms also increase with atomic number, the opposite is the case for mean excitation energies for molecules and molecular ions. The origin of these effects is explained by considering the spectral representation of the excited state contributing to the mean excitation energy.

  13. First-principles elastic constants of α- and θ-Al2O3

    NASA Astrophysics Data System (ADS)

    Shang, Shunli; Wang, Yi; Liu, Zi-Kui

    2007-03-01

    Using an efficient strain-stress method, the first-principles elastic constants cij's of α-Al2O3 and θ-Al2O3 have been predicted within the local density approximation and the generalized gradient approximation. It is indicated that more accurate calculations of cij's can be accomplished by the local density approximation. The predicted cij's of θ-Al2O3 provide helpful guidance for future measurements, especially the predicted negative c15. The present results make the stress estimation in thermally grown oxides containing of α- and θ-Al2O3 possible, which in turn provide helpful insights for preventing the failure of thermal barrier coatings on components in gas-turbine engines.

  14. Effect of molecular conformations on the electronic transport in oxygen-substituted alkanethiol molecular junctions

    NASA Astrophysics Data System (ADS)

    Wang, Minglang; Wang, Hao; Zhang, Guangping; Wang, Yongfeng; Sanvito, Stefano; Hou, Shimin

    2018-05-01

    The relationship between the molecular structure and the electronic transport properties of molecular junctions based on thiol-terminated oligoethers, which are obtained by replacing every third methylene unit in the corresponding alkanethiols with an oxygen atom, is investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that the low-bias conductance depends strongly on the conformation of the oligoethers in the junction. Specifically, in the cases of trans-extended conformation, the oxygen-dominated transmission peaks are very sharp and well below the Fermi energy, EF, thus hardly affect the transmission around EF; the Au-S interface hybrid states couple with σ-bonds in the molecular backbone forming the conduction channel at EF, resulting in a conductance decay against the molecular length close to that for alkanethiols. By contrast, for junctions with oligoethers in helical conformations, some π-type oxygen orbitals coupling with the Au-S interface hybrid states contribute to the transmission around EF. The molecule-electrode electronic coupling is also enhanced at the non-thiol side due to the specific spatial orientation introduced by the twist of the molecular backbone. This leads to a much smaller conductance decay constant. Our findings highlight the important role of the molecular conformation of oligoethers in their electronic transport properties and are also helpful for the design of molecular wires with heteroatom-substituted alkanethiols.

  15. Gravitational lensing limits on the cosmological constant in a flat universe

    NASA Technical Reports Server (NTRS)

    Turner, Edwin L.

    1990-01-01

    Inflationary cosmological theories predict, and some more general aesthetic criteria suggest, that the large-scale spatial curvature of the universe k should be accurately zero (i.e., flat), a condition which is satisfied when the universe's present mean density and the value of the cosmological constant Lambda have certain pairs of values. Available data on the frequency of multiple image-lensing of high-redshift quasars by galaxies suggest that the cosmological constant cannot make a dominant contribution to producing a flat universe. In particular, if the mean density of the universe is as small as the baryon density inferred from standard cosmic nucleosynthesis calculations or as determined from typical dynamical studies of galaxies and galaxy clusters, then a value of Lambda large enough to produce a k = 0 universe would result in a substantially higher frequency of multiple-image lensing of quasars than has been observed so far. Shortcomings of the available lens data and uncertainties concerning galaxy properties allow some possibility of escaping this conclusion, but systematic searches for a gravitational lenses and continuing investigations of galaxy mass distributions should soon provide decisive information. It is also noted that nonzero-curvature cosmological models can account for the observed frequency of galaxy-quasar lens systems and for a variety of other constraints.

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

    PubMed

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

    2011-10-14

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

  17. Primary gas thermometry by means of laser-absorption spectroscopy: determination of the Boltzmann constant.

    PubMed

    Casa, G; Castrillo, A; Galzerano, G; Wehr, R; Merlone, A; Di Serafino, D; Laporta, P; Gianfrani, L

    2008-05-23

    We report on a new optical implementation of primary gas thermometry based on laser-absorption spectrometry in the near infrared. The method consists in retrieving the Doppler broadening from highly accurate observations of the line shape of the R(12) nu1+2nu2(0)+nu3 transition in CO2 gas at thermodynamic equilibrium. Doppler width measurements as a function of gas temperature, ranging between the triple point of water and the gallium melting point, allowed for a spectroscopic determination of the Boltzmann constant with a relative accuracy of approximately 1.6 x 10(-4).

  18. Primary Gas Thermometry by Means of Laser-Absorption Spectroscopy: Determination of the Boltzmann Constant

    NASA Astrophysics Data System (ADS)

    Casa, G.; Castrillo, A.; Galzerano, G.; Wehr, R.; Merlone, A.; di Serafino, D.; Laporta, P.; Gianfrani, L.

    2008-05-01

    We report on a new optical implementation of primary gas thermometry based on laser-absorption spectrometry in the near infrared. The method consists in retrieving the Doppler broadening from highly accurate observations of the line shape of the R(12) ν1+2ν20+ν3 transition in CO2 gas at thermodynamic equilibrium. Doppler width measurements as a function of gas temperature, ranging between the triple point of water and the gallium melting point, allowed for a spectroscopic determination of the Boltzmann constant with a relative accuracy of ˜1.6×10-4.

  19. Diffusion-controlled interface kinetics-inclusive system-theoretic propagation models for molecular communication systems

    NASA Astrophysics Data System (ADS)

    Chude-Okonkwo, Uche A. K.; Malekian, Reza; Maharaj, B. T.

    2015-12-01

    Inspired by biological systems, molecular communication has been proposed as a new communication paradigm that uses biochemical signals to transfer information from one nano device to another over a short distance. The biochemical nature of the information transfer process implies that for molecular communication purposes, the development of molecular channel models should take into consideration diffusion phenomenon as well as the physical/biochemical kinetic possibilities of the process. The physical and biochemical kinetics arise at the interfaces between the diffusion channel and the transmitter/receiver units. These interfaces are herein termed molecular antennas. In this paper, we present the deterministic propagation model of the molecular communication between an immobilized nanotransmitter and nanoreceiver, where the emission and reception kinetics are taken into consideration. Specifically, we derived closed-form system-theoretic models and expressions for configurations that represent different communication systems based on the type of molecular antennas used. The antennas considered are the nanopores at the transmitter and the surface receptor proteins/enzymes at the receiver. The developed models are simulated to show the influence of parameters such as the receiver radius, surface receptor protein/enzyme concentration, and various reaction rate constants. Results show that the effective receiver surface area and the rate constants are important to the system's output performance. Assuming high rate of catalysis, the analysis of the frequency behavior of the developed propagation channels in the form of transfer functions shows significant difference introduce by the inclusion of the molecular antennas into the diffusion-only model. It is also shown that for t > > 0 and with the information molecules' concentration greater than the Michaelis-Menten kinetic constant of the systems, the inclusion of surface receptors proteins and enzymes in the models

  20. 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

  1. Constants for mercury binding by organic matter isolates from the Florida Everglades

    USGS Publications Warehouse

    Benoit, J.M.; Mason, R.P.; Gilmour, C.C.; Aiken, G.R.

    2001-01-01

    Dissolved organic matter (DOM) has been implicated as an important complexing agent for Hg that can affect its mobility and bioavailability in aquatic ecosystems. However, binding constants for natural Hg-DOM complexes are not well known. We employed a competitive ligand approach to estimate conditional stability constants for Hg complexes with DOM isolates collected from Florida Everglades surface waters. The isolates examined were the hydrophobic fraction of DOM from a eutrophic, sulfidic site (F1-HPoA) and the hydrophilic fraction from an oligotrophic, low-sulfide site (2BS-HPiA). Our experimental determinations utilized overall octanol-water partitioning coefficients (Dow) for 203Hg at 0.01 M chloride and across pH and DOM concentration gradients. Use of this radioisotope allowed rapid determinations of Hg concentrations in both water and octanol phases without problems of matrix interference. Conditional stability constants (1 = 0.06, 23??C) were log K??? = 11.8 for F1-HPoA and log K' = 10.6 for 2BS-HPiA. These are similar to previously published stability constants for Hg binding to low-molecular-weight thiols. Further, F1-HPoA showed a pH-dependent decline in Dow that was consistent with models of Hg complexation with thiol groups as the dominant Hg binding sites in DOM. These experiments demonstrate that the DOM isolates are stronger ligands for Hg than chloride ion or ethylenediamine-tetraacetic acid. Speciation calculations indicate that at the DOM concentrations frequently measured in Everglades, 20 to 40 ??M, significant complexation of Hg by DOM would be expected in aerobic (sulfide-free) surface waters. Copyright ?? 2001 Elsevier Science Ltd.

  2. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

    PubMed Central

    Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

    2012-01-01

    It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

  3. 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.

  4. Diffusion and binding constants for acetylcholine derived from the falling phase of miniature endplate currents.

    PubMed Central

    Land, B R; Harris, W V; Salpeter, E E; Salpeter, M M

    1984-01-01

    In previous papers we studied the rising phase of a miniature endplate current (MEPC) to derive diffusion and forward rate constants controlling acetylcholine (AcCho) in the intact neuromuscular junction. The present study derives similar values (but with smaller error ranges) for these constants by including experimental results from the falling phase of the MEPC. We find diffusion to be 4 X 10(-6) cm2 s-1, slightly slower than free diffusion, forward binding to be 3.3 X 10(7) M-1 s-1, and the distance from an average release site to the nearest exit from the cleft to be 1.6 micron. We also estimate the back reaction rates. From our values we can accurately describe the shape of MEPCs under different conditions of receptor and esterase concentration. Since we suggest that unbinding is slower than isomerization, we further predict that there should be several short "closing flickers" during the total open time for an AcCho-ligated receptor channel. PMID:6584895

  5. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

    PubMed Central

    2017-01-01

    Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. PMID:28637852

  6. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

    PubMed

    Warnock, Rachel C M; Yang, Ziheng; Donoghue, Philip C J

    2017-06-28

    Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. © 2017 The Authors.

  7. High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

    PubMed Central

    Chen, Alan A.; García, Angel E.

    2013-01-01

    We report the de novo folding of three hyperstable RNA tetraloops to 1–3 Å rmsd from their experimentally determined structures using molecular dynamics simulations initialized in the unfolded state. RNA tetraloops with loop sequences UUCG, GCAA, or CUUG are hyperstable because of the formation of noncanonical loop-stabilizing interactions, and they are all faithfully reproduced to angstrom-level accuracy in replica exchange molecular dynamics simulations, including explicit solvent and ion molecules. This accuracy is accomplished using unique RNA parameters, in which biases that favor rigid, highly stacked conformations are corrected to accurately capture the inherent flexibility of ssRNA loops, accurate base stacking energetics, and purine syn-anti interconversions. In a departure from traditional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated directly from thermodynamic and kinetic measurements of intra- and internucleotide structural transitions. The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations. PMID:24043821

  8. Fast, accurate, and reliable molecular docking with QuickVina 2.

    PubMed

    Alhossary, Amr; Handoko, Stephanus Daniel; Mu, Yuguang; Kwoh, Chee-Keong

    2015-07-01

    The need for efficient molecular docking tools for high-throughput screening is growing alongside the rapid growth of drug-fragment databases. AutoDock Vina ('Vina') is a widely used docking tool with parallelization for speed. QuickVina ('QVina 1') then further enhanced the speed via a heuristics, requiring high exhaustiveness. With low exhaustiveness, its accuracy was compromised. We present in this article the latest version of QuickVina ('QVina 2') that inherits both the speed of QVina 1 and the reliability of the original Vina. We tested the efficacy of QVina 2 on the core set of PDBbind 2014. With the default exhaustiveness level of Vina (i.e. 8), a maximum of 20.49-fold and an average of 2.30-fold acceleration with a correlation coefficient of 0.967 for the first mode and 0.911 for the sum of all modes were attained over the original Vina. A tendency for higher acceleration with increased number of rotatable bonds as the design variables was observed. On the accuracy, Vina wins over QVina 2 on 30% of the data with average energy difference of only 0.58 kcal/mol. On the same dataset, GOLD produced RMSD smaller than 2 Å on 56.9% of the data while QVina 2 attained 63.1%. The C++ source code of QVina 2 is available at (www.qvina.org). aalhossary@pmail.ntu.edu.sg Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. Using molecular recognition of beta-cyclodextrin to determine molecular weights of low-molecular-weight explosives by MALDI-TOF mass spectrometry.

    PubMed

    Zhang, Min; Shi, Zhen; Bai, Yinjuan; Gao, Yong; Hu, Rongzu; Zhao, Fenqi

    2006-02-01

    This study presents a novel method for determining the molecular weights of low molecular weight (MW) energetic compounds through their complexes of beta-cyclodextrin (beta-CD) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in a mass range of 500 to 1700 Da, avoiding matrix interference. The MWs of one composite explosive composed of 2,6-DNT, TNT, and RDX, one propellant with unknown components, and 14 single-compound explosives (RDX, HMX, 3,4-DNT, 2,6-DNT, 2,5-DNT, 2,4,6-TNT, TNAZ, DNI, BTTN, NG, TO, NTO, NP, and 662) were measured. The molecular recognition and inclusion behavior of beta-CD to energetic materials (EMs) were investigated. The results show that (1) the established method is sensitive, simple, accurate, and suitable for determining the MWs of low-MW single-compound explosives and energetic components in composite explosives and propellants; and (2) beta-CD has good inclusion and modular recognition abilities to the above EMs.

  10. Molecular dynamics simulations to study the solvent influence on protein structure

    NASA Astrophysics Data System (ADS)

    Dominguez, Hector

    2016-05-01

    Molecular simulations were carried out to study the influence of different water models in two protein systems. Most of the solvents used in protein simulations, e.g., SPC/E or TIP3P, fail to reproduce the bulk water static dielectric constant. Recently a new water model, TIP4P/ɛ, which reproduces the experimental dielectric constant was reported. Therefore, simulations for two different proteins, Lysozyme and Ubiquitin with SPC/E, TIP3P and TIP4P/ɛ solvents were carried out. Dielectric constants and structural properties were calculated and comparisons were conducted. The structural properties between the three models are very similar, however, the dielectric constants are different in each case.

  11. Base de linhas moleculares para síntese espectral estelar

    NASA Astrophysics Data System (ADS)

    Milone, A.; Sanzovo, G.

    2003-08-01

    A análise das abundâncias quí micas fotosféricas em estrelas do tipo solar ou tardia, através do cálculo teórico de seus espectros, emprega a espectroscopia de alta resolução e necessita de uma base representativa de linhas atômicas e moleculares com suas respectivas constantes bem determinadas. Nesse trabalho, utilizamos como ponto de partida as extensas listas de linhas espectrais de sistemas eletrônicos de algumas moléculas diatômicas compiladas por Kurucz para a construção de uma base de linhas moleculares para a sí ntese espectral estelar. Revisamos as determinações dos fatores rotacionais de Honl-London das forças de oscilador das linhas moleculares, para cada banda vibracional de alguns sistemas eletrônicos, seguindo a regra usual de normalização. Usamos as forças de oscilador eletrônicas da literatura. Os fatores vibracionais de Franck-Condon de cada banda foram especialmente recalculados empregando-se novas constantes moleculares. Reproduzimos, com êxito, as absorções espectrais de determinadas bandas eletrônicas-vibracionais das espécies moleculares C12C12, C12N14 e Mg24H em espectros de estrelas de referência como o Sol e Arcturus.

  12. Molecular hydrodynamics: Vortex formation and sound wave propagation

    DOE PAGES

    Han, Kyeong Hwan; Kim, Changho; Talkner, Peter; ...

    2018-01-14

    In the present study, quantitative feasibility tests of the hydrodynamic description of a two-dimensional fluid at the molecular level are performed, both with respect to length and time scales. Using high-resolution fluid velocity data obtained from extensive molecular dynamics simulations, we computed the transverse and longitudinal components of the velocity field by the Helmholtz decomposition and compared them with those obtained from the linearized Navier-Stokes (LNS) equations with time-dependent transport coefficients. By investigating the vortex dynamics and the sound wave propagation in terms of these field components, we confirm the validity of the LNS description for times comparable to ormore » larger than several mean collision times. The LNS description still reproduces the transverse velocity field accurately at smaller times, but it fails to predict characteristic patterns of molecular origin visible in the longitudinal velocity field. Based on these observations, we validate the main assumptions of the mode-coupling approach. The assumption that the velocity autocorrelation function can be expressed in terms of the fluid velocity field and the tagged particle distribution is found to be remarkably accurate even for times comparable to or smaller than the mean collision time. This suggests that the hydrodynamic-mode description remains valid down to the molecular scale.« less

  13. Molecular hydrodynamics: Vortex formation and sound wave propagation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Han, Kyeong Hwan; Kim, Changho; Talkner, Peter

    In the present study, quantitative feasibility tests of the hydrodynamic description of a two-dimensional fluid at the molecular level are performed, both with respect to length and time scales. Using high-resolution fluid velocity data obtained from extensive molecular dynamics simulations, we computed the transverse and longitudinal components of the velocity field by the Helmholtz decomposition and compared them with those obtained from the linearized Navier-Stokes (LNS) equations with time-dependent transport coefficients. By investigating the vortex dynamics and the sound wave propagation in terms of these field components, we confirm the validity of the LNS description for times comparable to ormore » larger than several mean collision times. The LNS description still reproduces the transverse velocity field accurately at smaller times, but it fails to predict characteristic patterns of molecular origin visible in the longitudinal velocity field. Based on these observations, we validate the main assumptions of the mode-coupling approach. The assumption that the velocity autocorrelation function can be expressed in terms of the fluid velocity field and the tagged particle distribution is found to be remarkably accurate even for times comparable to or smaller than the mean collision time. This suggests that the hydrodynamic-mode description remains valid down to the molecular scale.« less

  14. Universe of constant

    NASA Astrophysics Data System (ADS)

    Yongquan, Han

    2016-10-01

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

  15. Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties

    NASA Technical Reports Server (NTRS)

    Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

    1992-01-01

    The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.

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

    PubMed

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

    2015-03-01

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

  17. Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.

    Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less

  18. Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics

    DOE PAGES

    Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.; ...

    2015-04-21

    Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less

  19. Numerical determination of visible/NIR optical constants from laboratory spectra of HED meteorites

    NASA Astrophysics Data System (ADS)

    Davalos, Jorge A. G.; Carvano, Jorge Márcio; Blanco, Julio

    2017-03-01

    Radiative transfer models in particulate media (Hapke, 1981, 1993, 2012b; Shkuratov et al., 1999) are the most versatile tool that can be used to retrieve both composition and surface physical properties from observation of asteroids and other atmosphereless bodies of the Solar System. One caveat is that these methods require as input a sufficiently comprehensive set of optical constants of suitable template materials. These optical constants are the real and imaginary parts of the refractive indexes of the material as function of wavelength, and have to be derived from laboratory measurements of samples of minerals and meteorites. Optical constants can be calculated from a variety of types of measurements, and each has its problems and limitations. In particular, a problem with the determination of optical constants from measurement of reflectance is that the measurements need to be themselves interpreted using radiative transfer models. This is an issue because the number of parameters used in the most accurate versions of the radiative transfer models is large, and for most of the samples many of these parameters were not measured independently. As a result, attempts in the literature to retrieve optical constants from reflectance measurements tend to assume values for the unknown parameters, which can lead to uncertainties in the retrieved optical constants that can be difficult to quantify. In this work we propose a numerical method that allows the simultaneous inversion of the optical constant and the model parameters. This model is then applied to a set of reflectance spectra of 5 HED meteorites from the RELAB database that were measured with the same setup for samples with several particle size intervals. Our results indicate that our method is able to retrieve optical constants which are able to reproduce the measured reflectance of the samples over a large range (25-500 μm) of particle diameters. It is also found that the solutions obtained in this way

  20. Larson-Miller Constant of Heat-Resistant Steel

    NASA Astrophysics Data System (ADS)

    Tamura, Manabu; Abe, Fujio; Shiba, Kiyoyuki; Sakasegawa, Hideo; Tanigawa, Hiroyasu

    2013-06-01

    Long-term rupture data for 79 types of heat-resistant steels including carbon steel, low-alloy steel, high-alloy steel, austenitic stainless steel, and superalloy were analyzed, and a constant for the Larson-Miller (LM) parameter was obtained in the current study for each material. The calculated LM constant, C, is approximately 20 for heat-resistant steels and alloys except for high-alloy martensitic steels with high creep resistance, for which C ≈ 30 . The apparent activation energy was also calculated, and the LM constant was found to be proportional to the apparent activation energy with a high correlation coefficient, which suggests that the LM constant is a material constant possessing intrinsic physical meaning. The contribution of the entropy change to the LM constant is not small, especially for several martensitic steels with large values of C. Deformation of such martensitic steels should accompany a large entropy change of 10 times the gas constant at least, besides the entropy change due to self-diffusion.

  1. On the accurate long-time solution of the wave equation in exterior domains: Asymptotic expansions and corrected boundary conditions

    NASA Technical Reports Server (NTRS)

    Hagstrom, Thomas; Hariharan, S. I.; Maccamy, R. C.

    1993-01-01

    We consider the solution of scattering problems for the wave equation using approximate boundary conditions at artificial boundaries. These conditions are explicitly viewed as approximations to an exact boundary condition satisfied by the solution on the unbounded domain. We study the short and long term behavior of the error. It is provided that, in two space dimensions, no local in time, constant coefficient boundary operator can lead to accurate results uniformly in time for the class of problems we consider. A variable coefficient operator is developed which attains better accuracy (uniformly in time) than is possible with constant coefficient approximations. The theory is illustrated by numerical examples. We also analyze the proposed boundary conditions using energy methods, leading to asymptotically correct error bounds.

  2. Role of Molecular Profiling in Soft Tissue Sarcoma.

    PubMed

    Lindsay, Timothy; Movva, Sujana

    2018-05-01

    Diagnosis and treatment of soft tissue sarcoma (STS) is a particularly daunting task, largely due to the profound heterogeneity that characterizes these malignancies. Molecular profiling has emerged as a useful tool to confirm histologic diagnoses and more accurately classify these malignancies. Recent large-scale, multiplatform analyses have begun the work of establishing a more complete understanding of molecular profiling in STS subtypes and to identify new molecular alterations that may guide the development of novel targeted therapies. This review provides a brief and general overview of the role that molecular profiling has in STS, highlighting select sarcoma subtypes that are notable for recent developments. The role of molecular profiling as it relates to diagnostic strategies is discussed, along with ways that molecular profiling may provide guidance for potential therapeutic interventions. Copyright © 2018 by the National Comprehensive Cancer Network.

  3. Value and Methods for Molecular Subtyping of Bacteria

    NASA Astrophysics Data System (ADS)

    Moorman, Mark; Pruett, Payton; Weidman, Martin

    Tracking sources of microbial contaminants has been a concern since the early days of commercial food processing; however, recent advances in the development of molecular subtyping methods have provided tools that allow more rapid and highly accurate determinations of these sources. Only individuals with an understanding of the molecular subtyping methods, and the epidemiological techniques used, can evaluate the reliability of a link between a food-manufacturing plant, a food, and a foodborne disease outbreak.

  4. Evaluation of kinetic constants of biomolecular interaction on optical surface plasmon resonance sensor with Newton Iteration Method

    NASA Astrophysics Data System (ADS)

    Zhao, Yuanyuan; Jiang, Guoliang; Hu, Jiandong; Hu, Fengjiang; Wei, Jianguang; Shi, Liang

    2010-10-01

    In the immunology, there are two important types of biomolecular interaction: antigens-antibodies and receptors-ligands. Monitoring the response rate and affinity of biomolecular interaction can help analyze the protein function, drug discover, genomics and proteomics research. Moreover the association rate constant and dissociation rate constant of receptors-ligands are the important parameters for the study of signal transmission between cells. Recent advances in bioanalyzer instruments have greatly simplified the measurement of the kinetics of molecular interactions. Non-destructive and real-time monitoring the response to evaluate the parameters between antigens and antibodies can be performed by using optical surface plasmon resonance (SPR) biosensor technology. This technology provides a quantitative analysis that is carried out rapidly with label-free high-throughput detection using the binding curves of antigens-antibodies. Consequently, the kinetic parameters of interaction between antigens and antibodies can be obtained. This article presents a low cost integrated SPR-based bioanalyzer (HPSPR-6000) designed by ourselves. This bioanalyzer is mainly composed of a biosensor TSPR1K23, a touch-screen monitor, a microprocessor PIC24F128, a microflow cell with three channels, a clamp and a photoelectric conversion device. To obtain the kinetic parameters, sensorgrams may be modeled using one of several binding models provided with BIAevaluation software 3.0, SensiQ or Autolab. This allows calculation of the association rate constant (ka) and the dissociation rate constant (kd). The ratio of ka to kd can be used to estimate the equilibrium constant. Another kind is the analysis software OriginPro, which can process the obtained data by nonlinear fitting and then get some correlative parameters, but it can't be embedded into the bioanalyzer, so the bioanalyzer don't support the use of OriginPro. This paper proposes a novel method to evaluate the kinetic parameters

  5. Constant potential pulse polarography

    USGS Publications Warehouse

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

    1976-01-01

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

  6. Theoretical study of the reaction mechanism and kinetics of low-molecular-weight atmospheric aldehydes (C1-C4) with NO2

    NASA Astrophysics Data System (ADS)

    Ji, Yuemeng; Gao, Yanpeng; Li, Guiying; An, Taicheng

    2012-07-01

    Accurate description of atmospheric reactions of a series of low-molecular-weight (LMW) aldehydes (C1-C4) with NO2 has been modeled using a direct dynamic approach. The profiles of the potential energy surface were constructed at the BMC-CCSD//MPWB1K/6-311G(d,p) level of theory, and two different pathways have been found: H-abstraction and NO2-addition. The modeling results found that the contribution of NO2-addition reaction pathway to the total rate constant is very small and thus this kind of pathway is insignificant in atmospheric conditions. The predicted H-abstraction products are mainly reactive acyl radical and nitrous acid (HONO) which is very mutagenic and carcinogenic pollutant as well as the precursor of acid deposition. The rate constants of both pathways were also deduced by using canonical variational transition state theory incorporating with the small curvature tunneling correction within 200-360 and 360-2000 K. Theoretical overall rate constants are in good agreement with the available experimental values, whose increase in the order of kformaldehyde < kacetaldehyde < kpropanal < kbutanal, implying that relative long-chain LMW aldehydes are more reactive toward NO2 than those short-chain LMW aldehydes in the atmospheric condition. At 298 K, the total rate constants of LMW aldehydes (C1-C4) with NO2 are obtained as 1.65 × 10-25, 1.43 × 10-24, 3.39 × 10-24 and 1.83 × 10-23 cm3 molecule-1 s-1, respectively.

  7. Persimmon breeding in Japan for pollination-constant non-astringent (PCNA) type with marker-assisted selection

    PubMed Central

    Sato, Akihiko; Yamada, Masahiko

    2016-01-01

    Oriental persimmon (Diospyros kaki) originated in Eastern Asia, and many indigenous cultivars have been developed in China, Japan, and Korea. These cultivars are classified into four groups based on their natural astringency loss on the tree and seed formation: pollination-constant non-astringent (PCNA), pollination-variant non-astringent (PVNA), pollination-constant astringent (PCA), and pollination-variant astringent (PVA). PCNA is the most desirable type because the fruit can be eaten without any postharvest treatment; therefore, one of the goals of our persimmon breeding programs is to release superior PCNA cultivars. The PCNA genotype is recessive to the other three non-PCNA genotypes, and PCNA-type F1 offspring are obtained exclusively from crosses among PCNA genotypes. Moreover, the number of superior PCNA cross-parents have been limited. In the late 1980s, inbreeding depression became obvious, especially in terms of fruit size, tree vigor, and productivity. To mitigate the inbreeding, a backcross program using PCNA [(non-PCNA × PCNA) × PCNA] was started in 1990. This process, however, was inefficient because only 15% of the offspring were PCNA, and all offspring had to be grown to the fruiting stage. Therefore, molecular markers linked to the PCNA locus were developed for discriminating PCNA offspring. A molecular marker linked to Chinese PCNA has also been developed. PMID:27069391

  8. Constant-roll tachyon inflation and observational constraints

    NASA Astrophysics Data System (ADS)

    Gao, Qing; Gong, Yungui; Fei, Qin

    2018-05-01

    For the constant-roll tachyon inflation, we derive the analytical expressions for the scalar and tensor power spectra, the scalar and tensor spectral tilts and the tensor to scalar ratio to the first order of epsilon1 by using the method of Bessel function approximation. The derived ns-r results are compared with the observations, we find that only the constant-roll inflation with ηH being a constant is consistent with the observations and observations constrain the constant-roll inflation to be slow-roll inflation. The tachyon potential is also reconstructed for the constant-roll inflation which is consistent with the observations.

  9. Elastic constants and pressure derivative of elastic constants of Si1-xGex solid solution

    NASA Astrophysics Data System (ADS)

    Jivani, A. R.; Baria, J. K.; Vyas, P. S.; Jani, A. R.

    2013-02-01

    Elastic properties of Si1-xGex solid solution with arbitrary (atomic) concentration (x) are studied using the pseudo-alloy atom model based on the pseudopotential theory and on the higher-order perturbation scheme with the application of our own proposed model potential. We have used local-field correction function proposed by Sarkar et al to study Si-Ge system. The Elastic constants and pressure derivatives of elastic constants of the solid solution is investigated with different concentration x of Ge. It is found in the present study that the calculated numerical values of the aforesaid physical properties of Si-Ge system are function of x. The elastic constants (C11, C12 and C44) decrease linearly with increase in concentration x and pressure derivative of elastic constants (C11, C12 and C44) increase with the concentration x of Ge. This study provides better set of theoretical results for such solid solution for further comparison either with theoretical or experimental results.

  10. Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

    ERIC Educational Resources Information Center

    Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

    2016-01-01

    Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

  11. Present status of astronomical constants

    NASA Astrophysics Data System (ADS)

    Fukushima, T.

    Given was the additional information to the previous report on the recent progress in the determinations of astronomical constants (Fukushima 2000). First noted was the revision of LG as 6.969290134×10-10 based on the proposal to shift its status from a primary to a defining constant (Petit 2000). Next focused was the significant update of the correction to the current precession constant, Δp, based on the recent LLR-based determination (Chapront et al. 2000) as -0.3164+/-0.0030"/cy. By combining this and the equal weighted average of VLBI determinations (Mathews et al. 2000; Petrov 2000; Shirai and Fukushima 2000; Vondrak and Ron 2000) as -0.2968+/-0.0043"/cy, we derived the best estimate of precession constant as p = 5028.790+/-0.005"/cy. Also redetermined were some other quantities related to the precession formula; namely the offsets of Celestial Ephemeris Pole of the International Celestial Reference System as &Deltaψ0sinɛ0 = (-17.0+/-0.3) mas and Δɛ0 = (-5.1+/-0.3) mas. As a result, the obliquity of the ecliptic at the epoch J2000.0 was estimated as ɛ0 = 23°26'21."4059+/-0."0003. As a summary, presented was the (revised) IAU 2000 File of Current Best Estimates of astronomical constants, which is to replace the former 1994 version (Standish 1995).

  12. Accurate potentiometric determination of lipid membrane-water partition coefficients and apparent dissociation constants of ionizable drugs: electrostatic corrections.

    PubMed

    Elsayed, Mustafa M A; Vierl, Ulrich; Cevc, Gregor

    2009-06-01

    Potentiometric lipid membrane-water partition coefficient studies neglect electrostatic interactions to date; this leads to incorrect results. We herein show how to account properly for such interactions in potentiometric data analysis. We conducted potentiometric titration experiments to determine lipid membrane-water partition coefficients of four illustrative drugs, bupivacaine, diclofenac, ketoprofen and terbinafine. We then analyzed the results conventionally and with an improved analytical approach that considers Coulombic electrostatic interactions. The new analytical approach delivers robust partition coefficient values. In contrast, the conventional data analysis yields apparent partition coefficients of the ionized drug forms that depend on experimental conditions (mainly the lipid-drug ratio and the bulk ionic strength). This is due to changing electrostatic effects originating either from bound drug and/or lipid charges. A membrane comprising 10 mol-% mono-charged molecules in a 150 mM (monovalent) electrolyte solution yields results that differ by a factor of 4 from uncharged membranes results. Allowance for the Coulombic electrostatic interactions is a prerequisite for accurate and reliable determination of lipid membrane-water partition coefficients of ionizable drugs from potentiometric titration data. The same conclusion applies to all analytical methods involving drug binding to a surface.

  13. Graviton fluctuations erase the cosmological constant

    NASA Astrophysics Data System (ADS)

    Wetterich, C.

    2017-10-01

    Graviton fluctuations induce strong non-perturbative infrared renormalization effects for the cosmological constant. The functional renormalization flow drives a positive cosmological constant towards zero, solving the cosmological constant problem without the need to tune parameters. We propose a simple computation of the graviton contribution to the flow of the effective potential for scalar fields. Within variable gravity, with effective Planck mass proportional to the scalar field, we find that the potential increases asymptotically at most quadratically with the scalar field. The solutions of the derived cosmological equations lead to an asymptotically vanishing cosmological "constant" in the infinite future, providing for dynamical dark energy in the present cosmological epoch. Beyond a solution of the cosmological constant problem, our simplified computation also entails a sizeable positive graviton-induced anomalous dimension for the quartic Higgs coupling in the ultraviolet regime, substantiating the successful prediction of the Higgs boson mass within the asymptotic safety scenario for quantum gravity.

  14. Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Soudackov, Alexander; Hammes-Schiffer, Sharon

    2015-11-17

    Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency regimes for the proton donor-acceptor vibrational mode. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term does not significantly impact the rate constants derived using the cumulant expansion approachmore » in any of the regimes studied. The effects of the quadratic term may become significant when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant, however, particularly at high temperatures and for proton transfer interfaces with extremely soft proton donor-acceptor modes that are associated with extraordinarily weak hydrogen bonds. Even with the thermal averaging procedure, the effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances, and the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to proton transfer and proton-coupled electron transfer in chemical and biological processes. We are grateful for support from National Institutes of Health Grant GM056207 (applications to enzymes) and the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of

  15. Unmasking molecular profiles of bladder cancer.

    PubMed

    Piao, Xuan-Mei; Byun, Young Joon; Kim, Wun-Jae; Kim, Jayoung

    2018-03-01

    Precision medicine is designed to tailor treatments for individual patients by factoring in each person's specific biology and mechanism of disease. This paradigm shifted from a "one size fits all" approach to "personalized and precision care" requires multiple layers of molecular profiling of biomarkers for accurate diagnosis and prediction of treatment responses. Intensive studies are also being performed to understand the complex and dynamic molecular profiles of bladder cancer. These efforts involve looking bladder cancer mechanism at the multiple levels of the genome, epigenome, transcriptome, proteome, lipidome, metabolome etc. The aim of this short review is to outline the current technologies being used to investigate molecular profiles and discuss biomarker candidates that have been investigated as possible diagnostic and prognostic indicators of bladder cancer.

  16. Effects of Constant Flow vs. Constant Pressure Perfusion on Fluid Filtration in Severe Hypothermic Isolated Blood-Perfused Rat Lungs.

    PubMed

    Halsøy, Kathrine; Kondratiev, Timofey; Tveita, Torkjel; Bjertnaes, Lars J

    2016-01-01

    Victims of severe accidental hypothermia are prone to fluid extravasation but rarely develop lung edema. We hypothesize that combined hypothermia-induced increase in pulmonary vascular resistance (PVR) and a concomitant fall in cardiac output protect the lungs against edema development. Our aim was to explore in hypothermic-isolated blood-perfused rat lungs whether perfusion at constant pressure influences fluid filtration differently from perfusion at constant flow. Isolated blood-perfused rat lungs were hanging freely in a weight transducer for measuring weight changes (ΔW). Fluid filtration coefficient (Kfc), was determined by transiently elevating left atrial pressure (Pla) by 5.8 mmHg two times each during normothermia (37°C) and during hypothermia (15°C). The lung preparations were randomized to two groups. One group was perfused with constant flow (Constant flow group) and the other group with constant pulmonary artery pressure (Constant PPA group). Microvascular pressure (Pmv) was determined before and during elevation of Pla (ΔPmv) by means of the double occlusion technique. Kfc was calculated with the formula Kfc = ΔW/ΔPmv/min. All Kfc values were normalized to predicted lung weight (P LW ), which was based on body weight (BW) according to the formula: P LW  = 0.0053 BW - 0.48 and presented as Kfc PLW in mg/min/mmHg/g. At cessation, bronchoalveolar lavage (BAL) fluid/perfusate protein concentration (B/P) ratio was determined photometrically. Data were analyzed with parametric or non-parametric tests as appropriate. p  < 0.05 considered as significant. Perfusate flow remained constant in the Constant flow group, but was more than halved during hypothermia in the Constant PPA group concomitant with a more fold increase in PVR. In the Constant flow group, Kfc PLW and B/P ratio increased significantly by more than 10-fold during hypothermia concerted by visible signs of edema in the trachea. Hemoglobin and hematocrit increased within

  17. Molecular structure of liquid alcohols

    NASA Astrophysics Data System (ADS)

    Huyskens, P.

    1983-07-01

    A new thermodynamic treatment of continuous association is presented, where the various equilibria between i-mers are replaced by a single equilibrium between an OH groups in the bonded and the non-bonded states, linked in both cases to an indefinite ensemble of molecules. The treatment leads to an association constant K which differs from those considered in the theories of Kretschmer and Wiebe and of Wiehe and Bagley. For pure alcohols the association constant can be estimated from the vapor pressure of the alcohol and that of the homomorphous hydrocarbon. The fraction γ of free OH groups determined in this way is markedly smaller than those calculated from the other theories. For the normal alcohols the product K VA is approximately constant at a given temperature, VA being the molar volume. This can be expected from the increasing of the standard entropy of the non-bonded molecules when the molecular volume increases. For secondary and tertiary alcohols the product K VA is significantly lower due to steric hindrances. However for all the alcohols considered here the enthalpy of the hydrogen bond remains nearly constant — δ H being equal to 24.8 ± 2 kJ mol -1.

  18. CODATA recommended values of the fundamental constants

    NASA Astrophysics Data System (ADS)

    Mohr, Peter J.; Taylor, Barry N.

    2000-11-01

    A review is given of the latest Committee on Data for Science and Technology (CODATA) adjustment of the values of the fundamental constants. The new set of constants, referred to as the 1998 values, replaces the values recommended for international use by CODATA in 1986. The values of the constants, and particularly the Rydberg constant, are of relevance to the calculation of precise atomic spectra. The standard uncertainty (estimated standard deviation) of the new recommended value of the Rydberg constant, which is based on precision frequency metrology and a detailed analysis of the theory, is approximately 1/160 times the uncertainty of the 1986 value. The new set of recommended values as well as a searchable bibliographic database that gives citations to the relevant literature is available on the World Wide Web at physics.nist.gov/constants and physics.nist.gov/constantsbib, respectively. .

  19. The Henry's constant of monochloramine.

    PubMed

    Garcia, Miguel A; Anderson, Michael A

    2018-02-01

    Monochloramine is a secondary disinfectant used in drinking water and is also formed in chlorinated wastewater. While known to hydrolyze over time and react with dissolved organic matter, its partitioning between the aqueous and gas phase has not been extensively studied. Preliminary experiments demonstrated that monochloramine concentrations in solutions open to the atmosphere or actively aerated decreased more rapidly than in sealed solutions, indicating significant losses to the atmosphere. For example, a monochloramine solution open to the atmosphere yielded a loss rate constant of 0.08 d -1 , a value twice that for sealed samples without headspace (0.04 d -1 ) where loss occurs exclusively as a result of hydrolysis. A solution aerated at 10 mL s -1 had a loss rate constant nearly 10× greater than that for hydrolysis alone (0.35 d -1 ). To better understand partitioning of monochloramine to the gas phase and potential for volatilization, the dimensionless Henry's law constants of monochloramine (K H ) were determined using an equilibrium headspace technique at five different temperatures (11, 16, 21, 27, and 32 °C). The resulting values ranged from 8 × 10 -3 to 4 × 10 -2 , indicating a semi-volatile compound, and were found to be consistent with quantitative structure activity relationship predictions. At 20 °C, monochloramine exhibits a dimensionless Henry's constant of about 1.7 × 10 -2 which is 35 times greater than ammonia but comparable to the Henry's constant of inorganic semi-volatile compounds such sulfur dioxide. The Henry's constant values for monochloramine suggests that volatilization could be a relevant loss process in open systems such as rivers receiving chlorinated wastewater effluent, swimming pools and cooling towers. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Constant voltage electro-slag remelting control

    DOEpatents

    Schlienger, M.E.

    1996-10-22

    A system for controlling electrode gap in an electro-slag remelt furnace has a constant regulated voltage and an electrode which is fed into the slag pool at a constant rate. The impedance of the circuit through the slag pool is directly proportional to the gap distance. Because of the constant voltage, the system current changes are inversely proportional to changes in gap. This negative feedback causes the gap to remain stable. 1 fig.

  1. Constant voltage electro-slag remelting control

    DOEpatents

    Schlienger, Max E.

    1996-01-01

    A system for controlling electrode gap in an electro-slag remelt furnace has a constant regulated voltage and an eletrode which is fed into the slag pool at a constant rate. The impedance of the circuit through the slag pool is directly proportional to the gap distance. Because of the constant voltage, the system current changes are inversely proportional to changes in gap. This negative feedback causes the gap to remain stable.

  2. Full-order observer for direct torque control of induction motor based on constant V/F control technique.

    PubMed

    Pimkumwong, Narongrit; Wang, Ming-Shyan

    2018-02-01

    This paper presents another control method for the three-phase induction motor that is direct torque control based on constant voltage per frequency control technique. This method uses the magnitude of stator flux and torque errors to generate the stator voltage and phase angle references for controlling the induction motor by using constant voltage per frequency control method. Instead of hysteresis comparators and optimum switching table, the PI controllers and space vector modulation technique are used to reduce torque and stator-flux ripples and achieve constant switching frequency. Moreover, the coordinate transformations are not required. To implement this control method, a full-order observer is used to estimate stator flux and overcome the problems from drift and saturation in using pure integrator. The feedback gains are designed by simple manner to improve the convergence of stator flux estimation, especially in low speed range. Furthermore, the necessary conditions to maintain the stability for feedback gain design are introduced. The simulation and experimental results show accurate and stable operation of the introduced estimator and good dynamic response of the proposed control method. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  3. Delayed Shutters For Dual-Beam Molecular Epitaxy

    NASA Technical Reports Server (NTRS)

    Grunthaner, Frank J.; Liu, John L.; Hancock, Bruce

    1989-01-01

    System of shutters for dual-molecular-beam epitaxy apparatus delays start of one beam with respect to another. Used in pulsed-beam equipment for deposition of low-dislocation layers of InAs on GaAs substrates, system delays application of arsenic beam with respect to indium beam to assure proper stoichiometric proportions on newly forming InAs surface. Reflectance high-energy electron diffraction (RHEED) instrument used to monitor condition of evolving surface of deposit. RHEED signal used to time pulsing of molecular beams in way that minimizes density of defects and holds lattice constant of InAs to that of GaAs substrate.

  4. Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment

    PubMed Central

    Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L.; Yao, Xuebiao

    2015-01-01

    The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C–MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression. PMID:26240331

  5. Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment.

    PubMed

    Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L; Yao, Xuebiao

    2015-08-18

    The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C-MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression.

  6. New perspectives on constant-roll inflation

    NASA Astrophysics Data System (ADS)

    Cicciarella, Francesco; Mabillard, Joel; Pieroni, Mauro

    2018-01-01

    We study constant-roll inflation using the β-function formalism. We show that the constant rate of the inflaton roll is translated into a first order differential equation for the β-function which can be solved easily. The solutions to this equation correspond to the usual constant-roll models. We then construct, by perturbing these exact solutions, more general classes of models that satisfy the constant-roll equation asymptotically. In the case of an asymptotic power law solution, these corrections naturally provide an end to the inflationary phase. Interestingly, while from a theoretical point of view (in particular in terms of the holographic interpretation) these models are intrinsically different from standard slow-roll inflation, they may have phenomenological predictions in good agreement with present cosmological data.

  7. Constant speed control of four-stroke micro internal combustion swing engine

    NASA Astrophysics Data System (ADS)

    Gao, Dedong; Lei, Yong; Zhu, Honghai; Ni, Jun

    2015-09-01

    The increasing demands on safety, emission and fuel consumption require more accurate control models of micro internal combustion swing engine (MICSE). The objective of this paper is to investigate the constant speed control models of four-stroke MICSE. The operation principle of the four-stroke MICSE is presented based on the description of MICSE prototype. A two-level Petri net based hybrid model is proposed to model the four-stroke MICSE engine cycle. The Petri net subsystem at the upper level controls and synchronizes the four Petri net subsystems at the lower level. The continuous sub-models, including breathing dynamics of intake manifold, thermodynamics of the chamber and dynamics of the torque generation, are investigated and integrated with the discrete model in MATLAB Simulink. Through the comparison of experimental data and simulated DC voltage output, it is demonstrated that the hybrid model is valid for the four-stroke MICSE system. A nonlinear model is obtained from the cycle average data via the regression method, and it is linearized around a given nominal equilibrium point for the controller design. The feedback controller of the spark timing and valve duration timing is designed with a sequential loop closing design approach. The simulation of the sequential loop closure control design applied to the hybrid model is implemented in MATLAB. The simulation results show that the system is able to reach its desired operating point within 0.2 s, and the designed controller shows good MICSE engine performance with a constant speed. This paper presents the constant speed control models of four-stroke MICSE and carries out the simulation tests, the models and the simulation results can be used for further study on the precision control of four-stroke MICSE.

  8. Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields

    NASA Astrophysics Data System (ADS)

    Steffen, Julien; Hartke, Bernd

    2017-10-01

    Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.

  9. Accurate Binding Free Energy Predictions in Fragment Optimization.

    PubMed

    Steinbrecher, Thomas B; Dahlgren, Markus; Cappel, Daniel; Lin, Teng; Wang, Lingle; Krilov, Goran; Abel, Robert; Friesner, Richard; Sherman, Woody

    2015-11-23

    Predicting protein-ligand binding free energies is a central aim of computational structure-based drug design (SBDD)--improved accuracy in binding free energy predictions could significantly reduce costs and accelerate project timelines in lead discovery and optimization. The recent development and validation of advanced free energy calculation methods represents a major step toward this goal. Accurately predicting the relative binding free energy changes of modifications to ligands is especially valuable in the field of fragment-based drug design, since fragment screens tend to deliver initial hits of low binding affinity that require multiple rounds of synthesis to gain the requisite potency for a project. In this study, we show that a free energy perturbation protocol, FEP+, which was previously validated on drug-like lead compounds, is suitable for the calculation of relative binding strengths of fragment-sized compounds as well. We study several pharmaceutically relevant targets with a total of more than 90 fragments and find that the FEP+ methodology, which uses explicit solvent molecular dynamics and physics-based scoring with no parameters adjusted, can accurately predict relative fragment binding affinities. The calculations afford R(2)-values on average greater than 0.5 compared to experimental data and RMS errors of ca. 1.1 kcal/mol overall, demonstrating significant improvements over the docking and MM-GBSA methods tested in this work and indicating that FEP+ has the requisite predictive power to impact fragment-based affinity optimization projects.

  10. A molecular signaling model of platelet phosphoinositide and calcium regulation during homeostasis and P2Y1 activation.

    PubMed

    Purvis, Jeremy E; Chatterjee, Manash S; Brass, Lawrence F; Diamond, Scott L

    2008-11-15

    To quantify how various molecular mechanisms are integrated to maintain platelet homeostasis and allow responsiveness to adenosine diphosphate (ADP), we developed a computational model of the human platelet. Existing kinetic information for 77 reactions, 132 fixed kinetic rate constants, and 70 species was combined with electrochemical calculations, measurements of platelet ultrastructure, novel experimental results, and published single-cell data. The model accurately predicted: (1) steady-state resting concentrations for intracellular calcium, inositol 1,4,5-trisphosphate, diacylglycerol, phosphatidic acid, phosphatidylinositol, phosphatidylinositol phosphate, and phosphatidylinositol 4,5-bisphosphate; (2) transient increases in intracellular calcium, inositol 1,4,5-trisphosphate, and G(q)-GTP in response to ADP; and (3) the volume of the platelet dense tubular system. A more stringent test of the model involved stochastic simulation of individual platelets, which display an asynchronous calcium spiking behavior in response to ADP. Simulations accurately reproduced the broad frequency distribution of measured spiking events and demonstrated that asynchronous spiking was a consequence of stochastic fluctuations resulting from the small volume of the platelet. The model also provided insights into possible mechanisms of negative-feedback signaling, the relative potency of platelet agonists, and cell-to-cell variation across platelet populations. This integrative approach to platelet biology offers a novel and complementary strategy to traditional reductionist methods.

  11. An accurate estimation method of kinematic viscosity for standard viscosity liquids

    NASA Astrophysics Data System (ADS)

    Kurano, Y.; Kobayashi, H.; Yoshida, K.; Imai, H.

    1992-07-01

    Deming's method of least squares is introduced to make an accurate kinematic viscosity estimation for a series of 13 standard-viscosity liquids at any desired temperature. The empirical ASTM kinematic viscosity-temperature equation is represented in the form loglog( v+c)=a-b log T, where v (in mm2. s-1) is the kinematic viscosity at temperature T (in K), a and b are the constants for a given liquid, and c has a variable value. In the present application, however, c is assumed to have a constant value for each standard-viscosity liquid, as do a and b in the ASTM equation. This assumption has since been verified experimentally for all standard-viscosity liquids. The kinematic viscosities for the 13 standard-viscosity liquids have been measured with a high accuracy in the temperature range of 20 40°C using a series of the NRLM capillary master viscometers with an automatic flow time detection system. The deviations between measured and estimated kinematic viscosities were less than ±0.04% for the 10 standard-viscosity liquids JS2.5 to JS2000 and ±0.11% for the 3 standard-viscosity liquids JS15H to JS200H, respectively. From the above investigation, it was revealed that the uncertainty in the present estimation method is less than one-third that in the usual ASTM method.

  12. The variation of the fine-structure constant from disformal couplings

    NASA Astrophysics Data System (ADS)

    van de Bruck, Carsten; Mifsud, Jurgen; Nunes, Nelson J.

    2015-12-01

    We study a theory in which the electromagnetic field is disformally coupled to a scalar field, in addition to a usual non-minimal electromagnetic coupling. We show that disformal couplings modify the expression for the fine-structure constant, α. As a result, the theory we consider can explain the non-zero reported variation in the evolution of α by purely considering disformal couplings. We also find that if matter and photons are coupled in the same way to the scalar field, disformal couplings itself do not lead to a variation of the fine-structure constant. A number of scenarios are discussed consistent with the current astrophysical, geochemical, laboratory and the cosmic microwave background radiation constraints on the cosmological evolution of α. The models presented are also consistent with the current type Ia supernovae constraints on the effective dark energy equation of state. We find that the Oklo bound in particular puts strong constraints on the model parameters. From our numerical results, we find that the introduction of a non-minimal electromagnetic coupling enhances the cosmological variation in α. Better constrained data is expected to be reported by ALMA and with the forthcoming generation of high-resolution ultra-stable spectrographs such as PEPSI, ESPRESSO, and ELT-HIRES. Furthermore, an expected increase in the sensitivity of molecular and nuclear clocks will put a more stringent constraint on the theory.

  13. Hyperfine interaction constants of 14NO2 in 14 500-16 800 cm-1 energy region

    NASA Astrophysics Data System (ADS)

    Tada, Kohei; Hirata, Michihiro; Kasahara, Shunji

    2017-10-01

    We observed hyperfine-resolved high-resolution fluorescence excitation spectra of k = 0, N = 1 ← 0 transitions in 82 vibronic bands of the à 2B2 ← X ˜ 2A1 system of 14NO2 in the 14 500-16 800 cm-1 region by crossing a jet-cooled molecular beam and a single-mode dye laser beam at right angles. We determined hyperfine interaction constants of the lower and upper states for all the observed vibronic bands based on the analysis of the hyperfine structures of k = 0, N = 1 ← 0 transitions. Most of the determined Fermi contact interaction constants were found to be distributed in 0.0013-0.0038 cm-1, which are intermediate in magnitude between those in lower and higher energy region reported by other groups. A sharp decreasing of the Fermi contact interaction constant was found in 16 200-16 600 cm-1, and it may be caused by the interaction with the dark C ˜ 2A2 state. The hyperfine interaction constants are powerful clues to obtain reliable vibronic assignment. We tentatively assigned vibronic bands located at 14 836 cm-1, 15 586 cm-1, and 16 322 cm-1 as the transitions to the intrinsic (0,7,0), (0,8,0), and (0,9,0) vibrational levels of the à 2B2 state, respectively.

  14. 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.

  15. The Hubble Constant.

    PubMed

    Jackson, Neal

    2015-01-01

    I review the current state of determinations of the Hubble constant, which gives the length scale of the Universe by relating the expansion velocity of objects to their distance. There are two broad categories of measurements. The first uses individual astrophysical objects which have some property that allows their intrinsic luminosity or size to be determined, or allows the determination of their distance by geometric means. The second category comprises the use of all-sky cosmic microwave background, or correlations between large samples of galaxies, to determine information about the geometry of the Universe and hence the Hubble constant, typically in a combination with other cosmological parameters. Many, but not all, object-based measurements give 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.

  16. Relativistic problems on astronomical constants.

    NASA Astrophysics Data System (ADS)

    Tao, Jinhe; Huang, Tianyi

    1999-06-01

    The fact that modern astronomical observational technique has made rapid progress and the 1PN approximation of general relativity has been extensively applied in celestial mechanics and astrometry, makes it is necessary to investigate and examine the system of astronomical constants carefully and rigorously in the relativistic framework. The mass of a celestial body in the solar system should be defined as its BD mass that changes relatively in an amount less than 10-19 and could be considered as a constant. The equations satisfied by the gravitational potentials are not Poisson equations anymore but depend on the choice of the coordinate gauge. Therefore the gravitational potentials cannot be expanded in the traditional harmonics. It is neccessary to choose the coordinate gauge and take BD multipole moments as astronomical constants. The obliquity of the ecliptic has been determined in high precision and it would be neccessary to give a conventional definition of the 1PN ecliptic. A relativistic definition of the geoid is important and left to be discussed. The astronomical constants that relate the units of time and length have been clearly defined but need to be clarified to avoid their misuse.

  17. Spatially resolved dielectric constant of confined water and its connection to the non-local nature of bulk water

    NASA Astrophysics Data System (ADS)

    Schaaf, Christian; Gekle, Stephan

    2016-08-01

    We use molecular dynamics simulations to compute the spatially resolved static dielectric constant of water in cylindrical and spherical nanopores as occurring, e.g., in protein water pockets or carbon nanotubes. For this, we derive a linear-response formalism which correctly takes into account the dielectric boundary conditions in the considered geometries. We find that in cylindrical confinement, the axial component behaves similar as the local density akin to what is known near planar interfaces. The radial dielectric constant shows some oscillatory features when approaching the surface if their radius is larger than about 2 nm. Most importantly, however, the radial component exhibits pronounced oscillations at the center of the cavity. These surprising features are traced back quantitatively to the non-local dielectric nature of bulk water.

  18. Methods for constraining fine structure constant evolution with OH microwave transitions.

    PubMed

    Darling, Jeremy

    2003-07-04

    We investigate the constraints that OH microwave transitions in megamasers and molecular absorbers at cosmological distances may place on the evolution of the fine structure constant alpha=e(2)/ variant Planck's over 2pi c. The centimeter OH transitions are a combination of hyperfine splitting and lambda doubling that can constrain the cosmic evolution of alpha from a single species, avoiding systematic errors in alpha measurements from multiple species which may have relative velocity offsets. The most promising method compares the 18 and 6 cm OH lines, includes a calibration of systematic errors, and offers multiple determinations of alpha in a single object. Comparisons of OH lines to the HI 21 cm line and CO rotational transitions also show promise.

  19. MATHEMATICAL CONSTANTS.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Robinson, H.P.; Potter, Elinor

    1971-03-01

    This collection of mathematical data consists of two tables of decimal constants arranged according to size rather than function, a third table of integers from 1 to 1000, giving some of their properties, and a fourth table listing some infinite series arranged according to increasing size of the coefficients of the terms. The decimal values of Tables I and II are given to 20 D.

  20. Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.

    PubMed

    Lopes, J S; Arenas, M; Posada, D; Beaumont, M A

    2014-03-01

    The estimation of parameters in molecular evolution may be biased when some processes are not considered. For example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. Here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate Bayesian computation (ABC). We describe the implementation of a regression-based strategy for choosing subsets of summary statistics for coding data, and show that this approach can accurately infer recombination allowing for intracodon recombination breakpoints, molecular adaptation and codon substitution rates. We demonstrate that our ABC approach can outperform other analytical methods under a variety of evolutionary scenarios. We also show that although the choice of the codon-substitution model is important, our inferences are robust to a moderate degree of model misspecification. In addition, we demonstrate that our approach can accurately choose the evolutionary model that best fits the data, providing an alternative for when the use of full-likelihood methods is impracticable. Finally, we applied our ABC method to co-estimate recombination, substitution and molecular adaptation rates from 24 published human immunodeficiency virus 1 coding data sets.

  1. The 1% concordance Hubble constant

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    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. Amore » 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.« less

  2. An improved electronic determination of the Boltzmann constant by Johnson noise thermometry

    NASA Astrophysics Data System (ADS)

    Qu, Jifeng; Benz, Samuel P.; Coakley, Kevin; Rogalla, Horst; Tew, Weston L.; White, Rod; Zhou, Kunli; Zhou, Zhenyu

    2017-08-01

    Recent measurements using acoustic gas thermometry have determined the value of the Boltzmann constant, k, with a relative uncertainty less than 1  ×  10-6. These results have been supported by a measurement with a relative uncertainty of 1.9  ×  10-6 made with dielectric-constant gas thermometry. Together, the measurements meet the requirements of the International Committee for Weights and Measures and enable them to proceed with the redefinition of the kelvin in 2018. In further support, we provide a new determination of k using a purely electronic approach, Johnson noise thermometry, in which the thermal noise power generated by a sensing resistor immersed in a triple-point-of-water cell is compared to the noise power of a quantum-accurate pseudo-random noise waveform of nominally equal noise power. The experimental setup differs from that of the 2015 determination in several respects: a 100 Ω resistor is used as the thermal noise source, identical thin coaxial cables made of solid beryllium-copper conductors and foam dielectrics are used to connect the thermal and quantum-accurate noise sources to the correlator so as to minimize the temperature and frequency sensitivity of the impedances in the connecting leads, and no trimming capacitors or inductors are inserted into the connecting leads. The combination of reduced uncertainty due to spectral mismatches in the connecting leads and reduced statistical uncertainty due to a longer integration period of 100 d results in an improved determination of k  =  1.380 649 7(37)  ×  10-23 J K-1 with a relative standard uncertainty of 2.7  ×  10-6 and a relative offset of 0.89  ×  10-6 from the CODATA 2014 recommended value. The most significant terms in the uncertainty budget, the statistical uncertainty and the spectral-mismatch uncertainty, are uncorrelated with the corresponding uncertainties in the 2015 measurements.

  3. Carbene footprinting accurately maps binding sites in protein-ligand and protein-protein interactions

    NASA Astrophysics Data System (ADS)

    Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.

    2016-11-01

    Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

  4. Carter constant and angular momentum

    NASA Astrophysics Data System (ADS)

    Mukherjee, Sajal; Nayak, K. Rajesh

    We investigate the Carter-like constant in the case of a particle moving in a nonrelativistic dipolar potential. This special case is a missing link between the Carter constant in stationary and axially symmetric spacetimes (SASS) such as Kerr solution and its possible Newtonian counterpart. We use this system to carry over the definition of angular momentum from the Newtonian mechanics to the relativistic SASS.

  5. Molecular hyperfine fields in organic magnetoresistance devices

    NASA Astrophysics Data System (ADS)

    Giro, Ronaldo; Rosselli, Flávia P.; dos Santos Carvalho, Rafael; Capaz, Rodrigo B.; Cremona, Marco; Achete, Carlos A.

    2013-03-01

    We calculate molecular hyperfine fields in organic magnetoresistance (OMAR) devices using ab initio calculations. To do so, we establish a protocol for the accurate determination of the average hyperfine field Bhf and apply it to selected molecular ions: NPB, TPD, and Alq3. Then, we make devices with precisely the same molecules and perform measurements of the OMAR effect, in order to address the role of hole-transport layer in the characteristic magnetic field B0 of OMAR. Contrary to common belief, we find that molecular hyperfine fields are not only caused by hydrogen nuclei. We also find that dipolar contributions to the hyperfine fields can be comparable to the Fermi contact contributions. However, such contributions are restricted to nuclei located in the same molecular ion as the charge carrier (intramolecular), as extramolecular contributions are negligible.

  6. Ab Initio Calculation of Accurate Vibrational Frequencies for Molecules of Interest in Atmospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1996-01-01

    Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within +/- 8 cm(sup -1) on average, and molecular bond distances are accurate to within +/- 0.001-0.003 A, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as rovibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy win be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

  7. A modification of the Hammett equation for predicting ionisation constants of p-vinyl phenols.

    PubMed

    Sipilä, Julius; Nurmi, Harri; Kaukonen, Ann Marie; Hirvonen, Jouni; Taskinen, Jyrki; Yli-Kauhaluoma, Jari

    2005-01-01

    Currently there are several compounds used as drugs or studied as new chemical entities, which have an electron withdrawing group connected to a vinylic double bond in a phenolic or catecholic core structure. These compounds share a common feature--current computational methods utilizing the Hammett type equation for the prediction of ionisation constants fail to give accurate prediction of pK(a)'s for compounds containing the vinylic moiety. The hypothesis was that the effect of electron-withdrawing substituents on the pK(a) of p-vinyl phenols is due to the delocalized electronic structure of these compounds. Thus, this effect should be additive for multiple substituents attached to the vinylic double bond and quantifiable by LFER-based methods. The aim of this study was to produce an improved equation with a reduced tendency to underestimate the effect of the double bond on the ionisation of the phenolic hydroxyl. To this end a set of 19 para-substituted vinyl phenols was used. The ionisation constants were measured potentiometrically, and a training set of 10 compounds was selected to build a regression model (r2 = 0.987 and S.E. = 0.09). The average error with an external test set of six compounds was 0.19 for our model and 1.27 for the ACD-labs 7.0. Thus, we have been able to significantly improve the existing model for prediction of the ionisation constants of substituted p-vinyl phenols.

  8. High-Temperature Slow Crack Growth of Silicon Carbide Determined by Constant-Stress-Rate and Constant-Stress Testing

    NASA Technical Reports Server (NTRS)

    Choi, Sung H.; Salem, J. A.; Nemeth, N. N.

    1998-01-01

    High-temperature slow-crack-growth behaviour of hot-pressed silicon carbide was determined using both constant-stress-rate ("dynamic fatigue") and constant-stress ("static fatigue") testing in flexure at 1300 C in air. Slow crack growth was found to be a governing mechanism associated with failure of the material. Four estimation methods such as the individual data, the Weibull median, the arithmetic mean and the median deviation methods were used to determine the slow crack growth parameters. The four estimation methods were in good agreement for the constant-stress-rate testing with a small variation in the slow-crack-growth parameter, n, ranging from 28 to 36. By contrast, the variation in n between the four estimation methods was significant in the constant-stress testing with a somewhat wide range of n= 16 to 32.

  9. REACTOR PHYSICS CONSTANTS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    None

    1963-07-01

    This second edition is based on data available on March 15, 1961. Sections on constants necessary for the interpretation of experimental data and on digital computer programs for reactor design and reactor physics have been added. 1344 references. (D.C.W.)

  10. Adjoint-based constant-mass partial derivatives

    DOE PAGES

    Favorite, Jeffrey A.

    2017-09-01

    In transport theory, adjoint-based partial derivatives with respect to mass density are constant-volume derivatives. Likewise, adjoint-based partial derivatives with respect to surface locations (i.e., internal interface locations and the outer system boundary) are constant-density derivatives. This study derives the constant-mass partial derivative of a response with respect to an internal interface location or the outer system boundary and the constant-mass partial derivative of a response with respect to the mass density of a region. Numerical results are given for a multiregion two-dimensional (r-z) cylinder for three very different responses: the uncollided gamma-ray flux at an external detector point, k effmore » of the system, and the total neutron leakage. Finally, results from the derived formulas compare extremely well with direct perturbation calculations.« less

  11. Systematics of constant roll inflation

    NASA Astrophysics Data System (ADS)

    Anguelova, Lilia; Suranyi, Peter; Wijewardhana, L. C. R.

    2018-02-01

    We study constant roll inflation systematically. This is a regime, in which the slow roll approximation can be violated. It has long been thought that this approximation is necessary for agreement with observations. However, recently it was understood that there can be inflationary models with a constant, and not necessarily small, rate of roll that are both stable and compatible with the observational constraint ns ≈ 1. We investigate systematically the condition for such a constant-roll regime. In the process, we find a whole new class of inflationary models, in addition to the known solutions. We show that the new models are stable under scalar perturbations. Finally, we find a part of their parameter space, in which they produce a nearly scale-invariant scalar power spectrum, as needed for observational viability.

  12. Determination of association constants at moderately fast chemical exchange: complexation of camphor enantiomers by alpha-cyclodextrin.

    PubMed

    Bernatowicz, Piotr; Nowakowski, Michał; Dodziuk, Helena; Ejchart, Andrzej

    2006-08-01

    Association constants in weak molecular complexes can be determined by analysis of chemical shifts variations resulting from changes of guest to host concentration ratio. In the regime of very fast exchange, i.e., when exchange rate is several orders of magnitude larger than the Larmor angular frequency difference of the observed resonance in free and complexed molecule, the apparent position of averaged resonance is a population-weighted mean of resonances of particular forms involved in the equilibrium. The assumption of very fast exchange is often, however, tacitly admitted in literature even in cases where the process of interest is much slower than required. We show that such an unjustified simplification may, under certain circumstances, lead to significant underestimation of association constant and, in consequence, to non-negligible errors in Gibbs free energy under determination. We present a general method, based on iterative numerical NMR line shape analysis, which allows one for the compensation of chemical exchange effects, and delivers both the correct association constants and the exchange rates. The latter are not delivered by the other mentioned method. Practical application of our algorithm is illustrated by the case of camphor-alpha-cyclodextrin complexes.

  13. Molecular Detection of Chilo infuscatellus

    PubMed Central

    Wang, Weizhong; Wang, Rong; Zheng, Haotian; Gao, Sanji

    2017-01-01

    Abstract The Chilo infuscatellus (Snellen; Lepidoptera: Pyralidae) is the main pest of sugarcane in China. The shortage of easily distinguishable morphological characters especially in early stage make it challenging to diagnosed and promptly take steps for pest management. In the present study, we described a PCR method for the molecular identification of based on barcode region of COI sequences between C. infuscatellus and four other sugarcane borer species. A 285bp fragment was successfully amplified from all life stages and different geographical populations. Sensitivity tests revealed that diagnostic bands were generated as low as the DNA template concentration of 5 ng/µl. Our work demonstrated a rapid and accurate way for the molecular diagnosis of C. infuscatellus. PMID:29117377

  14. Conformational analysis of a condensed macrocyclic β-lactam by NMR and molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Keserű, György M.; Vásárhelyi, Helga; Makara, Gergely

    1994-09-01

    The conformation of the new macrocyclic β-lactam ( 1) was investigated by NMR and molecular dynamics (MD) calculations. Restraints obtained from NOESY and ROESY experiments were introduced into MD simulations which led to well-defined conformations. The preference for the calculated minimum energy conformation was confirmed by the analysis of vicinal coupling constants. Experimental coupling constants agreed with computed values.

  15. 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.

  16. Inflation with a constant rate of roll

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Motohashi, Hayato; Starobinsky, Alexei A.; Yokoyama, Jun'ichi, E-mail: motohashi@kicp.uchicago.edu, E-mail: alstar@landau.ac.ru, E-mail: yokoyama@resceu.s.u-tokyo.ac.jp

    2015-09-01

    We consider an inflationary scenario where the rate of inflaton roll defined by {sup ··}φ/H φ-dot remains constant. The rate of roll is small for slow-roll inflation, while a generic rate of roll leads to the interesting case of 'constant-roll' inflation. We find a general exact solution for the inflaton potential required for such inflaton behaviour. In this model, due to non-slow evolution of background, the would-be decaying mode of linear scalar (curvature) perturbations may not be neglected. It can even grow for some values of the model parameter, while the other mode always remains constant. However, this always occurs formore » 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.« less

  17. Guidance for laboratories performing molecular pathology for cancer patients

    PubMed Central

    Cree, Ian A; Deans, Zandra; Ligtenberg, Marjolijn J L; Normanno, Nicola; Edsjö, Anders; Rouleau, Etienne; Solé, Francesc; Thunnissen, Erik; Timens, Wim; Schuuring, Ed; Dequeker, Elisabeth; Murray, Samuel; Dietel, Manfred; Groenen, Patricia; Van Krieken, J Han

    2014-01-01

    Molecular testing is becoming an important part of the diagnosis of any patient with cancer. The challenge to laboratories is to meet this need, using reliable methods and processes to ensure that patients receive a timely and accurate report on which their treatment will be based. The aim of this paper is to provide minimum requirements for the management of molecular pathology laboratories. This general guidance should be augmented by the specific guidance available for different tumour types and tests. Preanalytical considerations are important, and careful consideration of the way in which specimens are obtained and reach the laboratory is necessary. Sample receipt and handling follow standard operating procedures, but some alterations may be necessary if molecular testing is to be performed, for instance to control tissue fixation. DNA and RNA extraction can be standardised and should be checked for quality and quantity of output on a regular basis. The choice of analytical method(s) depends on clinical requirements, desired turnaround time, and expertise available. Internal quality control, regular internal audit of the whole testing process, laboratory accreditation, and continual participation in external quality assessment schemes are prerequisites for delivery of a reliable service. A molecular pathology report should accurately convey the information the clinician needs to treat the patient with sufficient information to allow for correct interpretation of the result. Molecular pathology is developing rapidly, and further detailed evidence-based recommendations are required for many of the topics covered here. PMID:25012948

  18. Accurate van der Waals force field for gas adsorption in porous materials.

    PubMed

    Sun, Lei; Yang, Li; Zhang, Ya-Dong; Shi, Qi; Lu, Rui-Feng; Deng, Wei-Qiao

    2017-09-05

    An accurate van der Waals force field (VDW FF) was derived from highly precise quantum mechanical (QM) calculations. Small molecular clusters were used to explore van der Waals interactions between gas molecules and porous materials. The parameters of the accurate van der Waals force field were determined by QM calculations. To validate the force field, the prediction results from the VDW FF were compared with standard FFs, such as UFF, Dreiding, Pcff, and Compass. The results from the VDW FF were in excellent agreement with the experimental measurements. This force field can be applied to the prediction of the gas density (H 2 , CO 2 , C 2 H 4 , CH 4 , N 2 , O 2 ) and adsorption performance inside porous materials, such as covalent organic frameworks (COFs), zeolites and metal organic frameworks (MOFs), consisting of H, B, N, C, O, S, Si, Al, Zn, Mg, Ni, and Co. This work provides a solid basis for studying gas adsorption in porous materials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  19. [Planar molecular arrangements aid the design of MHC class II binding peptides].

    PubMed

    Cortés, A; Coral, J; McLachlan, C; Benítez, R; Pinilla, L

    2017-01-01

    The coupling between peptides and MHC-II proteins in the human immune system is not well understood. This work presents an evidence-based hypothesis of a guiding intermolecular force present in every human MHC-II protein (HLA-II). Previously, we examined the spatial positions of the fully conserved residues in all HLA-II protein types. In each one, constant planar patterns were revealed. These molecular planes comprise of amino acid groups of the same chemical species (for example, Gly) distributed across the protein structure. Each amino acid plane has a unique direction and this directional element offers spatial selectivity. Constant within all planes, too, is the presence of an aromatic residue possessing electrons in movement, leading the authors to consider that the planes generate electromagnetic fields that could serve as an attractive force in a single direction. Selection and attraction between HLA-II molecules and antigen peptides would, therefore, be non-random, resulting in a coupling mechanism as effective and rapid as is clearly required in the immune response. On the basis of planar projections onto the HLA-II groove, modifications were made by substituting the key residues in the class II-associated invariant chain peptide-a peptide with a universal binding affinity-resulting in eight different modified peptides with affinities greater than that of the unmodified peptide. Accurate and reliable prediction of MHC class II-binding peptides may facilitate the design of universal vaccine-peptides with greatly enhanced binding affinities. The proposed mechanisms of selection, attraction and coupling between HLA-II and antigen peptides are explained further in the paper.

  20. Extensions to the instantaneous normal mode analysis of cluster dynamics: Diffusion constants and the role of rotations in clusters

    NASA Astrophysics Data System (ADS)

    Adams, John E.; Stratt, Richard M.

    1990-08-01

    For the instantaneous normal mode analysis method to be generally useful in studying the dynamics of clusters of arbitrary size, it ought to yield values of atomic self-diffusion constants which agree with those derived directly from molecular dynamics calculations. The present study proposes that such agreement indeed can be obtained if a sufficiently sophisticated formalism for computing the diffusion constant is adopted, such as the one suggested by Madan, Keyes, and Seeley [J. Chem. Phys. 92, 7565 (1990)]. In order to implement this particular formalism, however, we have found it necessary to pay particular attention to the removal from the computed spectra of spurious rotational contributions. The utility of the formalism is demonstrated via a study of small argon clusters, for which numerous results generated using other approaches are available. We find the same temperature dependence of the Ar13 self-diffusion constant that Beck and Marchioro [J. Chem. Phys. 93, 1347 (1990)] do from their direct calculation of the velocity autocorrelation function: The diffusion constant rises quickly from zero to a liquid-like value as the cluster goes through (the finite-size equivalent of) the melting transition.

  1. Constant-head pumping test of a multiaquifer well to determine characteristics of individual aquifers

    USGS Publications Warehouse

    Bennett, Gordon D.; Patten, E.P.

    1962-01-01

    This report describes the theory and field procedures for determining the transmissibility and storage coefficients and the original hydrostatic head of each aquifer penetrated by a multiaquifer well. The procedure involves pumping the well in such a manner that the drawdown of water level is constant while the discharges of the different aquifers are measured by means of borehole flowmeters. The theory is developed by analogy to the heat-flow problem solved by Smith. The internal discharge between aquifers after the well is completed is analyzed as the first step. Pumping at constant, drawdown constitutes the second step. Transmissibility and storage coefficients are determined by a method described by Jacob and Lohman, after the original internal discharge to or from the aquifer has been compensated for in the calculations. The original hydrostatic head of each aquifer is then determined by resubstituting the transmissibility and storage coefficients into the first step of the analysis. The method was tested on a well in Chester County, Pa., but the results were not entirely satisfactory, owing to the lack of sufficiently accurate methods of flow measurement and, probably, to the effects of entrance losses in the well. The determinations of the transmissibility coefficient and static head can be accepted as having order-of-magnitude significance, but the determinations of the storage coefficient, which is highly sensitive to experimental error, must be rejected. It is felt that better results may be achieved in the future, as more reliable devices for metering the flow become available and as more is learned concerning the nature of entrance losses. If accurate data can be obtained, recently developed techniques of digital or analog computation may permit determination of the response of each aquifer in the well to any form of pumping.

  2. Computational IR spectroscopy of water: OH stretch frequencies, transition dipoles, and intermolecular vibrational coupling constants

    NASA Astrophysics Data System (ADS)

    Choi, Jun-Ho; Cho, Minhaeng

    2013-05-01

    The Hessian matrix reconstruction method initially developed to extract the basis mode frequencies, vibrational coupling constants, and transition dipoles of the delocalized amide I, II, and III vibrations of polypeptides and proteins from quantum chemistry calculation results is used to obtain those properties of delocalized O-H stretch modes in liquid water. Considering the water symmetric and asymmetric O-H stretch modes as basis modes, we here develop theoretical models relating vibrational frequencies, transition dipoles, and coupling constants of basis modes to local water configuration and solvent electric potential. Molecular dynamics simulation was performed to generate an ensemble of water configurations that was in turn used to construct vibrational Hamiltonian matrices. Obtaining the eigenvalues and eigenvectors of the matrices and using the time-averaging approximation method, which was developed by the Skinner group, to calculating the vibrational spectra of coupled oscillator systems, we could numerically simulate the O-H stretch IR spectrum of liquid water. The asymmetric line shape and weak shoulder bands were quantitatively reproduced by the present computational procedure based on vibrational exciton model, where the polarization effects on basis mode transition dipoles and inter-mode coupling constants were found to be crucial in quantitatively simulating the vibrational spectra of hydrogen-bond networking liquid water.

  3. Theoretical Evaluation of the Transient Response of Constant Head and Constant Flow-Rate Permeability Tests

    USGS Publications Warehouse

    Zhang, M.; Takahashi, M.; Morin, R.H.; Esaki, T.

    1998-01-01

    A theoretical analysis is presented that compares the response characteristics of the constant head and the constant flowrate (flow pump) laboratory techniques for quantifying the hydraulic properties of geologic materials having permeabilities less than 10-10 m/s. Rigorous analytical solutions that describe the transient distributions of hydraulic gradient within a specimen are developed, and equations are derived for each method. Expressions simulating the inflow and outflow rates across the specimen boundaries during a constant-head permeability test are also presented. These solutions illustrate the advantages and disadvantages of each method, including insights into measurement accuracy and the validity of using Darcy's law under certain conditions. The resulting observations offer practical considerations in the selection of an appropriate laboratory test method for the reliable measurement of permeability in low-permeability geologic materials.

  4. A full set of langatate high-temperature acoustic wave constants: elastic, piezoelectric, dielectric constants up to 900°C.

    PubMed

    Davulis, Peter M; da Cunha, Mauricio Pereira

    2013-04-01

    A full set of langatate (LGT) elastic, dielectric, and piezoelectric constants with their respective temperature coefficients up to 900°C is presented, and the relevance of the dielectric and piezoelectric constants and temperature coefficients are discussed with respect to predicted and measured high-temperature SAW propagation properties. The set of constants allows for high-temperature acoustic wave (AW) propagation studies and device design. The dielectric constants and polarization and conductive losses were extracted by impedance spectroscopy of parallel-plate capacitors. The measured dielectric constants at high temperatures were combined with previously measured LGT expansion coefficients and used to determine the elastic and piezoelectric constants using resonant ultrasound spectroscopy (RUS) measurements at temperatures up to 900°C. The extracted LGT piezoelectric constants and temperature coefficients show that e11 and e14 change by up to 62% and 77%, respectively, for the entire 25°C to 900°C range when compared with room-temperature values. The LGT high-temperature constants and temperature coefficients were verified by comparing measured and predicted phase velocities (vp) and temperature coefficients of delay (TCD) of SAW delay lines fabricated along 6 orientations in the LGT plane (90°, 23°, Ψ) up to 900°C. For the 6 tested orientations, the predicted SAW vp agree within 0.2% of the measured vp on average and the calculated TCD is within 9.6 ppm/°C of the measured value on average over the temperature range of 25°C to 900°C. By including the temperature dependence of both dielectric and piezoelectric constants, the average discrepancies between predicted and measured SAW properties were reduced, on average: 77% for vp, 13% for TCD, and 63% for the turn-over temperatures analyzed.

  5. Acetylated Lysozyme as Impurity in Lysozyme Crystals: Constant Distribution Coefficient

    NASA Technical Reports Server (NTRS)

    Thomas, B. R.; Chernov, A. A.

    2000-01-01

    Hen egg white lysozyme (HEWL) was acetylated to modify molecular charge keeping the molecular size and weight nearly constant. Two derivatives, A and B, more and less acetylated, respectively, were obtained, separated, purified and added to the solution from which crystals of tetragonal HEWL crystals were grown. Amounts of the A or B impurities added were 0.76, 0.38 and 0.1 milligram per millimeter while HEWL concentration were 20, 30 and 40 milligram per milliliter. The crystals grown in 18 experiments for each impurity were dissolved and quantities of A or B additives in these crystals were analyzed by cation exchange high performance liquid chromatography. All the data for each set of 18 samples with the different impurity and regular HEWL concentrations is well described by one distribution coefficient K = 2.15 plus or minus 0.13 for A and K = 3.42 plus or minus 0.25 for B. The observed independence of the distribution coefficient on both the impurity concentration and supersaturation is explained by the dilution model described in this paper. It shows that impurity adsorption and incorporation rate is proportional to the impurity concentration and that the growth rate is proportional to the crystallizing protein in solution. With the kinetic coefficient for crystallization, beta = 5.10(exp -7) centimeters per second, the frequency at which an impurity molecule near the growing interface irreversibly joins a molecular site on the crystal was found to be 3 1 per second, much higher than the average frequency for crystal molecules. For best quality protein crystals it is better to have low microheterogeneous protein impurity concentration and high supers aturation.

  6. Molecular switching behavior in isosteric DNA base pairs.

    PubMed

    Jissy, A K; Konar, Sukanya; Datta, Ayan

    2013-04-15

    The structures and proton-coupled behavior of adenine-thymine (A-T) and a modified base pair containing a thymine isostere, adenine-difluorotoluene (A-F), are studied in different solvents by dispersion-corrected density functional theory. The stability of the canonical Watson-Crick base pair and the mismatched pair in various solvents with low and high dielectric constants is analyzed. It is demonstrated that A-F base pairing is favored in solvents with low dielectric constant. The stabilization and conformational changes induced by protonation are also analyzed for the natural as well as the mismatched base pair. DNA sequences capable of changing their sequence conformation on protonation are used in the construction of pH-based molecular switches. An acidic medium has a profound influence in stabilizing the isostere base pair. Such a large gain in stability on protonation leads to an interesting pH-controlled molecular switch, which can be incorporated in a natural DNA tract. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. An independent determination of the local Hubble constant

    NASA Astrophysics Data System (ADS)

    Fernández Arenas, David; Terlevich, Elena; Terlevich, Roberto; Melnick, Jorge; Chávez, Ricardo; Bresolin, Fabio; Telles, Eduardo; Plionis, Manolis; Basilakos, Spyros

    2018-02-01

    The relationship between the integrated H β line luminosity and the velocity dispersion of the ionized gas of H II galaxies and giant H II regions represents an exciting standard candle that presently can be used up to redshifts z ˜ 4. Locally it is used to obtain precise measurements of the Hubble constant by combining the slope of the relation obtained from nearby (z ≤ 0.2) H II galaxies with the zero-point determined from giant H II regions belonging to an `anchor sample' of galaxies for which accurate redshift-independent distance moduli are available. We present new data for 36 giant H II regions in 13 galaxies of the anchor sample that includes the megamaser galaxy NGC 4258. Our data are the result of the first 4 yr of observation of our primary sample of 130 giant H II regions in 73 galaxies with Cepheid determined distances. Our best estimate of the Hubble parameter is 71.0 ± 2.8(random) ± 2.1(systematic) km s- 1Mpc- 1. This result is the product of an independent approach and, although at present less precise than the latest SNIa results, it is amenable to substantial improvement.

  8. Wormholes and the cosmological constant problem.

    NASA Astrophysics Data System (ADS)

    Klebanov, I.

    The author reviews the cosmological constant problem and the recently proposed wormhole mechanism for its solution. Summation over wormholes in the Euclidean path integral for gravity turns all the coupling parameters into dynamical variables, sampled from a probability distribution. A formal saddle point analysis results in a distribution with a sharp peak at the cosmological constant equal to zero, which appears to solve the cosmological constant problem. He discusses the instabilities of the gravitational Euclidean path integral and the difficulties with its interpretation. He presents an alternate formalism for baby universes, based on the "third quantization" of the Wheeler-De Witt equation. This approach is analyzed in a minisuperspace model for quantum gravity, where it reduces to simple quantum mechanics. Once again, the coupling parameters become dynamical. Unfortunately, the a priori probability distribution for the cosmological constant and other parameters is typically a smooth function, with no sharp peaks.

  9. Thermo-acoustical molecular interaction study in binary mixtures of glycerol and ethylene glycol

    NASA Astrophysics Data System (ADS)

    Kaur, Kirandeep; Juglan, K. C.; Kumar, Harsh

    2017-07-01

    Ultrasonic velocity, density and viscosity are measured over the entire composition range for binary liquid mixtures of glycerol (CH2OH-CHOH-CH2OH) and ethylene glycol (HOCH2CH2OH) at different temperatures and constant frequency of 2MHz using ultrasonic interferometer, specific gravity bottle and viscometer respectively. Measured experimental values are used to obtained various acoustical parameters such as adiabatic compressibility, acoustic impedance, intermolecular free length, relaxation time, ultrasonic attenuation, effective molar weight, free volume, available volume, molar volume, Wada's constant, Rao's constant, Vander Waal's constant, internal pressure, Gibb's free energy and enthalpy. The variation in acoustical parameters are interpreted in terms of molecular interactions between the components of molecules of binary liquid mixtures.

  10. Calculation of kinetic rate constants from thermodynamic data

    NASA Technical Reports Server (NTRS)

    Marek, C. John

    1995-01-01

    A new scheme for relating the absolute value for the kinetic rate constant k to the thermodynamic constant Kp is developed for gases. In this report the forward and reverse rate constants are individually related to the thermodynamic data. The kinetic rate constants computed from thermodynamics compare well with the current kinetic rate constants. This method is self consistent and does not have extensive rules. It is first demonstrated and calibrated by computing the HBr reaction from H2 and Br2. This method then is used on other reactions.

  11. Constant-roll (quasi-)linear inflation

    NASA Astrophysics Data System (ADS)

    Karam, A.; Marzola, L.; Pappas, T.; Racioppi, A.; Tamvakis, K.

    2018-05-01

    In constant-roll inflation, the scalar field that drives the accelerated expansion of the Universe is rolling down its potential at a constant rate. Within this framework, we highlight the relations between the Hubble slow-roll parameters and the potential ones, studying in detail the case of a single-field Coleman-Weinberg model characterised by a non-minimal coupling of the inflaton to gravity. With respect to the exact constant-roll predictions, we find that assuming an approximate slow-roll behaviour yields a difference of Δ r = 0.001 in the tensor-to-scalar ratio prediction. Such a discrepancy is in principle testable by future satellite missions. As for the scalar spectral index ns, we find that the existing 2-σ bound constrains the value of the non-minimal coupling to ξphi ~ 0.29–0.31 in the model under consideration.

  12. Precision Spectroscopy of Molecular Hydrogen and the Search for New Physics

    NASA Astrophysics Data System (ADS)

    Ubachs, Wim

    2017-06-01

    The hydrogen molecule is the smallest neutral chemical entity and a benchmark system of molecular spectroscopy. The comparison between highly accurate measurements of transition frequencies and level energies with quantum calculations including all known phenomena (relativistic, vacuum polarization and self energy) provides a tool to search for physical phenomena in the realm of the unknown: are there forces beyond the three included in the Standard Model of physics plus gravity [1], are there extra dimensions beyond the 3+1 describing space time [2] ? Comparison of laboratory wavelengths of transitions in hydrogen may be compared with the lines observed during the epoch of the early Universe to verify whether fundamental constants of Nature have varied over cosmological time [3]. These concepts, as well as the precision laboratory experiments and the astronomical observations used for such searches of new physics [4] will be discussed. [1] E.J. Salumbides, J.C.J. Koelemeij, J. Komasa, K. Pachucki, K.S.E. Eikema, W. Ubachs, Bounds on fifth forces from precision measurements on molecules, Phys. Rev. D87, 112008 (2013). [2] E.J. Salumbides, A.N. Schellekens, B. Gato-Rivera, W. Ubachs Constraints on extra dimensions from molecular spectroscopy, New. J. Phys. 17, 033015 (2015). [3] W. Ubachs, J. Bagdonaite, E.J. Salumbides, M.T. Murphy, L. Kaper, Search for a drifting proton-electron mass ratio from H_2, Rev. Mod. Phys. 88, 021003 (2016). [4] W. Ubachs, J.C.J. Koelemeij, K.S.E. Eikema, E.J. Salumbides, Physics beyond the Standard Model from hydrogen spectroscopy, J. Mol. Spectr. 320, 1 (2016).

  13. Equivalent refractive-index structure constant of non-Kolmogorov turbulence.

    PubMed

    Li, Yujie; Zhu, Wenyue; Wu, Xiaoqing; Rao, Ruizhong

    2015-09-07

    The relationship between the non-Kolmogorov refractive-index structure constant and the Kolmogorov refractive-index structure constant is derived by using the refractive-index structure function and the variance of refractive-index fluctuations. It shows that the non-Kolmogorov structure constant is proportional to the Kolmogorov structure constant and the scaling factor depends on the outer scale and the spectral power law. For a fixed Kolmogorov structure constant, the non-Kolmogorov structure constant increases with a increasing outer scale for the power law less than 11/3, the trend is opposite for the power law greater than 11/3. This equivalent relation provides a way of obtaining the non-Kolmogorov structure constant by using the Kolmogorov structure constant.

  14. On the influences of key modelling constants of large eddy simulations for large-scale compartment fires predictions

    NASA Astrophysics Data System (ADS)

    Yuen, Anthony C. Y.; Yeoh, Guan H.; Timchenko, Victoria; Cheung, Sherman C. P.; Chan, Qing N.; Chen, Timothy

    2017-09-01

    An in-house large eddy simulation (LES) based fire field model has been developed for large-scale compartment fire simulations. The model incorporates four major components, including subgrid-scale turbulence, combustion, soot and radiation models which are fully coupled. It is designed to simulate the temporal and fluid dynamical effects of turbulent reaction flow for non-premixed diffusion flame. Parametric studies were performed based on a large-scale fire experiment carried out in a 39-m long test hall facility. Several turbulent Prandtl and Schmidt numbers ranging from 0.2 to 0.5, and Smagorinsky constants ranging from 0.18 to 0.23 were investigated. It was found that the temperature and flow field predictions were most accurate with turbulent Prandtl and Schmidt numbers of 0.3, respectively, and a Smagorinsky constant of 0.2 applied. In addition, by utilising a set of numerically verified key modelling parameters, the smoke filling process was successfully captured by the present LES model.

  15. Systematic harmonic power laws inter-relating multiple fundamental constants

    NASA Astrophysics Data System (ADS)

    Chakeres, Donald; Buckhanan, Wayne; Andrianarijaona, Vola

    2017-01-01

    Power laws and harmonic systems are ubiquitous in physics. We hypothesize that 2, π, the electron, Bohr radius, Rydberg constant, neutron, fine structure constant, Higgs boson, top quark, kaons, pions, muon, Tau, W, and Z when scaled in a common single unit are all inter-related by systematic harmonic powers laws. This implies that if the power law is known it is possible to derive a fundamental constant's scale in the absence of any direct experimental data of that constant. This is true for the case of the hydrogen constants. We created a power law search engine computer program that randomly generated possible positive or negative powers searching when the product of logical groups of constants equals 1, confirming they are physically valid. For 2, π, and the hydrogen constants the search engine found Planck's constant, Coulomb's energy law, and the kinetic energy law. The product of ratios defined by two constants each was the standard general format. The search engine found systematic resonant power laws based on partial harmonic fraction powers of the neutron for all of the constants with products near 1, within their known experimental precision, when utilized with appropriate hydrogen constants. We conclude that multiple fundamental constants are inter-related within a harmonic power law system.

  16. A model-updating procedure to stimulate piezoelectric transducers accurately.

    PubMed

    Piranda, B; Ballandras, S; Steichen, W; Hecart, B

    2001-09-01

    The use of numerical calculations based on finite element methods (FEM) has yielded significant improvements in the simulation and design of piezoelectric transducers piezoelectric transducer utilized in acoustic imaging. However, the ultimate precision of such models is directly controlled by the accuracy of material characterization. The present work is dedicated to the development of a model-updating technique adapted to the problem of piezoelectric transducer. The updating process is applied using the experimental admittance of a given structure for which a finite element analysis is performed. The mathematical developments are reported and then applied to update the entries of a FEM of a two-layer structure (a PbZrTi-PZT-ridge glued on a backing) for which measurements were available. The efficiency of the proposed approach is demonstrated, yielding the definition of a new set of constants well adapted to predict the structure response accurately. Improvement of the proposed approach, consisting of the updating of material coefficients not only on the admittance but also on the impedance data, is finally discussed.

  17. A hundred years with the cosmological constant

    NASA Astrophysics Data System (ADS)

    Grøn, Øyvind G.

    2018-07-01

    The main points in the history of the cosmological constant are briefly discussed. As a conceptual background, useful for teaching of physics at an elementary college and university level, Newton’s theory formulated locally in terms of the Poisson equation is presented, and it is shown how it is modified by the introduction of the cosmological constant. The different physical interpretations of the cosmological constant, as introduced by Einstein in 1917 and interpreted by Lemaître in 1934, are presented. Energy conservation in an expanding universe dominated by vacuum energy is discussed. The connection between the cosmological constant and the quantum mechanical vacuum energy is mentioned, together with the problem that a quantum mechanical calculation of the density of the vacuum energy gives a vastly too large value of the cosmological constant. The article is concluded by reviewing a solution of this problem that was presented on May 11, 2017.

  18. Effect of molecular anisotropy on beam scattering measurements

    NASA Technical Reports Server (NTRS)

    Goldflam, R.; Green, S.; Kouri, D. J.; Monchick, L.

    1978-01-01

    Within the energy sudden approximation, the total integral and total differential scattering cross sections are given by the angle average of scattering cross sections computed at fixed rotor orientations. Using this formalism the effect of molecular anisotropy on scattering of He by HCl and by CO is examined. Comparisons with accurate close coupling calculations indicate that this approximation is quite reliable, even at very low collision energies, for both of these systems. Comparisons are also made with predictions based on the spherical average of the interaction. For HCl the anisotropy is rather weak and its main effect is a slight quenching of the oscillations in the differential cross sections relative to predictions of the spherical averaged potential. For CO the anisotropy is much stronger, so that the oscillatory pattern is strongly quenched and somewhat shifted. It appears that the sudden approximation provides a simple yet accurate method for describing the effect of molecular anisotropy on scattering measurements.

  19. Ligands of low electronegativity in the vsepr model: molecular pseudohalides

    NASA Astrophysics Data System (ADS)

    Glidewell, Christopher; Holden, H. Diane

    Equilibrium structures and force constants at linearity, for the skeletal bending mode δ(RNX) have been calculated in the MNDO approximation for 67 isocyanates, isothio-cyanates and azides, RNXY (XY = CO, CS or N 2) and the corresponding structures and force constants, δ(RCN), for 12 fulminates RCNO. Fulminates all have linear skeletons, but for RNXY the molecular skeleton is linear at atom X only if it is linear at N also ; otherwise the skeleton RNXY has a trans planar structure. Bending force constants are large and negative for all azides studied, negative for methyl and substituted methyl isocyanates and isothiocyanates and very small and positive for silyl and substituted silyl isothiocyanates: for silyl and substituted silyl isocyanales, the force constant is small and positive when the R group has effective C2v symmetry, but small and negative when the R group has only effective Cs symmetry.

  20. Measurement of the fine-structure constant as a test of the Standard Model.

    PubMed

    Parker, Richard H; Yu, Chenghui; Zhong, Weicheng; Estey, Brian; Müller, Holger

    2018-04-13

    Measurements of the fine-structure constant α require methods from across subfields and are thus powerful tests of the consistency of theory and experiment in physics. Using the recoil frequency of cesium-133 atoms in a matter-wave interferometer, we recorded the most accurate measurement of the fine-structure constant to date: α = 1/137.035999046(27) at 2.0 × 10 -10 accuracy. Using multiphoton interactions (Bragg diffraction and Bloch oscillations), we demonstrate the largest phase (12 million radians) of any Ramsey-Bordé interferometer and control systematic effects at a level of 0.12 part per billion. Comparison with Penning trap measurements of the electron gyromagnetic anomaly g e - 2 via the Standard Model of particle physics is now limited by the uncertainty in g e - 2; a 2.5σ tension rejects dark photons as the reason for the unexplained part of the muon's magnetic moment at a 99% confidence level. Implications for dark-sector candidates and electron substructure may be a sign of physics beyond the Standard Model that warrants further investigation. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.